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.
-
__init__
(atoms, ref)[source]
Initialize object.
Parameters: |
- atoms ([Atom]) – A list of
Atom objects to be stored in this
object
- ref (Residue) – The reference object for the amino acid.
Used to convert from the alternate naming scheme to the main naming
scheme.
|
-
letter_code
()[source]
Return letter code for amino acid.
Returns: | amino acid 1-letter code |
Return type: | str |
-
class
pdb2pqr.aa.
ARG
(atoms, ref)[source]
Arginine class.
-
__init__
(atoms, ref)[source]
Initialize object.
Parameters: |
- atoms ([Atom]) – A list of
Atom objects to be stored in this
object
- ref (Residue) – The reference object for the amino acid.
Used to convert from the alternate naming scheme to the main naming
scheme.
|
-
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.
-
class
pdb2pqr.aa.
ASN
(atoms, ref)[source]
Asparagine class.
-
__init__
(atoms, ref)[source]
Initialize object.
Parameters: |
- atoms ([Atom]) – A list of
Atom objects to be stored in this
object
- ref (Residue) – The reference object for the amino acid.
Used to convert from the alternate naming scheme to the main naming
scheme.
|
-
letter_code
()[source]
Return letter code for amino acid.
Returns: | amino acid 1-letter code |
Return type: | str |
-
class
pdb2pqr.aa.
ASP
(atoms, ref)[source]
Aspartic acid class.
-
__init__
(atoms, ref)[source]
Initialize object.
Parameters: |
- atoms ([Atom]) – A list of
Atom objects to be stored in this
object
- ref (Residue) – The reference object for the amino acid.
Used to convert from the alternate naming scheme to the main naming
scheme.
|
-
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.
-
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
called
Parameters: |
- atoms ([Atom]) – A list of
Atom objects to be stored in this
object
- ref (Residue) – The reference object for the amino acid.
Used to convert from the alternate naming scheme to the main naming
scheme.
|
-
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: |
- atomname (str) – name of atom
- newcoords ([float, float, float]) – new coordinates for atom
|
-
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 |
-
set_state
()[source]
Set the name to use for the forcefield based on the current state.
Uses N*
and C*
for termini.
-
class
pdb2pqr.aa.
CYS
(atoms, ref)[source]
Cysteine class.
-
__init__
(atoms, ref)[source]
Initialize object.
Parameters: |
- atoms ([Atom]) – A list of
Atom objects to be stored in this
object
- ref (Residue) – The reference object for the amino acid.
Used to convert from the alternate naming scheme to the main naming
scheme.
|
-
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 state.
If SS-bonded, use CYX. If negatively charged, use CYM. If HG is not
present, use CYX.
-
class
pdb2pqr.aa.
GLN
(atoms, ref)[source]
Glutamine class.
-
__init__
(atoms, ref)[source]
Initialize object.
Parameters: |
- atoms ([Atom]) – A list of
Atom objects to be stored in this
object
- ref (Residue) – The reference object for the amino acid.
Used to convert from the alternate naming scheme to the main naming
scheme.
|
-
letter_code
()[source]
Return letter code for amino acid.
Returns: | amino acid 1-letter code |
Return type: | str |
-
class
pdb2pqr.aa.
GLU
(atoms, ref)[source]
Glutamic acid class.
-
__init__
(atoms, ref)[source]
Initialize object.
Parameters: |
- atoms ([Atom]) – A list of
Atom objects to be stored in this
object
- ref (Residue) – The reference object for the amino acid.
Used to convert from the alternate naming scheme to the main naming
scheme.
|
-
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.
-
class
pdb2pqr.aa.
GLY
(atoms, ref)[source]
Glycine class.
-
__init__
(atoms, ref)[source]
Initialize object.
Parameters: |
- atoms ([Atom]) – A list of
Atom objects to be stored in this
object
- ref (Residue) – The reference object for the amino acid.
Used to convert from the alternate naming scheme to the main naming
scheme.
|
-
letter_code
()[source]
Return letter code for amino acid.
Returns: | amino acid 1-letter code |
Return type: | str |
-
class
pdb2pqr.aa.
HIS
(atoms, ref)[source]
Histidine class.
-
__init__
(atoms, ref)[source]
Initialize object.
Parameters: |
- atoms ([Atom]) – A list of
Atom objects to be stored in this
object
- ref (Residue) – The reference object for the amino acid.
Used to convert from the alternate naming scheme to the main naming
scheme.
|
-
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.
-
__init__
(atoms, ref)[source]
Initialize object.
Parameters: |
- atoms ([Atom]) – A list of
Atom objects to be stored in this
object
- ref (Residue) – The reference object for the amino acid.
Used to convert from the alternate naming scheme to the main naming
scheme.
|
-
letter_code
()[source]
Return letter code for amino acid.
Returns: | amino acid 1-letter code |
Return type: | str |
-
class
pdb2pqr.aa.
LEU
(atoms, ref)[source]
Leucine class.
-
__init__
(atoms, ref)[source]
Initialize object.
Parameters: |
- atoms ([Atom]) – A list of
Atom objects to be stored in this
object
- ref (Residue) – The reference object for the amino acid.
Used to convert from the alternate naming scheme to the main naming
scheme.
|
-
letter_code
()[source]
Return letter code for amino acid.
Returns: | amino acid 1-letter code |
Return type: | str |
-
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: |
- atoms ([Atom]) – A list of
Atom objects to be stored in this
object
- ref (Residue) – The reference object for the residue.
Used to convert from the alternate naming scheme to the main naming
scheme.
|
-
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 ligand atom.
Parameters: |
- atomname (str) – name of atom to be added
- newcoords ([float, float, float]) – coordinates for new atom
|
-
class
pdb2pqr.aa.
LYS
(atoms, ref)[source]
Lysine class.
-
__init__
(atoms, ref)[source]
Initialize object.
Parameters: |
- atoms ([Atom]) – A list of
Atom objects to be stored in this
object
- ref (Residue) – The reference object for the amino acid.
Used to convert from the alternate naming scheme to the main naming
scheme.
|
-
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.
-
class
pdb2pqr.aa.
MET
(atoms, ref)[source]
Methionine class.
-
__init__
(atoms, ref)[source]
Initialize object.
Parameters: |
- atoms ([Atom]) – A list of
Atom objects to be stored in this
object
- ref (Residue) – The reference object for the amino acid.
Used to convert from the alternate naming scheme to the main naming
scheme.
|
-
letter_code
()[source]
Return letter code for amino acid.
Returns: | amino acid 1-letter code |
Return type: | str |
-
class
pdb2pqr.aa.
PHE
(atoms, ref)[source]
Phenylalanine class.
-
__init__
(atoms, ref)[source]
Initialize object.
Parameters: |
- atoms ([Atom]) – A list of
Atom objects to be stored in this
object
- ref (Residue) – The reference object for the amino acid.
Used to convert from the alternate naming scheme to the main naming
scheme.
|
-
letter_code
()[source]
Return letter code for amino acid.
Returns: | amino acid 1-letter code |
Return type: | str |
-
class
pdb2pqr.aa.
PRO
(atoms, ref)[source]
Proline class.
-
__init__
(atoms, ref)[source]
Initialize object.
Parameters: |
- atoms ([Atom]) – A list of
Atom objects to be stored in this
object
- ref (Residue) – The reference object for the amino acid.
Used to convert from the alternate naming scheme to the main naming
scheme.
|
-
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 the current state.
Uses N*
and C*
for termini.
-
class
pdb2pqr.aa.
SER
(atoms, ref)[source]
Serine class.
-
__init__
(atoms, ref)[source]
Initialize object.
Parameters: |
- atoms ([Atom]) – A list of
Atom objects to be stored in this
object
- ref (Residue) – The reference object for the amino acid.
Used to convert from the alternate naming scheme to the main naming
scheme.
|
-
letter_code
()[source]
Return letter code for amino acid.
Returns: | amino acid 1-letter code |
Return type: | str |
-
class
pdb2pqr.aa.
THR
(atoms, ref)[source]
Threonine class.
-
__init__
(atoms, ref)[source]
Initialize object.
Parameters: |
- atoms ([Atom]) – A list of
Atom objects to be stored in this
object
- ref (Residue) – The reference object for the amino acid.
Used to convert from the alternate naming scheme to the main naming
scheme.
|
-
letter_code
()[source]
Return letter code for amino acid.
Returns: | amino acid 1-letter code |
Return type: | str |
-
class
pdb2pqr.aa.
TRP
(atoms, ref)[source]
Tryptophan class.
-
__init__
(atoms, ref)[source]
Initialize object.
Parameters: |
- atoms ([Atom]) – A list of
Atom objects to be stored in this
object
- ref (Residue) – The reference object for the amino acid.
Used to convert from the alternate naming scheme to the main naming
scheme.
|
-
letter_code
()[source]
Return letter code for amino acid.
Returns: | amino acid 1-letter code |
Return type: | str |
-
class
pdb2pqr.aa.
TYR
(atoms, ref)[source]
Tyrosine class.
-
__init__
(atoms, ref)[source]
Initialize object.
Parameters: |
- atoms ([Atom]) – A list of
Atom objects to be stored in this
object
- ref (Residue) – The reference object for the amino acid.
Used to convert from the alternate naming scheme to the main naming
scheme.
|
-
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.
-
class
pdb2pqr.aa.
VAL
(atoms, ref)[source]
Valine class.
-
__init__
(atoms, ref)[source]
Initialize object.
Parameters: |
- atoms ([Atom]) – A list of
Atom objects to be stored in this
object
- ref (Residue) – The reference object for the amino acid.
Used to convert from the alternate naming scheme to the main naming
scheme.
|
-
letter_code
()[source]
Return letter code for amino acid.
Returns: | amino acid 1-letter code |
Return type: | str |
-
class
pdb2pqr.aa.
WAT
(atoms, ref)[source]
Water class.
Todo
Why is water in the amino acid module?
-
__init__
(atoms, ref)[source]
Initialize object.
Parameters: |
- atoms ([Atom]) – A list of
Atom objects to be stored in this
object
- ref (Residue) – The reference object for the residue.
Used to convert from the alternate naming scheme to the main naming
scheme.
|
-
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: |
- atomname (str) – name of atom to be added
- newcoords ([float, float, float]) – coordinates for new atom
|
-
water_residue_names
= ['HOH', 'WAT']