354 lines
11 KiB
Python
354 lines
11 KiB
Python
"""
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Atom
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====
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The :class:`Atom` class contains all atom information found in the PDB file.
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"""
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import string
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from typing import cast, List, NoReturn, Optional, TYPE_CHECKING
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from propka.lib import make_tidy_atom_label
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from . import hybrid36
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if TYPE_CHECKING:
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from propka.group import Group
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from propka.molecular_container import MolecularContainer
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from propka.conformation_container import ConformationContainer
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# Format strings that get used in multiple places (or are very complex)
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PDB_LINE_FMT1 = (
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"{type:6s}{r.numb:>5d} {atom_label} {r.res_name}{r.chain_id:>2s}"
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"{r.res_num:>4d}{r.x:>12.3f}{r.y:>8.3f}{r.z:>8.3f}{r.occ:>6s}"
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"{r.beta:>6s}\n")
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MOL2_LINE_FMT = (
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"{id:<4d} {atom_label:4s} "
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"{r.x:>10.4f} {r.y:>10.4f} {r.z:>10.4f} "
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"{r.sybyl_type:>6s} {r.res_num:>6d} {r.res_name:>10s} 0.0000\n")
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PDB_LINE_FMT2 = (
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"ATOM {numb:>6d} {atom_label} {res_name}{chain_id:>2s}{res_num:>4d}"
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"{x:>12.3f}{y:>8.3f}{z:>8.3f}{occ:>6.2f}{beta:>6.2f}\n")
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STR_FMT = (
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"{r.numb:>5d}-{r.name:>4s} {r.res_num:>5d}-{r.res_name:>3s} "
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"({r.chain_id:1s}) [{r.x:>8.3f} {r.y:>8.3f} {r.z:>8.3f}] {r.element:s}")
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class Atom:
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"""Atom class - contains all atom information found in the PDB file
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.. versionchanged:: 3.4.0
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:meth:`make_input_line` and :meth:`get_input_parameters` have been
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removed as reading/writing PROPKA input is no longer supported.
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"""
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def __init__(self, line: Optional[str] = None):
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"""Initialize Atom object.
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Args:
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line: Line from a PDB file to set properties of atom.
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"""
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self.number_of_bonded_elements: NoReturn = cast(NoReturn, {}) # FIXME unused?
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self.group: Optional[Group] = None
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self.group_type: Optional[str] = None
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self.cysteine_bridge: bool = False
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self.bonded_atoms: List[Atom] = []
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self.residue = None
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self.conformation_container: Optional[ConformationContainer] = None
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self.molecular_container: Optional[MolecularContainer] = None
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self.is_protonated = False
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self.steric_num_lone_pairs_set = False
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self.terminal: Optional[str] = None
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self.charge = 0.0
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self.charge_set = False
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self.steric_number = 0
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self.number_of_lone_pairs = 0
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self.number_of_protons_to_add = 0
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self.num_pi_elec_2_3_bonds = 0
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self.num_pi_elec_conj_2_3_bonds = 0
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self.groups_extracted = 0
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self.set_properties(line)
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fmt = "{r.name:3s}{r.res_num:>4d}{r.chain_id:>2s}"
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self.residue_label = fmt.format(r=self)
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# ligand atom types
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self.sybyl_type = ''
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self.sybyl_assigned = False
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self.marvin_pka = False
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def set_properties(self, line: Optional[str]):
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"""Line from PDB file to set properties of atom.
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Args:
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line: PDB file line
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"""
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self.name = ''
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self.numb = 0
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self.x = 0.0
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self.y = 0.0
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self.z = 0.0
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self.res_num = 0
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self.res_name = ''
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self.chain_id = 'A'
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self.type = ''
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self.occ = '1.0'
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self.beta = '0.0'
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self.element = ''
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self.icode = ''
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if line:
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self.name = line[12:16].strip()
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self.numb = int(hybrid36.decode(line[6:11]))
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self.x = float(line[30:38].strip())
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self.y = float(line[38:46].strip())
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self.z = float(line[46:54].strip())
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self.res_num = int(line[22:26].strip())
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self.res_name = "{0:<3s}".format(line[17:20].strip())
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# Set chain id to "_" if it is just white space.
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self.chain_id = line[21].strip() or '_'
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self.type = line[:6].strip().lower()
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# TODO - define nucleic acid residue names elsewhere
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if self.res_name in ['DA ', 'DC ', 'DG ', 'DT ']:
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self.type = 'hetatm'
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self.occ = line[55:60].strip()
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self.beta = line[60:66].strip()
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self.icode = line[26:27]
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# Set the element using the position of the name in the pdb file
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self.element = line[12:14].strip().strip(string.digits)
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if len(self.name) == 4:
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self.element = self.element[0]
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if len(self.element) == 2:
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self.element = '{0:1s}{1:1s}'.format(
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self.element[0], self.element[1].lower())
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def set_group_type(self, type_: str):
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"""Set group type of atom.
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Args:
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type_: group type of atom
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"""
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self.group_type = type_
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def count_bonded_elements(self, element):
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"""Count number of bonded atoms with same element.
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Args:
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element: element type for test.
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Returns:
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number of bonded atoms.
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"""
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return len(self.get_bonded_elements(element))
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def get_bonded_elements(self, element):
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"""Get bonded atoms with same element.
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Args:
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element: element type for test.
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Returns:
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array of bonded atoms.
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"""
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res = []
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for bond_atom in self.bonded_atoms:
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if bond_atom.element == element:
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res.append(bond_atom)
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return res
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def get_bonded_heavy_atoms(self):
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"""Get the atoms bonded to this one that aren't hydrogen.
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Returns:
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list of atoms.
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"""
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return [ba for ba in self.bonded_atoms if ba.element != 'H']
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def is_atom_within_bond_distance(self, other_atom, max_bonds, cur_bond):
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"""Check if <other_atom> is found within <max_bonds> bonds of self.
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Args:
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other_atom: atom to check
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max_bonds: number of bonds to check for other atom bonding to self
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Returns:
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Boolean for atom bond distance
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"""
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for ba in self.bonded_atoms:
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if ba == other_atom:
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return True
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if max_bonds > cur_bond:
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if ba.is_atom_within_bond_distance(other_atom, max_bonds,
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cur_bond+1):
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return True
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return False
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def set_property(self, numb=None, name=None, res_name=None, chain_id=None,
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res_num=None, x=None, y=None, z=None, occ=None,
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beta=None):
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"""Set properties of the atom object.
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Args:
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numb: Atom number
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name: Atom name
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res_name: residue name
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chain_id: chain ID
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res_num: residue number
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x: atom x-coordinate
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y: atom y-coordinate
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z: atom z-coordinate
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occ: atom occupancy
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beta: atom temperature factor
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"""
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if numb is not None:
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self.numb = numb
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if name is not None:
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self.name = name
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if res_name is not None:
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self.res_name = res_name
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if chain_id is not None:
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self.chain_id = chain_id
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if res_num is not None:
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self.res_num = res_num
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if x is not None:
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self.x = x
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if y is not None:
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self.y = y
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if z is not None:
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self.z = z
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if occ is not None:
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self.occ = occ
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if beta is not None:
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self.beta = beta
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def make_copy(self):
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"""Make a copy of this atom.
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Returns:
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Another atom object copy of this one.
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"""
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new_atom = Atom()
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new_atom.type = self.type
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new_atom.numb = self.numb
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new_atom.name = self.name
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new_atom.element = self.element
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new_atom.res_name = self.res_name
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new_atom.res_num = self.res_num
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new_atom.chain_id = self.chain_id
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new_atom.x = self.x
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new_atom.y = self.y
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new_atom.z = self.z
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new_atom.occ = self.occ
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new_atom.beta = self.beta
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new_atom.terminal = self.terminal
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new_atom.residue_label = self.residue_label
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new_atom.icode = self.icode
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return new_atom
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def make_conect_line(self):
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"""PDB line for bonding within this molecule.
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Returns:
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String with PDB line.
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"""
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res = 'CONECT{0:5d}'.format(self.numb)
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bonded = []
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for atom in self.bonded_atoms:
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bonded.append(atom.numb)
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bonded.sort()
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for bond in bonded:
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res += '{0:5d}'.format(bond)
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res += '\n'
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return res
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def make_pdb_line(self):
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"""Create PDB line.
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TODO - this could/should be a @property method/attribute
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TODO - figure out difference between make_pdb_line, and make_pdb_line2
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Returns:
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String with PDB line.
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"""
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str_ = PDB_LINE_FMT1.format(
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type=self.type.upper(), r=self,
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atom_label=make_tidy_atom_label(self.name, self.element))
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return str_
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def make_mol2_line(self, id_):
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"""Create MOL2 line.
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Format: 1 S1 3.6147 2.0531 1.4795 S.3 1 noname -0.1785
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TODO - this could/should be a @property method/attribute
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Returns:
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String with MOL2 line.
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"""
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str_ = MOL2_LINE_FMT.format(
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id=id_, r=self,
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atom_label=make_tidy_atom_label(self.name, self.element))
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return str_
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def make_pdb_line2(self, numb=None, name=None, res_name=None, chain_id=None,
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res_num=None, x=None, y=None, z=None, occ=None,
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beta=None):
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"""Create a PDB line.
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TODO - this could/should be a @property method/attribute
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TODO - figure out difference between make_pdb_line, and make_pdb_line2
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Returns:
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String with PDB line.
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"""
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if numb is None:
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numb = self.numb
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if name is None:
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name = self.name
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if res_name is None:
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res_name = self.res_name
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if chain_id is None:
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chain_id = self.chain_id
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if res_num is None:
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res_num = self.res_num
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if x is None:
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x = self.x
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if y is None:
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y = self.y
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if z is None:
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z = self.z
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if occ is None:
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occ = self.occ
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if beta is None:
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beta = self.beta
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str_ = PDB_LINE_FMT2.format(
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numb=numb, res_name=res_name, chain_id=chain_id, res_num=res_num,
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x=x, y=y, z=z, occ=occ, beta=beta,
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atom_label=make_tidy_atom_label(name, self.element)
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)
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return str_
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def get_tidy_label(self):
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"""Returns a 'tidier' atom label for printing the new pdbfile
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TODO - this could/should be a @property method/attribute
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Returns:
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String with label"""
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return make_tidy_atom_label(self.name, self.element)
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def __str__(self):
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"""Return an undefined-format string version of this atom."""
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return STR_FMT.format(r=self)
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def set_residue(self, residue):
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""" Makes a reference to the parent residue
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Args:
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residue: the parent residue
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"""
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if self.residue is None:
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self.residue = residue
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