Fix some pylint issues for propka.atom.
Only implemented fixes that do not change functonality. Avoided changing numbers of arguments, numbers of attribute, variable/function names, etc.
This commit is contained in:
Nathan Baker
469
propka/atom.py
469
propka/atom.py
@@ -1,36 +1,43 @@
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from __future__ import division
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from __future__ import print_function
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import string, propka.lib, propka.group
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"""Atom class - contains all atom information found in the PDB file"""
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import string
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import propka.lib
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import propka.group
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from . import hybrid36
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class Atom:
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"""
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Atom class - contains all atom information found in the pdbfile
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"""
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class Atom(object):
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"""Atom class - contains all atom information found in the PDB file"""
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def __init__(self, line=None, verbose=False):
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"""Initialize Atom object.
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self.set_properties(line)
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self.residue_label = "%-3s%4d%2s" % (self.name,self.resNumb, self.chainID)
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self.groups_extracted = 0
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Args:
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line: Line from a PDB file to set properties of atom.
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verbose: TODO - this does not appear to be used. Can we remove it?
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"""
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self.occ = None
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self.numb = None
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self.resName = None
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self.type = None
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self.chainID = None
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self.beta = None
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self.icode = None
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self.resNumb = None
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self.name = None
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self.element = None
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self.x = None
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self.y = None
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self.z = None
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self.group = None
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self.group_type = None
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self.number_of_bonded_elements = {}
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self.cysteine_bridge = False
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self.bonded_atoms = []
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self.residue = None
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self.conformation_container = None
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self.molecular_container = None
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self.is_protonated = False
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self.steric_number_and_lone_pairs_set = False
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self.terminal = None
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self.charge = 0
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self.charge_set = False
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@@ -39,20 +46,21 @@ class Atom:
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self.number_of_protons_to_add = 0
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self.number_of_pi_electrons_in_double_and_triple_bonds = 0
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self.number_of_pi_electrons_in_conjugate_double_and_triple_bonds = 0
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self.groups_extracted = 0
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self.set_properties(line)
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self.residue_label = "%-3s%4d%2s" % (self.name, self.resNumb, self.chainID)
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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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return
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def set_properties(self, line):
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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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@@ -69,11 +77,11 @@ class Atom:
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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.resNumb = int( line[22:26].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.resNumb = int(line[22:26].strip())
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self.resName = "%-3s" % (line[17:20].strip())
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self.chainID = line[21]
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# Set chain id to "_" if it is just white space.
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@@ -81,7 +89,7 @@ class Atom:
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self.chainID = '_'
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self.type = line[:6].strip().lower()
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if self.resName in ['DA ','DC ','DG ','DT ']:
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if self.resName 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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@@ -92,24 +100,42 @@ class Atom:
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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 = '%1s%1s'%(self.element[0], self.element[1].lower())
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if len(self.element) == 2:
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self.element = '%1s%1s' % (self.element[0], self.element[1].lower())
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return
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def set_group_type(self, type_):
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"""Set group type of atom.
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def set_group_type(self, type):
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self.group_type = type
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return
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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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TODO - this function is silly. It should just be the len() of the
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array returned by get_bonded_elements()
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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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res = 0
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for ba in self.bonded_atoms:
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if element == ba.element:
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res +=1
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res += 1
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return res
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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 ba in self.bonded_atoms:
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if ba.element == element:
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@@ -117,55 +143,78 @@ class Atom:
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return res
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def get_bonded_heavy_atoms(self):
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return [ba for ba in self.bonded_atoms if ba.element!='H']
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"""Get the atoms bonded to this one that aren't hydrogen.
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TODO - this could be a @property attribute/method
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Returns:
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list of atoms.
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"""
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array = [ba for ba in self.bonded_atoms if ba.element != 'H']
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return array
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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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"""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, cur_bond+1):
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return True
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return False
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def setProperty(self, numb=None, name=None, resName=None, chainID=None,
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resNumb=None, x=None, y=None, z=None, occ=None, beta=None):
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"""Set properties of the atom object.
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def setProperty(self,
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numb = None,
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name = None,
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resName = None,
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chainID = None,
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resNumb = None,
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x = None,
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y = None,
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z = None,
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occ = None,
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beta = None):
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Args:
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numb: Atom number
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name: Atom name
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resName: residue name
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chainId: chain ID
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resNumb: 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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sets properties of the atom object
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"""
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if numb != None: self.numb = numb
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if name != None: self.name = name
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if resName != None: self.resName = resName
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if chainID != None: self.chainID = chainID
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if resNumb != None: self.resNumb = resNumb
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if x != None: self.x = x
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if y != None: self.y = y
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if z != None: self.z = z
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if occ != None: self.occ = occ
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if beta != None: self.beta = beta
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if numb != None:
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self.numb = numb
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if name != None:
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self.name = name
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if resName != None:
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self.resName = resName
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if chainID != None:
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self.chainID = chainID
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if resNumb != None:
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self.resNumb = resNumb
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if x != None:
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self.x = x
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if y != None:
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self.y = y
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if z != None:
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self.z = z
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if occ != None:
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self.occ = occ
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if beta != None:
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self.beta = beta
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def makeCopy(self):
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"""
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making a copy of this atom
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"""
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"""Make a copy of this atom.
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TODO - this could be a property method/attribute
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Returns:
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Another atom object copy of this one.
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"""
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newAtom = Atom()
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newAtom.type = self.type
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newAtom.numb = self.numb
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@@ -182,14 +231,17 @@ class Atom:
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newAtom.terminal = self.terminal
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newAtom.residue_label = self.residue_label
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newAtom.icode = self.icode
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return newAtom
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def make_input_line(self):
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# making string
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"""PDB line for this atom.
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TODO - Could be @property method/attribute
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TODO - figure out difference between make_pdb_line, make_input_line, and makePDBLine
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Returns:
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String with PDB-format line.
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"""
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group = '-'
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model_pka = '-'
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if self.group:
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@@ -199,197 +251,168 @@ class Atom:
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if self.group.titratable:
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model_pka = '%6.2f'%self.group.model_pka
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str = "%-6s%5d %s %s%2s%4d%12.3lf%8.3lf%8.3lf%6s%6s \n" % (self.type.upper(),
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self.numb,
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propka.lib.makeTidyAtomLabel(self.name,
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self.element),
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self.resName,
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self.chainID,
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self.resNumb,
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self.x,
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self.y,
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self.z,
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group,
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model_pka)
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return str
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str_ = "%-6s%5d %s " % (self.type.upper(), self.numb,
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propka.lib.makeTidyAtomLabel(self.name, self.element))
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str_ += "%s%2s%4d%12.3lf%8.3lf%8.3lf%6s%6s \n" % (self.resName, self.chainID,
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self.resNumb, self.x, self.y,
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self.z, group, model_pka)
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return str_
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def make_conect_line(self):
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res = 'CONECT%5d'%self.numb
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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%5d' % self.numb
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# extract and sort numbers of bonded residues
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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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# write 'em out
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for b in bonded:
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res += '%5d'%b
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res += '\n'
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return res
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def get_input_parameters(self):
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""" Method for getting the input parameters stored in the
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occupancy and b-factor fields in input files"""
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"""Extract the input parameters stored in the occupancy and b-factor
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fields in input files"""
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# Set the group type
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if self.occ != '-':
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# make sure to set the terminal
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if self.occ in ['N+','C-']:
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if self.occ in ['N+', 'C-']:
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self.terminal = self.occ
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# save the ligand group charge
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if self.occ =='BLG':
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self.charge=+1
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elif self.occ =='ALG':
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self.charge=-1
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if self.occ == 'BLG':
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self.charge = +1
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elif self.occ == 'ALG':
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self.charge = -1
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# generic ions
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if self.occ in ['1P','2P','1N','2N']:
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self.resName=self.occ
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self.occ='Ion'
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if self.occ in ['1P', '2P', '1N', '2N']:
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self.resName = self.occ
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self.occ = 'Ion'
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# correct the group type
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self.occ = self.occ.replace('N+','Nterm')
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self.occ = self.occ.replace('C-','Cterm')
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self.occ = self.occ.replace('ION','Ion')
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self.occ = self.occ.replace('ALG','titratable_ligand')
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self.occ = self.occ.replace('BLG','titratable_ligand')
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self.occ = self.occ.replace('LG','non_titratable_ligand')
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self.occ = self.occ.replace('N+', 'Nterm')
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self.occ = self.occ.replace('C-', 'Cterm')
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self.occ = self.occ.replace('ION', 'Ion')
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self.occ = self.occ.replace('ALG', 'titratable_ligand')
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self.occ = self.occ.replace('BLG', 'titratable_ligand')
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self.occ = self.occ.replace('LG', 'non_titratable_ligand')
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# try to initialise the group
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try:
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exec('self.group = propka.group.%s_group(self)'%self.occ)
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# TODO - get rid of this exec() statement for security reasons
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exec('self.group = propka.group.%s_group(self)' % self.occ)
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except:
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raise Exception('%s in input_file is not recognized as a group'%self.occ)
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raise Exception('%s in input_file is not recognized as a group' % self.occ)
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# set the model pKa value
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if self.beta != '-':
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self.group.model_pka = float(self.beta)
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self.group.model_pka_set = True
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# set occ and beta to standard values
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self.occ = '1.00'
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self.beta = '0.00'
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return
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def make_pdb_line(self):
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"""Create PDB line.
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# making string
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str = "%-6s%5d %s %s%2s%4d%12.3lf%8.3lf%8.3lf%6s%6s\n" % (self.type.upper(),
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self.numb,
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propka.lib.makeTidyAtomLabel(self.name,
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self.element),
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self.resName,
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self.chainID,
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self.resNumb,
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self.x,
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self.y,
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self.z,
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self.occ,
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self.beta)
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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, make_input_line, and makePDBLine
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return str
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def make_mol2_line(self,id):
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#1 S1 3.6147 2.0531 1.4795 S.3 1 noname -0.1785
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# making string
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str = "%-4d %-4s %10.4f %10.4f %10.4f %6s %6d %10s %10.4f\n" % (id,
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propka.lib.makeTidyAtomLabel(self.name,
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self.element),
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self.x,
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self.y,
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self.z,
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self.sybyl_type.replace('-',''),
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self.resNumb,
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self.resName,
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0.0)#self.charge)
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return str
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def makePDBLine(self,
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numb = None,
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name = None,
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resName = None,
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chainID = None,
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resNumb = None,
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x = None,
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y = None,
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z = None,
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occ = None,
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beta = None):
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Returns:
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String with PDB line.
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"""
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returns a pdb ATOM-line for various purposes;
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specifying arguments over-writes.
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str_ = "%-6s%5d " % (self.type.upper(), self.numb)
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str_ += "%s %s" % (propka.lib.makeTidyAtomLabel(self.name, self.element),
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self.resName)
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str_ += "%2s%4d%12.3lf%8.3lf%8.3lf%6s%6s\n" % (self.chainID, self.resNumb,
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self.x, self.y, self.z,
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self.occ, self.beta)
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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/shoudl be a @property method/attribute
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Returns:
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String with MOL2 line.
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"""
|
||||
if numb == None: numb = self.numb
|
||||
if name == None: name = self.name
|
||||
if resName == None: resName = self.resName
|
||||
if chainID == None: chainID = self.chainID
|
||||
if resNumb == None: resNumb = self.resNumb
|
||||
if x == None: x = self.x
|
||||
if y == None: y = self.y
|
||||
if z == None: z = self.z
|
||||
if occ == None: occ = self.occ
|
||||
if beta == None: beta = self.beta
|
||||
str_ = "%-4d %-4s " % (id_, propka.lib.makeTidyAtomLabel(self.name,
|
||||
self.element))
|
||||
str_ += "%10.4f %10.4f %10.4f " % (self.x, self.y, self.z)
|
||||
str_ += "%6s %6d %10s %10.4f\n" % (self.sybyl_type.replace('-', ''),
|
||||
self.resNumb, self.resName, 0.0)
|
||||
return str_
|
||||
|
||||
# making string
|
||||
str = "ATOM "
|
||||
str += "%6d" % (numb)
|
||||
str += " %s" % (propka.lib.makeTidyAtomLabel(name,self.element))
|
||||
str += " %s" % (resName)
|
||||
str += "%2s" % (chainID)
|
||||
str += "%4d" % (resNumb)
|
||||
str += "%12.3lf" % (x)
|
||||
str += "%8.3lf" % (y)
|
||||
str += "%8.3lf" % (z)
|
||||
str += "%6.2lf" % (occ)
|
||||
str += "%6.2lf" % (beta)
|
||||
str += '\n'
|
||||
return str
|
||||
def makePDBLine(self, numb=None, name=None, resName=None, chainID=None,
|
||||
resNumb=None, x=None, y=None, z=None, occ=None, beta=None):
|
||||
"""Create a PDB line.
|
||||
|
||||
TODO - this could/should be a @property method/attribute
|
||||
TODO - figure out difference between make_pdb_line, make_input_line, and makePDBLine
|
||||
|
||||
Returns:
|
||||
String with PDB line.
|
||||
"""
|
||||
if numb is None:
|
||||
numb = self.numb
|
||||
if name is None:
|
||||
name = self.name
|
||||
if resName is None:
|
||||
resName = self.resName
|
||||
if chainID is None:
|
||||
chainID = self.chainID
|
||||
if resNumb is None:
|
||||
resNumb = self.resNumb
|
||||
if x is None:
|
||||
x = self.x
|
||||
if y is None:
|
||||
y = self.y
|
||||
if z is None:
|
||||
z = self.z
|
||||
if occ is None:
|
||||
occ = self.occ
|
||||
if beta is None:
|
||||
beta = self.beta
|
||||
str_ = "ATOM "
|
||||
str_ += "%6d" % (numb)
|
||||
str_ += " %s" % (propka.lib.makeTidyAtomLabel(name, self.element))
|
||||
str_ += " %s" % (resName)
|
||||
str_ += "%2s" % (chainID)
|
||||
str_ += "%4d" % (resNumb)
|
||||
str_ += "%12.3lf" % (x)
|
||||
str_ += "%8.3lf" % (y)
|
||||
str_ += "%8.3lf" % (z)
|
||||
str_ += "%6.2lf" % (occ)
|
||||
str_ += "%6.2lf" % (beta)
|
||||
str_ += '\n'
|
||||
return str_
|
||||
|
||||
def getTidyLabel(self):
|
||||
"""
|
||||
Returns a 'tidier' atom label for printing the new pdbfile
|
||||
"""
|
||||
return propka.lib.makeTidyAtomLabel(self.name,self.element)
|
||||
"""Returns a 'tidier' atom label for printing the new pdbfile
|
||||
|
||||
TODO - this could/should be a @property method/attribute
|
||||
|
||||
Returns:
|
||||
String with label"""
|
||||
return propka.lib.makeTidyAtomLabel(self.name, self.element)
|
||||
|
||||
def __str__(self):
|
||||
return '%5d-%4s %5d-%3s (%1s) [%8.3f %8.3f %8.3f] %s' %(self.numb, self.name, self.resNumb, self.resName, self.chainID, self.x, self.y, self.z,self.element)
|
||||
|
||||
|
||||
# def get_element(self):
|
||||
# """ try to extract element if not already done"""
|
||||
# if self.element == '':
|
||||
# self.element = self.name.strip(string.digits)[0]
|
||||
# return self.element
|
||||
|
||||
"""Return an undefined-format string version of this atom."""
|
||||
return '%5d-%4s %5d-%3s (%1s) [%8.3f %8.3f %8.3f] %s' % (self.numb, self.name,
|
||||
self.resNumb, self.resName,
|
||||
self.chainID, self.x, self.y,
|
||||
self.z, self.element)
|
||||
|
||||
def set_residue(self, residue):
|
||||
""" Makes a references to the parent residue"""
|
||||
if self.residue == None:
|
||||
""" Makes a reference to the parent residue
|
||||
|
||||
Args:
|
||||
residue: the parent residue
|
||||
"""
|
||||
if self.residue is None:
|
||||
self.residue = residue
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
Reference in New Issue
Block a user