PDB2PQR¶
Overview¶
The use of continuum solvation methods such as APBS requires accurate and complete structural data as well as force field parameters such as atomic charges and radii. Unfortunately, the limiting step in continuum electrostatics calculations is often the addition of missing atomic coordinates to molecular structures from the Protein Data Bank and the assignment of parameters to these structures. To address this problem, we have developed PDB2PQR. This software automates many of the common tasks of preparing structures for continuum solvation calculations as well as many other types of biomolecular structure modeling, analysis, and simulation. These tasks include:
- Adding a limited number of missing heavy (non-hydrogen) atoms to biomolecular structures.
- Estimating titration states and protonating biomolecules in a manner consistent with favorable hydrogen bonding.
- Assigning charge and radius parameters from a variety of force fields.
- Generating “PQR” output compatible with several popular computational modeling and analysis packages.
- This service is intended to facilitate the setup and execution of electrostatics calculations for both experts and non-experts and thereby broaden the accessibility of biomolecular solvation and electrostatics analyses to the biomedical community.
Contents¶
Getting PDB2PQR¶
Note
Before you begin! PDB2PQR funding is dependent on your help for continued development and support. Please register before using the software so we can accurately report the number of users to our funding agencies.
Web servers¶
Most functionality is available through our online web servers.
The PDB2PQR web server offers a simple way to use both APBS and PDB2PQR without the need to download and install additional programs.
After registering, please visit http://server.poissonboltzmann.org/ to access the web server.
Python Package Installer (PIP)¶
Most users who want to use the software offline should install it via pip with the following command
pip install pdb2pqr
from within your favorite virtual environment.
The PIP package provides the pdb2pqr Python module as well as the pdb2pqr30 program which can be used from the command line.
Installation from source code¶
You can also download the source code from GitHub (we recommend using a tagged release) and building the code yourself with:
pip install .
from the top-level of the source code directory. Note that developers may want to install the code in “editable” mode with
pip install -e .
Testing¶
The software can be tested for correct functioning via Coverage.py with
or pytest
from the top level of the source directory.
Using PDB2PQR¶
Note
Before you begin! PDB2PQR funding is dependent on your help for continued development and support. Please register before using the software so we can accurately report the number of users to our funding agencies.
PDB2PQR is often used together with the APBS software; e.g., ,in the following type of workflow
- Start with a PDB ID or locally generated PDB file (see PDB molecular structure format).
- Assign titration states and parameters with pdb2pqr to convert the biomolecule and ligands to PQR format (see PQR molecular structure format).
- Perform electrostatics calculations with apbs (can be done from within the PDB2PQR web server).
- Visualize results from within PDB2PQR web server or with Other software.
Web server use¶
Most users will use PDB2PQR through the web server (after registering, of course). However, it is also possible to install local versions of PDB2PQR and run these through the command line.
Command line use¶
pdb2pqr30 [options] --ff={forcefield} {path} {output-path}
This module takes a PDB file as input and performs optimizations before yielding a new PQR-style file in {output-path}.
If {path} is a PDB ID it will automatically be retrieved from the online PDB archive.
In addition to the required {path} and {output-path} arguments, pdb2pqr30 requires one of the following options:
--ff=FIELD_NAMEspecifying the forcefield to use. Runpdb2pqr30 --helpto see specific options.--userff=USER_FIELD_FILEspecifying a user-created forcefield file. Requires--usernamesand overrides--ff.--cleanspecifying no optimization, atom addition, or parameter assignment, just return the original PDB file in aligned format. Overrides--ffand--userffoptions.
Information about additional options can be obtained by running:
pdb2pqr30 --help
Additional command-line tools¶
The following tools are also provided with PDB2PQR.
They all accept the --help option which provides information about usage of these tools.
dx2cube¶
Converts an OpenDX volumetric (e.g., as generated by APBS) to a Gaussian cube-format file.
inputgen¶
Generates an APBS input file with recommended settings.
psize¶
Provides size information about the molecular system and suggests APBS settings.
Examples and algorithms¶
Examples¶
In order to perform electrostatics calculations on your biomolecular structure of interest, you need to provide atomic charge and radius information to APBS. Charges are used to form the biomolecular charge distribution for the Poisson-Boltzmann (PB) equation while the radii are used to construct the dielectric and ionic accessibility functions.
The PDB2PQR web service and software will convert most PDB files into PQR format with some caveats. Although PDB2PQR can fix some missing heavy atoms in sidechains, it does not currently have the (nontrivial) capability to model in large regions of missing backbone and sidechain coordinates. Be patient and make certain that the job you submitted to the PDB2PQR website has finished and you have downloaded the resulting PQR file correctly. It usually takes less than 10 minutes for the job to finish.
These examples assume that you have registered and have access to the PDB2PQR web server.
Adding hydrogens and assigning parameters with the PDB2PQR web server¶
This example uses http://server.poissonboltzmann.org.
Start by choosing a PDB file to process. Either enter the 4-character PDB ID into PDB2PQR or accession number (1FAS is a good starting choice) or upload your own PDB file. Note that, if you choose to enter a 4-character PDB ID, PDB2PQR will process all recognizable chains of PDB file as it was deposited in the PDB (e.g., not the biological unit, any related transformations, etc.).
For most applications, the choice is easy: PARSE. This forcefield has been optimized for implicit solvent calculation and is probably the best choice for visualization of biomolecular electrostatics and many common types of energetic calculations for biomolecules. However, AMBER and CHARMM may be more appropriate if you are attempting to compare directly to simulations performed with those force fields, require nucleic acid support, are simulating ligands parameterized with those force fields, etc.
It is also possible to upload a user-defined forcefield (e.g., to define radii and charges for ligands or unusual residues). Please see Extending PDB2PQR for more information.
This choice is largely irrelevant to electrostatics calculations but may be important for some visualization programs. When in doubt, choose the “Internal naming scheme” which attempts to conform to IUPAC standards.
Under options, be sure the “Ensure that new atoms are not rebuilt too close to existing atoms” and “Optimize the hydrogen bonding network” options are selected. You can select other options as well, if interested.
Download the resulting PQR file and visualize in a molecular graphics program to examine how the hydrogens were added and how hydrogen bonds were optimized.
Parameterizing ligands with the PDB2PQR web server¶
This section outlines the parameterization of ligands using the PEOE_PB methods (see Czodrowski et al, 2006 for more information).
The PDB structure 1HPX includes HIV-1 protease complexed with an inhibitor at 2.0 Å resolution. HIV-1 protease has two chains; residue D25 is anionic on one chain and neutral on the other – these titration states are important in the role of D25 as an acid in the catalytic mechanism.
If we don’t want to include the ligand, then the process is straightforward:
- From the PDB2PQR server web page, enter
1HPXinto the PDB ID field. - Choose whichever forcefield and naming schemes you prefer.
- Under options, be sure the “Ensure that new atoms are not rebuilt too close to existing atoms”, “Optimize the hydrogen bonding network”, and “Use PROPKA to assign protonation states at pH” options are selected. Choose pH 7 for your initial calculations. You can select other options as well, if interested.
- Hit the “Submit” button.
- Once the calculations are complete, you should see a web page with a link to the PROPKA output, a new PQR file, and warnings about the ligand KNI (since we didn’t choose to parameterize it in this calculation). For comparison, you might download the the original PDB file and compare the PDB2PQR-generated structure with the original to see where hydrogens were placed.
This section outlines the parameterization of ligands using the PEOE_PB methods (see DOI:10.1002/prot.21110).
Ligand parameterization currently requires a MOL2-format representation of the ligand to provide the necessary bonding information. MOL2-format files can be obtained through the PRODRG web server or some molecular modeling software packages. PRODRG provides documentation as well as several examples on ligand preparation on its web page.
We’re now ready to look at the 1HPV crystal structure from above and parameterize its ligand, KNI-272.
- From the PDB2PQR server web page, enter
1HPXinto the PDB ID field. - Choose whichever forcefield and naming schemes you prefer.
- Under options, be sure the “Ensure that new atoms are not rebuilt too close to existing atoms”, “Optimize the hydrogen bonding network”, and “Assign charges to the ligand specified in a MOL2 file” options are selected. You can select other options as well, if interested.
- Hit the “Submit” button.
- Once the calculations are complete, you should see a web page with a link to the new PQR file with a warning about debumping P81 (but no warnings about ligand parameterization!).
As a second example, we use the PDB structure 1ABF of L-arabinose binding protein in complex with a sugar ligand at 1.90 Å resolution. To parameterize both this protein and its ligand:
- From the PDB2PQR server web page, enter 1ABF into the PDB ID field.
- Choose whichever forcefield and naming schemes you prefer.
- Under options, be sure the “Ensure that new atoms are not rebuilt too close to existing atoms”, “Optimize the hydrogen bonding network”, and “Assign charges to the ligand specified in a MOL2 file” options are selected. You can select other options as well, if interested.
- Hit the “Submit” button.
- Once the calculations are complete, you should see a web page with a link to the new PQR file with a warning about debumping P66, K295, and K306 (but no warnings about ligand parameterization!).
Algorithms used by PDB2PQR¶
Debumping¶
Unless otherwise instructed with --nodebump, PDB2PQR will attempt to remove steric clashes (debump) between residues.
To determine if a residue needs to be debumped, PDB2PQR compares its atoms to all nearby atoms. With the exception of donor/acceptor pairs and CYS residue SS bonded pairs, a residue needs to be debumped if any of its atoms are within cutoff distance of any other atoms. The cutoff is 1.0 angstrom for hydrogen/hydrogen collisions, 1.5 angstrom for hydrogen/heavy collisions, and 2.0 angstrom otherwise.
Considering the atoms that are conflicted, PDB2PQR changes selected dihedral angle configurations in increments of 5.0 degrees, looking for positions where the residue does not conflict with other atoms. If modifying a dihedral angle does not result in a debumped configuration then the dihedral angle is reset and the next one is tried. If 10 angles are tried without success the algorithm reports failure.
Warning
It should be noted that this is not an optimal solution. This method is not guaranteed to find a solution if it exists and will accept the first completely debumped state found, not the optimal state.
Additionally, PDB2PQR does not consider water atoms when looking for conflicts.
Hydrogen bond optimization¶
Unless otherwise indicated with --noopts, PDB2PQR will attempt to add hydrogens in a way that optimizes hydrogen bonding.
The hydrogen bonding network optimization seeks, as the name suggests, to optimize the hydrogen bonding network of the biomolecule. Currently this entails manipulating the following residues:
- Flipping the side chains of HIS (including user defined HIS states), ASN, and GLN residues;
- Rotating the sidechain hydrogen on SER, THR, TYR, and CYS (if available);
- Determining the best placement for the sidechain hydrogen on neutral HIS, protonated GLU, and protonated ASP;
- Optimizing all water hydrogens.
Titration state assignment¶
Versions 2.1 and earlier of PDB2PQR offered the following methods to assign titration states to molecules at a specified pH.
- PROPKA. This method uses the PROPKA software to assign titration states. More information about PROPKA can be found on its website.
- PDB2PKA. Uses a Poisson-Boltzmann method to assign titration states. This approach is loosely related to the method described by Nielsen and Vriend (2001) doi:10.1002/prot.10.
The current version () of PDB2PQR currently only supports PROPKA while we address portability issues in PDB2PKA.
PDB2PQR has the ability to recognize certain protonation states and keep them fixed during optimization. To use this feature manually rename the residue name in the PDB file as follows:
- Neutral ASP: ASH
- Negative CYS: CYM
- Neutral GLU: GLH
- Neutral HIS: HIE or HSE (epsilon-protonated); HID or HSD (delta-protonated)
- Positive HIS: HIP or HSP
- Neutral LYS: LYN
- Negative TYR: TYM
PDB2PQR is unable to assign charges and radii when they are not available in the forcefield - thus this warning message will occur for most ligands unless a MOL2 file is provided for the ligand with the --ligand option.
Occasionally this message will occur in error for a standard amino acid residue where an atom or residue may be misnamed.
However, some of the protonation states derived from the PROPKA results are not supported in the requested forcefield and thus PDB2PQR is unable to get charges and radii for that state.
PDB2PQR currently supports the following states as derived from PROPKA:
| Protonation State | AMBER Support | CHARMM Support | PARSE Support |
|---|---|---|---|
| Neutral N-Terminus | No | No | Yes |
| Neutral C-Terminus | No | No | Yes |
| Neutral ARG | No | No | No |
| Neutral ASP | Yes [1] | Yes | Yes |
| Negative CYS | Yes [1] | No | Yes |
| Neutral GLU | Yes [1] | Yes | Yes |
| Neutral HIS | Yes | Yes | Yes |
| Neutral LYS | Yes [1] | No | Yes |
| Negative TYR | No | No | Yes |
| [1] | (1, 2, 3, 4) Only if residue is not a terminal residue; if the residue is terminal it will not be set to this state. |
Other software¶
A variety of other software can be used to visualize and process the results of PDB2PQR and APBS calculations.
Visualization software¶
Examples of visualization software that work with output from PDB2PQR and APBS:
Dynamics simulations¶
As an example of PDB2PQR and APBS integration with molecular mechanics sofware, the iAPBS library was developed to facilitate the integration of APBS with other molecular simulation packages. This library has enabled the integration of APBS with several molecular dynamics packages, including NAMD, AMBER, and CHARMM.
APBS is also used directly by Brownian dynamics software such as SDA and BrownDye.
Getting help¶
GitHub issues¶
Our preferred mechanism for user questions and feedback is via GitHub issues. We monitor these issues daily and usually respond within a few days.
Announcements¶
Announcements about updates to the APBS-PDB2PQR software and related news are available through our mailing list; please register for updates.
Contacting the authors¶
If all else fails, feel free to contact nathanandrewbaker@gmail.com.
Supporting PDB2PQR¶
Please register as a user!¶
Please help ensure continued support for APBS-PDB2PQR by registering your use of our software.
Citing our software¶
If you use PDB2PQR in your research, please cite one or more of the following papers:
- Jurrus E, Engel D, Star K, Monson K, Brandi J, Felberg LE, Brookes DH, Wilson L, Chen J, Liles K, Chun M, Li P, Gohara DW, Dolinsky T, Konecny R, Koes DR, Nielsen JE, Head-Gordon T, Geng W, Krasny R, Wei G-W, Holst MJ, McCammon JA, Baker NA. Improvements to the APBS biomolecular solvation software suite. Protein Sci, 27 (1), 112-128, 2018. https://doi.org/10.1002/pro.3280
- Unni S, Huang Y, Hanson RM, Tobias M, Krishnan S, Li WW, Nielsen JE, Baker NA. Web servers and services for electrostatics calculations with APBS and PDB2PQR. J Comput Chem, 32 (7), 1488-1491, 2011. http://dx.doi.org/10.1002/jcc.21720
- Dolinsky TJ, Czodrowski P, Li H, Nielsen JE, Jensen JH, Klebe G, Baker NA. PDB2PQR: Expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res, 35, W522-5, 2007. http://dx.doi.org/10.1093/nar/gkm276
- Dolinsky TJ, Nielsen JE, McCammon JA, Baker NA. PDB2PQR: an automated pipeline for the setup, execution, and analysis of Poisson-Boltzmann electrostatics calculations. Nucleic Acids Res, 32, W665-7, 2004. http://dx.doi.org/10.1093/nar/gkh381
Supporting organizations¶
The PDB2PQR authors would like to give special thanks to the supporting organizations behind the APBS and PDB2PQR software:
- National Institutes of Health
- Primary source of funding for APBS via grant GM069702
- National Biomedical Computation Resource
- Deployment and computational resources support from 2002 to 2020
- National Partnership for Advanced Computational Infrastructure
- Funding and computational resources
- Washington University in St. Louis
- Start-up funding
Extending PDB2PQR¶
Adding new forcefield parameters¶
If you are just adding the parameters of a few residues and atoms to an existing forcefield (e.g., AMBER), you can open the forcefield data file distributed with PDB2PQR (dat/AMBER.DAT) directly and add your parameters.
After the parameter addition, save the force field data file with your changes.
You should also update the corresponding .names file (dat/AMBER.names) if your added residue or atom naming scheme is different from the PDB2PQR canonical naming scheme.
Adding an entirely new forcefield¶
The following steps outline how to add a new force field to PDB2PQR.
You will need to generate a forcefield data file (e.g., myff.DAT) and, if your atom naming scheme of the forcefield is different from the PDB2PQR canonical naming scheme, you will also need to provide a names files (myFF.names).
The format of the names file is described in PDB2PQR NAMES files.
It is recommended to build your own forcefield data and names files based on existing PDB2PQR .DAT and .names examples provided with PDB2PQR in the dat directory.
After finishing your forcefield data file and names file, these can be used with either the command line or the web server versions of PDB2PQR.
Helping with development¶
Adding new functionality¶
PDB2PQR welcomes new contributions; the software API is documented in API Reference. To contribute code, submit a pull request against the master branch in the PDB2PQR repository. Please be sure to run PDB2PQR tests, as described in Testing, before submitting new code.
Helping with to-do items¶
A list of “to-do” items for the code is available in GitHub Issues. A loosely maintained list auto-generated from the documentation is also presented below.
Todo
need to see whether super().__init__() should be
called
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/pdb2pqr/checkouts/v3.1.0/pdb2pqr/aa.py:docstring of pdb2pqr.aa.Amino.__init__, line 3.)
Todo
Determine why this is different than superclass method.
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/pdb2pqr/checkouts/v3.1.0/pdb2pqr/aa.py:docstring of pdb2pqr.aa.Amino.create_atom, line 3.)
Todo
why is the force field name “WAT” for this?
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/pdb2pqr/checkouts/v3.1.0/pdb2pqr/aa.py:docstring of pdb2pqr.aa.LIG.__init__, line 3.)
Todo
Why is water in the amino acid module?
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/pdb2pqr/checkouts/v3.1.0/pdb2pqr/aa.py:docstring of pdb2pqr.aa.WAT, line 3.)
Todo
There is a huge amount of duplicated code in this module.
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/pdb2pqr/checkouts/v3.1.0/pdb2pqr/aa.py:docstring of pdb2pqr.aa.WAT.create_atom, line 5.)
Todo
This module should be broken into separate files.
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/pdb2pqr/checkouts/v3.1.0/pdb2pqr/biomolecule.py:docstring of pdb2pqr.biomolecule, line 3.)
Todo
Since the misslist is used to identify incorrect charge assignments, this routine does not list the 3 and 5 termini of nucleic acid chains as having non-integer charge even though they are (correctly) non-integer.
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/pdb2pqr/checkouts/v3.1.0/pdb2pqr/biomolecule.py:docstring of pdb2pqr.biomolecule.Biomolecule.charge, line 3.)
Todo
Figure out if this is redundant with
Biomolecule.num_bio_atoms()
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/pdb2pqr/checkouts/v3.1.0/pdb2pqr/biomolecule.py:docstring of pdb2pqr.biomolecule.Biomolecule.num_heavy, line 3.)
Todo
This function needs to be cleaned and simplified
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/pdb2pqr/checkouts/v3.1.0/pdb2pqr/biomolecule.py:docstring of pdb2pqr.biomolecule.Biomolecule.set_termini, line 6.)
Todo
Why are we setting residue types to numeric values (see code)?
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/pdb2pqr/checkouts/v3.1.0/pdb2pqr/biomolecule.py:docstring of pdb2pqr.biomolecule.Biomolecule.update_residue_types, line 3.)
Todo
Manage several blocks of data.
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/pdb2pqr/checkouts/v3.1.0/pdb2pqr/cif.py:docstring of pdb2pqr.cif.read_cif, line 3.)
Todo
This class needs to be susbtantially refactored in to multiple classes with clear responsibilities.
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/pdb2pqr/checkouts/v3.1.0/pdb2pqr/debump.py:docstring of pdb2pqr.debump.Debump, line 3.)
Todo
Why are files being loaded so deep in this function?
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/pdb2pqr/checkouts/v3.1.0/pdb2pqr/forcefield.py:docstring of pdb2pqr.forcefield.Forcefield.__init__, line 3.)
Todo
Should this be a staticmethod or a classmethod?
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/pdb2pqr/checkouts/v3.1.0/pdb2pqr/forcefield.py:docstring of pdb2pqr.forcefield.Forcefield.get_amber_params, line 3.)
Todo
Figure out why residue.type has int values
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/pdb2pqr/checkouts/v3.1.0/pdb2pqr/forcefield.py:docstring of pdb2pqr.forcefield.Forcefield.get_amber_params, line 5.)
Todo
Should this be a staticmethod or a classmethod?
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/pdb2pqr/checkouts/v3.1.0/pdb2pqr/forcefield.py:docstring of pdb2pqr.forcefield.Forcefield.get_charmm_params, line 3.)
Todo
Figure out why residue.type has int values
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/pdb2pqr/checkouts/v3.1.0/pdb2pqr/forcefield.py:docstring of pdb2pqr.forcefield.Forcefield.get_charmm_params, line 5.)
Todo
Why do both get_params() and get_params1() exist?
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/pdb2pqr/checkouts/v3.1.0/pdb2pqr/forcefield.py:docstring of pdb2pqr.forcefield.Forcefield.get_params, line 7.)
Todo
Why do both get_params() and get_params1() exist?
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/pdb2pqr/checkouts/v3.1.0/pdb2pqr/forcefield.py:docstring of pdb2pqr.forcefield.Forcefield.get_params1, line 7.)
Todo
Should this be a staticmethod or a classmethod?
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/pdb2pqr/checkouts/v3.1.0/pdb2pqr/forcefield.py:docstring of pdb2pqr.forcefield.Forcefield.get_parse_params, line 3.)
Todo
Should this be a staticmethod instead of classmethod?
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/pdb2pqr/checkouts/v3.1.0/pdb2pqr/forcefield.py:docstring of pdb2pqr.forcefield.ForcefieldHandler.find_matching_names, line 3.)
Todo
Should this be a staticmethod instead of classmethod?
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/pdb2pqr/checkouts/v3.1.0/pdb2pqr/forcefield.py:docstring of pdb2pqr.forcefield.ForcefieldHandler.update_map, line 4.)
Todo
This module has too many lines and should be simplified.
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/pdb2pqr/checkouts/v3.1.0/pdb2pqr/hydrogens/__init__.py:docstring of pdb2pqr.hydrogens, line 5.)
Todo
This class really needs to be refactored.
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/pdb2pqr/checkouts/v3.1.0/pdb2pqr/hydrogens/__init__.py:docstring of pdb2pqr.hydrogens.HydrogenRoutines, line 3.)
Todo
Remove hard-coded progress threshold and increment values.
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/pdb2pqr/checkouts/v3.1.0/pdb2pqr/hydrogens/__init__.py:docstring of pdb2pqr.hydrogens.HydrogenRoutines.optimize_hydrogens, line 6.)
Todo
This function needs to be simplified.
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/pdb2pqr/checkouts/v3.1.0/pdb2pqr/hydrogens/__init__.py:docstring of pdb2pqr.hydrogens.HydrogenRoutines.optimize_hydrogens, line 10.)
Todo
The type of the res appears to be incorrect.
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/pdb2pqr/checkouts/v3.1.0/pdb2pqr/hydrogens/__init__.py:docstring of pdb2pqr.hydrogens.HydrogenRoutines.parse_hydrogen, line 6.)
Todo
This function is too long and needs to be simplified.
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/pdb2pqr/checkouts/v3.1.0/pdb2pqr/hydrogens/__init__.py:docstring of pdb2pqr.hydrogens.HydrogenRoutines.parse_hydrogen, line 9.)
Todo
Lots of code in this function could be accelerated with
numpy.
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/pdb2pqr/checkouts/v3.1.0/pdb2pqr/hydrogens/optimize.py:docstring of pdb2pqr.hydrogens.optimize.Optimize.get_pair_energy, line 3.)
Todo
Lots of hard-coded parameters in this function that need to be abstracted out.
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/pdb2pqr/checkouts/v3.1.0/pdb2pqr/hydrogens/optimize.py:docstring of pdb2pqr.hydrogens.optimize.Optimize.get_pair_energy, line 7.)
Todo
Should this be a staticmethod rather than a classmethod?
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/pdb2pqr/checkouts/v3.1.0/pdb2pqr/hydrogens/optimize.py:docstring of pdb2pqr.hydrogens.optimize.Optimize.get_position_with_three_bonds, line 3.)
Todo
Remove hard-coded values in function.
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/pdb2pqr/checkouts/v3.1.0/pdb2pqr/hydrogens/optimize.py:docstring of pdb2pqr.hydrogens.optimize.Optimize.get_position_with_three_bonds, line 6.)
Todo
Remove some hard-coded values in this function.
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/pdb2pqr/checkouts/v3.1.0/pdb2pqr/hydrogens/optimize.py:docstring of pdb2pqr.hydrogens.optimize.Optimize.get_positions_with_two_bonds, line 3.)
Todo
Remove hard-coded hydrogen bond distance and angles.
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/pdb2pqr/checkouts/v3.1.0/pdb2pqr/hydrogens/optimize.py:docstring of pdb2pqr.hydrogens.optimize.Optimize.is_hbond, line 3.)
Todo
Does this need to be a classmethod or could it be a staticmethod?
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/pdb2pqr/checkouts/v3.1.0/pdb2pqr/hydrogens/optimize.py:docstring of pdb2pqr.hydrogens.optimize.Optimize.make_atom_with_one_bond_h, line 3.)
Todo
Does this need to be a classmethod or could it be a staticmethod?
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/pdb2pqr/checkouts/v3.1.0/pdb2pqr/hydrogens/optimize.py:docstring of pdb2pqr.hydrogens.optimize.Optimize.make_atom_with_one_bond_lp, line 3.)
Todo
Does this need to be a classmethod or could it be a staticmethod?
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/pdb2pqr/checkouts/v3.1.0/pdb2pqr/hydrogens/optimize.py:docstring of pdb2pqr.hydrogens.optimize.Optimize.make_water_with_one_bond, line 5.)
Todo
Remove some hard-coded values in this function.
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/pdb2pqr/checkouts/v3.1.0/pdb2pqr/hydrogens/optimize.py:docstring of pdb2pqr.hydrogens.optimize.Optimize.try_single_alcoholic_h, line 3.)
Todo
Remove some hard-coded values in this function and figure out where others (e.g., “72”) come from.
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/pdb2pqr/checkouts/v3.1.0/pdb2pqr/hydrogens/optimize.py:docstring of pdb2pqr.hydrogens.optimize.Optimize.try_single_alcoholic_lp, line 3.)
Todo
Replace hard-coded values in the function.
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/pdb2pqr/checkouts/v3.1.0/pdb2pqr/hydrogens/structures.py:docstring of pdb2pqr.hydrogens.structures.Alcoholic.finalize, line 3.)
Todo
Rename this and related methods to conform with PEP8
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/pdb2pqr/checkouts/v3.1.0/pdb2pqr/hydrogens/structures.py:docstring of pdb2pqr.hydrogens.structures.HydrogenHandler.endElement, line 3.)
Todo
Rename this and related methods to conform with PEP8
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/pdb2pqr/checkouts/v3.1.0/pdb2pqr/hydrogens/structures.py:docstring of pdb2pqr.hydrogens.structures.HydrogenHandler.startElement, line 3.)
Todo
This looks like a bug: donorh ends up being the last item in donor.bonds. This may be fixed by setting a best_donorh to go with bestdist and using best_donorh in the function below
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/pdb2pqr/checkouts/v3.1.0/pdb2pqr/hydrogens/structures.py:docstring of pdb2pqr.hydrogens.structures.Water.try_acceptor, line 3.)
Todo
Remove hard-coded parameters.
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/pdb2pqr/checkouts/v3.1.0/pdb2pqr/inputgen.py:docstring of pdb2pqr.inputgen.Elec.__init__, line 3.)
Todo
is this function still useful?
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/pdb2pqr/checkouts/v3.1.0/pdb2pqr/inputgen.py:docstring of pdb2pqr.inputgen.Input.dump_pickle, line 3.)
Todo
This should be a context manager (to close the open file).
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/pdb2pqr/checkouts/v3.1.0/pdb2pqr/io.py:docstring of pdb2pqr.io.get_pdb_file, line 7.)
Todo
Remove hard-coded parameters.
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/pdb2pqr/checkouts/v3.1.0/pdb2pqr/io.py:docstring of pdb2pqr.io.get_pdb_file, line 8.)
Todo
This function should be moved into the APBS code base.
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/pdb2pqr/checkouts/v3.1.0/pdb2pqr/io.py:docstring of pdb2pqr.io.read_dx, line 9.)
Todo
This function should be moved into the APBS code base.
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/pdb2pqr/checkouts/v3.1.0/pdb2pqr/io.py:docstring of pdb2pqr.io.write_cube, line 6.)
Todo
Some of the definitions in this module belong in a configuration file other than here.
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/pdb2pqr/checkouts/v3.1.0/pdb2pqr/ligand/__init__.py:docstring of pdb2pqr.ligand, line 3.)
Todo
It seems inconsistent that this function pulls radii from a dictionary and the biomolecule routines use force field files.
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/pdb2pqr/checkouts/v3.1.0/pdb2pqr/ligand/mol2.py:docstring of pdb2pqr.ligand.mol2.Mol2Atom.assign_radius, line 3.)
Todo
Need separate argparse groups for PDB2PKA and PROPKA. These exist but need real options.
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/pdb2pqr/checkouts/v3.1.0/pdb2pqr/main.py:docstring of pdb2pqr.main.build_main_parser, line 3.)
Todo
this module is already too long but this function fits better here. Other possible place would be utilities.
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/pdb2pqr/checkouts/v3.1.0/pdb2pqr/main.py:docstring of pdb2pqr.main.drop_water, line 3.)
Todo
This function should be moved into the APBS code base.
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/pdb2pqr/checkouts/v3.1.0/pdb2pqr/main.py:docstring of pdb2pqr.main.dx_to_cube, line 8.)
Todo
These routines should be generalized to biomolecules; none of them are specific to biomolecules.
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/pdb2pqr/checkouts/v3.1.0/pdb2pqr/main.py:docstring of pdb2pqr.main.non_trivial, line 3.)
Todo
Move this to another module (io)
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/pdb2pqr/checkouts/v3.1.0/pdb2pqr/main.py:docstring of pdb2pqr.main.print_pdb, line 3.)
Todo
Move this to another module (io)
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/pdb2pqr/checkouts/v3.1.0/pdb2pqr/main.py:docstring of pdb2pqr.main.print_pqr, line 3.)
Todo
I wish this could be done with argparse.
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/pdb2pqr/checkouts/v3.1.0/pdb2pqr/main.py:docstring of pdb2pqr.main.transform_arguments, line 3.)
Todo
This code is duplicated in several places.
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/pdb2pqr/checkouts/v3.1.0/pdb2pqr/na.py:docstring of pdb2pqr.na.Nucleic.create_atom, line 5.)
Todo
If multiple modifications are present, only the last one in the file is preserved.
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/pdb2pqr/checkouts/v3.1.0/pdb2pqr/pdb.py:docstring of pdb2pqr.pdb.REVDAT.__init__, line 3.)
Todo
This code could be combined with inputgen.
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/pdb2pqr/checkouts/v3.1.0/pdb2pqr/psize.py:docstring of pdb2pqr.psize, line 3.)
Todo
This code should be moved to the APBS code base.
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/pdb2pqr/checkouts/v3.1.0/pdb2pqr/psize.py:docstring of pdb2pqr.psize, line 5.)
Todo
This is messed up. Why are we parsing the PQR manually here when we already have other routines to do that? This function should be replaced by a call to existing routines.
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/pdb2pqr/checkouts/v3.1.0/pdb2pqr/psize.py:docstring of pdb2pqr.psize.Psize.parse_lines, line 3.)
Todo
remove hard-coded values from this function.
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/pdb2pqr/checkouts/v3.1.0/pdb2pqr/psize.py:docstring of pdb2pqr.psize.Psize.set_fine_grid_points, line 3.)
Todo
Replace hard-coded values in this function.
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/pdb2pqr/checkouts/v3.1.0/pdb2pqr/psize.py:docstring of pdb2pqr.psize.Psize.set_length, line 3.)
Todo
Remove hard-coded values from this function.
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/pdb2pqr/checkouts/v3.1.0/pdb2pqr/psize.py:docstring of pdb2pqr.psize.Psize.set_smallest, line 9.)
Todo
There are many unnecessary parameters in this module due to FORTRAN/C assumptions about how the code should behave.
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/pdb2pqr/checkouts/v3.1.0/pdb2pqr/quatfit.py:docstring of pdb2pqr.quatfit, line 13.)
Todo
Remove hard-coded parameters of function.
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/pdb2pqr/checkouts/v3.1.0/pdb2pqr/quatfit.py:docstring of pdb2pqr.quatfit.qfit, line 4.)
Todo
Should this class have a member variable for dihedrals? Pylint complains!
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/pdb2pqr/checkouts/v3.1.0/pdb2pqr/residue.py:docstring of pdb2pqr.residue.Residue, line 3.)
File formats¶
Molecular structure formats¶
PQR molecular structure format¶
This format is a modification of the PDB format which allows users to add charge and radius parameters to existing PDB data while keeping it in a format amenable to visualization with standard molecular graphics programs. The origins of the PQR format are somewhat uncertain, but has been used by several computational biology software programs, including MEAD and AutoDock. UHBD uses a very similar format called QCD.
APBS reads very loosely-formatted PQR files: all fields are whitespace-delimited rather than the strict column formatting mandated by the PDB format. This more liberal formatting allows coordinates which are larger/smaller than ± 999 Å. APBS reads data on a per-line basis from PQR files using the following format::
Field_name Atom_number Atom_name Residue_name Chain_ID Residue_number X Y Z Charge Radius
where the whitespace is the most important feature of this format. The fields are:
Field_name- A string which specifies the type of PQR entry and should either be ATOM or HETATM in order to be parsed by APBS.
Atom_number- An integer which provides the atom index.
Atom_name- A string which provides the atom name.
Residue_name- A string which provides the residue name.
Chain_ID- An optional string which provides the chain ID of the atom. Note that chain ID support is a new feature of APBS 0.5.0 and later versions.
Residue_number- An integer which provides the residue index.
X Y Z- 3 floats which provide the atomic coordinates (in Å)
Charge- A float which provides the atomic charge (in electrons).
Radius- A float which provides the atomic radius (in Å).
Clearly, this format can deviate wildly from PDB due to the use of whitespaces rather than specific column widths and alignments. This deviation can be particularly significant when large coordinate values are used. However, in order to maintain compatibility with most molecular graphics programs, the PDB2PQR program and the utilities provided with APBS attempt to preserve the PDB format as much as possible.
PDB molecular structure format¶
The PDB file format is described in detail in the Protein Data Bank documentation.
MOL2 molecular structure format¶
The MOL2 file format is a popular method for specifying chemical structure, including atom types, positions, and bonding. It is described in detail in the Tripos documentation.
Parameter formats¶
PDB2PQR NAMES files¶
Much of the difficulty in adding a new forcefield to PDB2PQR depends on the naming scheme used in that forcefield.
XML file format¶
To start, either a flat file or XML file containing the desired forcefield’s parameters should be made - see AMBER.DAT and AMBER.xml for examples.
If the forcefield’s naming scheme matches the canonical naming scheme, that’s all that is necessary.
If the naming schemes differ, however, conversions must be made. These are made in the *.names file (see CHARMM.names, for example).
In this file you will see sections like:</p>
<residue>
<name>WAT</name>
<useresname>TP3M</useresname>
<atom>
<name>O</name>
<useatomname>OH2</useatomname>
</atom>
</residue>
This section tells PDB2PQR that for the oxygen atom O in WAT, CHARMM uses the names OH2 and TP3M, respectively. When the XML file is read in, PDB2PQR ensures that the WAT/O pair points to TP3M/OH2 such that the appropriate parameters are returned. But for naming schemes that greatly differ from the PDB2PQR canonical naming scheme, this could get really ugly. As a result, PDB2PQR can use regular expressions to simplify the renaming process, i.e.:
<residue>
<name>[NC]?...$</name>
<atom>
<name>H</name>
<useatomname>HN</useatomname>
</atom>
</residue>
This section of code will ensure that the H atom of all canonical residue names that match the [NC]?...$ regular expression point to HN instead.
This regular expression matches all three-letter residue names, residue names with an ‘N’ prepended (N-Termini), and residue names with a ‘C’ prepended (C-Termini).
For twenty amino acids, sixty residue name changes can all be done by a single section.
The use of regular expressions is therefore a much more powerful method of handling naming scheme differences than working on a one to one basis.
There are a few other additional notes when using the .names file.
First, the $group variable is used to denote the matching group of a regular expression, for instance:
<residue>
<name>HI([PDE])$</name>
<useresname>HS$group</useresname>
</residue>
This section replaces HIP/HID/HIE with HSP/HSD/HSE by first matching the HI([PDE])$ regular expression and then using the group that is enclosed by parantheses to fill in the name to use.
Second, sections are cumulative - since CHARMM, for instance, has a patch-based naming scheme, one single canonical residue name can map to multiple forcefield-scheme names. Let’s look at how to map an SS-bonded Cysteine (canonical name CYX) to the CHARMM naming scheme:
<residue>
<name>CYX</name>
<useresname>CYS</useresname>
</residue>
<residue>
<name>CYX</name>
<useresname>DISU</useresname>
<atom>
<name>CB</name>
<useatomname>1CB</useatomname>
</atom>
<atom>
<name>SG</name>
<useatomname>1SG</useatomname>
</atom>
</residue>
The CYX residue is first mapped to CHARMM’s CYS, and then to CHARMM’s DISU object. All atom names that are found in DISU overwrite those found in CYS - in effect, the DISU patch is applied to CYS, yielding the desired CYX. This cumulative can be repeated as necessary.
Caveats about atom naming¶
In an ideal world each individual residue and atom would have a standard, distinct name. Unfortunately several naming schemes for atoms exist, particularly for hydrogens. As such, in order to detect the presence/absence of atoms in a biomolecule, an internal canonical naming scheme is used. The naming scheme used in PDB2PQR is the one recommended by the PDB itself, and derives from the IUPAC naming recommendations [1]
| [1] |
|
This canonical naming scheme is used as the default PDB2PQR output. All conversions in PDB2PQR use the internal canonical naming scheme to determine distinct atom names. In previous versions of PDB2PQR, these conversions were stored in long lists of if statements, but for transparency and editing this is a bad thing. Instead, all conversions can now be found in XML as described above.
There are a few additions to the canonical naming scheme, mirrored after the AMBER naming scheme (chosen since for the most part it follows the IUPAC recommendations).
These changes are made in PATCHES.xml, and allow any of the following to be patched as necessary as well as detected on input:
N*- N-Terminal Residue (i.e. NALA, NLEU)
NEUTRAL-N*- Neutral N-Terminal Residue
C*- C-Terminal Residue (i.e. CLYS, CTYR)
NEUTRAL-C*- Neutral C-Terminal Residue
*5- 5-Terminus for Nucleic Acids (i.e. DA5)
*3- 3-Terminus for Nucleic Acids (i.e. DA3)
ASH- Neutral ASP
CYX- SS-bonded CYS
CYM- Negative CYS
GLH- Neutral GLU
HIP- Positive HIS
HID- Neutral HIS, proton HD1 present
HIE- Neutral HIS, proton HE2 present
LYN- Neutral LYS
TYM- Negative TYR
PDB2PQR DAT files¶
A PDB2PQR .DAT file has the following whitespace-delimited columns:
- Name of the residue (
str, e.g., RU, ARG, WAT, etc.) - Name of the atom (
str, e.g., HB3, CA, HA, etc.) - Charge of the atom (
float, in electrons) - Radius of the atom (
float, in Å) - (optional) Atom type (
str, e.g., HT, etc.)
Lines that start with # are treated as comments.
API Reference¶
The pdb2pqr30 command provides a command-line interface to PDB2PQR’s functionality.
It is built on classes and functions in the pdb2pqr module.
The API of pdb2pqr is documented here for developers who might want to directly use the PDB2PQR code.
Note
The API is still changing and there is currently no guarantee that it will remain stable between minor releases.
Forcefield support modules¶
definitions¶
XML handling for biomolecular residue topology definitions.
Code author: Jens Erik Nielsen
Code author: Todd Dolinsky
Code author: Yong Huang
-
class
pdb2pqr.definitions.Definition(aa_file, na_file, patch_file)[source]¶ Force field topology definitions.
The Definition class contains the structured definitions found in the files and several mappings for easy access to the information.
-
class
pdb2pqr.definitions.DefinitionAtom(name=None, x=None, y=None, z=None)[source]¶ Store force field atom topology definitions.
-
class
pdb2pqr.definitions.DefinitionHandler[source]¶ Handle definition XML file content.
-
endElement(name)[source]¶ End XML element parsing.
Parameters: name (str) – element name
Raises: - KeyError – for invalid atom or residue names
- RuntimeError – for unexpected XML features or format
-
forcefield¶
Force fields are fun.
The forcefield structure is modeled off of the structures.py file, where each forcefield is considered a chain of residues of atoms.
Code author: Todd Dolinsky
Code author: Yong Huang
-
class
pdb2pqr.forcefield.Forcefield(ff_name, definition, userff, usernames=None)[source]¶ Parameter definitions for a given forcefield.
Note
Pass ff and ff names file like objects rather than sorting out whether to use user-created files here.
The forcefield class contains definitions for a given forcefield. Each forcefield object contains a dictionary of residues, with each residue containing a dictionary of atoms. Dictionaries are used instead of lists as the ordering is not important. The forcefield definition files are unedited, directly from the forcefield - all transformations are done within.
-
__init__(ff_name, definition, userff, usernames=None)[source]¶ Initialize the class by parsing the definition file.
Todo
Why are files being loaded so deep in this function?
Parameters: - ff_name (str) – the name of the forcefield (can be None)
- definition (Definition) – the definition object for the Forcefield
- userff (str) – path for user-defined forcefields file
- usernames (str) – path to user-defined atom/residue names file
Raises: ValueError – if invalid force field names specified
-
classmethod
get_amber_params(residue, name)[source]¶ Get AMBER forcefield definitions.
Todo
Should this be a staticmethod or a classmethod?
Todo
Figure out why residue.type has
intvaluesParameters: Returns: (forcefield name of residue, forcefield name of atom)
Return type:
-
classmethod
get_charmm_params(residue, name)[source]¶ Get CHARMM forcefield definitions.
Todo
Should this be a staticmethod or a classmethod?
Todo
Figure out why residue.type has
intvaluesParameters: Returns: (forcefield name of residue, forcefield name of atom)
Return type:
-
get_group(resname, atomname)[source]¶ Get the group/type associated with the input fields.
Parameters: Returns: group name or empty string
Return type:
-
get_names(resname, atomname)[source]¶ Get forcefield names associated with residue and atom.
The names passed in point to ForcefieldResidue and ForcefieldAtom objects which may have different names; grab these names and return.
Parameters: Returns: (forcefield’s name for this residue, forcefield’s name for this atom)
Return type:
-
get_params(resname, atomname)[source]¶ Get the charge and radius parameters for an atom in a residue.
The residue itself is needed instead of simply its name because the forcefield may use a different residue name than the standard amino acid name.
Todo
Why do both
get_params()andget_params1()exist?Parameters: Returns: (charge of the atom, radius of the atom)
Return type:
-
get_params1(residue, name)[source]¶ Get the charge and radius parameters for an atom in a residue.
The residue itself is needed instead of simply its name because the forcefield may use a different residue name than the standard amino acid name.
Todo
Why do both
get_params()andget_params1()exist?Parameters: Returns: (charge of the atom, radius of the atom)
Return type:
-
classmethod
get_parse_params(residue, name)[source]¶ Get PARSE forcefield definitions.
Todo
Should this be a staticmethod or a classmethod?
Parameters: Returns: (forcefield name of residue, forcefield name of atom)
Return type:
-
get_residue(resname)[source]¶ Return the residue object with the given resname.
Parameters: resname (str) – the name of the residue Returns: residue object Return type: ForcefieldResidue
-
-
class
pdb2pqr.forcefield.ForcefieldAtom(name, charge, radius, resname, group='')[source]¶ ForcefieldAtom class.
Contains fields that are related to the forcefield at the atom level.
-
get(name)[source]¶ Get a member of the ForcefieldAtom class.
Parameters: name (str) – the name of the member, including:
- name: The atom name (returns string)
- charge: The charge on the atom (returns float)
- radius: The radius of the atom (returns float)
- epsilon: The epsilon assocaited with the atom (returns float)
Returns: the value of the member Raises: KeyError – if member does not exist
-
-
class
pdb2pqr.forcefield.ForcefieldHandler(map_, reference)[source]¶ Process XML-format force field parameter files.
-
characters(text)[source]¶ Parse text information within XML tag.
Parameters: text – the text value between the XML tags
-
classmethod
find_matching_names(regname, map_)[source]¶ Find strings in the map that match the given regular expression.
Todo
Should this be a staticmethod instead of classmethod?
Parameters: Returns: a list of regular expression match objects for dictionary keys that match the regular expression.
Return type: [re.Match]
-
-
class
pdb2pqr.forcefield.ForcefieldResidue(name)[source]¶ ForcefieldResidue class
The ForceFieldResidue class contains a mapping of all atoms within the residue for easy searching.
-
__init__(name)[source]¶ Initialize the ForceFieldResidue object.
Parameters: name (str) – the name of the residue
-
add_atom(atom)[source]¶ Add an atom to the ForcefieldResidue object.
Parameters: atom (Atom) – the atom to be added
-
get_atom(atomname)[source]¶ Return the atom object with the given atomname.
Parameters: resname (str) – the name of the atom Returns: the atom object Return type: ForcefieldAtom
-
Molecular structure modules¶
aa¶
Amino Acid Structures for PDB2PQR
This module contains the base amino acid structures for pdb2pqr.
Code author: Todd Dolinsky
Code author: Nathan Baker
-
class
pdb2pqr.aa.ALA(atoms, ref)[source]¶ Alanine class.
-
class
pdb2pqr.aa.ARG(atoms, ref)[source]¶ Arginine class.
-
class
pdb2pqr.aa.ASN(atoms, ref)[source]¶ Asparagine class.
-
class
pdb2pqr.aa.ASP(atoms, ref)[source]¶ Aspartic acid class.
-
class
pdb2pqr.aa.Amino(atoms, ref)[source]¶ Amino acid class
This class provides standard features of the amino acids.
-
__init__(atoms, ref)[source]¶ Initialize object.
Todo
need to see whether
super().__init__()should be calledParameters:
-
add_atom(atom)[source]¶ Add atom to residue.
Override the existing add_atom; include the link to the reference object.
Parameters: atom (Atom) – atom to add
-
add_dihedral_angle(value)[source]¶ Add a dihedral angle to the residue list.
Parameters: value (float) – dihedral angle (in degrees) to add
-
create_atom(atomname, newcoords)[source]¶ Create an atom.
Todo
Determine why this is different than superclass method.
Override the generic residue’s version of create_atom().
Parameters:
-
rebuild_tetrahedral(atomname)[source]¶ Rebuild a tetrahedral hydrogen group.
This is necessary due to the shortcomings of the quatfit routine - given a tetrahedral geometry and two existing hydrogens, the quatfit routines have two potential solutions. This function uses basic tetrahedral geometry to fix this issue.
Parameters: atomname (str) – the atom name to add Returns: indication of whether this was successful Return type: bool
-
-
class
pdb2pqr.aa.CYS(atoms, ref)[source]¶ Cysteine class.
-
class
pdb2pqr.aa.GLN(atoms, ref)[source]¶ Glutamine class.
-
class
pdb2pqr.aa.GLU(atoms, ref)[source]¶ Glutamic acid class.
-
class
pdb2pqr.aa.GLY(atoms, ref)[source]¶ Glycine class.
-
class
pdb2pqr.aa.HIS(atoms, ref)[source]¶ Histidine class.
-
letter_code()[source]¶ Return letter code for amino acid.
Returns: amino acid 1-letter code Return type: str
-
set_state()[source]¶ Set forcefield name based on current titration state.
Histidines are a special case due to the presence of several different forms. This function sets all neutral forms of HIS to neutral HIS by checking to see if optimization removed hacceptor or hdonor flags. Otherwise HID is used as the default.
-
-
class
pdb2pqr.aa.ILE(atoms, ref)[source]¶ Isoleucine class.
-
class
pdb2pqr.aa.LEU(atoms, ref)[source]¶ Leucine class.
-
class
pdb2pqr.aa.LIG(atoms, ref)[source]¶ Generic ligand class.
-
__init__(atoms, ref)[source]¶ Initialize this object.
Todo
why is the force field name “WAT” for this?
Parameters:
-
-
class
pdb2pqr.aa.LYS(atoms, ref)[source]¶ Lysine class.
-
class
pdb2pqr.aa.MET(atoms, ref)[source]¶ Methionine class.
-
class
pdb2pqr.aa.PHE(atoms, ref)[source]¶ Phenylalanine class.
-
class
pdb2pqr.aa.PRO(atoms, ref)[source]¶ Proline class.
-
class
pdb2pqr.aa.SER(atoms, ref)[source]¶ Serine class.
-
class
pdb2pqr.aa.THR(atoms, ref)[source]¶ Threonine class.
-
class
pdb2pqr.aa.TRP(atoms, ref)[source]¶ Tryptophan class.
-
class
pdb2pqr.aa.TYR(atoms, ref)[source]¶ Tyrosine class.
-
class
pdb2pqr.aa.VAL(atoms, ref)[source]¶ Valine class.
-
class
pdb2pqr.aa.WAT(atoms, ref)[source]¶ Water class.
Todo
Why is water in the amino acid module?
-
add_atom(atom)[source]¶ Add an atom to the residue.
Override the existing add_atom - include the link to the reference object.
Parameters: atom (Atom) – add atom to residue
-
create_atom(atomname, newcoords)[source]¶ Create a water atom.
Note the HETATM field.
Todo
There is a huge amount of duplicated code in this module.
Parameters:
-
water_residue_names= ['HOH', 'WAT']¶
-
hydrogens and submodule contents¶
hydrogens¶
Hydrogen optimization module for PDB2PQR.
This is an module for hydrogen optimization routines.
Todo
This module has too many lines and should be simplified.
Code author: Todd Dolinsky
Code author: Jens Erik Nielsen
Code author: Yong Huang
Code author: Nathan Baker
-
class
pdb2pqr.hydrogens.HydrogenRoutines(debumper, handler)[source]¶ The main routines for hydrogen optimization.
Todo
This class really needs to be refactored.
-
__init__(debumper, handler)[source]¶ Initialize object.
Parameters: - debumper (debump.Debump) – Debump object
- handler (HydrogenHandler) – HydrogenHandler object
-
cleanup()[source]¶ Delete extra carboxylic atoms.
If there are any extra carboxlyic
*1atoms, delete them. This may occur when no optimization is chosen.
-
initialize_full_optimization()[source]¶ Initialize the full optimization.
Detects all optimizeable donors and acceptors and sets the internal optlist.
-
initialize_wat_optimization()[source]¶ Initialize optimization for waters only.
Detects all optimizeable donors and acceptors and sets the internal optlist.
-
is_optimizeable(residue)[source]¶ Check to see if the given residue is optimizeable. There are three ways to identify a residue:
- By name (i.e., HIS)
- By reference name - a PDB file HSP has a HIS reference name
- By patch - applied by propka, terminal selection
Parameters: residue (Residue) – the residue in question Returns: None if not optimizeable, otherwise the OptimizationHolder instance that corresponds to the residue. Return type: None or OptimizationHolder
-
optimize_hydrogens()[source]¶ The main driver for the optimization.
Note
Should be called only after the optlist has been initialized.
Todo
Remove hard-coded progress threshold and increment values.
Todo
This function needs to be simplified.
-
parse_hydrogen(res, topo)[source]¶ Parse a list of lines in order to make a hydrogen definition.
This is the current definition:
Name Ttyp A R # Stdconf HT Chi OPTmTodo
The type of the res appears to be incorrect.
Todo
This function is too long and needs to be simplified.
Parameters: - res (unknown) – the lines to parse (list)
- topo (pdb2pqr.topology.Topology) – Topology object
Returns: the hydrogen definition object
Return type:
-
classmethod
pka_switchstate(amb, state_id_)[source]¶ Switch a residue to a new state by first removing all hydrogens. This routine is used in pKa calculations only!
Parameters: - amb (tup) – the amibiguity to switch
- state_id (int) – the state id to switch to
-
read_hydrogen_def(topo)[source]¶ Read the hydrogen definition file
Parameters: topo (Topology object) – Topology object
-
set_optimizeable_hydrogens()[source]¶ Set any hydrogen listed in HYDROGENS.xml that is optimizeable.
Used BEFORE hydrogen optimization to label atoms so that they won’t be debumped - i.e. if SER HG is too close to another atom, don’t debump but wait for optimization.
Note
This function should not be used if full optimization is not taking place.
-
-
pdb2pqr.hydrogens.create_handler(hyd_path='HYDROGENS.xml')[source]¶ Create and populate a hydrogen handler.
Parameters: hyd_def_file (string or pathlib.Path object) – path to hydrogen definition file Returns: HydrogenHandler object Return type: HydrogenHandler
hydrogens.optimize¶
Hydrogen optimization routines.
Code author: Todd Dolinsky
Code author: Jens Erik Nielsen
Code author: Yong Huang
Code author: Nathan Baker
-
class
pdb2pqr.hydrogens.optimize.Optimize[source]¶ The holder class for the hydrogen optimization routines.
Individual optimization types inherit off of this class. Any functions used by multiple types appear here.
-
static
get_hbond_angle(atom1, atom2, atom3)[source]¶ Get the angle between three atoms
Parameters: Returns: the angle between the atoms in degrees
Return type:
-
static
get_pair_energy(donor, acceptor)[source]¶ Get the energy between two atoms
Todo
Lots of code in this function could be accelerated with
numpy.Todo
Lots of hard-coded parameters in this function that need to be abstracted out.
Parameters: Returns: the energy of the pair
Return type:
-
classmethod
get_position_with_three_bonds(atom)[source]¶ Find position for last bond in tetrahedral geometry.
Todo
Should this be a staticmethod rather than a classmethod?
Todo
Remove hard-coded values in function.
If there’s three bonds in a tetrahedral geometry, there’s only one available position. Find that position.
Parameters: atom (Atom) – atom to check Returns: coordinates Return type: (float, float, float)
-
classmethod
get_positions_with_two_bonds(atom)[source]¶ Return possible coordinates for new bonds.
Todo
Remove some hard-coded values in this function.
Given a tetrahedral geometry with two existing bonds, return the two potential sets of coordinates that are possible for a new bond.
Parameters: atom (Atom) – atom to test for bonds Returns: 2-tuple of coordinates (floats) Return type: tuple
-
is_hbond(donor, acc)[source]¶ Determine whether this donor acceptor pair is a hydrogen bond.
Todo
Remove hard-coded hydrogen bond distance and angles.
Parameters: - donor – donor atom
- acc – acceptor atom
Returns: whether this pair is a hydrogen bond
Return type:
-
make_atom_with_no_bonds(atom, closeatom, addname)[source]¶ Create an atom with no bonds.
Called for water oxygen atoms with no current bonds. Uses the closeatom to place the new atom directly colinear with the atom and the closeatom.
Parameters:
-
classmethod
make_atom_with_one_bond_h(atom, addname)[source]¶ Add a hydrogen to an alcoholic donor with one existing bond.
Todo
Does this need to be a classmethod or could it be a staticmethod?
Parameters:
-
classmethod
make_atom_with_one_bond_lp(atom, addname)[source]¶ Add a lone pair to an alcoholic donor with one existing bond.
Todo
Does this need to be a classmethod or could it be a staticmethod?
Parameters:
-
classmethod
make_water_with_one_bond(atom, addname)[source]¶ Add an atom to a water residue that already has one bond.
Uses the water reference structure to align the new atom.
Todo
Does this need to be a classmethod or could it be a staticmethod?
Parameters:
-
try_positions_three_bonds_h(donor, acc, newname, loc)[source]¶ Try making a hydrogen bond with the lone available position.
Parameters: Returns: indication of whether atom was added
Return type:
-
try_positions_three_bonds_lp(acc, donor, newname, loc)[source]¶ Make a hydrogen bond in the only position possible.
Try making a hydrogen bond using the lone available hydrogen position.
Parameters: Returns: indication whether atom was added
Return type:
-
try_positions_with_two_bonds_h(donor, acc, newname, loc1, loc2)[source]¶ Try adding a new hydrogen to the two potential locations. If both form hydrogen bonds, place at whatever returns the best bond as determined by get_pair_energy.
Parameters: Returns: indication whether atom was added
Return type:
-
try_positions_with_two_bonds_lp(acc, donor, newname, loc1, loc2)[source]¶ Attempt to place a LP on an atom.
Try placing an LP on a tetrahedral geometry with two existing bonds. If this isn’t a hydrogen bond it can return - otherwise ensure that the H(D)-A-LP angle is minimized.
Parameters: Returns: indication of whether LP was added
Return type:
-
try_single_alcoholic_h(donor, acc, newatom)[source]¶ Attempt to add an atom to make a hydrogen bond.
Todo
Remove some hard-coded values in this function.
After a new bond has been added using
makeAtomWithOneBond(), try to find the best orientation by rotating to form a hydrogen bond. If a bond cannot be formed, remove the newatom (thereby returning to a single bond).Parameters: Returns: indication whether atom was added
Return type:
-
try_single_alcoholic_lp(acc, donor, newatom)[source]¶ Attempt to add an atom to make a hydrogen bond.
Todo
Remove some hard-coded values in this function and figure out where others (e.g., “72”) come from.
After a new bond has been added using
makeAtomWithOneBond(), ensure that a hydrogen bond has been made. If so, try to minimze the H(D)-A-LP angle. If that cannot be minimized, ignore the bond and remove the atom.Parameters: Returns: indication whether atom was added
Return type:
-
static
hydrogens.structures¶
Topology-related classes for hydrogen optimization.
-
class
pdb2pqr.hydrogens.structures.Alcoholic(residue, optinstance, routines)[source]¶ The class for alcoholic residue.
-
__init__(residue, optinstance, routines)[source]¶ Initialize the alcoholic class by removing the alcoholic hydrogen if it exists.
Parameters:
-
complete()[source]¶ Complete an alcoholic optimization.
Call
finalize()and then remove all extra LP atoms.
-
finalize()[source]¶ Finalize an alcoholic residue.
Todo
Replace hard-coded values in the function.
Try to minimize conflict with nearby atoms by building away from them. Called when LPs are still present so as to account for their bonds.
-
try_acceptor(acc, donor)[source]¶ Add a lone pair to an optimizeable residue.
Parameters: Returns: indication of whether addition was successful
Return type:
-
try_both(donor, acc, accobj)[source]¶ Attempt to optimize both the donor and acceptor.
If one is fixed, we only need to try one side. Otherwise first try to satisfy the donor - if that’s succesful, try to satisfy the acceptor. An undo may be necessary if the donor is satisfied and the acceptor isn’t.
Parameters: Returns: indication of whether hydrogen was added
Return type:
-
-
class
pdb2pqr.hydrogens.structures.Carboxylic(residue, optinstance, routines)[source]¶ The class for carboxylic residues
-
__init__(residue, optinstance, routines)[source]¶ Initialize carboxylic optimization class.
Initialize a case where the lone hydrogen atom can have four different orientations. Works similar to
initializeFlip()by pre-adding the necessary atoms.This also takes into account that the carboxyl group has different bond lengths for the two C-O bonds - this is probably due to one bond being assigned as a C=O. As a result hydrogens are only added to the C-O (longer) bond.
Parameters:
-
is_carboxylic_hbond(donor, acc)[source]¶ Determine whether this donor acceptor pair is a hydrogen bond.
Parameters: Returns: indication of whether hydrogen was added
Return type:
-
rename(hydatom)[source]¶ Rename the optimized atoms appropriately.
This is done since the forcefields tend to require that the hydrogen is linked to a specific oxygen, and this atom may have different parameter values.
Parameters: hydatom (Atom) – the hydrogen atom that was added
-
try_acceptor(acc, donor)[source]¶ Add lone pair to an optimizable residue.
Parameters: Returns: indication of whether addition was successful
Return type:
-
try_both(donor, acc, accobj)[source]¶ Attempt to optimize donor and acceptor.
Called when both the donor and acceptor are optimizeable. If one is fixed, we only need to try one side. Otherwise first try to satisfy the donor - if that’s succesful, try to satisfy the acceptor. An undo may be necessary if the donor is satisfied and the acceptor isn’t.
Parameters: Returns: indication of whether hydrogen was added
Return type:
-
-
class
pdb2pqr.hydrogens.structures.Flip(residue, optinstance, routines)[source]¶ The holder for optimization of flippable residues.
-
__init__(residue, optinstance, routines)[source]¶ Initialize a potential flip.
Rather than flipping the given residue back and forth, take each atom that would be flipped and pre-flip it, making a new
*FLIPatom in its place.Parameters:
-
complete()[source]¶ Complete the flippable residue optimization.
Call the
finalize()function, and then rename allFLIPatoms back to their standard names.
-
finalize()[source]¶ Finalize a flippable group back to its original state.
Since the original atoms are now
*FLIP, it deletes the*atoms and renames the*FLIPatoms back to*.
-
fix_flip(bondatom)[source]¶ Remove atoms if hydrogen bond has been found for specified atom.
If bondatom is of type
*FLIP, remove all*atoms, otherwise remove all*FLIPatoms.Parameters: bondatom (Atom) – atom to flip
-
try_acceptor(acc, donor)[source]¶ Aa lone pair to an optimizable residue.
Parameters: Returns: indication of whether addition was successful
Return type:
-
try_both(donor, acc, accobj)[source]¶ Try to optimize both donor and acceptor bonds.
Called when both the donor and acceptor are optimizeable. If one is fixed, we only need to try one side. Otherwise first try to satisfy the donor - if that’s succesful, try to satisfy the acceptor. An undo may be necessary if the donor is satisfied and the acceptor isn’t.
Parameters: Returns: indication of whether hydrogen was added
Return type:
-
-
class
pdb2pqr.hydrogens.structures.Generic(residue, optinstance, routines)[source]¶ Generic optimization class
-
class
pdb2pqr.hydrogens.structures.HydrogenAmbiguity(residue, hdef, routines)[source]¶ Contains information about ambiguities in hydrogen conformations.
-
class
pdb2pqr.hydrogens.structures.HydrogenConformation(hname, boundatom, bondlength)[source]¶ Class for possible hydrogen conformations.
The
HydrogenConformationclass contains data about possible hydrogen conformations as specified in the hydrogen data file.-
__init__(hname, boundatom, bondlength)[source]¶ Parameters: - hname – The hydrogen name (string)
- boundatom – The atom the hydrogen is bound to (string)
- bondlength – The bond length (float)
-
add_atom(atom)[source]¶ Add an atom to the list of atoms.
Parameters: atom (DefinitionAtom) – the atom to be added
-
-
class
pdb2pqr.hydrogens.structures.HydrogenDefinition(name, opttype, optangle, map_)[source]¶ Class for potential ambiguities in amino acid hydrogens.
It is essentially the hydrogen definition file in object form.
-
__init__(name, opttype, optangle, map_)[source]¶ Initialize the object with information from the definition file.
See
HYDROGENS.XMLfor more information.Parameters:
-
add_conf(conf)[source]¶ Add a hydrogen conformation to the list.
Parameters: conf (HydrogenConformation) – the conformation to be added
-
-
class
pdb2pqr.hydrogens.structures.HydrogenHandler[source]¶ Extends the SAX XML Parser to parse the Hydrogens.xml class.
-
characters(text)[source]¶ Set a given attribute of the object to the text.
Parameters: text (str) – value of the attribute
-
-
class
pdb2pqr.hydrogens.structures.PotentialBond(atom1, atom2, dist)[source]¶ A class containing the hydrogen bond structure.
-
class
pdb2pqr.hydrogens.structures.Water(residue, optinstance, routines)[source]¶ The class for water residues.
-
__init__(residue, optinstance, routines)[source]¶ Initialize the water optimization class.
Parameters:
-
finalize()[source]¶ Finalize a water residue.
Try to minimize conflict with nearby atoms by building away from them. Called when LPs are still present so as to account for their bonds.
-
try_acceptor(acc, donor)[source]¶ The main driver for adding an LP to an optimizeable residue.
Todo
This looks like a bug: donorh ends up being the last item in donor.bonds. This may be fixed by setting a best_donorh to go with bestdist and using best_donorh in the function below
Parameters: Returns: indication of whether addition was successful
Return type:
-
try_both(donor, acc, accobj)[source]¶ Attempt to optimize both the donor and the acceptor.
If one is fixed, we only need to try one side. Otherwise first try to satisfy the donor - if that’s successful, try to satisfy the acceptor. An undo may be necessary if the donor is satisfied and the acceptor isn’t.
Parameters: Returns: indication of whether hydrogen was added
Return type:
-
ligand and submodule contents¶
ligand¶
Ligand support functions.
Todo
Some of the definitions in this module belong in a configuration file other than here.
Code author: Jens Erik Nielsen
hydrogens.ligand.mol2¶
Support molecules in Tripos MOL2 format.
For further information look at (web page exists: 25 August 2005): http://www.tripos.com/index.php?family=modules,SimplePage,,,&page=sup_mol2&s=0
-
class
pdb2pqr.ligand.mol2.Mol2Atom[source]¶ MOL2 molecule atoms.
-
assign_radius(primary_dict, secondary_dict)[source]¶ Assign radius to atom.
Todo
It seems inconsistent that this function pulls radii from a dictionary and the biomolecule routines use force field files.
Parameters:
-
bond_order¶ Total number of electrons in bonds with other atoms.
Returns: total number of electrons in bonds with other atoms Return type: int
-
coords¶ Coordinates.
Returns: coordinates Return type: numpy.ndarray
-
distance(other)[source]¶ Get distance between two atoms.
Parameters: other (Mol2Atom) – other atom for distance measurement Returns: distance Return type: float
-
-
class
pdb2pqr.ligand.mol2.Mol2Bond(atom1, atom2, bond_type, bond_id=0)[source]¶ MOL2 molecule bonds.
-
class
pdb2pqr.ligand.mol2.Mol2Molecule[source]¶ Tripos MOL2 molecule.
-
assign_parameters(primary_dict={'C': 1.87, 'Cl': 1.82, 'F': 2.4, 'H': 1.1, 'I': 2.65, 'N': 1.4, 'O.co2': 1.76, 'S': 2.15}, secondary_dict={'Ar': 1.88, 'As': 1.85, 'Br': 1.85, 'C': 1.7, 'Cl': 1.75, 'F': 1.47, 'H': 1.2, 'He': 1.4, 'I': 1.98, 'Kr': 2.02, 'N': 1.55, 'Ne': 1.54, 'O': 1.52, 'P': 1.8, 'S': 1.8, 'Se': 1.9, 'Si': 2.1, 'Te': 2.06, 'Xe': 2.16})[source]¶ Assign charges and radii to atoms in molecule.
Parameters: - primary_dict – primary dictionary of radii indexed by atom type or element
- secondary_dict – backup dictionary for radii not found in primary dictionary
-
find_atom_torsions(start_atom)[source]¶ Set the torsion angles that start with this atom (name).
Parameters: start_atom (str) – starting atom name Returns: list of 4-tuples containing atom names comprising torsions
-
find_new_rings(path, rings, level=0)[source]¶ Find new rings in molecule.
This was borrowed from StackOverflow: https://j.mp/2AHaukj
Parameters: - path (list of str) – list of atom names
- rings (list of str) – current list of rings
- level (int) – recursion level
Returns: new list of rings
Return type:
-
parse_atoms(mol2_file)[source]¶ Parse @<TRIPOS>ATOM section of file.
Parameters: mol2_file – file-like object with MOL2 data
Returns: file-like object advanced to bonds section
Raises: - ValueError – for bad MOL2 ATOM lines
- TypeError – for bad charge entries
-
parse_bonds(mol2_file)[source]¶ Parse @<TRIPOS>BOND section of file.
Atoms must already have been parsed. Also sets up torsions and rings.
Parameters: mol2_file – file-like object with MOL2 data Returns: file-like object advanced to SUBSTRUCTURE section
-
read(mol2_file)[source]¶ Routines for reading MOL2 file.
Parameters: mol2_file – file-like object with MOL2 data
-
static
rotate_to_smallest(path)[source]¶ Rotate cycle path so that it begins with the smallest node.
This was borrowed from StackOverflow: https://j.mp/2AHaukj
Parameters: path (list of str) – list of atom names Returns: rotated path Return type: list of str
-
set_rings()[source]¶ Set all rings in molecule.
This was borrowed from StackOverflow: https://j.mp/2AHaukj
-
hydrogens.ligand.peoe¶
Implements the PEOE method.
The PEOE method is described in: Paul Czodrowski, Ingo Dramburg, Christoph A. Sotriffer Gerhard Klebe. Development, validation, and application of adapted PEOE charges to estimate pKa values of functional groups in protein–ligand complexes. Proteins, 65, 424-437, 2006. https://doi.org/10.1002/prot.21110
-
pdb2pqr.ligand.peoe.assign_terms(atoms, term_dict)[source]¶ Assign polynomial terms to each atom.
Parameters: Returns: modified list of atoms
Return type:
-
pdb2pqr.ligand.peoe.electronegativity(charge, poly_terms, atom_type)[source]¶ Calculate the electronegativity.
Calculation is based on a third-order polynomial in the atomic charge as described in Equation 2 of https://doi.org/10.1002/prot.21110.
Parameters: Returns: electronegativity value
Return type: Raises: IndexError – if incorrect number of poly_terms given
-
pdb2pqr.ligand.peoe.equilibrate(atoms, damp=0.778, scale=1.56, num_cycles=6, term_dict={'BR': (10.88, 8.47, 1.16, 19.71), 'C.1': (10.39, 9.45, 0.73, 20.57), 'C.2': (9.29, 9.32, 1.51, 19.62), 'C.3': (7.98, 9.18, 1.88, 19.04), 'C.AR': (8.530000000000001, 9.18, 1.88, 19.04), 'C.CAT': (7.98, 9.18, 1.88, 19.04), 'CL': (10.38, 9.69, 1.35, 22.04), 'F': (12.36, 13.85, 2.31, 30.82), 'H': (7.17, 6.24, -0.56, 12.85), 'I': (10.9, 7.96, 0.96, 18.82), 'N.1': (15.68, 11.7, -0.27, 27.11), 'N.2': (12.87, 11.15, 0.85, 24.87), 'N.3': (17.54, 10.28, 1.36, 28.0), 'N.4': (17.54, 10.28, 1.36, 28.0), 'N.AM': (16.369999999999997, 11.15, 0.85, 24.87), 'N.AR': (11.579999999999998, 11.15, 0.85, 24.87), 'N.PL3': (13.37, 11.15, 0.85, 24.87), 'O.2': (14.18, 12.92, 1.39, 28.49), 'O.3': (11.08, 12.92, 1.39, 28.49), 'O.CO2': (15.25, 13.79, 0.47, 31.33), 'O.OH': (14.98, 12.92, 1.39, 28.49), 'P.3': (10.63, 9.13, 1.38, 20.65), 'S.2': (10.63, 9.13, 1.38, 20.65), 'S.3': (10.63, 9.13, 1.38, 20.65), 'S.O2': (10.63, 9.13, 1.38, 20.65)})[source]¶ Equilibrate the atomic charges.
Parameters: Returns: revised list of atoms
Return type:
na¶
Nucleic Acid Structures for PDB2PQR
This module contains the base nucleic acid structures for pdb2pqr.
Code author: Todd Dolinsky
Code author: Nathan Baker
-
class
pdb2pqr.na.ADE(atoms, ref)[source]¶ Adenosine class.
-
class
pdb2pqr.na.CYT(atoms, ref)[source]¶ Cytidine class
-
pdb2pqr.na.DA¶ alias of
pdb2pqr.na.ADE
-
pdb2pqr.na.DC¶ alias of
pdb2pqr.na.CYT
-
pdb2pqr.na.DG¶ alias of
pdb2pqr.na.GUA
-
pdb2pqr.na.DT¶ alias of
pdb2pqr.na.THY
-
class
pdb2pqr.na.GUA(atoms, ref)[source]¶ Guanosine class
-
class
pdb2pqr.na.Nucleic(atoms, ref)[source]¶ This class provides standard features of the nucleic acids listed below.
-
__init__(atoms, ref)[source]¶ Initialize the class
Parameters: atoms (list) – list of atom-like ( HETATMorATOM) objects to be stored
-
add_atom(atom)[source]¶ Add existing atom to system.
Override the existing add_atom - include the link to the reference object.
Parameters: atom (Atom) – atom to add to system.
-
add_dihedral_angle(value)[source]¶ Add the value to the list of chi angles.
Parameters: value (float) – dihedral angle to add to list (in degrees)
-
-
pdb2pqr.na.RA¶ alias of
pdb2pqr.na.URA
-
pdb2pqr.na.RC¶ alias of
pdb2pqr.na.CYT
-
pdb2pqr.na.RG¶ alias of
pdb2pqr.na.GUA
-
class
pdb2pqr.na.THY(atoms, ref)[source]¶ Thymine class
biomolecule¶
The biomolecule object used in PDB2PQR and associated methods.
Todo
This module should be broken into separate files.
Authors: Todd Dolinsky, Yong Huang
-
class
pdb2pqr.biomolecule.Biomolecule(pdblist, definition)[source]¶ Biomolecule class.
This class represents the parsed PDB, and provides a hierarchy of information - each Biomolecule object contains a list of Chain objects as provided in the PDB file. Each Chain then contains its associated list of Residue objects, and each Residue contains a list of Atom objects, completing the hierarchy.
-
__init__(pdblist, definition)[source]¶ Initialize using parsed PDB file
Parameters: - pdblist (list) – list of objects from
pdbfrom lines of PDB file - definition (Definition) – topology definition object
- pdblist (list) – list of objects from
-
add_hydrogens()[source]¶ Add the hydrogens to the biomolecule.
This requires either the rebuild_tetrahedral function for tetrahedral geometries or the standard quatfit methods. These methods use three nearby bonds to rebuild the atom; the closer the bonds, the more accurate the results. As such the peptide bonds are used when available.
-
apply_force_field(forcefield_)[source]¶ Apply the forcefield to the atoms within the biomolecule.
Parameters: forcefield (Forcefield) – forcefield object Returns: (list of atoms that were found in the forcefield, list of atoms that were not found in the forcefield) Return type: (list, list)
-
apply_name_scheme(forcefield_)[source]¶ Apply the naming scheme of the given forcefield.
Parameters: forcefield (Forcefield) – forcefield object
-
apply_patch(patchname, residue)[source]¶ Apply a patch to the given residue.
This is one of the key functions in PDB2PQR. A similar function appears in
definitions- that version is needed for residue level subtitutions so certain protonation states (i.e. CYM, HSE) are detectatble on input.This version looks up the particular patch name in the patch_map stored in the biomolecule, and then applies the various commands to the reference and actual residue structures.
See the inline comments for a more detailed explanation.
Parameters:
-
apply_pka_values(force_field, ph, pkadic)[source]¶ Apply calculated pKa values to assign titration states.
Parameters:
-
assign_termini(chain, neutraln=False, neutralc=False)[source]¶ Assign the termini for the given chain.
Assignment made by looking at the start and end residues.
Parameters:
-
calculate_dihedral_angles()[source]¶ Calculate dihedral angles for every residue in the biomolecule.
-
charge¶ Get the total charge on the biomolecule
Todo
Since the misslist is used to identify incorrect charge assignments, this routine does not list the 3 and 5 termini of nucleic acid chains as having non-integer charge even though they are (correctly) non-integer.
Returns: (list of residues with non-integer charges, the total charge on the biomolecule) Return type: (list, float)
-
create_html_typemap(definition, outfilename)[source]¶ Create an HTML typemap file at the desired location.
If a type cannot be found for an atom a blank is listed.
Parameters: - definition (Definition) – the definition objects.
- outfilename (str) – the name of the file to write
-
create_residue(residue, resname)[source]¶ Create a residue object.
If the resname is a known residue type, try to make that specific object, otherwise just make a standard residue object.
Parameters: Returns: the residue object
Return type:
-
hold_residues(hlist)[source]¶ Set fixed state of specified residues.
Parameters: hlist ([(str, str, str)]) – list of (res_seq, chainid, ins_code) specifying the residues for altering fixed state status.
-
num_bio_atoms¶ Return the number of ATOM (not HETATM) records in the biomolecule.
Returns: number of ATOM records Return type: int
-
num_heavy¶ Return number of biomolecular heavy atoms in structure.
Todo
Figure out if this is redundant with
Biomolecule.num_bio_atoms()Note
Includes hydrogens (but those are stripped off eventually)
Returns: number of heavy atoms Return type: int
-
num_missing_heavy¶ Return number of missing biomolecular heavy atoms in structure.
Returns: number of missing heavy atoms in structure Return type: int
-
repair_heavy()[source]¶ Repair all heavy atoms.
Unfortunately the first time we get to an atom we might not be able to rebuild it - it might depend on other atoms to be rebuild first (think side chains). As such a ‘seenmap’ is used to keep track of what we’ve already seen and subsequent attempts to rebuild the atom.
Raises: ValueError – missing atoms prevent reconstruction
-
set_reference_distance()[source]¶ Set the distance to the CA atom in the residue.
This is necessary for determining which atoms are allowed to move during rotations. Uses the
shortest_path()algorithm found inutilities.Raises: ValueError – if shortest path cannot be found (e.g., if the atoms are not connected)
-
set_states()[source]¶ Set the state of each residue.
This is the last step before assigning the forcefield, but is necessary so as to distinguish between various protonation states.
See
aafor residue-specific functions.
-
set_termini(neutraln=False, neutralc=False)[source]¶ Set the termini for a protein.
First set all known termini by looking at the ends of the chain. Then examine each residue, looking for internal chain breaks.
Todo
This function needs to be cleaned and simplified
Parameters:
-
update_bonds()[source]¶ Update the bonding network of the biomolecule.
This happens in 3 steps:
- Apply the PEPTIDE patch to all Amino residues to add reference for the N(i+1) and C(i-1) atoms
- UpdateInternal_bonds for inter-residue linking
- Set the links to the N(i+1) and C(i-1) atoms
-
update_internal_bonds()[source]¶ Update the internal bonding network.
Update using the reference objects in each atom.
-
residue¶
Biomolecular residue class.
Code author: Todd Dolinsky
Code author: Nathan Baker
-
class
pdb2pqr.residue.Residue(atoms)[source]¶ Residue class
Todo
Should this class have a member variable for dihedrals? Pylint complains!
The residue class contains a list of Atom objects associated with that residue and other helper functions.
-
__init__(atoms)[source]¶ Initialize the class
Parameters: atoms (list) – list of atom-like ( HETATMorATOM) objects to be stored
-
add_atom(atom)[source]¶ Add the atom object to the residue.
Parameters: atom – atom-like object, e.g., HETATMorATOM
-
charge¶ Get the total charge of the residue.
In order to get rid of floating point rounding error, do a string transformation.
Returns: The charge of the residue (float) Return type: charge
-
get_atom(name)[source]¶ Retrieve a residue atom based on its name.
Parameters: resname (str) – name of the residue to retrieve Returns: residue Return type: structures.Atom
-
get_moveable_names(pivot)[source]¶ Return all atom names that are further away than the pivot atom.
Parameters: Returns: names of atoms further away than pivot atom
Return type: [str]
-
has_atom(name)[source]¶ Return True if atom in residue.
Parameters: name (str) – atom name in question Returns: True if atom in residue Return type: bool
-
static
letter_code()[source]¶ Default letter code for residue.
Returns: letter code for residue Return type: str
-
pick_dihedral_angle(conflict_names, oldnum=None)[source]¶ Choose an angle number to use in debumping.
Instead of simply picking a random chiangle, this function uses a more intelligent method to improve efficiency. The algorithm uses the names of the conflicting atoms within the residue to determine which angle number has the best chance of fixing the problem(s). The method also insures that the same chiangle will not be run twice in a row.
Parameters: Returns: new dihedral angle number
Return type:
-
remove_atom(atomname)[source]¶ Remove an atom from the residue object.
Parameters: atomname (str) – the name of the atom to be removed
-
rename_residue(name)[source]¶ Rename the residue.
Parameters: name (str) – the new name of the residue
-
classmethod
rotate_tetrahedral(atom1, atom2, angle)[source]¶ Rotate about the atom1-atom2 bond by a given angle.
All atoms connected to atom2 will rotate.
Parameters: - atom1 (structures.Atom) – first atom of the bond to rotate about
- atom2 (structures.Atom) – second atom of the bond to rotate about
- angle (float) – degrees to rotate
-
structures¶
Simple biomolecular structures.
This module contains the simpler structure objects used in PDB2PQR and their associated methods.
Code author: Todd Dolinsky
Code author: Nathan Baker
-
class
pdb2pqr.structures.Atom(atom=None, type_='ATOM', residue=None)[source]¶ Represent an atom.
The Atom class inherits from the
ATOMobject inpdb. This class used for adding fields not found in the PDB that may be useful for analysis. This class also simplifies code by combiningATOMandHETATMobjects into a single class.-
__init__(atom=None, type_='ATOM', residue=None)[source]¶ Initialize the new Atom object by using the old object.
Parameters:
-
add_bond(bondedatom)[source]¶ Add a bond to the list of bonds.
Parameters: bondedatom (ATOM) – the atom to bond to
-
coords¶ Return the x,y,z coordinates of the atom.
Returns: list of the coordinates Return type: [float, float, float]
-
classmethod
from_pqr_line(line)[source]¶ Create an atom from a PQR line.
Parameters: Returns: new atom or None (for REMARK and similar lines)
Return type: Raises: ValueError – for problems parsing
-
classmethod
from_qcd_line(line, atom_serial)[source]¶ Create an atom from a QCD (UHBD QCARD format) line.
Parameters: Returns: new atom or None (for REMARK and similar lines)
Return type: Raises: ValueError – for problems parsing
-
get_common_string_rep(chainflag=False)[source]¶ Returns a string of the common column of the new atom type.
Uses the
ATOMstring output but changes the first field to either beATOMorHETATMas necessary. This is used to create the output for PQR and PDB files.Returns: string with ATOM/HETATM field set appropriately Return type: str
-
get_pdb_string()[source]¶ Returns a string of the atom type.
Uses the
ATOMstring output but changes the first field to either beATOMorHETATMas necessary. This is for the PDB representation of the atom. Thepropkamodule depends on this being correct.Returns: string with ATOM/HETATM field set appropriately Return type: str
-
get_pqr_string(chainflag=False)[source]¶ Returns a string of the atom type.
Uses the
ATOMstring output but changes the first field to either beATOMorHETATMas necessary. This is used to create the output for PQR files.Returns: string with ATOM/HETATM field set appropriately Return type: str
-
has_reference¶ Determine if the object has a reference object or not.
All known atoms should have reference objects.
Returns: whether atom has reference object Return type: bool
-
-
class
pdb2pqr.structures.Chain(chain_id)[source]¶ Chain class
The chain class contains information about each chain within a given
Biomoleculeobject.-
__init__(chain_id)[source]¶ Initialize the class.
Parameters: chain_id (str) – ID for this chain as denoted in the PDB
-
add_residue(residue)[source]¶ Add a residue to the chain
Parameters: residue (Residue) – residue to be added
-
topology¶
Parser for topology XML files.
Code author: Nathan Baker
Code author: Yong Huang
-
class
pdb2pqr.topology.Topology(topology_file)[source]¶ Contains the structured definitions of residue reference coordinates as well as alternate titration, conformer, and tautomer states.
-
class
pdb2pqr.topology.TopologyAtom(parent)[source]¶ A class for atom topology information.
-
__init__(parent)[source]¶ Initialize with an upper-level class that contains an atom array.
For example, initialize with
TopologyReferenceorTopologyConformerAdditionParameters: parent – parent object with atom array
-
-
class
pdb2pqr.topology.TopologyConformer(topology_tautomer)[source]¶ A class for topology conformer information.
-
__init__(topology_tautomer)[source]¶ Initialize object.
Parameters: topology_tautomer (TopologyTautomer) – tautomer for which to evaluate conformers
-
-
class
pdb2pqr.topology.TopologyConformerAdd(topology_conformer)[source]¶ A class for adding atoms to a conformer.
-
__init__(topology_conformer)[source]¶ Initialize object.
Parameters: topology_conformer (TopologyConformer) – conformer to which to add atoms
-
-
class
pdb2pqr.topology.TopologyConformerRemove(topology_conformer)[source]¶ A class for removing atoms from a conformer.
-
__init__(topology_conformer)[source]¶ Initialize object.
Parameters: topology_conformer (TopologyConformer) – conformer to which to add atoms
-
-
class
pdb2pqr.topology.TopologyDihedral(parent)[source]¶ A class for dihedral angle topology information.
-
class
pdb2pqr.topology.TopologyHandler[source]¶ Handler for XML-based topology files.
Assumes the following hierarchy of tags:
- topology
- residue
- reference
- titrationstate
- tautomer
- conformer
- tautomer
- residue
-
characters(text)[source]¶ Parse characters in topology XML file.
Parameters: text (str) – XML character data
- topology
-
class
pdb2pqr.topology.TopologyReference(topology_residue)[source]¶ A class for the reference structure of a residue.
-
__init__(topology_residue)[source]¶ Initialize object.
Parameters: topology_residue (TopologyResidue) – reference residue
-
-
class
pdb2pqr.topology.TopologyResidue(topology_)[source]¶ A class for residue topology information.
-
class
pdb2pqr.topology.TopologyTautomer(topology_titration_state)[source]¶ A class for topology tautomer information.
-
__init__(topology_titration_state)[source]¶ Initialize object.
Parameters: topology_titration_state (TopologyTitrationState) – titration state of this residue
-
-
class
pdb2pqr.topology.TopologyTitrationState(topology_residue)[source]¶ A class for the titration state of a residue.
-
__init__(topology_residue)[source]¶ Initialize object.
Parameters: topology_residue (TopologyResidue) – residue topology
-
I/O modules¶
cif¶
CIF parsing methods.
This methods use the pdbx/cif parser provided by WWPDB (http://mmcif.wwpdb.org/docs/sw-examples/python/html/index.html)
Code author: Juan Brandi
-
pdb2pqr.cif.atom_site(block)[source]¶ Handle ATOM_SITE block.
Data items in the ATOM_SITE category record details about the atom sites in a macromolecular crystal structure, such as the positional coordinates, atomic displacement parameters, magnetic moments and directions. (Source: https://j.mp/2Zprx41)
Parameters: block ([str]) – PDBx data block Returns: (array of pdb.ATOM objects, array of things that weren’t handled by parser) Return type: ([Atom], [str])
Handle AUTHOR block.
Parameters: block ([str]) – PDBx data block Returns: (array of pdb.conect objects, array of things that did not parse) Return type: ([pdb.CONECT], [str])
-
pdb2pqr.cif.cispep(block)[source]¶ Handle CISPEP block.
Parameters: block ([str]) – PDBx data block Returns: (array of pdb.conect objects, array of things that did not parse) Return type: ([pdb.CONECT], [str])
-
pdb2pqr.cif.compnd(block)[source]¶ Handle COMPND block.
Parameters: block ([str]) – PDBx data block Returns: (array of pdb.conect objects, array of things that did not parse) Return type: ([pdb.CONECT], [str])
-
pdb2pqr.cif.conect(block)[source]¶ Handle CONECT block.
Data items in the STRUCT_CONN category record details about the connections between portions of the structure. These can be hydrogen bonds, salt bridges, disulfide bridges and so on.
The
STRUCT_CONN_TYPErecords define the criteria used to identify these connections. (Source: https://j.mp/3gPkJT5)Parameters: block ([str]) – PDBx data block Returns: (array of pdb.conect objects, array of things that did not parse) Return type: ([pdb.CONECT], [str])
-
pdb2pqr.cif.count_models(block)[source]¶ Count models in structure file block.
Parameters: block ([str]) – PDBx data block Returns: number of models in block Return type: int
-
pdb2pqr.cif.cryst1(block)[source]¶ Handle CRYST1 block.
Parameters: block ([str]) – PDBx data block Returns: (array of pdb.conect objects, array of things that did not parse) Return type: ([pdb.CONECT], [str])
-
pdb2pqr.cif.expdata(block)[source]¶ Handle EXPDTA block.
Parameters: block ([str]) – PDBx data block Returns: (array of pdb.conect objects, array of things that did not parse) Return type: ([pdb.CONECT], [str])
-
pdb2pqr.cif.header(block)[source]¶ Handle HEADER block.
Parameters: block ([str]) – PDBx data block Returns: (array of pdb.conect objects, array of things that did not parse) Return type: ([pdb.CONECT], [str])
-
pdb2pqr.cif.keywds(block)[source]¶ Handle KEYWDS block.
Parameters: block ([str]) – PDBx data block Returns: (array of pdb.conect objects, array of things that did not parse) Return type: ([pdb.CONECT], [str])
-
pdb2pqr.cif.origxn(block)[source]¶ Handle ORIGXn block.
Parameters: block ([str]) – PDBx data block Returns: (array of pdb.conect objects, array of things that did not parse) Return type: ([pdb.CONECT], [str])
-
pdb2pqr.cif.read_cif(cif_file)[source]¶ Parse CIF-format data into array of Atom objects.
Todo
Manage several blocks of data.
Parameters: file (file) – open file-like object Returns: (a dictionary indexed by PDBx/CIF record names, a list of record names that couldn’t be parsed) Return type: (dict, [str])
-
pdb2pqr.cif.scalen(block)[source]¶ Handle SCALEn block.
Parameters: block ([str]) – PDBx data block Returns: (array of pdb.conect objects, array of things that did not parse) Return type: ([pdb.CONECT], [str])
-
pdb2pqr.cif.source(block)[source]¶ Handle SOURCE block.
Parameters: block ([str]) – PDBx data block Returns: (array of pdb.conect objects, array of things that did not parse) Return type: ([pdb.CONECT], [str])
-
pdb2pqr.cif.ssbond(block)[source]¶ Handle SSBOND block.
Parameters: block ([str]) – PDBx data block Returns: (array of pdb.conect objects, array of things that did not parse) Return type: ([pdb.CONECT], [str])
-
pdb2pqr.cif.title(block)[source]¶ Handle TITLE block.
Parameters: block ([str]) – PDBx data block Returns: (array of pdb.conect objects, array of things that did not parse) Return type: ([pdb.CONECT], [str])
io¶
Functions related to reading and writing data.
-
class
pdb2pqr.io.DuplicateFilter[source]¶ Filter duplicate messages.
-
pdb2pqr.io.dump_apbs(output_pqr, output_path)[source]¶ Generate and dump APBS input files related to output_pqr.
Parameters:
-
pdb2pqr.io.get_definitions(aa_path='AA.xml', na_path='NA.xml', patch_path='PATCHES.xml')[source]¶ Load topology definition files.
Parameters: Returns: topology Definitions object.
Return type:
-
pdb2pqr.io.get_molecule(input_path)[source]¶ Get molecular structure information as a series of parsed lines.
Parameters: input_path – structure file PDB ID or path Returns: (list of molecule records, Boolean indicating whether entry is CIF) Return type: ([str], bool) Raises: RuntimeError – problems with structure file
-
pdb2pqr.io.get_old_header(pdblist)[source]¶ Get old header from list of
pdbobjects.Parameters: pdblist ([]) – list of pdbblock objectsReturns: old header as string Return type: str
-
pdb2pqr.io.get_pdb_file(name)[source]¶ Obtain a PDB file.
First check the path given on the command line - if that file is not available, obtain the file from the PDB webserver at http://www.rcsb.org/pdb/
Todo
This should be a context manager (to close the open file).
Todo
Remove hard-coded parameters.
Parameters: name (str) – name of PDB file (path) or PDB ID Returns: file-like object containing PDB file Return type: file
-
pdb2pqr.io.print_biomolecule_atoms(atomlist, chainflag=False, pdbfile=False)[source]¶ Get PDB-format text lines for specified atoms.
Parameters: Returns: list of strings, each representing an atom PDB line
Return type: [str]
-
pdb2pqr.io.print_pqr_header(pdblist, atomlist, reslist, charge, force_field, ph_calc_method, ph, ffout, include_old_header=False)[source]¶ Print the header for the PQR file.
Parameters: - pdblist ([str]) – list of lines from original PDB with header
- atomlist ([Atom]) – a list of atoms that were unable to have charges assigned
- reslist ([Residue]) – a list of residues with non-integral charges
- charge (float) – the total charge on the biomolecule
- force_field (str) – the forcefield name
- ph_calc_method (str) – pKa calculation method
- ph (float) – pH value, if any
- ffout (str) – forcefield used for naming scheme
Returns: the header for the PQR file
Return type:
-
pdb2pqr.io.print_pqr_header_cif(atomlist, reslist, charge, force_field, ph_calc_method, ph, ffout, include_old_header=False)[source]¶ Print the header for the PQR file in CIF format.
Parameters: - atomlist ([Atom]) – a list of atoms that were unable to have charges assigned
- reslist ([Residue]) – a list of residues with non-integral charges
- charge (float) – the total charge on the biomolecule
- force_field (str) – the forcefield name
- ph_calc_method (str) – pKa calculation method
- ph (float) – pH value, if any
- ffout (str) – forcefield used for naming scheme
Returns: the header for the PQR file
Return type:
-
pdb2pqr.io.read_dx(dx_file)[source]¶ Read DX-format volumetric information.
The OpenDX file format is defined at <https://www.idvbook.com/wp-content/uploads/2010/12/opendx.pdf`.
Note
This function is not a general-format OpenDX file parser and makes many assumptions about the input data type, grid structure, etc.
Todo
This function should be moved into the APBS code base.
Parameters: dx_file (file) – file object for DX file, ready for reading as text Returns: dictionary with data from DX file Return type: dict Raises: ValueError – on parsing error
-
pdb2pqr.io.read_pqr(pqr_file)[source]¶ Read PQR file.
Parameters: pqr_file (file) – file object ready for reading as text Returns: list of atoms read from file Return type: [Atom]
-
pdb2pqr.io.read_qcd(qcd_file)[source]¶ Read QCD (UHDB QCARD format) file.
Parameters: qcd_file (file) – file object ready for reading as text Returns: list of atoms read from file Return type: [Atom]
-
pdb2pqr.io.setup_logger(output_pqr, level='DEBUG')[source]¶ Setup the logger.
Setup logger to output the log file to the same directory as PQR output.
Parameters:
-
pdb2pqr.io.test_dat_file(name)[source]¶ Test for the forcefield file with a few name permutations.
Parameters: name (str) – the name of the dat file Returns: the path to the file Return type: Path Raises: FileNotFoundError – file not found
-
pdb2pqr.io.test_for_file(name, type_)[source]¶ Test for the existence of a file with a few name permutations.
Parameters: Returns: path to file
Raises: FileNotFoundError – if file not found
Return type: Path
-
pdb2pqr.io.test_names_file(name)[source]¶ Test for the .names file that contains the XML mapping.
Parameters: name (str) – the name of the forcefield Returns: the path to the file Return type: Path Raises: FileNotFoundError – file not found
-
pdb2pqr.io.test_xml_file(name)[source]¶ Test for the XML file with a few name permutations.
Parameters: name (str) – the name of the dat file Returns: the path to the file Return type: Path Raises: FileNotFoundError – file not found
-
pdb2pqr.io.write_cube(cube_file, data_dict, atom_list, comment='CPMD CUBE FILE.')[source]¶ Write a Cube-format data file.
Cube file format is defined at <https://docs.chemaxon.com/display/Gaussian_Cube_format.html>.
Todo
This function should be moved into the APBS code base.
Parameters:
inputgen¶
Create an APBS input file using psize data.
Code author: Todd Dolinsky
Code author: Nathan Baker
-
class
pdb2pqr.inputgen.Elec(pqrpath, size, method, asyncflag, istrng=0, potdx=False)[source]¶ An object for the ELEC section of an APBS input file.
-
__init__(pqrpath, size, method, asyncflag, istrng=0, potdx=False)[source]¶ Initialize object.
Todo
Remove hard-coded parameters.
Parameters: - pqrpath (str) – path to PQR file
- size (Psize) – parameter sizing object
- method (str) – solution method (e.g., mg-para, mg-auto, etc.)
- asyncflag (bool) – perform an asynchronous parallel focusing calculation
- istrng – ionic strength/concentration (M)
- potdx (bool) – whether to write out potential information in DX format
-
-
class
pdb2pqr.inputgen.Input(pqrpath, size, method, asyncflag, istrng=0, potdx=False)[source]¶ Each object of this class is one APBS input file.
-
__init__(pqrpath, size, method, asyncflag, istrng=0, potdx=False)[source]¶ Initialize the input file class.
Each input file contains a PQR name, a list of elec objects, and a list of strings containing print statements. For starters, assume two ELEC statements are needed, one for the inhomgenous and the other for the homogenous dielectric calculations.
Note
This assumes you have already run psize, either by
size.run_psize(...)()orsize.parse_string(...)()followed bysize.set_all().Parameters: - pqrpath (str) – path to PQR file
- size (Psize) – parameter sizing object
- method (str) – solution method (e.g., mg-para, mg-auto, etc.)
- asyncflag (bool) – perform an asynchronous parallel focusing calculation
- istrng – ionic strength/concentration (M)
- potdx (bool) – whether to write out potential information in DX format
-
pdb¶
PDB parsing class
This module parses PDBs in accordance to PDB Format Description Version 2.2 (1996); it is not very forgiving. Each class in this module corresponds to a record in the PDB Format Description. Much of the documentation for the classes is taken directly from the above PDB Format Description.
Code author: Todd Dolinsky
Code author: Yong Huang
Code author: Nathan Baker
-
class
pdb2pqr.pdb.ANISOU(line)[source]¶ ANISOU class
The ANISOU records present the anisotropic temperature factors.
-
__init__(line)[source]¶ Initialize by parsing line:
COLUMNS TYPE FIELD DEFINITION 7-11 int serial Atom serial number. 13-16 string name Atom name. 17 string alt_loc Alternate location indicator. 18-20 string res_name Residue name. 22 string chain_id Chain identifier. 23-26 int res_seq Residue sequence number. 27 string ins_code Insertion code. 29-35 int u00 U(1,1) 36-42 int u11 U(2,2) 43-49 int u22 U(3,3) 50-56 int u01 U(1,2) 57-63 int u02 U(1,3) 64-70 int u12 U(2,3) 73-76 string seg_id Segment identifier, left-justified. 77-78 string element Element symbol, right-justified. 79-80 string charge Charge on the atom. Parameters: line (str) – line with PDB class
-
-
class
pdb2pqr.pdb.ATOM(line)[source]¶ ATOM class
The ATOM records present the atomic coordinates for standard residues. They also present the occupancy and temperature factor for each atom. Heterogen coordinates use the HETATM record type. The element symbol is always present on each ATOM record; segment identifier and charge are optional.
-
__init__(line)[source]¶ Initialize by parsing line
COLUMNS TYPE FIELD DEFINITION 7-11 int serial Atom serial number. 13-16 string name Atom name. 17 string alt_loc Alternate location indicator. 18-20 string res_name Residue name. 22 string chain_id Chain identifier. 23-26 int res_seq Residue sequence number. 27 string ins_code Code for insertion of residues. 31-38 float x Orthogonal coordinates for X in Angstroms. 39-46 float y Orthogonal coordinates for Y in Angstroms. 47-54 float z Orthogonal coordinates for Z in Angstroms. 55-60 float occupancy Occupancy. 61-66 float temp_factor Temperature factor. 73-76 string seg_id Segment identifier, left-justified. 77-78 string element Element symbol, right-justified. 79-80 string charge Charge on the atom. Parameters: line (str) – line with PDB class
-
-
class
pdb2pqr.pdb.AUTHOR(line)[source]¶ AUTHOR field
The AUTHOR record contains the names of the people responsible for the contents of the entry.
-
class
pdb2pqr.pdb.BaseRecord(line)[source]¶ Base class for all records.
Verifies the received record type.
-
class
pdb2pqr.pdb.CAVEAT(line)[source]¶ CAVEAT field
CAVEAT warns of severe errors in an entry. Use caution when using an entry containing this record.
-
class
pdb2pqr.pdb.CISPEP(line)[source]¶ CISPEP field
CISPEP records specify the prolines and other peptides found to be in the cis conformation. This record replaces the use of footnote records to list cis peptides.
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__init__(line)[source]¶ Initialize by parsing line
COLUMNS TYPE FIELD DEFINITION 8-10 int ser_num Record serial number. 12-14 string pep1 Residue name. 16 string chain_id1 Chain identifier. 18-21 int seq_num1 Residue sequence number. 22 string icode1 Insertion code. 26-28 string pep2 Residue name. 30 string chain_id2 Chain identifier. 32-35 int seq_num2 Residue sequence number. 36 string icode2 Insertion code. 44-46 int mod_num Identifies the specific model. 54-59 float measure Measure of the angle in degrees. Parameters: line (str) – line with PDB class
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class
pdb2pqr.pdb.COMPND(line)[source]¶ COMPND field
The COMPND record describes the macromolecular contents of an entry. Each macromolecule found in the entry is described by a set of token: value pairs, and is referred to as a COMPND record component. Since the concept of a molecule is difficult to specify exactly, PDB staff may exercise editorial judgment in consultation with depositors in assigning these names.
For each macromolecular component, the molecule name, synonyms, number assigned by the Enzyme Commission (EC), and other relevant details are specified.
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class
pdb2pqr.pdb.CONECT(line)[source]¶ CONECT class
The CONECT records specify connectivity between atoms for which coordinates are supplied. The connectivity is described using the atom serial number as found in the entry. CONECT records are mandatory for HET groups (excluding water) and for other bonds not specified in the standard residue connectivity table which involve atoms in standard residues (see Appendix 4 for the list of standard residues). These records are generated by the PDB.
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__init__(line)[source]¶ Initialize by parsing line
COLUMNS TYPE FIELD DEFINITION 7-11 int serial Atom serial number 12-16 int serial1 Serial number of bonded atom 17-21 int serial2 Serial number of bonded atom 22-26 int serial3 Serial number of bonded atom 27-31 int serial4 Serial number of bonded atom 32-36 int serial5 Serial number of hydrogen bonded atom 37-41 int serial6 Serial number of hydrogen bonded atom 42-46 int serial7 Serial number of salt bridged atom 47-51 int serial8 Serial number of hydrogen bonded atom 52-56 int serial9 Serial number of hydrogen bonded atom 57-61 int serial10 Serial number of salt bridged atom Parameters: line (str) – line with PDB class
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class
pdb2pqr.pdb.CRYST1(line)[source]¶ CRYST1 class
The CRYST1 record presents the unit cell parameters, space group, and Z value. If the structure was not determined by crystallographic means, CRYST1 simply defines a unit cube.
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__init__(line)[source]¶ Initialize by parsing line
COLUMNS TYPE FIELD DEFINITION 7-15 float a a (Angstroms). 16-24 float b b (Angstroms). 25-33 float c c (Angstroms). 34-40 float alpha alpha (degrees). 41-47 float beta beta (degrees). 48-54 float gamma gamma (degrees). 56-66 string space_group Space group. 67-70 int z Z value. Parameters: line (str) – line with PDB class
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class
pdb2pqr.pdb.DBREF(line)[source]¶ DBREF field
The DBREF record provides cross-reference links between PDB sequences and the corresponding database entry or entries. A cross reference to the sequence database is mandatory for each peptide chain with a length greater than ten (10) residues. For nucleic acid entries a DBREF record pointing to the Nucleic Acid Database (NDB) is mandatory when the corresponding entry exists in NDB.
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__init__(line)[source]¶ Initialize by parsing a line.
COLUMNS TYPE FIELD DEFINITION 8-11 string id_code ID code of this entry. 13 string chain_id Chain identifier. 15-18 int seq_begin Initial sequence number of the PDB sequence segment. 19 string insert_begin Initial insertion code of the PDB sequence segment. 21-24 int seq_end Ending sequence number of the PDB sequence segment. 25 string insert_end Ending insertion code of the PDB sequence segment. 27-32 string database Sequence database name. “PDB” when a corresponding sequence database entry has not been identified. 34-41 string db_accession Sequence database accession code. For GenBank entries, this is the NCBI gi number. 43-54 string db_id_code Sequence database identification code. For GenBank entries, this is the accession code. 56-60 int db_seq_begin Initial sequence number of the database seqment. 61 string db_ins_begin Insertion code of initial residue of the segment, if PDB is the reference. 63-67 int dbseq_end Ending sequence number of the database segment. 68 string db_ins_end Insertion code of the ending residue of the segment, if PDB is the reference. Parameters: line (str) – line with PDB class
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class
pdb2pqr.pdb.END(line)[source]¶ END class
The END records are paired with MODEL records to group individual structures found in a coordinate entry.
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class
pdb2pqr.pdb.ENDMDL(line)[source]¶ ENDMDL class
The ENDMDL records are paired with MODEL records to group individual structures found in a coordinate entry.
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class
pdb2pqr.pdb.EXPDTA(line)[source]¶ EXPDTA field
The EXPDTA record identifies the experimental technique used. This may refer to the type of radiation and sample, or include the spectroscopic or modeling technique. Permitted values include:
- ELECTRON DIFFRACTION
- FIBER DIFFRACTION
- FLUORESCENCE TRANSFER
- NEUTRON DIFFRACTION
- NMR
- THEORETICAL MODEL
- X-RAY DIFFRACTION
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class
pdb2pqr.pdb.FORMUL(line)[source]¶ FORMUL field
The FORMUL record presents the chemical formula and charge of a non-standard group.
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class
pdb2pqr.pdb.HEADER(line)[source]¶ HEADER field
The HEADER record uniquely identifies a PDB entry through the id_code field. This record also provides a classification for the entry. Finally, it contains the date the coordinates were deposited at the PDB.
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__init__(line)[source]¶ Initialize by parsing a line.
COLUMNS TYPE FIELD DEFINITION 11-50 string classification Classifies the molecule(s) 51-59 string dep_date Deposition date. This is the date the coordinates were received by the PDB 63-66 string id_code This identifier is unique wihin within PDB Parameters: line (str) – line with PDB class
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class
pdb2pqr.pdb.HELIX(line)[source]¶ HELIX field
HELIX records are used to identify the position of helices in the molecule. Helices are both named and numbered. The residues where the helix begins and ends are noted, as well as the total length.
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__init__(line)[source]¶ Initialize by parsing line
COLUMNS TYPE FIELD DEFINITION 8-10 int ser_num Serial number of the helix. This starts at 1 and increases incrementally. 12-14 string helix_id Helix identifier. In addition to a serial number, each helix is given an alphanumeric character helix identifier. 16-18 string init_res_name Name of the initial residue. 20 string init_chain_id Chain identifier for the chain containing this helix. 22-25 int init_seq_num Sequence number of the initial residue. 26 string init_i_code Insertion code of the initial residue. 28-30 string end_res_name Name of the terminal residue of the helix. 32 string end_chain_id Chain identifier for the chain containing this helix. 34-37 int end_seq_num Sequence number of the terminal residue. 38 string end_i_code Insertion code of the terminal residue. 39-40 int helix_class Helix class (see below). 41-70 string comment Comment about this helix. 72-76 int length Length of this helix. Parameters: line (str) – line with PDB class
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class
pdb2pqr.pdb.HET(line)[source]¶ HET field
HET records are used to describe non-standard residues, such as prosthetic groups, inhibitors, solvent molecules, and ions for which coordinates are supplied. Groups are considered HET if they are:
- not one of the standard amino acids, and
- not one of the nucleic acids (C, G, A, T, U, and I), and
- not one of the modified versions of nucleic acids (+C, +G, +A, +T, +U, and +I), and
- not an unknown amino acid or nucleic acid where UNK is used to indicate the unknown residue name.
Het records also describe heterogens for which the chemical identity is unknown, in which case the group is assigned the hetatm_id UNK.
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__init__(line)[source]¶ Initialize by parsing line
COLUMNS TYPE FIELD DEFINITION 8-10 string hetatm_id Het identifier, right-justified. 13 string ChainID Chain identifier. 14-17 int seq_num Sequence number. 18 string ins_code Insertion code. 21-25 int num_het_atoms Number of HETATM records. 31-70 string text Text describing Het group. Parameters: line (str) – line with PDB class
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class
pdb2pqr.pdb.HETATM(line, sybyl_type='A.aaa', l_bonds=[], l_bonded_atoms=[])[source]¶ HETATM class
The HETATM records present the atomic coordinate records for atoms within “non-standard” groups. These records are used for water molecules and atoms presented in HET groups.
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__init__(line, sybyl_type='A.aaa', l_bonds=[], l_bonded_atoms=[])[source]¶ Initialize by parsing line
COLUMNS TYPE FIELD DEFINITION 7-11 int serial Atom serial number. 13-16 string name Atom name. 17 string alt_loc Alternate location indicator. 18-20 string res_name Residue name. 22 string chain_id Chain identifier. 23-26 int res_seq Residue sequence number. 27 string ins_code Code for insertion of residues. 31-38 float x Orthogonal coordinates for X in Angstroms. 39-46 float y Orthogonal coordinates for Y in Angstroms. 47-54 float z Orthogonal coordinates for Z in Angstroms. 55-60 float occupancy Occupancy. 61-66 float temp_factor Temperature factor. 73-76 string seg_id Segment identifier, left- justified. 77-78 string element Element symbol, right-justified. 79-80 string charge Charge on the atom. Parameters: line (str) – line with PDB class
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class
pdb2pqr.pdb.HETNAM(line)[source]¶ HETNAM field
This record gives the chemical name of the compound with the given hetatm_id.
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class
pdb2pqr.pdb.HETSYN(line)[source]¶ HETSYN field
This record provides synonyms, if any, for the compound in the corresponding (i.e., same hetatm_id) HETNAM record. This is to allow greater flexibility in searching for HET groups.
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class
pdb2pqr.pdb.HYDBND(line)[source]¶ HYDBND field
The HYDBND records specify hydrogen bonds in the entry.
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__init__(line)[source]¶ Initialize by parsing line
COLUMNS TYPE FIELD DEFINITION 13-16 string name1 Atom name. 17 string alt_loc1 Alternate location indicator. 18-20 string res_name1 Residue name. 22 string chain1 Chain identifier. 23-27 int res_seq1 Residue sequence number. 28 string i_code1 Insertion code. 30-33 string name_h Hydrogen atom name. 34 string alt_loc_h Alternate location indicator. 36 string chain_h Chain identifier. 37-41 int res_seq_h Residue sequence number. 42 string ins_codeH Insertion code. 44-47 string name2 Atom name. 48 string alt_loc2 Alternate location indicator. 49-51 string res_name2 Residue name. 53 string chain_id2 Chain identifier. 54-58 int res_seq2 Residue sequence number. 59 string ins_code2 Insertion code. 60-65 string sym1 Symmetry operator for 1st non-hydrogen atom. 67-72 string sym2 Symmetry operator for 2nd non-hydrogen atom. Parameters: line (str) – line with PDB class
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class
pdb2pqr.pdb.JRNL(line)[source]¶ JRNL field
The JRNL record contains the primary literature citation that describes the experiment which resulted in the deposited coordinate set. There is at most one JRNL reference per entry. If there is no primary reference, then there is no JRNL reference. Other references are given in REMARK 1.
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class
pdb2pqr.pdb.KEYWDS(line)[source]¶ KEYWDS field
The KEYWDS record contains a set of terms relevant to the entry. Terms in the KEYWDS record provide a simple means of categorizing entries and may be used to generate index files. This record addresses some of the limitations found in the classification field of the HEADER record. It provides the opportunity to add further annotation to the entry in a concise and computer-searchable fashion.
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class
pdb2pqr.pdb.LINK(line)[source]¶ LINK field
The LINK records specify connectivity between residues that is not implied by the primary structure. Connectivity is expressed in terms of the atom names. This record supplements information given in CONECT records and is provided here for convenience in searching.
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__init__(line)[source]¶ Initialize by parsing line
COLUMNS TYPE FIELD DEFINITION 13-16 string name1 Atom name. 17 string alt_loc1 Alternate location indicator. 18-20 string res_name1 Residue name. 22 string chain_id1 Chain identifier. 23-26 int res_seq1 Residue sequence number. 27 string ins_code1 Insertion code. 43-46 string name2 Atom name. 47 string alt_loc2 Alternate location indicator. 48-50 string res_name2 Residue name. 52 string chain_id2 Chain identifier. 53-56 int res_seq2 Residue sequence number. 57 string ins_code2 Insertion code. 60-65 string sym1 Symmetry operator for 1st atom. 67-72 string sym2 Symmetry operator for 2nd atom. Parameters: line (str) – line with PDB class
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class
pdb2pqr.pdb.MASTER(line)[source]¶ MASTER class
The MASTER record is a control record for bookkeeping. It lists the number of lines in the coordinate entry or file for selected record types.
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__init__(line)[source]¶ Initialize by parsing line
COLUMNS TYPE FIELD DEFINITION 11-15 int num_remark Number of REMARK records 21-25 int num_het Number of HET records 26-30 int numHelix Number of HELIX records 31-35 int numSheet Number of SHEET records 36-40 int numTurn Number of TURN records 41-45 int numSite Number of SITE records 46-50 int numXform Number of coordinate transformation records (ORIGX+SCALE+MTRIX) 51-55 int numCoord Number of atomic coordinate records (ATOM+HETATM) 56-60 int numTer Number of TER records 61-65 int numConect Number of CONECT records 66-70 int numSeq Number of SEQRES records Parameters: line (str) – line with PDB class
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class
pdb2pqr.pdb.MODEL(line)[source]¶ MODEL class
The MODEL record specifies the model serial number when multiple structures are presented in a single coordinate entry, as is often the case with structures determined by NMR.
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class
pdb2pqr.pdb.MODRES(line)[source]¶ MODRES field
The MODRES record provides descriptions of modifications (e.g., chemical or post-translational) to protein and nucleic acid residues. Included are a mapping between residue names given in a PDB entry and standard residues.
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__init__(line)[source]¶ Initialize by parsing a line
COLUMNS TYPE FIELD DEFINITION 8-11 string id_code ID code of this entry. 13-15 string res_name Residue name used in this entry. 17 string chain_id Chain identifier. 19-22 int seq_num Sequence number. 23 string ins_code Insertion code. 25-27 string stdRes Standard residue name. 30-70 string comment Description of the residue modification. Parameters: line (str) – line with PDB class
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class
pdb2pqr.pdb.MTRIXn(line)[source]¶ MTRIXn baseclass
The MTRIXn (n = 1, 2, or 3) records present transformations expressing non-crystallographic symmetry.
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__init__(line)[source]¶ Initialize by parsing line
COLUMNS TYPE FIELD DEFINITION 8-10 int serial Serial number 11-20 float mn1 M31 21-30 float mn2 M32 31-40 float mn3 M33 46-55 float vn V3 60 int i_given 1 if coordinates for the representations which are approximately related by the transformations of the molecule are contained in the entry. Otherwise, blank. Parameters: line (str) – line with PDB class
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class
pdb2pqr.pdb.NUMMDL(line)[source]¶ NUMMDL class
The NUMMDL record indicates total number of models in a PDB entry.
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class
pdb2pqr.pdb.OBSLTE(line)[source]¶ OBSLTE field
This record acts as a flag in an entry which has been withdrawn from the PDB’s full release. It indicates which, if any, new entries have replaced the withdrawn entry.
The format allows for the case of multiple new entries replacing one existing entry.
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__init__(line)[source]¶ Initialize by parsing a line.
COLUMNS TYPE FIELD DEFINITION 12-20 string replace_date Date that this entry was replaced. 22-25 string id_code ID code of this entry. 32-35 string rid_code ID code of entry that replaced this one. 37-40 string rid_code ID code of entry that replaced this one. 42-45 string rid_code ID code of entry that replaced this one. 47-50 string rid_code ID code of entry that replaced this one. 52-55 string rid_code ID code of entry that replaced this one. 57-60 string rid_code ID code of entry that replaced this one. 62-65 string rid_code ID code of entry that replaced this one. 67-70 string rid_code ID code of entry that replaced this one. Parameters: line (str) – line with PDB class
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class
pdb2pqr.pdb.ORIGXn(line)[source]¶ ORIGXn class
The ORIGXn (n = 1, 2, or 3) records present the transformation from the orthogonal coordinates contained in the entry to the submitted coordinates.
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class
pdb2pqr.pdb.REMARK(line)[source]¶ REMARK field
REMARK records present experimental details, annotations, comments, and information not included in other records. In a number of cases, REMARKs are used to expand the contents of other record types. A new level of structure is being used for some REMARK records. This is expected to facilitate searching and will assist in the conversion to a relational database.
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class
pdb2pqr.pdb.REVDAT(line)[source]¶ REVDAT field
REVDAT records contain a history of the modifications made to an entry since its release.
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__init__(line)[source]¶ Initialize by parsing a line.
Todo
If multiple modifications are present, only the last one in the file is preserved.
COLUMNS TYPE FIELD DEFINITION 8-10 int mod_num Modification number. 14-22 string mod_date Date of modification (or release for new entries). 24-28 string mod_id Identifies this particular modification. It links to the archive used internally by PDB. 32 int mod_type An integer identifying the type of modification. In case of revisions with more than one possible mod_type, the highest value applicable will be assigned. 40-45 string record Name of the modified record. 47-52 string record Name of the modified record. 54-59 string record Name of the modified record. 61-66 string record Name of the modified record. Parameters: line (str) – line with PDB class
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class
pdb2pqr.pdb.SCALEn(line)[source]¶ SCALEn baseclass
The SCALEn (n = 1, 2, or 3) records present the transformation from the orthogonal coordinates as contained in the entry to fractional crystallographic coordinates. Non-standard coordinate systems should be explained in the remarks.
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class
pdb2pqr.pdb.SEQADV(line)[source]¶ SEQADV field
The SEQADV record identifies conflicts between sequence information in the ATOM records of the PDB entry and the sequence database entry given on DBREF. Please note that these records were designed to identify differences and not errors. No assumption is made as to which database contains the correct data. PDB may include REMARK records in the entry that reflect the depositor’s view of which database has the correct sequence.
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__init__(line)[source]¶ Initialize by parsing line
COLUMNS TYPE FIELD DEFINITION 8-11 string id_code ID code of this entry. 13-15 string res_name Name of the PDB residue in conflict. 17 string chain_id PDB chain identifier. 19-22 int seq_num PDB sequence number. 23 string ins_code PDB insertion code. 25-28 string database Sequence database name. 30-38 string db_id_code Sequence database accession number. 40-42 string db_res Sequence database residue name. 44-48 int db_seq Sequence database sequence number. 50-70 string conflict Conflict comment. Parameters: line (str) – line with PDB class
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class
pdb2pqr.pdb.SEQRES(line)[source]¶ SEQRES field
SEQRES records contain the amino acid or nucleic acid sequence of residues in each chain of the macromolecule that was studied.
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__init__(line)[source]¶ Initialize by parsing a line
COLUMNS TYPE FIELD DEFINITION 9-10 int ser_num Serial number of the SEQRES record for the current chain. Starts at 1 and increments by one each line. Reset to 1 for each chain. 12 string chain_id Chain identifier. This may be any single legal character, including a blank which is used if there is only one chain. 14-17 int num_res Number of residues in the chain. This value is repeated on every record. 20-22 string res_name Residue name. 24-26 string res_name Residue name. 28-30 string res_name Residue name. 32-34 string res_name Residue name. 36-38 string res_name Residue name. 40-42 string res_name Residue name. 44-46 string res_name Residue name. 48-50 string res_name Residue name. 52-54 string res_name Residue name. 56-58 string res_name Residue name. 60-62 string res_name Residue name. 64-66 string res_name Residue name. 68-70 string res_name Residue name. Parameters: line (str) – line with PDB class
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class
pdb2pqr.pdb.SHEET(line)[source]¶ SHEET field
SHEET records are used to identify the position of sheets in the molecule. Sheets are both named and numbered. The residues where the sheet begins and ends are noted.
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__init__(line)[source]¶ Initialize by parsing line
COLUMNS TYPE FIELD DEFINITION 8-10 int strand Strand number which starts at 1 for each strand within a sheet and increases by one. 12-14 string sheet_id Sheet identifier. 15-16 int num_strands Number of strands in sheet. 18-20 string init_res_name Residue name of initial residue. 22 string init_chain_id Chain identifier of initial residue in strand. 23-26 int init_seq_num Sequence number of initial residue in strand. 27 string init_i_code Insertion code of initial residue in strand. 29-31 string end_res_name Residue name of terminal residue. 33 string end_chain_id Chain identifier of terminal residue. 34-37 int end_seq_num Sequence number of terminal residue. 38 string end_i_code Insertion code of terminal residue. 39-40 int sense Sense of strand with respect to previous strand in the sheet. 0 if first strand, 1 if parallel, -1 if anti-parallel. 42-45 string cur_atom Registration. Atom name in current strand. 46-48 string curr_res_name Registration. Residue name in current strand. 50 string curChainId Registration. Chain identifier in current strand. 51-54 int curr_res_seq Registration. Residue sequence number in current strand. 55 string curr_ins_code Registration. Insertion code in current strand. 57-60 string prev_atom Registration. Atom name in previous strand. 61-63 string prev_res_name Registration. Residue name in previous strand. 65 string prevChainId Registration. Chain identifier in previous strand. 66-69 int prev_res_seq Registration. Residue sequence number in previous strand. 70 string prev_ins_code Registration. Insertion code in previous strand. Parameters: line (str) – line with PDB class
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class
pdb2pqr.pdb.SIGATM(line)[source]¶ SIGATM class
The SIGATM records present the standard deviation of atomic parameters as they appear in ATOM and HETATM records.
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__init__(line)[source]¶ Initialize by parsing line
COLUMNS TYPE FIELD DEFINITION 7-11 int serial Atom serial number. 13-16 string name Atom name. 17 string alt_loc Alternate location indicator. 18-20 string res_name Residue name. 22 string chain_id Chain identifier. 23-26 int res_seq Residue sequence number. 27 string ins_code Code for insertion of residues. 31-38 float sig_x Standard deviation of orthogonal coordinates for X in Angstroms. 39-46 float sig_y Standard deviation of orthogonal coordinates for Y in Angstroms. 47-54 float sig_z Standard deviation of orthogonal coordinates for Z in Angstroms. 55-60 float sig_occ Standard deviation of occupancy. 61-66 float sig_temp Standard deviation of temperature factor. 73-76 string seg_id Segment identifier, left-justified. 77-78 string element Element symbol, right-justified. 79-80 string charge Charge on the atom. Parameters: line (str) – line with PDB class
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class
pdb2pqr.pdb.SIGUIJ(line)[source]¶ SIGUIJ class
The SIGUIJ records present the anisotropic temperature factors.
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__init__(line)[source]¶ Initialize by parsing line:
COLUMNS TYPE FIELD DEFINITION 7-11 int serial Atom serial number. 13-16 string name Atom name. 17 string alt_loc Alternate location indicator. 18-20 string res_name Residue name. 22 string chain_id Chain identifier. 23-26 int res_seq Residue sequence number. 27 string ins_code Insertion code. 29-35 int sig11 Sigma U(1,1) 36-42 int sig22 Sigma U(2,2) 43-49 int sig33 Sigma U(3,3) 50-56 int sig12 Sigma U(1,2) 57-63 int sig13 Sigma U(1,3) 64-70 int sig23 Sigma U(2,3) 73-76 string seg_id Segment identifier, left-justified. 77-78 string el.ment Element symbol, right-justified. 79-80 string charge Charge on the atom. Parameters: line (str) – line with PDB class
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class
pdb2pqr.pdb.SITE(line)[source]¶ SITE class
The SITE records supply the identification of groups comprising important sites in the macromolecule.
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__init__(line)[source]¶ Initialize by parsing the line
COLUMNS 8-10 TYPE int FIELD seq_num DEFINITION Sequence number. 12-14 string site_id Site name. 16-17 int num_res Number of residues comprising site. 19-21 string res_name1 Residue name for first residue comprising site. 23 string chain_id1 Chain identifier for first residue comprising site. 24-27 int seq1 Residue sequence number for first residue comprising site. 28 string ins_code1 Insertion code for first residue comprising site. 30-32 string res_name2 Residue name for second residue comprising site. 34 string chain_id2 Chain identifier for second residue comprising site. 35-38 int seq2 Residue sequence number for second residue comprising site. 39 string ins_code2 Insertion code for second residue comprising site. 41-43 string res_name3 Residue name for third residue comprising site. 45 string chain_id3 Chain identifier for third residue comprising site. 46-49 int seq3 Residue sequence number for third residue comprising site. 50 string ins_code3 Insertion code for third residue comprising site. 52-54 string res_name4 Residue name for fourth residue comprising site. 56 string chain_id4 Chain identifier for fourth residue comprising site. 57-60 int seq4 Residue sequence number for fourth residue comprising site. 61 string ins_code4 Insertion code for fourth residue comprising site. Parameters: line (str) – line with PDB class
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class
pdb2pqr.pdb.SLTBRG(line)[source]¶ SLTBRG field
The SLTBRG records specify salt bridges in the entry. records and is provided here for convenience in searching.
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__init__(line)[source]¶ Initialize by parsing line
COLUMNS TYPE FIELD DEFINITION 13-16 string name1 Atom name. 17 string alt_loc1 Alternate location indicator. 18-20 string res_name1 Residue name. 22 string chain_id1 Chain identifier. 23-26 int res_seq1 Residue sequence number. 27 string ins_code1 Insertion code. 43-46 string name2 Atom name. 47 string alt_loc2 Alternate location indicator. 48-50 string res_name2 Residue name. 52 string chain_id2 Chain identifier. 53-56 int res_seq2 Residue sequence number. 57 string ins_code2 Insertion code. 60-65 string sym1 Symmetry operator for 1st atom. 67-72 string sym2 Symmetry operator for 2nd atom. Parameters: line (str) – line with PDB class
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class
pdb2pqr.pdb.SOURCE(line)[source]¶ SOURCE field
The SOURCE record specifies the biological and/or chemical source of each biological molecule in the entry. Sources are described by both the common name and the scientific name, e.g., genus and species. Strain and/or cell-line for immortalized cells are given when they help to uniquely identify the biological entity studied.
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class
pdb2pqr.pdb.SPRSDE(line)[source]¶ SPRSDE field
The SPRSDE records contain a list of the ID codes of entries that were made obsolete by the given coordinate entry and withdrawn from the PDB release set. One entry may replace many. It is PDB policy that only the principal investigator of a structure has the authority to withdraw it.
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__init__(line)[source]¶ Initialize by parsing line
COLUMNS TYPE FIELD DEFINITION 12-20 string super_date Date this entry superseded the listed entries. 22-25 string id_code ID code of this entry. 32-35 string sid_code ID code of a superseded entry. 37-40 string sid_code ID code of a superseded entry. 42-45 string sid_code ID code of a superseded entry. 47-50 string sid_code ID code of a superseded entry. 52-55 string sid_code ID code of a superseded entry. 57-60 string sid_code ID code of a superseded entry. 62-65 string sid_code ID code of a superseded entry. 67-70 string sid_code ID code of a superseded entry. Parameters: line (str) – line with PDB class
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class
pdb2pqr.pdb.SSBOND(line)[source]¶ SSBOND field
The SSBOND record identifies each disulfide bond in protein and polypeptide structures by identifying the two residues involved in the bond.
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__init__(line)[source]¶ Initialize by parsing line
COLUMNS TYPE FIELD DEFINITION 8-10 int ser_num Serial number. 16 string chain_id1 Chain identifier. 18-21 int seq_num1 Residue sequence number. 22 string icode1 Insertion code. 30 string chain_id2 Chain identifier. 32-35 int seq_num2 Residue sequence number. 36 string icode2 Insertion code. 60-65 string sym1 Symmetry operator for 1st residue. 67-72 string sym2 Symmetry operator for 2nd residue. Parameters: line (str) – line with PDB class
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class
pdb2pqr.pdb.TER(line)[source]¶ TER class
The TER record indicates the end of a list of ATOM/HETATM records for a chain.
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__init__(line)[source]¶ Initialize by parsing line:
COLUMNS TYPE FIELD DEFINITION 7-11 int serial Serial number. 18-20 string res_name Residue name. 22 string chain_id Chain identifier. 23-26 int res_seq Residue sequence number. 27 string ins_code Insertion code. Parameters: line (str) – line with PDB class
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class
pdb2pqr.pdb.TITLE(line)[source]¶ TITLE field
The TITLE record contains a title for the experiment or analysis that is represented in the entry. It should identify an entry in the PDB in the same way that a title identifies a paper.
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class
pdb2pqr.pdb.TURN(line)[source]¶ TURN field
The TURN records identify turns and other short loop turns which normally connect other secondary structure segments.
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__init__(line)[source]¶ Initialize by parsing line
COLUMNS TYPE FIELD DEFINITION 8-10 int seq Turn number; starts with 1 and increments by one. 12-14 string turn_id Turn identifier. 16-18 string init_res_name Residue name of initial residue in turn. 20 string init_chain_id Chain identifier for the chain containing this turn. 21-24 int init_seq_num Sequence number of initial residue in turn. 25 string init_i_code Insertion code of initial residue in turn. 27-29 string end_res_name Residue name of terminal residue of turn. 31 string end_chain_id Chain identifier for the chain containing this turn. 32-35 int end_seq_num Sequence number of terminal residue of turn. 36 string end_i_code Insertion code of terminal residue of turn. 41-70 string comment Associated comment. Parameters: line (str) – line with PDB class
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class
pdb2pqr.pdb.TVECT(line)[source]¶ TVECT class
The TVECT records present the translation vector for infinite covalently connected structures.
-
__init__(line)[source]¶ Initialize by parsing line
COLUMNS TYPE FIELD DEFINITION 8-10 int serial Serial number 11-20 float t1 Components of translation vector 21-30 float t2 Components of translation vector 31-40 float t2 Components of translation vector 41-70 string text Comments Parameters: line (str) – line with PDB class
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pdb2pqr.pdb.read_atom(line)[source]¶ If the ATOM/HETATM is not column-formatted, try to get some information by parsing whitespace from the right. Look for five floating point numbers followed by the residue number.
Parameters: line (str) – the line to parse
Other modules¶
cells¶
Cell list to facilitate neighbor searching.
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class
pdb2pqr.cells.Cells(cellsize)[source]¶ Accelerate the search for nearby atoms.
A pure all versus all search is O(n^2) - for every atom, every other atom must be searched. This is rather inefficient, especially for large biomolecules where cells may be tens of angstroms apart. The cell class breaks down the xyz biomolecule space into several 3-D cells of desired size - then by simply examining atoms that fall into the adjacent cells one can quickly find nearby cells.
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__init__(cellsize)[source]¶ Initialize the cells.
Parameters: cellsize (int) – the size of each cell (in Angstroms)
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assign_cells(biomolecule)[source]¶ Place each atom in a virtual cell for easy neighbor comparison.
Parameters: biomolecule (Biomolecule) – biomolecule with atoms to assign to cells
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debump¶
Routines for biomolecule optimization.
Code author: Jens Erik Nielsen
Code author: Todd Dolinsky
Code author: Yong Huang
Code author: Nathan Baker
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class
pdb2pqr.debump.Debump(biomolecule, definition=None)[source]¶ Grab bag of random stuff that apparently didn’t fit elsewhere.
Todo
This class needs to be susbtantially refactored in to multiple classes with clear responsibilities.
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__init__(biomolecule, definition=None)[source]¶ Initialize the Debump object.
Parameters: - biomolecule (Biomolecule) – the biomolecule to debump
- definition (Definition) – topology definition file
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debump_biomolecule()[source]¶ Minimize bump score for molecule.
Make sure that none of the added atoms were rebuilt on top of existing atoms. See each called function for more information.
Raises: ValueError – if missing (backbone) atoms are encountered
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debump_residue(residue, conflict_names)[source]¶ Debump a specific residue.
Only should be called if the residue has been detected to have a conflict. If called, try to rotate about dihedral angles to resolve the conflict.
Parameters: Returns: True if successful, False otherwise
Return type:
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find_nearby_atoms(atom)[source]¶ Find nearby atoms for conflict-checking.
Uses neighboring cells to compare atoms rather than an all versus all O(n^2) algorithm, which saves a great deal of time. There are several instances where we ignore potential conflicts; these include donor/acceptor pairs, atoms in the same residue, and bonded CYS bridges.
Parameters: atom (Atom) – find nearby atoms to this atom Returns: a dictionary of Atom too closetoamount of overlap for that atomReturn type: dict
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find_residue_conflicts(residue, write_conflict_info=False)[source]¶ Find conflicts between residues.
Parameters: Returns: list of conflicts
Return type: [str]
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get_bump_score(residue)[source]¶ Get a bump score for a residue.
Parameters: residue (Residue) – residue with bumping to evaluate Returns: bump score Return type: float
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get_bump_score_atom(atom)[source]¶ Find nearby atoms for conflict-checking.
Uses neighboring cells to compare atoms rather than an all versus all O(n^2) algorithm, which saves a great deal of time. There are several instances where we ignore potential conflicts; these include donor/acceptor pairs, atoms in the same residue, and bonded CYS bridges.
Parameters: atom (Atom) – find nearby atoms to this atom Returns: a bump score sum((dist-cutoff)**20 for all nearby atoms Return type: float
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get_closest_atom(atom)[source]¶ Get the closest atom that does not form a donor/acceptor pair.
Used to detect potential conflicts.
Note
Cells must be set before using this function.
Parameters: atom (Atom) – the atom to test Returns: the closest atom to the input atom that does not satisfy a donor/acceptor pair. Return type: Atom
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main¶
Perform functions related to _main_ execution of PDB2PQR.
This module is intended for functions that directly touch arguments provided at the invocation of PDB2PQR. It was created to avoid cluttering the __init__.py file.
Code author: Nathan Baker (et al.)
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pdb2pqr.main.build_main_parser()[source]¶ Build an argument parser.
Todo
Need separate argparse groups for PDB2PKA and PROPKA. These exist but need real options.
Returns: argument parser Return type: argparse.ArgumentParser
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pdb2pqr.main.check_files(args)[source]¶ Check for other necessary files.
Parameters: args (argparse.Namespace) – command-line arguments
Raises: - FileNotFoundError – necessary files not found
- RuntimeError – input argument or file parsing problems
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pdb2pqr.main.check_options(args)[source]¶ Sanity check options.
Parameters: args (argparse.Namespace) – command-line arguments Raises: RuntimeError – silly option combinations were encountered.
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pdb2pqr.main.drop_water(pdblist)[source]¶ Drop waters from a list of PDB records.
Todo
this module is already too long but this function fits better here. Other possible place would be utilities.
Parameters: pdb_list ([str]) – list of PDB records as returned by io.get_molecule Returns: new list of PDB records with waters removed. Return type: [str]
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pdb2pqr.main.dx_to_cube()[source]¶ Convert DX file format to Cube file format.
The OpenDX file format is defined at <https://www.idvbook.com/wp-content/uploads/2010/12/opendx.pdf` and the Cube file format is defined at <https://docs.chemaxon.com/display/Gaussian_Cube_format.html>.
Todo
This function should be moved into the APBS code base.
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pdb2pqr.main.is_repairable(biomolecule, has_ligand)[source]¶ Determine if the biomolecule can be (or needs to be) repaired.
Parameters: - biomolecule (biomol.Biomolecule) – biomolecule object
- has_ligand (bool) – does the system contain a ligand?
Returns: indication of whether biomolecule can be repaired
Return type: Raises: ValueError – if there are insufficient heavy atoms or a significant part of the biomolecule is missing
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pdb2pqr.main.main_driver(args)[source]¶ Main driver for running program from the command line.
Validate inputs, launch PDB2PQR, handle output.
Parameters: args (argparse.Namespace) – command-line arguments
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pdb2pqr.main.non_trivial(args, biomolecule, ligand, definition, is_cif)[source]¶ Perform a non-trivial PDB2PQR run.
Todo
These routines should be generalized to biomolecules; none of them are specific to biomolecules.
Parameters: - args (argparse.Namespace) – command-line arguments
- biomolecule (Biomolecule) – biomolecule
- ligand (Mol2Molecule) – ligand object or None
- definition (Definition) – topology definition
- is_cif (bool) – indicates whether file is CIF format
Raises: ValueError – for missing atoms that prevent debumping
Returns: dictionary with results
Return type:
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pdb2pqr.main.print_pdb(args, pdb_lines, header_lines, missing_lines, is_cif)[source]¶ Print PDB-format output to specified file
Todo
Move this to another module (io)
Parameters: - args (argparse.Namespace) – command-line arguments
- pdb_lines ([str]]) – output lines (records)
- header_lines ([str]) – header lines
- missing_lines ([str]) – lines describing missing atoms (should go in header)
- is_cif (bool) – flag indicating CIF format
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pdb2pqr.main.print_pqr(args, pqr_lines, header_lines, missing_lines, is_cif)[source]¶ Print PQR-format output to specified file
Todo
Move this to another module (io)
Parameters: - args (argparse.Namespace) – command-line arguments
- pqr_lines ([str]) – output lines (records)
- header_lines ([str]) – header lines
- missing_lines ([str]) – lines describing missing atoms (should go in header)
- is_cif (bool) – flag indicating CIF format
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pdb2pqr.main.print_splash_screen(args)[source]¶ Print argument overview and citation information.
Parameters: args (argparse.Namespace) – command-line arguments
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pdb2pqr.main.run_propka(args, biomolecule)[source]¶ Run a PROPKA calculation.
Parameters: - args (argparse.Namespace) – command-line arguments
- biomolecule (Biomolecule) – biomolecule object
Returns: (DataFrame of assigned pKa values, pKa information from PROPKA)
Return type: (pandas.DataFrame, str)
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pdb2pqr.main.setup_molecule(pdblist, definition, ligand_path)[source]¶ Set up the molecular system.
Parameters: - pdblist (list) – list of PDB records
- definition (Definition) – topology definition
- ligand_path (str) – path to ligand (may be None)
Returns: (biomolecule object, definition object–revised if ligand was parsed, ligand object–may be None)
Return type: (Biomolecule, Definition, Ligand)
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pdb2pqr.main.transform_arguments(args)[source]¶ Transform arguments with logic not provided by argparse.
Todo
I wish this could be done with argparse.
Parameters: args (argparse.Namespace) – command-line arguments Returns: modified arguments Return type: argparse.Namespace
psize¶
Get dimensions and other information from a PQR file.
Todo
This code could be combined with inputgen.
Todo
This code should be moved to the APBS code base.
Code author: Dave Sept
Code author: Nathan Baker
Code author: Todd Dolinksy
Code author: Yong Huang
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class
pdb2pqr.psize.Psize(cfac=1.7, fadd=20.0, space=0.5, gmemfac=200, gmemceil=400, ofrac=0.1, redfac=0.25)[source]¶ Class for parsing input files and suggesting settings.
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__init__(cfac=1.7, fadd=20.0, space=0.5, gmemfac=200, gmemceil=400, ofrac=0.1, redfac=0.25)[source]¶ Initialize.
Parameters: - cfac (float) – factor by which to expand molecular dimensions to get coarse grid dimensions
- fadd (float) – amount (in Angstroms) to add to molecular dimensions to get the fine grid dimensions
- space (float) – desired fine mesh resolution (in Angstroms)
- gmemfac (float) – number of bytes per grid point required for a sequential multigrid calculation
- gmemceil (float) – maximum memory (in MB) allowed for sequential multigrid calculation. Adjust this value to force the script to perform faster calculations (which require more parallelism).
- ofrac (float) – overlap factor between mesh partitions in parallel focusing calculation
- redfac (float) – the maximum factor by which a domain dimension can be reduced during focusing
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parse_input(filename)[source]¶ Parse input structure file in PDB or PQR format.
Parameters: filename (str) – string with path to PDB- or PQR-format file.
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parse_lines(lines)[source]¶ Parse the PQR/PDB lines.
Todo
This is messed up. Why are we parsing the PQR manually here when we already have other routines to do that? This function should be replaced by a call to existing routines.
Parameters: lines ([str]) – PDB/PQR lines to parse
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parse_string(structure)[source]¶ Parse the input structure as a string in PDB or PQR format.
Parameters: structure (str) – input structure as string in PDB or PQR format.
-
run_psize(filename)[source]¶ Parse input PQR file and set parameters.
Parameters: filename (str) – path of PQR file
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set_center(maxlen, minlen)[source]¶ Compute molecular center.
Parameters: Returns: center of molecule
Return type:
-
set_coarse_grid_dims(mol_length)[source]¶ Compute coarse mesh lengths.
Parameters: mol_length ([float, float, float]) – input molecule lengths Returns: coarse grid dimensions Return type: [float, float, float]
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set_fine_grid_dims(mol_length, coarse_length)[source]¶ Compute fine mesh lengths.
Parameters: Returns: fine grid lengths
Return type:
-
set_fine_grid_points(fine_length)[source]¶ Compute mesh grid points, assuming 4 levels in multigrid hierarchy.
Todo
remove hard-coded values from this function.
Parameters: fine_length ([float, float, float]) – lengths of the fine grid Returns: number of grid points in each direction Return type: [int, int, int]
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set_focus(fine_length, nproc, coarse_length)[source]¶ Calculate the number of levels of focusing required for each processor subdomain.
Parameters:
-
set_length(maxlen, minlen)[source]¶ Compute molecular dimensions, adjusting for zero-length values.
Todo
Replace hard-coded values in this function.
Parameters: Returns: molecular dimensions
Return type:
-
set_proc_grid(ngrid, nsmall)[source]¶ Calculate the number of processors required in a parallel focusing calculation to span each dimension of the grid given the grid size suitable for memory constraints.
Parameters: Returns: number of processors needed in each direction
Return type:
-
set_smallest(ngrid)[source]¶ Set smallest dimensions.
Compute parallel division of domain in case the memory requirements for the calculation are above the memory ceiling. Find the smallest dimension and see if the number of grid points in that dimension will fit below the memory ceiling Reduce nsmall until an nsmall^3 domain will fit into memory.
Todo
Remove hard-coded values from this function.
Parameters: ngrid ([int, int, int]) – number of grid points Returns: smallest number of grid points in each direction to fit in memory Return type: [int, int, int]
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-
pdb2pqr.psize.build_parser()[source]¶ Build argument parser.
Returns: argument parser Return type: argparse.ArgumentParser
quatfit¶
Quatfit routines for PDB2PQR
This module is used to find the coordinates of a new atom based on a reference set of coordinates and a definition set of coordinates.
Original Code by David J. Heisterberg, The Ohio Supercomputer Center, 1224 Kinnear Rd., Columbus, OH 43212-1163, (614)292-6036, djh@osc.edu, djh@ohstpy.bitnet, ohstpy::djh
Translated to C from fitest.f program and interfaced with Xmol program by Jan Labanowski, jkl@osc.edu, jkl@ohstpy.bitnet, ohstpy::jkl
Todo
There are many unnecessary parameters in this module due to FORTRAN/C assumptions about how the code should behave.
Code author: David Heisterberg
Code author: Jan Labanowski
Code author: Jens Erik Nielsen
Code author: Todd Dolinsky
-
pdb2pqr.quatfit.center(numpoints, refcoords)[source]¶ Center a molecule using equally weighted points.
Parameters: Returns: (center of the set of points, moved refcoords relative to refcenter)
-
pdb2pqr.quatfit.find_coordinates(numpoints, refcoords, defcoords, defatomcoords)[source]¶ Driver for the quaternion file.
Provide the coordinates as inputs and obtain the coordinates for the new atom as output.
Parameters: - numpoints (int) – the number of points in each list
- refcoords ([[float, float, float]]) – the reference coordinates, a list of lists of form [x,y,z]
- defcoords ([[float, float, float]]) – the definition coordinates, a list of lists of form [x,y,z]
- defatomcoords ([[float, float, float]]) – the definition coordinates for the atom to be placed in the reference frame
Returns: the coordinates of the new atom in the reference frame
Return type:
-
pdb2pqr.quatfit.jacobi(amat, nrot)[source]¶ Jacobi diagonalizer with sorted output, only good for 4x4 matrices.
Parameters: - amat – Matrix to diagonalize
- nrot (int) – maximum number of sweeps
Returns: (eigenvalues, eigenvectors)
-
pdb2pqr.quatfit.q2mat(quat)[source]¶ Generate a left rotation matrix from a normalized quaternion
Parameters: quat ([[float, float, float, float]]) – the normalized quaternion Returns: the rotation matrix
-
pdb2pqr.quatfit.qchichange(initcoords, refcoords, angle)[source]¶ Change the chiangle of the reference coordinate.
Change the chiangle of the reference coordinate using the initcoords and the given angle.
Parameters: Returns: the new coordinates of the atoms
Return type:
-
pdb2pqr.quatfit.qfit(numpoints, refcoords, defcoords)[source]¶ Method for getting new atom coordinates from sets of reference and definition coordinates.
Todo
Remove hard-coded parameters of function.
Parameters: Returns: (reference center, definition center, left rotation matrix)
Return type: ([[float, float, float]], [[float, float, float]], [[float, float, float]])
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pdb2pqr.quatfit.qtransform(numpoints, defcoords, refcenter, fitcenter, rotation)[source]¶ Transform coordinates using the reference.
Transform the set of defcoords using the reference center, the fit center, and a rotation matrix.
Parameters: - numpoints (int) – the number of points in each list
- defcoords ([[float, float, float]]) – set of coordinates to be transformed using the reference center and a rotation matrix
- refcenter ([[float, float, float]]) – the reference center
- fitcenter ([float, float, float]) – the definition center
- rotation ([[float, float, float]]) – the rotation matrix
Returns: the coordinates of the new point
Return type:
-
pdb2pqr.quatfit.qtrfit(numpoints, defcoords, refcoords, nrot)[source]¶ Find the best-fit quaternion.
Find the quaternion, q, [and left rotation matrix, u] that minimizes
\[| qTXq - Y | ^ 2 [|uX - Y| ^ 2]\]This is equivalent to maximizing
\[Re(q^T X^T q Y)\]The left rotation matrix, u, is obtained from q by
\[u = qT1q\]Parameters: - numpoints (int) – the number of points in each list
- defcoords ([[float, float, float]]) – list of definition coordinates, with each set a list of form [x,y,z]
- refcoords ([[float, float, float]]) – list of fitted coordinates, with each set a list of form [x,y,z]
- nrot (int) – the maximum number of Jacobi sweeps
Returns: (the best-fit quaternion, the best-fit left rotation matrix)
-
pdb2pqr.quatfit.rotmol(numpoints, coor, lrot)[source]¶ Rotate a molecule
Parameters: Returns: the rotated coordinates
Return type:
run¶
Routines for running the code with a given set of options and PDB files.
utilities¶
Utilities for the PDB2PQR software suite.
Code author: Todd Dolinsky
Code author: Yong Huang
Code author: Nathan Baker
-
pdb2pqr.utilities.add(coords1, coords2)[source]¶ Add one 3-dimensional point to another.
Parameters: Returns: list of coordinates equal to coords2 + coords1
Return type: numpy.ndarray
-
pdb2pqr.utilities.analyze_connectivity(map_, key)[source]¶ Analyze the connectivity of a given map using the key value.
Parameters: Returns: list of connected values to the key
Return type:
-
pdb2pqr.utilities.angle(coords1, coords2, coords3)[source]¶ Get the angle between three coordinates.
Parameters: Returns: angle between the atoms (in degrees)
Return type:
-
pdb2pqr.utilities.cross(coords1, coords2)[source]¶ Find the cross-product of one 3-dimensional point with another.
Parameters: Returns: list of coordinates equal to coords2 cross coords1
Return type: numpy.ndarray
-
pdb2pqr.utilities.dihedral(coords1, coords2, coords3, coords4)[source]¶ Calculate the dihedral angle from four atoms’ coordinates.
Parameters: Returns: the angle (in degrees)
Return type:
-
pdb2pqr.utilities.distance(coords1, coords2)[source]¶ Calculate the distance between two coordinates.
Parameters: Returns: distance between the two coordinates
Return type:
-
pdb2pqr.utilities.dot(coords1, coords2)[source]¶ Find the dot-product of one 3-dimensional point with another.
Parameters: Returns: list of coordinates equal to the inner product of coords2 with coords1
Return type: numpy.ndarray
-
pdb2pqr.utilities.factorial(num)[source]¶ Returns the factorial of the given number.
Parameters: num (int) – number for which to compute factorial Returns: factorial of number Return type: int
-
pdb2pqr.utilities.normalize(coords)[source]¶ Normalize a set of coordinates to unit vector.
Parameters: coords ([float, float, float]) – coordinates of form [x,y,z] Returns: normalized coordinates Return type: numpy.ndarray
-
pdb2pqr.utilities.shortest_path(graph, start, end, path=[])[source]¶ Find the shortest path between two nodes.
Uses recursion to find the shortest path from one node to another in an unweighted graph. Adapted from http://www.python.org/doc/essays/graphs.html
Parameters: - graph (dict) – a mapping of the graph to analyze, of the form {0: [1,2], 1:[3,4], …} . Each key has a list of edges.
- start (str) – the ID of the key to start the analysis from
- end (str) – the ID of the key to end the analysis
- path (list) – optional argument used during the recursive step to keep the current path up to that point
Returns: list of the shortest path or
Noneif start and end are not connectedReturn type:
-
pdb2pqr.utilities.sort_dict_by_value(inputdict)[source]¶ Sort a dictionary by its values.
Parameters: inputdict (dict) – the dictionary to sort Returns: list of keys sorted by value Return type: list
Release history¶
3.1.0 (2020-12-22)¶
Additions¶
- Created Sphinx documentation of usage and API at http://pdb2pqr.readthedocs.io (#88, #90).
- New command line tools added with documentation (#163).
- Added support for reading QCD-format structure files (#137).
- Added versioneer support for versioning (#104).
- Made several APBS tools available as PDB2PQR scripts:
dx2cube(#98),inputgen(#105),psize(#106). - Added code of conduct document (#62).
Fixes¶
- Fixed faulty no-op logic in debumping routines (#162)
- Fixed problem with element type in PDB output (#159)
- Updated very out-of-date change log (#153).
- Fixed atom-ordering problem in PDB output (#134).
- Fixed REDVAT PDB record parsing (#119).
- Fixed broken
--apbs-inputoption (#94). - Fixed OS-specific file handing (#78).
Changes¶
- PDB2PKA is still removed from the code base while refactoring for a code base that is more friendly to multiple platforms.
- Added Python 3.9 to testing (#161).
- Enabled additional PROPKA output (#143).
- Moved mmCIF support to external module
mmcif-pdbx(#135). - Added formal PQR parser (#97).
- Made failure due to missing backbone atoms more graceful (#95).
- Moved some logging output from stdout/stderr to files (#74).
- Increased testing (#70, #73).
- Continued de-linting and refactoring (#56, #122).
3.0.0 (2020-07-03)¶
Additions¶
- Added ability to read mmCIF files.
Fixes¶
- Updated URL used to fetch PDB files from RCSB.
- Fixed naming error for CYS hydrogen.
- Replaced Python pickle with portable JSON.
Changes¶
- Upgraded to Python 3.
- Changed primary distribution mechanism into Python package (#45)
- Upgraded web interface.
- Upgraded to PROPKA 3.1 (and converted to
pipdependency rather than submodule). - Removed PDB2PKA support.
- Added coverage tests to testing.
- Removed support for extensions.
- Significant code refactoring.
- Changed output from
print()tologging. - Provided additional warnings when dropping HETATM entries.
- Improved build system.
- Increased list of proteins used in testing.
- Removed Opal support.
- Added GitHub actions for continuous integration testing.
2.1.1 (2016-03)¶
Additions¶
- Replaced the Monte Carlo method for generating titration curves with Graph Cut. See http://arxiv.org/1507.07021/
Fixes¶
- Added a check before calculating pKa’s for large interaction energies
Known bugs¶
- If more than one extension is run from the command line and one of the extensions modifies the protein data structure it could affect the output of the other extension. The only included extensions that exhibit this problem are resinter and newresinter.
- Running ligands and PDB2PKA at the same time is not currently supported.
- PDB2PKA currently leaks memory slowly. Small jobs will use about twice the normally required RAM (i.e. ~14 titratable residues will use 140MB). Big jobs will use about 5 times the normally required RAM (60 titratable residues will use 480MB). We are working on this.
2.1.0 (2015-12)¶
Additions¶
- Added alternate method to do visualization using 3dmol.
- Replaced the Monte Carlo method for generating titration curves with Graph Cut. See http://arxiv.org/abs/1507.07021. If you prefer the Monte Carlo Method, please use http://nbcr-222.ucsd.edu/pdb2pqr_2.0.0/
Fixes¶
- Added compile options to allow for arbitrary flags to be added. Helps work around some platforms where scons does not detect the needed settings correctly.
- Fixed broken links on APBS submission page.
- Added some missing files to query status page results.
- Fixed some pages to use the proper CSS file.
- Better error message for
--assign-onlyand HIS residues. - Fixed PROPKA crash for unrecognized residue.
- Debumping routines are now more consistent across platforms. This fixes pdb2pka not giving the same results on different platforms.
Changes¶
- Added
fabricscript used to build and test releases. - The
newtworkxlibrary is now required forpdb2pka.
Known bugs¶
- If more than one extension is run from the command line and one of the extensions modifies the protein data structure it could affect the output of the other extension. The only included extensions that exhibit this problem are resinter and newresinter.
- Running ligands and PDB2PKA at the same time is not currently supported.
- PDB2PKA currently leaks memory slowly. Small jobs will use about twice the normally required RAM (i.e. ~14 titratable residues will use 140MB). Big jobs will use about 5 times the normally required RAM (60 titratable residues will use 480MB). We are working on this.
2.0.0 (2014-12)¶
Additions¶
- Improved look of web interface.
- Option to automatically drop water from pdb file before processing.
- Integration of PDB2PKA into PDB2PQR as an alternative to PROPKA.
- Support for compiling with VS2008 in Windows.
- Option to build with debug headers.
- PDB2PKA now detects and reports non Henderson-Hasselbalch behavior.
- PDB2PKA can be instructed whether or not to start from scratch with
--pdb2pka-resume. - Can now specify output directory for PDB2PKA.
- Improved error regarding backbone in some cases.
- Changed time format on query status page.
- Improved error catching on web interface.
Fixes¶
- Fixed executable name when creating binaries for Unix based operating systems.
- Fixed potential crash when using
--cleanwith extensions. - Fixed MAXATOMS display on server home page.
- PDB2PKA now mostly respects the
--verbosesetting. - Fixed how hydrogens are added by PDB2PKA for state changes in some cases.
- Fixed :mode:`psize` error check.
- Will now build properly without ligand support if
numpyis not installed. - Removed old automake build files from all test ported to scons.
- Fixed broken opal backend.
Changes¶
- Command line interface to PROPKA changed to accommodate PDB2PKA.
PROPKA is now used with
--ph-calc-method=propka --with-phnow defaults to 7.0 and is only required if a different pH value is required. --ph-calc-methodto select optional method to calculate pH values used to protonate titratable residues. Possible options are “propka” and “pdb2pka”.- Dropped support for compilation with mingw. Building on Windows now requires VS 2008 installed in the default location.
- Updated included Scons to 2.3.3
- PDB2PKA can now be run directly (not integrated in PDB2PQR) with pka.py. Arguments are PDBfile and Output directory.
- No longer providing 32-bit binary build. PDB2PKA support is too memory-intensive to make this practical in many cases.
Known bugs¶
- If more than one extension is run from the command line and one of the extensions modifies the protein data structure it could affect the output of the other extension. The only included extensions that exhibit this problem are resinter and newresinter.
- Running ligands and PDB2PKA at the same time is not currently supported.
- PDB2PKA currently leaks memory slowly. Small jobs will use about twice the normally required RAM (i.e. ~14 titratable residues will use 140MB). Big jobs will use about 5 times the normally required RAM (60 titratable residues will use 480MB). We are working on this.
1.9 (2014-03)¶
Additions¶
- Added support for reference command line option for PROPKA.
- Added newresinter plugin to provide alternate methods for calculating interaction energies between residues.
- Added propka support for phosphorous sp3. Thanks to Dr. Stefan Henrich
Fixes¶
- Rolled back change that prevented plugins from interfering with each other. Large proteins would cause a stack overflow when trying to do a deep copy
- Fixed apbs input file to match what web interface produces.
- Fixed user specified mobile ion species not being passed to apbs input file.
- Removed ambiguous A, ADE, C, CYT, G, GUA, T, THY, U, URA as possible residue names.
- Fixed hbond extension output to include insertion code in residue name.
- Fixed debumping routines not including water in their checks. Fixes bad debump of ASN B 20 in 1gm9 when run with pH 7.0.
- Fixed debumping failing to use best angle for a specific dihedral angle when no tested angles are without conflict.
- Fixed debumping using asymmetrical cutoffs and too large cutoffs in many checks involving hydrogen.
- Fixed debumping accumulating rounding error while checking angles.
- Fixed inconsistencies in pdb parsing. Thanks to Dr. Stefan Henrich
- Fixed problems with propka handling of aromatic carbon/nitrogen. Thanks to Dr. Stefan Henrich
- Fixed case where certain apbs compile options would break web visualization.
- Fixed improper handling of paths with a ‘.’ or filenames with more than one ‘.’ in them.
Changes¶
- Updated INSTALL file to reflect no more need for Fortran.
- Removed eval from pdb parsing routines.
- Updated web links where appropriate.
- Binary builds do not require python or numpy be installed to use. Everything needed to run PDB2PQR is included. Just unpack and use.
- OSX binaries require OSX 10.6 or newer. The OSX binary is 64-bit.
- Linux binaries require CentOS 6 or newer and have been tested on Ubuntu 12.04 LTS and Linux Mint 13. If you are running 64-bit Linux use the 64-bit libraries. In some cases the needed 32-bit system libraries will not be installed on a 64-bit system.
- Windows binaries are 32 bit and were built and tested on Windows 7 64-bit but should work on Windows XP, Vista, and 8 both 32 and 64-bit systems.
- PDB2PQR can now be compiled and run on Windows using MinGW32. See http://mingw.org/ for details.
- PDB2PQR now uses Scons for compilations. With this comes improved automated testing.
- A ligand file with duplicate atoms will cause pdb2pqr to stop instead of issue a warning. Trust us, this is a feature, not a bug!
- Improved error reporting.
- Mol2 file handling is now case insensitive with atom names.
- PROPKA with a pH of 7 is now specified by default on the web service.
- Compilation is now done with scons.
- Verbose output now includes information on all patches applied during a run.
- Added stderr and stdout to web error page.
- Added warning to water optimization when other water is ignored.
- Command line used to generate a pqr is now duplicated in the comments of the output.
- Added support for NUMMDL in parser.
- Added complete commandline feature test. Use complete-test target.
- Added a PyInstaller spec file. Standalone pdb2pqr builds are now possible.
- Removed
numpyfrom contrib. The user is expected to havenumpyinstalled and available to python at configuration. - Support for
numericdropped.
Known bugs¶
- If more than one extension is run from the command line and one of the extensions modifies the protein data structure it could affect the output of the other extension. The only included extensions that exhibit this problem are resinter and newresinter.
1.8 (2012-01)¶
Additions¶
- Added residue interaction energy extension
- Added Opal configuration file.
Fixes¶
- Cleaned up white space in several files and some pydev warnings
- Creating print output no longer clears the chain id data from atoms in the data. (Affected resinter plugin)
- Removed possibility of one plug-in affecting the output of another
- Fixed
--protonation=newoption forpropka30 - Improved time reporting for apbs jobs
- Fixed opal runtime reporting
- Fixed misspelled command line options that prevented the use of PEOEPB and TYL06
- Fixed error handling when certain data files are missing
- Fixed LDFLAGS environment variable not being used along with python specific linker flags to link
Algorithms.oand_pMC_mult.so - Fixed possible Attribute error when applying naming scheme.
Changes¶
- Updated PROPKA to version 3.0
- Added protein summary extension
- Combined
hbondandhbondwhatifinto one extension (hbond) with new command line parameters - Combined
rama,phi,psiinto one extension (rama) with new command line parameters. - Extensions may now add their own command line arguments. Extensions with their own command line arguments will be grouped separately.
- Improved interface for extensions
1.7.1a (2011-09-13)¶
Additions¶
- Added force field example.
Fixes¶
- Fixed ligand command line option.
- Fixed capitalization of force field in PQR header.
- Fixed error handling for opal errors.
- Fixed web logging error when using ligand files, user force fields, and name files.
- Fixed extension template in documentation.
- Fixed 1a1p example README to reflect command line changes.
1.7.1 (2011-08)¶
Additions¶
- Switched Opal service urls from sccne.wustl.edu to NBCR.
- Added more JMol controls for visualization, JMol code and applets provided by Bob Hanson.
- Changed default forcefield to PARSE in web interface.
Fixes¶
- Fixed crash when opal returns an error.
- Fixed specific combinations of command-line arguments causing
pdb2pqr.pyto crash. - Fixed opal job failing when filenames have spaces or dashs.
- Fixed gap in backbone causing irrationally placed hydrogens.
- Fixed crash when too many fixes are needed when setting termini.
- Corrected web and command line error handling in many cases.
- Fixed
--usernamecommand line option. - Fixed ambiguous user created forcefield and name handling. Now
--usernameis required if--userffis used. - Fixed
querystatus.pynot redirecting to generated error page.
1.7 (2010-10)¶
Changes¶
- For PDB2PQR web interface users: the JMol web interface for APBS calculation visualization has been substantially improved, thanks to help from Bob Hanson. Those performing APBS calculations via the PDB2PQR web interface now have a much wider range of options for visualizing the output online – as well as downloading for offline analysis.
- For PDB2PQR command-line and custom web interface users: the Opal service URLs have changed to new NBCR addresses. Old services hosted at .wustl.edu addresses have been decommissioned. Please upgrade ASAP to use the new web service. Thank you as always to the staff at NBCR for their continuing support of APBS/PDB2PQR web servers and services.
1.6 (2010-04)¶
Additions¶
- Added Swanson force field based on Swanson et al paper (http://dx.doi.org/10.1021/ct600216k).
- Modified
printAtoms()method. Now “TER” is printed at the end of every chain. - Added Google Analytics code to get the statistics on the production server.
- Modified APBS calculation page layout to hide parameters by default and display PDB ID
- Added
make test-webserver, which tests a long list of PDBs (246 PDBs) on the production PDB2PQR web server. - Removed
nlevfrominputgen.pyandinputgen_pKa.pyas nlev keyword is now deprecated in APBS. - Added PARSE parameters for RNA, data from: Tang C. L., Alexov E, Pyle A. M., Honig B. Calculation of pKas in RNA: On the Structural Origins and Functional Roles of Protonated Nucleotides. Journal of Molecular Biology 366 (5) 1475-1496, 2007.
Fixes¶
- Fixed a minor bug: when starting
pka.pyfrom pdb2pka directory using command likepython pka.py [options] inputfile, we need to make sure scriptpath does not end with “/”. - Fixed a bug which caused “coercing to Unicode: need string or buffer, instance found” when submitting PDB2PQR jobs with user-defined force fields on Opal based web server.
- Fixed a bug in
main_cgi.py, now Opal-based PDB2PQR jobs should also be logged inusage.txtfile. - Updated
src/utilities.pywith a bug fix provided by Greg Cipriano, which prevents infinite loops in analyzing connected atoms in certain cases. - Fixed a bug related to neutraln and/or neutralc selections on the web server.
- Fixed a special case with
--ffoutand 1AIK, where the N-terminus is acetylated. - Fixed a bug in
psize.pyper Michael Lerner’s suggestion. The old version ofpsize.pygives wrong cglen and fglen results in special cases (e.g., all y coordinates are negative values). - Fixed a bug in
main_cgi.py, eliminated input/output file name confusions whether a PDB ID or a pdb file is provided on the web server. - Fixed a bug which causes run time error on the web server when user-defined force field and names files are provided.
- Fixed a bug in
apbs_cgi.py: pdb file names submitted by users are not always 4 characters long.
1.5 (2009-10)¶
Additions¶
- APBS calculations can be executed through the PDB2PQR web interface in the production version of the server
- APBS-calculated potentials can be visualized via the PDB2PQR web interface thanks to Jmol
- Disabled Typemap output by default, added –typemap flag to create typemap output if needed.
- Enabled “Create APBS Input File” by default on the web server, so that APBS calculation and visualization are more obvious to the users.
- Added warnings to stderr and the REMARK field in the output PQR file regarding multiple occupancy entries in PDB file.
- Added more informative messages in REMARK field, explaining why PDB2PQR was unable to assign charges to certain atoms.
- Added
make test-long, which runs PDB2PQR on a long list (246) of PDBs by default, it is also possible to let it run on specified number of PDBs, e.g.,export TESTNUM=50; make test-long - Merged PDB2PKA code, PDB2PKA is functional now.
- Added two new options:
--neutralnand--neutralc, so that users can manually make the N-termini or C-termini of their proteins neutral. - Added a
local-test, which addresses the issue of Debian-like Linux distros not allowing fetching PDBs from the web. - Added deprotonated Arginine form for post-PROPKA routines. This only works for PARSE forcefield as other forcefields lack deprotonated ARG parameters.
Fixes¶
- Verbosity outputs should be stdouts, not stderrs in web server interface.
Corrected this in
src/routines.py. - Fixed a bug in
psize.py: for a pqr file with no ATOM entries but only HETATM entries in it,inputgen.pyshould still create an APBS input file with reasonable grid lengths. - Added special handling for special mol2 formats (unwanted white spaces or blank lines in ATOM or BOND records).
- Added template file to doc directory, which fixed a broken link in programmer guide.
Changes¶
- Updated structures.py, now PDB2PQR keeps the insertion codes from PDB files.
- Updated NBCR opal service urls from http://ws.nbcr.net/opal/… to http://ws.nbcr.net/opal2/…
- Compressed APBS OpenDX output files in zip format, so that users can download zip files from the web server.
- Removed “EXPERIMENTAL” from APBS web solver interface and Jmol visualization interface.
- Updated all APBS related urls from http://apbs.sourceforge.net/… to http:/apbs.wustl.edu/…
- Updated inputgen.py with –potdx and –istrng options added, original modification code provided by Miguel Ortiz-Lombardía.
- Changed default Opal service from http://ws.nbcr.net/opal2/services/pdb2pqr_1.4.0 to http://sccne.wustl.edu:8082/opal2/services/pdb2pqr-1.5
1.4.0 (2009-03)¶
Additions¶
- Added a whitespace option by by putting whitespaces between atom name and residue name, between x and y, and between y and z.
- Added radius for Chlorine in ligff.py.
- Added PEOEPB forcefield, data provided by Paul Czodrowski.
- Updated inputgen.py to write out the electrostatic potential for APBS input file.
Fixes¶
- Fixed a legacy bug with the web server (web server doesn’t like ligand files generated on Windows or old Mac OS platforms).
- Fixed a bug in
configure.ac, so that PDB2PQR no longer checks forNumpy.pthat configure stage. - Updated
pdb2pka/substruct/Makefile.am. - Fixed
isBackbone()bug indefinitions.py. - Fixed a bug for
Carboxylicresidues inhydrogens.py. - Fixed a bug in
routines.py, which caused hydrogens added in LEU and ILE in eclipsed conformation rather than staggered. - Fixed a bug in
configure.ac, now it is OK to configure with double slashes in the prefix path, e.g.,--prefix=/foo/bar//another/path - Fixed a bug in nucleic acid naming scheme.
- Fixed a bug involving MET, GLY as NTERM, CTERM with
--ffoutoption. - Fixed a bug for PRO as C-terminus with PARSE forcefield.
- Fixed a bug for ND1 in HIS as hacceptor.
- Fixed the
--cleanoption bug. - Fixed a bug in CHARMM naming scheme.
- Fixed a bug in
test.cppof the simple test (which is related to recent modifications of 1AFS in Protein Data Bank).
Changes¶
- Updated
html/master-index.html, deletedhtml/index.php. - Updated pydoc by running
genpydoc.sh. - Updated CHARMM.DAT with two sets of phosphoserine parameters.
- Allowed amino acid chains with only one residue, using
--assign-onlyoption. - Updated
server.py.inso that the ligand option is also recorded inusage.txt. - Updated HE21, HE22 coordinates in GLN according to the results from AMBER Leap program.
- Updated
Makefile.amwith Manuel Prinz’s patch (removed distclean2 and appended its contents to distclean-local). - Updated
configure.ac,pdb2pqr-opal.py; addedAppService_client.pyandAppService_types.pywith Samir Unni’s changes, which fixed earlier problems in invoking Opal services. - Applied two patches from Manuel Prinz to
pdb2pka/pMC_mult.handpdb2pka/ligand_topology.py. - Updated
PARSE.DAT:file:with the source of parameters. - Created a
contribfolder withnumpy-1.1.0package. PDB2PQR will install numpy by default unless any of the following conditions is met:- Working version of NumPy dectected by autoconf.
- User requests no installation with
--disable-pdb2pkaoption. - User specifies external NumPy installation.
- Merged Samir Unni’s branch.
Now PDB2PQR Opal and APBS Opal services are available (through
--with-opaland/or--with-apbs,--with-apbs-opaloptions at configure stage). - Added error handling for residue name longer than 4 characters.
- Updated
hbond.pywith Mike Bradley’s definitions for ANGLE_CUTOFF and DIST_CUTOFF by default. - Removed PyXML-0.8.4, which is not required for ZSI installation.
- Updated propka error message for make adv-test – propka requires a version of Fortran compiler.
- Updated
na.pyandPATCHES.xmlso that PDB2PQR handles three lettered RNA residue names (ADE, CYT, GUA, THY, and URA) as well. - Updated NA.xml with HO2’ added as an alternative name for H2’’, and H5” added as an alternative name for H5’’.
- Updated version numbers in html/ and doc/pydoc/ .
- Updated web server.
When selecting user-defined forcefield file from the web server, users should also provide
.namesfile. - Removed http://enzyme.ucd.ie/Services/pdb2pqr/ from web server list.
- Eliminated the need for protein when processing other types (ligands, nucleic acids).
- Updated
psize.pywith Robert Konecny’s patch to fix inconsistent assignment of fine grid numbers in some (very) rare cases. - Made whitespace option available for both command line and web server versions.
- Updated
inputgen_pKa.pywith the latest version.
1.3.0 (2008-01)¶
Additions¶
- Added
make testandmake adv-test - Added integration with Opal for launching jobs as well as querying status
Fixes¶
- Fixed the line feed bug.
Now PDB2PQR handles different input files (
.pdband file:.mol2) created or saved on different platforms. - Fixed
hbondwhatifwarning at start up. - Fixed problems with
make dist - The default value of 7.00 for the pH on the server form is removed due to a problem with browser refershing.
Changes¶
- The user may use NUMPY to specify the location of NUMPY.
- Both PDB2PKA and PROPKA are enabled by default. PDB2PKA is enabled by default since ligand parameterization would fail without this option.
- For a regular user,
make installtells the user the exact command the system administrator will use to make the URL viewable. - Updated warning messages for lines beginning with SITE, TURN, SSBOND and LINK.
- Switched license from GPL to BSD.
- Made a new tar ball
pdb2pqr-1.3.0-1.tar.gzfor Windows users who cannot create file:pdb2pqr.py through configure process. - file:configure now automatically detects SRCPATH, WEBSITE, and the location of file:pdb2pqr.cgi. In version 1.2.1, LOCALPATH(SRCPATH) and WEBSITE were defined in file:src/server.py and the location of file:pdb2pqr.cgi was specified in file:html/server.html (file:index.html). Configure now uses variable substitution with new files file:src/server.py.in and file:html/server.html.in to create file:src/server.py and file:html/server.html (file:index.html).
- SRCPATH is automatically set to the current working directory. WEBSITE is automatically set to http://fully_qualified_domain_name/pdb2pqr. Path to CGI is automcailly set to http://fully_qualified_domain_name/pdb2pqr/pdb2pqr.cgi.
- In version 1.2.1, there were 3 variables that needed to be changed to set up a server at a location different from agave.wustl.edu. LOCALPATH, WEBSITE, and the location of the CGI file. In this version, LOCALPATH has been used to SRCPATH to avoid confusion, since LOCALPATH could be interpreted as the local path for source files or the localpath for the server.
- Since configure now automatically sets the locations of files/directories based on the machine and configure options, the default agave.wustl.edu locations are not used anymore.
- A copy of
pdb2pqr.cssis included. configureprints out information about parameters such as python flags, srcpath, localpath, website, etc.configurenow automatically creates tmp/ with r + w + x permissions.configurenow automatically copiespdb2pqr.pytopdb2pqr.cgi.configurenow automatically copieshtml/server.htmltoindex.htmlafter variable substitution. Insrc/server.py.in(src/server.py), WEBNAME is changed toindex.html.$HOME/pdb2pqris the default prefix for a regular user/var/www/htmlis the default prefix for root- http://FQDN/pdb2pqr as default website.
make installrunsmakefirst, and the copies the approprite files to--prefix.- If root did not specify
--prefixand/var/www/html/pdb2pqralready exists, then a warning is issued, and the user may choose to quit or overwrite that directory. - Similary, if a regular user did not specify
--prefixand$HOME/pdb2pqralready exists, then a warning is issued, and the user may choose to quit or overwrite that directory. - If root does not specify
--prefixto be a directory to be inside/var/www/html(for example,--prefix=/share/apps/pdb2pqr), then a symbolic link will be made to/var/www/html/pdb2pqrduringmake install. configureoption--with-urlcan be specified either as something like http://sandstone.ucsd.edu/pdb2pqr-test or sandstone.ucsd.edu/pdb2pqr-test. It also doesn’t matter if there’s a ‘/’ at the end.- If user is root, and the last part of URL and prefix are different, for example,
--with-url=athena.nbcr.net/test0 --prefix=/var/www/html/pdb2pqr-test, then a warning will be issued saying the server will be viewable from the URL specified, but not the URL based on pdb2pqr-test. In other words, the server will be viewable from athena.abcr.net/test0, but not athena.nbcr.net/pdb2pqr-test. Duringmake install, a symbolic link is created to enable users to view the server from--with-url. - When making a symbolic link for root, if then link destination already exists as a directory or a symoblic link, then the user may choose to continue with creating the link and overwrite the original directory or quit.
- If the user changes py_path when running configure for PDB2PQR, then the change also applies to PROPKA.
1.2.1 (2007-04)¶
Additions¶
- Added ligand examples to examples/ directory
- Added native support for the TYL06 forcefield. For more information on this forcefield please see Tan C, Yang L, Luo R. How well does Poisson-Boltzmann implicit solvent agree with explicit solvent? A quantitative analysis. Journal of Physical Chemistry B. 110 (37), 18680-7, 2006.
- Added a new HTML output page which relays the different atom types between the AMBER and CHARMM forcefields for a generated PQR file (thanks to the anonymous reviewers of the latest PDB2PQR paper).
Fixes¶
- Fixed bug where a segmentation fault would occur in PropKa if the N atom was not the first atom listed in the residue
- Fixed error message that occurred when a blank line was found in a parameter file.
- Better error handling in MOL2 file parsing.
- Fixed bug where ligands were not supported on PDB files with multiple MODEL fields.
Changes¶
- Updated documentation to include instructions for pdb2pka support, references, more pydoc documents.
1.2.0 (2007-01)¶
Additions¶
- Added new support for passing in a single ligand residue in MOL2 format via the
--ligandcommand. Also available from the web server (with link to PRODRG for unsupported ligands). - Numerous additions to examples directory (see
examples/index.html) and update to User Guide.
Fixes¶
- Fixed charge assignment error when dealing with LYN in AMBER.
- Fixed crash when a chain has a single amino acid residue. The code now reports the offending chain and residue before exiting.
- Fixed hydrogen optimization bug where waters with no nearby atoms at certain orientations caused missing hydrogens.
Changes¶
- Added autoconf support for
pdb2pkadirectory.
1.1.2 (2006-06)¶
Fixes¶
- Fixed a bug in the hydrogen bonding routines where PDB2PQR attempted to delete an atom that had already been deleted. (thanks to Rachel Burdge)
- Fixed a bug in chain detection routines where PDB2PQR was unable to detect multiple chains inside a single unnamed chain (thanks to Rachel Burdge)
- Fixed a second bug in chain detection routines where HETATM residues with names ending in “3” were improperly chosen for termini (thanks to Reut Abramovich)
- Fixed a bug where chains were improperly detected when only containing one HETATM residue (thanks to Reut Abramovich)
1.1.1 (2006-05)¶
Fixes¶
- Fixed a bug which prevented PDB2PQR from recognizing atoms from nucleic acids with “*” in their atom names. (thanks to Jaichen Wang)
- Fixed a bug in the hydrogen bonding routines where a misnamed object led to a crash for very specific cases. (thanks to Josh Swamidass)
1.1.0 (2006-04)¶
Additions¶
- Added an
extensionsdirectory for small scripts. Scripts in this directory will be automatically loaded into PDB2PQR has command line options for post-processing, and can be easily customized. - Pydoc documentation is now included in
html/pydoc. - A programmer’s guide has been included to explain programming decisions and ease future development.
- A
--ffoutflag has been added to allow users to output a PQR file in the naming scheme of the desired forcefield.
Fixes¶
- Updated
psize.pyto use centers and radii when calculating grid sizes (thanks to John Mongan) - Fixed bug where PDB2PQR could not read PropKa results from chains with more than 1000 residues (thanks to Michael Widmann)
Changes¶
- Structural data files have been moved to XML format. This should make it easier for users and developers to contribute to the project.
- Code has been greatly cleaned so as to minimize values hard-coded into functions and to allow greater customizability via external XML files. This includes a more object-oriented hierarchy of structures.
- Improved detection of the termini of chains.
- Assign-only now does just that - only assigns parameters to atoms without additions, debumping, or optimizations.
- Added a
--cleancommand line option which does no additions, optimizations, or forcefield assignment, but simply aligns the PDB columns on output. Useful for using post-processing scripts like those in the extensions directory without modifying the original input file. - The
--userffflag has been replaced by opening up the--ffoption to user-defined files. - User guide FAQ updated.
- The efficiency of the hydrogen bonding detection script (
--hbond) has been greatly improved. - Increased the number of options available to users via the PDB2PQR web server.
1.0.2 (2005-12)¶
Additions¶
- Added ability for users to add their own forcefield files. This should be particularly useful for HETATMs.
- Added sdens keyword to
inputgen.pyto make PDB2PQR compatibile with APBS 0.4.0. - Added a new examples directory with a basic runthrough on how to use the various features in PDB2PQR.
Fixes¶
- Fixed a bug that was unable to handle N-Terminal PRO residues with hydrogens already present.
- Fixed two instances in the PropKa routines where warnings were improperly handled due to a misspelling.
- Fixed instance where chain IDs were unable to be assigned to proteins with more than 26 chains.
1.0.1 (2005-10)¶
Fixes¶
- Fixed a bug during hydrogen optimization that left out H2 from water if the oxygen in question had already made 3 hydrogen bonds.
Changes¶
- Added citation information to PQR output.
1.0.0 (2005-08)¶
This is the initial version of the PDB2PQR conversion utility. There are several changes to the various “non-official” versions previously available:
- SourceForge has been chosen as a centralized location for all things related to PDB2PQR, including downloads, mailing lists, and bug reports.
- Several additions to the code have been made, including pKa support via PropKa, a new hydrogen optimization algorithm which should increase both accuracy and speed, and general bug fixes.