io

Functions related to reading and writing data.

class pdb2pqr.io.DuplicateFilter

Filter duplicate messages.

__init__()

Initialize a filter.

Initialize with the name of the logger which, together with its children, will have its events allowed through the filter. If no name is specified, allow every event.

filter(record)

Filter current record.

pdb2pqr.io.dump_apbs(output_pqr, output_path)

Generate and dump APBS input files related to output_pqr.

Parameters:

• output_pqr (str) – path to PQR file used to generate APBS input file
• output_path (str) – path for APBS input file output

pdb2pqr.io.get_definitions(aa_path='AA.xml', na_path='NA.xml', patch_path='PATCHES.xml')

Load topology definition files.

Parameters:

• aa_path (str) – likely location of amino acid topology definitions
• na_path (str) – likely location of nucleic acid topology definitions
• patch_path (str) – likely location of patch topology definitions

Returns:

topology Definitions object.

Return type:

Definition

pdb2pqr.io.get_molecule(input_path)

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)

Get old header from list of pdb objects.

Parameters:pdblist ([]) – list of pdb block objects Returns:old header as string Return type:str

pdb2pqr.io.get_pdb_file(name)

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)

Get PDB-format text lines for specified atoms.

Parameters:

• atomlist ([Atom]) – the list of atoms to include
• chainflag (bool) – flag whether to print chainid or not

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)

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:

str

pdb2pqr.io.print_pqr_header_cif(atomlist, reslist, charge, force_field, ph_calc_method, ph, ffout, include_old_header=False)

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:

str

pdb2pqr.io.read_dx(dx_file)

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)

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)

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')

Setup the logger.

Setup logger to output the log file to the same directory as PQR output.

Parameters:

• output_pqr (str) – path to PQR file
• level (str) – logging level

pdb2pqr.io.test_dat_file(name)

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_)

Test for the existence of a file with a few name permutations.

Parameters:

• name (str) – name of file
• type (str) – type of file

Returns:

path to file

Raises:

FileNotFoundError – if file not found

Return type:

Path

pdb2pqr.io.test_names_file(name)

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)

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.')

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:

• cube_file (file) – file object ready for writing text data
• data_dict (dict) – dictionary of volumetric data as produced by read_dx()
• comment (str) – comment for Cube file