omic/propka
1
0
Fork 0
Code Issues Pull Requests Actions 1 Packages Projects Releases Wiki Activity

Fix some pylint issues for propka.atom.

Browse Source 
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
2020-05-16 20:47:36 -07:00
parent 61c200c3f4
commit 22d83ae29e
1 changed files with 248 additions and 225 deletions
Download Patch File Download Diff File Expand all files Collapse all files

417
propka/atom.py
View File

@@ -1,36 +1,43 @@
"""Atom class - contains all atom information found in the PDB file"""
from __future__ import division import string
from __future__ import print_function import propka.lib
import propka.group
import string, propka.lib, propka.group
from . import hybrid36 from . import hybrid36
class Atom:
""" class Atom(object):
Atom class - contains all atom information found in the pdbfile """Atom class - contains all atom information found in the PDB file"""
"""
def __init__(self, line=None, verbose=False): def __init__(self, line=None, verbose=False):
"""Initialize Atom object.
self.set_properties(line) Args:
line: Line from a PDB file to set properties of atom.
self.residue_label = "%-3s%4d%2s" % (self.name,self.resNumb, self.chainID) verbose: TODO - this does not appear to be used. Can we remove it?
"""
self.groups_extracted = 0 self.occ = None
self.numb = None
self.resName = None
self.type = None
self.chainID = None
self.beta = None
self.icode = None
self.resNumb = None
self.name = None
self.element = None
self.x = None
self.y = None
self.z = None
self.group = None self.group = None
self.group_type = None self.group_type = None
self.number_of_bonded_elements = {} self.number_of_bonded_elements = {}
self.cysteine_bridge = False self.cysteine_bridge = False
self.bonded_atoms = [] self.bonded_atoms = []
self.residue = None self.residue = None
self.conformation_container = None self.conformation_container = None
self.molecular_container = None self.molecular_container = None
self.is_protonated = False self.is_protonated = False
self.steric_number_and_lone_pairs_set = False self.steric_number_and_lone_pairs_set = False
self.terminal = None self.terminal = None
self.charge = 0 self.charge = 0
self.charge_set = False self.charge_set = False
@@ -39,20 +46,21 @@ class Atom:
self.number_of_protons_to_add = 0 self.number_of_protons_to_add = 0
self.number_of_pi_electrons_in_double_and_triple_bonds = 0 self.number_of_pi_electrons_in_double_and_triple_bonds = 0
self.number_of_pi_electrons_in_conjugate_double_and_triple_bonds = 0 self.number_of_pi_electrons_in_conjugate_double_and_triple_bonds = 0
self.groups_extracted = 0
self.set_properties(line)
self.residue_label = "%-3s%4d%2s" % (self.name, self.resNumb, self.chainID)
# ligand atom types # ligand atom types
self.sybyl_type = '' self.sybyl_type = ''
self.sybyl_assigned = False self.sybyl_assigned = False
self.marvin_pka = False self.marvin_pka = False
return
def set_properties(self, line): def set_properties(self, line):
"""Line from PDB file to set properties of atom.
Args:
line: PDB file line
"""
self.name = '' self.name = ''
self.numb = 0 self.numb = 0
self.x = 0.0 self.x = 0.0
@@ -95,21 +103,39 @@ class Atom:
if len(self.element) == 2: if len(self.element) == 2:
self.element = '%1s%1s' % (self.element[0], self.element[1].lower()) self.element = '%1s%1s' % (self.element[0], self.element[1].lower())
return def set_group_type(self, type_):
"""Set group type of atom.
def set_group_type(self, type): Args:
self.group_type = type type_: group type of atom
return """
self.group_type = type_
def count_bonded_elements(self, element): def count_bonded_elements(self, element):
"""Count number of bonded atoms with same element.
TODO - this function is silly. It should just be the len() of the
array returned by get_bonded_elements()
Args:
element: element type for test.
Returns:
number of bonded atoms.
"""
res = 0 res = 0
for ba in self.bonded_atoms: for ba in self.bonded_atoms:
if element == ba.element: if element == ba.element:
res += 1 res += 1
return res return res
def get_bonded_elements(self, element): def get_bonded_elements(self, element):
"""Get bonded atoms with same element.
Args:
element: element type for test.
Returns:
array of bonded atoms.
"""
res = [] res = []
for ba in self.bonded_atoms: for ba in self.bonded_atoms:
if ba.element == element: if ba.element == element:
@@ -117,55 +143,78 @@ class Atom:
return res return res
def get_bonded_heavy_atoms(self): def get_bonded_heavy_atoms(self):
return [ba for ba in self.bonded_atoms if ba.element!='H'] """Get the atoms bonded to this one that aren't hydrogen.
TODO - this could be a @property attribute/method
Returns:
list of atoms.
"""
array = [ba for ba in self.bonded_atoms if ba.element != 'H']
return array
def is_atom_within_bond_distance(self, other_atom, max_bonds, cur_bond): def is_atom_within_bond_distance(self, other_atom, max_bonds, cur_bond):
""" check if <other_atom> is found within <max_bonds> bonds of self """ """Check if <other_atom> is found within <max_bonds> bonds of self.
Args:
other_atom: atom to check
max_bonds: number of bonds to check for other atom bonding to self
Returns:
Boolean for atom bond distance
"""
for ba in self.bonded_atoms: for ba in self.bonded_atoms:
if ba == other_atom: if ba == other_atom:
return True return True
if max_bonds > cur_bond: if max_bonds > cur_bond:
if ba.is_atom_within_bond_distance(other_atom, max_bonds, cur_bond+1): if ba.is_atom_within_bond_distance(other_atom, max_bonds, cur_bond+1):
return True return True
return False return False
def setProperty(self, numb=None, name=None, resName=None, chainID=None,
resNumb=None, x=None, y=None, z=None, occ=None, beta=None):
"""Set properties of the atom object.
Args:
def setProperty(self, numb: Atom number
numb = None, name: Atom name
name = None, resName: residue name
resName = None, chainId: chain ID
chainID = None, resNumb: residue number
resNumb = None, x: atom x-coordinate
x = None, y: atom y-coordinate
y = None, z: atom z-coordinate
z = None, occ: atom occupancy
occ = None, beta: atom temperature factor
beta = None):
""" """
sets properties of the atom object if numb != None:
""" self.numb = numb
if name != None:
if numb != None: self.numb = numb self.name = name
if name != None: self.name = name if resName != None:
if resName != None: self.resName = resName self.resName = resName
if chainID != None: self.chainID = chainID if chainID != None:
if resNumb != None: self.resNumb = resNumb self.chainID = chainID
if x != None: self.x = x if resNumb != None:
if y != None: self.y = y self.resNumb = resNumb
if z != None: self.z = z if x != None:
if occ != None: self.occ = occ self.x = x
if beta != None: self.beta = beta if y != None:
self.y = y
if z != None:
self.z = z
if occ != None:
self.occ = occ
if beta != None:
self.beta = beta
def makeCopy(self): def makeCopy(self):
""" """Make a copy of this atom.
making a copy of this atom
"""
TODO - this could be a property method/attribute
Returns:
Another atom object copy of this one.
"""
newAtom = Atom() newAtom = Atom()
newAtom.type = self.type newAtom.type = self.type
newAtom.numb = self.numb newAtom.numb = self.numb
@@ -182,14 +231,17 @@ class Atom:
newAtom.terminal = self.terminal newAtom.terminal = self.terminal
newAtom.residue_label = self.residue_label newAtom.residue_label = self.residue_label
newAtom.icode = self.icode newAtom.icode = self.icode
return newAtom return newAtom
def make_input_line(self): def make_input_line(self):
# making string """PDB line for this atom.
TODO - Could be @property method/attribute
TODO - figure out difference between make_pdb_line, make_input_line, and makePDBLine
Returns:
String with PDB-format line.
"""
group = '-' group = '-'
model_pka = '-' model_pka = '-'
if self.group: if self.group:
@@ -199,63 +251,48 @@ class Atom:
if self.group.titratable: if self.group.titratable:
model_pka = '%6.2f'%self.group.model_pka model_pka = '%6.2f'%self.group.model_pka
str_ = "%-6s%5d %s " % (self.type.upper(), self.numb,
propka.lib.makeTidyAtomLabel(self.name, self.element))
str = "%-6s%5d %s %s%2s%4d%12.3lf%8.3lf%8.3lf%6s%6s \n" % (self.type.upper(), str_ += "%s%2s%4d%12.3lf%8.3lf%8.3lf%6s%6s \n" % (self.resName, self.chainID,
self.numb, self.resNumb, self.x, self.y,
propka.lib.makeTidyAtomLabel(self.name, self.z, group, model_pka)
self.element), return str_
self.resName,
self.chainID,
self.resNumb,
self.x,
self.y,
self.z,
group,
model_pka)
return str
def make_conect_line(self): def make_conect_line(self):
"""PDB line for bonding within this molecule.
Returns:
String with PDB line.
"""
res = 'CONECT%5d' % self.numb res = 'CONECT%5d' % self.numb
# extract and sort numbers of bonded residues
bonded = [] bonded = []
for atom in self.bonded_atoms: for atom in self.bonded_atoms:
bonded.append(atom.numb) bonded.append(atom.numb)
bonded.sort() bonded.sort()
# write 'em out
for b in bonded: for b in bonded:
res += '%5d'%b res += '%5d'%b
res += '\n' res += '\n'
return res return res
def get_input_parameters(self): def get_input_parameters(self):
""" Method for getting the input parameters stored in the """Extract the input parameters stored in the occupancy and b-factor
occupancy and b-factor fields in input files""" fields in input files"""
# Set the group type # Set the group type
if self.occ != '-': if self.occ != '-':
# make sure to set the terminal # make sure to set the terminal
if self.occ in ['N+', 'C-']: if self.occ in ['N+', 'C-']:
self.terminal = self.occ self.terminal = self.occ
# save the ligand group charge # save the ligand group charge
if self.occ == 'BLG': if self.occ == 'BLG':
self.charge = +1 self.charge = +1
elif self.occ == 'ALG': elif self.occ == 'ALG':
self.charge = -1 self.charge = -1
# generic ions # generic ions
if self.occ in ['1P', '2P', '1N', '2N']: if self.occ in ['1P', '2P', '1N', '2N']:
self.resName = self.occ self.resName = self.occ
self.occ = 'Ion' self.occ = 'Ion'
# correct the group type # correct the group type
self.occ = self.occ.replace('N+', 'Nterm') self.occ = self.occ.replace('N+', 'Nterm')
self.occ = self.occ.replace('C-', 'Cterm') self.occ = self.occ.replace('C-', 'Cterm')
@@ -263,133 +300,119 @@ class Atom:
self.occ = self.occ.replace('ALG', 'titratable_ligand') self.occ = self.occ.replace('ALG', 'titratable_ligand')
self.occ = self.occ.replace('BLG', 'titratable_ligand') self.occ = self.occ.replace('BLG', 'titratable_ligand')
self.occ = self.occ.replace('LG', 'non_titratable_ligand') self.occ = self.occ.replace('LG', 'non_titratable_ligand')
# try to initialise the group # try to initialise the group
try: try:
# TODO - get rid of this exec() statement for security reasons
exec('self.group = propka.group.%s_group(self)' % self.occ) exec('self.group = propka.group.%s_group(self)' % self.occ)
except: except:
raise Exception('%s in input_file is not recognized as a group' % self.occ) raise Exception('%s in input_file is not recognized as a group' % self.occ)
# set the model pKa value # set the model pKa value
if self.beta != '-': if self.beta != '-':
self.group.model_pka = float(self.beta) self.group.model_pka = float(self.beta)
self.group.model_pka_set = True self.group.model_pka_set = True
# set occ and beta to standard values # set occ and beta to standard values
self.occ = '1.00' self.occ = '1.00'
self.beta = '0.00' self.beta = '0.00'
return
def make_pdb_line(self): def make_pdb_line(self):
"""Create PDB line.
# making string TODO - this could/should be a @property method/attribute
str = "%-6s%5d %s %s%2s%4d%12.3lf%8.3lf%8.3lf%6s%6s\n" % (self.type.upper(), TODO - figure out difference between make_pdb_line, make_input_line, and makePDBLine
self.numb,
propka.lib.makeTidyAtomLabel(self.name,
self.element),
self.resName,
self.chainID,
self.resNumb,
self.x,
self.y,
self.z,
self.occ,
self.beta)
Returns:
return str String with PDB line.
def make_mol2_line(self,id):
#1 S1 3.6147 2.0531 1.4795 S.3 1 noname -0.1785
# making string
str = "%-4d %-4s %10.4f %10.4f %10.4f %6s %6d %10s %10.4f\n" % (id,
propka.lib.makeTidyAtomLabel(self.name,
self.element),
self.x,
self.y,
self.z,
self.sybyl_type.replace('-',''),
self.resNumb,
self.resName,
0.0)#self.charge)
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):
""" """
returns a pdb ATOM-line for various purposes; str_ = "%-6s%5d " % (self.type.upper(), self.numb)
specifying arguments over-writes. str_ += "%s %s" % (propka.lib.makeTidyAtomLabel(self.name, self.element),
self.resName)
str_ += "%2s%4d%12.3lf%8.3lf%8.3lf%6s%6s\n" % (self.chainID, self.resNumb,
self.x, self.y, self.z,
self.occ, self.beta)
return str_
def make_mol2_line(self, id_):
"""Create MOL2 line.
Format: 1 S1 3.6147 2.0531 1.4795 S.3 1 noname -0.1785
TODO - this could/shoudl be a @property method/attribute
Returns:
String with MOL2 line.
""" """
if numb == None: numb = self.numb str_ = "%-4d %-4s " % (id_, propka.lib.makeTidyAtomLabel(self.name,
if name == None: name = self.name self.element))
if resName == None: resName = self.resName str_ += "%10.4f %10.4f %10.4f " % (self.x, self.y, self.z)
if chainID == None: chainID = self.chainID str_ += "%6s %6d %10s %10.4f\n" % (self.sybyl_type.replace('-', ''),
if resNumb == None: resNumb = self.resNumb self.resNumb, self.resName, 0.0)
if x == None: x = self.x return str_
if y == None: y = self.y
if z == None: z = self.z
if occ == None: occ = self.occ
if beta == None: beta = self.beta
# making string def makePDBLine(self, numb=None, name=None, resName=None, chainID=None,
str = "ATOM " resNumb=None, x=None, y=None, z=None, occ=None, beta=None):
str += "%6d" % (numb) """Create a PDB line.
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
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): def getTidyLabel(self):
""" """Returns a 'tidier' atom label for printing the new pdbfile
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) return propka.lib.makeTidyAtomLabel(self.name, self.element)
def __str__(self): 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) """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,
# def get_element(self): self.chainID, self.x, self.y,
# """ try to extract element if not already done""" self.z, self.element)
# if self.element == '':
# self.element = self.name.strip(string.digits)[0]
# return self.element
def set_residue(self, residue): def set_residue(self, residue):
""" Makes a references to the parent residue""" """ Makes a reference to the parent residue
if self.residue == None:
Args:
residue: the parent residue
"""
if self.residue is None:
self.residue = residue self.residue = residue