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

pdb2pqr.ligand.ELEMENT_BY_GROUP = {1: ['H', 'Li', 'Na', 'K', 'Rb', 'Cs', 'Fr'], 2: ['Be', 'Mg', 'Ca', 'Sr', 'Ba', 'Ra'], 13: ['B', 'Al', 'Ga', 'In', 'Tl', 'Nh'], 14: ['C', 'Si', 'Ge', 'Sn', 'Pb', 'Fl'], 15: ['N', 'P', 'As', 'Sb', 'Bi', 'Mc'], 16: ['O', 'S', 'Se', 'Te', 'Po', 'Lv'], 17: ['F', 'Cl', 'Br', 'I', 'At', 'Ts'], 18: ['He', 'Ne', 'Ar', 'Kr', 'Xe', 'Rn', 'Og']}

Groups of the periodic table

pdb2pqr.ligand.NONBONDED_BY_TYPE = {'Al': 0, 'Br': 6, 'C.1': 0, 'C.2': 0, 'C.3': 0, 'C.ar': 0, 'Ca': 0, 'Cl': 6, 'F': 6, 'H': 0, 'I': 6, 'K': 0, 'Li': 0, 'N.1': 2, 'N.2': 2, 'N.3': 2, 'N.4': 0, 'N.am': 0, 'N.ar': 2, 'N.pl3': 0, 'Na': 0, 'O.2': 4, 'O.3': 4, 'O.co2': 4.5, 'P.3': 0, 'S.2': 4, 'S.3': 4, 'S.o': 2, 'S.o2': 0, 'Si': 0}

Numbers of non-bonded electrons for Sybyl-type atoms. Adapted from https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.540100804 (Table I).

pdb2pqr.ligand.RADII = {'bondi': {'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}, 'bondi-zap': {'C': 1.7, 'Cl': 1.75, 'F': 1.47, 'H': 1.2, 'I': 1.98, 'N': 1.55, 'O.co2': 1.52, 'S': 1.8}, 'not parse - do not use': {'Br': 2.5, 'C': 1.7, 'Cl': 1.75, 'F': 1.2, 'H': 1.0, 'N': 1.5, 'O': 1.4, 'P': 1.9, 'S': 1.85}, 'parse': {'C': 1.7, 'C.1': 2.0, 'C.2': 2.0, 'C.3': 2.0, 'H': 1.0, 'N': 1.5, 'O': 1.4, 'S': 1.85}, 'zap9': {'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}}

Radii for different atom types. When using these tables, the most specific Sybyl atom type should be used first and then the generic element should be used

pdb2pqr.ligand.VALENCE_BY_ELEMENT = {'Al': 3, 'Ar': 8, 'As': 5, 'At': 7, 'B': 3, 'Ba': 2, 'Be': 2, 'Bi': 5, 'Br': 7, 'C': 4, 'Ca': 2, 'Cl': 7, 'Cs': 1, 'F': 7, 'Fl': 4, 'Fr': 1, 'Ga': 3, 'Ge': 4, 'H': 1, 'He': 8, 'I': 7, 'In': 3, 'K': 1, 'Kr': 8, 'Li': 1, 'Lv': 6, 'Mc': 5, 'Mg': 2, 'N': 5, 'Na': 1, 'Ne': 8, 'Nh': 3, 'O': 6, 'Og': 8, 'P': 5, 'Pb': 4, 'Po': 6, 'Ra': 2, 'Rb': 1, 'Rn': 8, 'S': 6, 'Sb': 5, 'Se': 6, 'Si': 4, 'Sn': 4, 'Sr': 2, 'Te': 6, 'Tl': 3, 'Ts': 7, 'Xe': 8}

Valence electrons by element

pdb2pqr.ligand.VALENCE_BY_GROUP = {1: 1, 2: 2, 13: 3, 14: 4, 15: 5, 16: 6, 17: 7, 18: 8}

Numbers of valence electrons for the groups of the periodic table

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.

__init__()[source]
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

  • primary_dict (dict) – primary dictionary of radii indexed by atom type or element

  • secondary_dict (dict) – backup dictionary for radii not found in primary dictionary

property bond_order

Total number of electrons in bonds with other atoms.

Returns

total number of electrons in bonds with other atoms

Return type

int

property bonded_atom_names

Bonded atom names.

Returns

bonded atom names

Return type

list

property 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

property element

Element for this atom (uppercase).

Returns

element for this atom

Return type

str

property formal_charge

Formal charge for this atom

Returns

formal charge for this atom

Return type

int

property num_bonded_heavy

Number of heavy atoms bonded to this atom.

Returns

number of heavy atoms

Return type

int

property num_bonded_hydrogen

Number of hydrogen atoms bonded to this atom.

Returns

number of hydrogen atoms

Return type

int

class pdb2pqr.ligand.mol2.Mol2Bond(atom1, atom2, bond_type, bond_id=0)[source]

MOL2 molecule bonds.

__init__(atom1, atom2, bond_type, bond_id=0)[source]

Initialize bond.

Parameters

  • atom1 (str) – name of first atom in bond

  • atom2 (str) – name of second atom in bond

  • bond_type (int) – type of bond: 1 (single), 2 (double), or ar (aromatic)

  • bond_id (int) – integer ID of bond

property atom_names

Get atom names in bond.

Returns

tuple with names of atoms in bond.

Return type

(str, str)

property length

Get bond length.

Returns

bond length

Return type

float

class pdb2pqr.ligand.mol2.Mol2Molecule[source]

Tripos MOL2 molecule.

__init__()[source]
assign_charges()[source]

Assign charges to atoms in 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

assign_radii(primary_dict, secondary_dict)[source]

Assign radii to atoms in molecule.

Parameters

  • primary_dict (dict) – primary dictionary of radii indexed by atom type or element

  • secondary_dict (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

int

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
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

set_torsions()[source]

Set all torsions in molecule.

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

  • atoms (list) – list of Mol2Atom atoms

  • term_dict (dict) – dictionary of polynomial terms

Returns

modified list of atoms

Return type

list

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

  • charge (float) – charge of atom

  • poly_terms – polynomial terms ordered from 0th- to 3rd-order

  • atom_type (str) – string with atom type

Returns

electronegativity value

Return type

float

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

  • atoms (list) – list of Mol2Atom atoms to equilibrate

  • damp (float) – damping factor for equilibration process

  • scale (float) – scaling factor for equilibration process

  • num_cycles (int) – number of PEOE cycles

  • term_dict (dict) – dictionary of polynomial terms

Returns

revised list of atoms

Return type

list

hydrogens.ligand.topology

Ligand topology classes.

class pdb2pqr.ligand.topology.Topology(molecule)[source]

Ligand topology class.

__init__(molecule)[source]

Initialize with molecule.

Parameters

molecule (Mol2Molecule) – Mol2Molecule object