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De-lint propka/atom.py

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Other changes are a result of Atom use in other files.
This commit is contained in:
Nathan Baker
2020-05-17 17:08:38 -07:00
parent 303aaae25a
commit 10efc3c7f9
10 changed files with 178 additions and 177 deletions
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157
propka/atom.py
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@@ -2,6 +2,7 @@
import string import string
import propka.lib import propka.lib
import propka.group import propka.group
# TODO - what is hybrid36?
from . import hybrid36 from . import hybrid36
@@ -17,12 +18,12 @@ class Atom(object):
""" """
self.occ = None self.occ = None
self.numb = None self.numb = None
self.resName = None self.res_name = None
self.type = None self.type = None
self.chainID = None self.chain_id = None
self.beta = None self.beta = None
self.icode = None self.icode = None
self.resNumb = None self.res_num = None
self.name = None self.name = None
self.element = None self.element = None
self.x = None self.x = None
@@ -37,18 +38,18 @@ class Atom(object):
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_num_lone_pairs_set = False
self.terminal = None self.terminal = None
self.charge = 0 self.charge = 0
self.charge_set = False self.charge_set = False
self.steric_number = 0 self.steric_number = 0
self.number_of_lone_pairs = 0 self.number_of_lone_pairs = 0
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.num_pi_elec_2_3_bonds = 0
self.number_of_pi_electrons_in_conjugate_double_and_triple_bonds = 0 self.num_pi_elec_conj_2_3_bonds = 0
self.groups_extracted = 0 self.groups_extracted = 0
self.set_properties(line) self.set_properties(line)
self.residue_label = "%-3s%4d%2s" % (self.name, self.resNumb, self.chainID) self.residue_label = "%-3s%4d%2s" % (self.name, self.res_num, self.chain_id)
# ligand atom types # ligand atom types
self.sybyl_type = '' self.sybyl_type = ''
@@ -66,9 +67,9 @@ class Atom(object):
self.x = 0.0 self.x = 0.0
self.y = 0.0 self.y = 0.0
self.z = 0.0 self.z = 0.0
self.resNumb = 0 self.res_num = 0
self.resName = '' self.res_name = ''
self.chainID = 'A' self.chain_id = 'A'
self.type = '' self.type = ''
self.occ = '1.0' self.occ = '1.0'
self.beta = '0.0' self.beta = '0.0'
@@ -81,15 +82,15 @@ class Atom(object):
self.x = float(line[30:38].strip()) self.x = float(line[30:38].strip())
self.y = float(line[38:46].strip()) self.y = float(line[38:46].strip())
self.z = float(line[46:54].strip()) self.z = float(line[46:54].strip())
self.resNumb = int(line[22:26].strip()) self.res_num = int(line[22:26].strip())
self.resName = "%-3s" % (line[17:20].strip()) self.res_name = "%-3s" % (line[17:20].strip())
self.chainID = line[21] self.chain_id = line[21]
# Set chain id to "_" if it is just white space. # Set chain id to "_" if it is just white space.
if not self.chainID.strip(): if not self.chain_id.strip():
self.chainID = '_' self.chain_id = '_'
self.type = line[:6].strip().lower() self.type = line[:6].strip().lower()
if self.resName in ['DA ', 'DC ', 'DG ', 'DT ']: if self.res_name in ['DA ', 'DC ', 'DG ', 'DT ']:
self.type = 'hetatm' self.type = 'hetatm'
self.occ = line[55:60].strip() self.occ = line[55:60].strip()
@@ -123,8 +124,8 @@ class Atom(object):
number of bonded atoms. number of bonded atoms.
""" """
res = 0 res = 0
for ba in self.bonded_atoms: for bonded_atom in self.bonded_atoms:
if element == ba.element: if element == bonded_atom.element:
res += 1 res += 1
return res return res
@@ -170,44 +171,44 @@ class Atom(object):
return True return True
return False return False
def setProperty(self, numb=None, name=None, resName=None, chainID=None, def set_property(self, numb=None, name=None, res_name=None, chain_id=None,
resNumb=None, x=None, y=None, z=None, occ=None, beta=None): res_num=None, x=None, y=None, z=None, occ=None, beta=None):
"""Set properties of the atom object. """Set properties of the atom object.
Args: Args:
numb: Atom number numb: Atom number
name: Atom name name: Atom name
resName: residue name res_name: residue name
chainId: chain ID chain_id: chain ID
resNumb: residue number res_num: residue number
x: atom x-coordinate x: atom x-coordinate
y: atom y-coordinate y: atom y-coordinate
z: atom z-coordinate z: atom z-coordinate
occ: atom occupancy occ: atom occupancy
beta: atom temperature factor beta: atom temperature factor
""" """
if numb != None: if numb is not None:
self.numb = numb self.numb = numb
if name != None: if name is not None:
self.name = name self.name = name
if resName != None: if res_name is not None:
self.resName = resName self.res_name = res_name
if chainID != None: if chain_id is not None:
self.chainID = chainID self.chain_id = chain_id
if resNumb != None: if res_num is not None:
self.resNumb = resNumb self.res_num = res_num
if x != None: if x is not None:
self.x = x self.x = x
if y != None: if y is not None:
self.y = y self.y = y
if z != None: if z is not None:
self.z = z self.z = z
if occ != None: if occ is not None:
self.occ = occ self.occ = occ
if beta != None: if beta is not None:
self.beta = beta self.beta = beta
def makeCopy(self): def make_copy(self):
"""Make a copy of this atom. """Make a copy of this atom.
TODO - this could be a property method/attribute TODO - this could be a property method/attribute
@@ -215,29 +216,29 @@ class Atom(object):
Returns: Returns:
Another atom object copy of this one. Another atom object copy of this one.
""" """
newAtom = Atom() new_atom = Atom()
newAtom.type = self.type new_atom.type = self.type
newAtom.numb = self.numb new_atom.numb = self.numb
newAtom.name = self.name new_atom.name = self.name
newAtom.element = self.element new_atom.element = self.element
newAtom.resName = self.resName new_atom.res_name = self.res_name
newAtom.resNumb = self.resNumb new_atom.res_num = self.res_num
newAtom.chainID = self.chainID new_atom.chain_id = self.chain_id
newAtom.x = self.x new_atom.x = self.x
newAtom.y = self.y new_atom.y = self.y
newAtom.z = self.z new_atom.z = self.z
newAtom.occ = self.occ new_atom.occ = self.occ
newAtom.beta = self.beta new_atom.beta = self.beta
newAtom.terminal = self.terminal new_atom.terminal = self.terminal
newAtom.residue_label = self.residue_label new_atom.residue_label = self.residue_label
newAtom.icode = self.icode new_atom.icode = self.icode
return newAtom return new_atom
def make_input_line(self): def make_input_line(self):
"""PDB line for this atom. """PDB line for this atom.
TODO - Could be @property method/attribute TODO - Could be @property method/attribute
TODO - figure out difference between make_pdb_line, make_input_line, and makePDBLine TODO - figure out difference between make_pdb_line, make_input_line, and make_pdb_line2
Returns: Returns:
String with PDB-format line. String with PDB-format line.
@@ -253,8 +254,8 @@ class Atom(object):
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, str_ = "%-6s%5d %s " % (self.type.upper(), self.numb,
propka.lib.makeTidyAtomLabel(self.name, self.element)) propka.lib.makeTidyAtomLabel(self.name, self.element))
str_ += "%s%2s%4d%12.3lf%8.3lf%8.3lf%6s%6s \n" % (self.resName, self.chainID, str_ += "%s%2s%4d%12.3lf%8.3lf%8.3lf%6s%6s \n" % (self.res_name, self.chain_id,
self.resNumb, self.x, self.y, self.res_num, self.x, self.y,
self.z, group, model_pka) self.z, group, model_pka)
return str_ return str_
@@ -291,7 +292,7 @@ class Atom(object):
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.res_name = 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')
@@ -318,15 +319,15 @@ class Atom(object):
"""Create PDB line. """Create PDB line.
TODO - this could/should be a @property method/attribute TODO - this could/should be a @property method/attribute
TODO - figure out difference between make_pdb_line, make_input_line, and makePDBLine TODO - figure out difference between make_pdb_line, make_input_line, and make_pdb_line2
Returns: Returns:
String with PDB line. String with PDB line.
""" """
str_ = "%-6s%5d " % (self.type.upper(), self.numb) str_ = "%-6s%5d " % (self.type.upper(), self.numb)
str_ += "%s %s" % (propka.lib.makeTidyAtomLabel(self.name, self.element), str_ += "%s %s" % (propka.lib.makeTidyAtomLabel(self.name, self.element),
self.resName) self.res_name)
str_ += "%2s%4d%12.3lf%8.3lf%8.3lf%6s%6s\n" % (self.chainID, self.resNumb, str_ += "%2s%4d%12.3lf%8.3lf%8.3lf%6s%6s\n" % (self.chain_id, self.res_num,
self.x, self.y, self.z, self.x, self.y, self.z,
self.occ, self.beta) self.occ, self.beta)
return str_ return str_
@@ -336,7 +337,7 @@ class Atom(object):
Format: 1 S1 3.6147 2.0531 1.4795 S.3 1 noname -0.1785 Format: 1 S1 3.6147 2.0531 1.4795 S.3 1 noname -0.1785
TODO - this could/shoudl be a @property method/attribute TODO - this could/should be a @property method/attribute
Returns: Returns:
String with MOL2 line. String with MOL2 line.
@@ -345,15 +346,15 @@ class Atom(object):
self.element)) self.element))
str_ += "%10.4f %10.4f %10.4f " % (self.x, self.y, self.z) str_ += "%10.4f %10.4f %10.4f " % (self.x, self.y, self.z)
str_ += "%6s %6d %10s %10.4f\n" % (self.sybyl_type.replace('-', ''), str_ += "%6s %6d %10s %10.4f\n" % (self.sybyl_type.replace('-', ''),
self.resNumb, self.resName, 0.0) self.res_num, self.res_name, 0.0)
return str_ return str_
def makePDBLine(self, numb=None, name=None, resName=None, chainID=None, def make_pdb_line2(self, numb=None, name=None, res_name=None, chain_id=None,
resNumb=None, x=None, y=None, z=None, occ=None, beta=None): res_num=None, x=None, y=None, z=None, occ=None, beta=None):
"""Create a PDB line. """Create a PDB line.
TODO - this could/should be a @property method/attribute TODO - this could/should be a @property method/attribute
TODO - figure out difference between make_pdb_line, make_input_line, and makePDBLine TODO - figure out difference between make_pdb_line, make_input_line, and make_pdb_line2
Returns: Returns:
String with PDB line. String with PDB line.
@@ -362,12 +363,12 @@ class Atom(object):
numb = self.numb numb = self.numb
if name is None: if name is None:
name = self.name name = self.name
if resName is None: if res_name is None:
resName = self.resName res_name = self.res_name
if chainID is None: if chain_id is None:
chainID = self.chainID chain_id = self.chain_id
if resNumb is None: if res_num is None:
resNumb = self.resNumb res_num = self.res_num
if x is None: if x is None:
x = self.x x = self.x
if y is None: if y is None:
@@ -381,9 +382,9 @@ class Atom(object):
str_ = "ATOM " str_ = "ATOM "
str_ += "%6d" % (numb) str_ += "%6d" % (numb)
str_ += " %s" % (propka.lib.makeTidyAtomLabel(name, self.element)) str_ += " %s" % (propka.lib.makeTidyAtomLabel(name, self.element))
str_ += " %s" % (resName) str_ += " %s" % (res_name)
str_ += "%2s" % (chainID) str_ += "%2s" % (chain_id)
str_ += "%4d" % (resNumb) str_ += "%4d" % (res_num)
str_ += "%12.3lf" % (x) str_ += "%12.3lf" % (x)
str_ += "%8.3lf" % (y) str_ += "%8.3lf" % (y)
str_ += "%8.3lf" % (z) str_ += "%8.3lf" % (z)
@@ -392,7 +393,7 @@ class Atom(object):
str_ += '\n' str_ += '\n'
return str_ return str_
def getTidyLabel(self): def get_tidy_label(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 TODO - this could/should be a @property method/attribute
@@ -404,8 +405,8 @@ class Atom(object):
def __str__(self): def __str__(self):
"""Return an undefined-format string version of this atom.""" """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, return '%5d-%4s %5d-%3s (%1s) [%8.3f %8.3f %8.3f] %s' % (self.numb, self.name,
self.resNumb, self.resName, self.res_num, self.res_name,
self.chainID, self.x, self.y, self.chain_id, self.x, self.y,
self.z, self.element) self.z, self.element)
def set_residue(self, residue): def set_residue(self, residue):

42
propka/bonds.py
View File

@@ -105,15 +105,15 @@ class bondmaker:
# side chains # side chains
for chain in protein.chains: for chain in protein.chains:
for residue in chain.residues: for residue in chain.residues:
if residue.resName.replace(' ', '') not in ['N+', 'C-']: if residue.res_name.replace(' ', '') not in ['N+', 'C-']:
self.find_bonds_for_side_chain(residue.atoms) self.find_bonds_for_side_chain(residue.atoms)
info('++++ Backbones ++++') info('++++ Backbones ++++')
# backbone # backbone
last_residues = [] last_residues = []
for chain in protein.chains: for chain in protein.chains:
for i in range(1, len(chain.residues)): for i in range(1, len(chain.residues)):
if chain.residues[i-1].resName.replace(' ', '') not in ['N+', 'C-']: if chain.residues[i-1].res_name.replace(' ', '') not in ['N+', 'C-']:
if chain.residues[i].resName.replace(' ', '') not in ['N+', 'C-']: if chain.residues[i].res_name.replace(' ', '') not in ['N+', 'C-']:
self.connect_backbone(chain.residues[i-1], chain.residues[i]) self.connect_backbone(chain.residues[i-1], chain.residues[i])
last_residues.append(chain.residues[i]) last_residues.append(chain.residues[i])
info('++++ terminal oxygen ++++') info('++++ terminal oxygen ++++')
@@ -124,9 +124,9 @@ class bondmaker:
# Cysteines # Cysteines
for chain in protein.chains: for chain in protein.chains:
for i in range(0, len(chain.residues)): for i in range(0, len(chain.residues)):
if chain.residues[i].resName == 'CYS': if chain.residues[i].res_name == 'CYS':
for j in range(0, len(chain.residues)): for j in range(0, len(chain.residues)):
if chain.residues[j].resName == 'CYS' and j != i: if chain.residues[j].res_name == 'CYS' and j != i:
self.check_for_cysteine_bonds(chain.residues[i], self.check_for_cysteine_bonds(chain.residues[i],
chain.residues[j]) chain.residues[j])
@@ -180,9 +180,9 @@ class bondmaker:
def find_bonds_for_residue_backbone(self, residue): def find_bonds_for_residue_backbone(self, residue):
for atom1 in residue.atoms: for atom1 in residue.atoms:
if atom1.name in list(self.number_of_pi_electrons_in_bonds_in_backbone.keys()): if atom1.name in list(self.number_of_pi_electrons_in_bonds_in_backbone.keys()):
atom1.number_of_pi_electrons_in_double_and_triple_bonds = self.number_of_pi_electrons_in_bonds_in_backbone[atom1.name] atom1.num_pi_elec_2_3_bonds = self.number_of_pi_electrons_in_bonds_in_backbone[atom1.name]
if atom1.name in list(self.number_of_pi_electrons_in_conjugate_bonds_in_backbone.keys()) and len(atom1.bonded_atoms)>1: # last part to avoid including N-term if atom1.name in list(self.number_of_pi_electrons_in_conjugate_bonds_in_backbone.keys()) and len(atom1.bonded_atoms)>1: # last part to avoid including N-term
atom1.number_of_pi_electrons_in_conjugate_double_and_triple_bonds = self.number_of_pi_electrons_in_conjugate_bonds_in_backbone[atom1.name] atom1.num_pi_elec_conj_2_3_bonds = self.number_of_pi_electrons_in_conjugate_bonds_in_backbone[atom1.name]
if atom1.name in self.backbone_atoms: if atom1.name in self.backbone_atoms:
for atom2 in residue.atoms: for atom2 in residue.atoms:
@@ -196,16 +196,16 @@ class bondmaker:
""" Finds bonds for a side chain """ """ Finds bonds for a side chain """
for atom1 in atoms: for atom1 in atoms:
key = '%s-%s'%(atom1.resName,atom1.name) key = '%s-%s'%(atom1.res_name,atom1.name)
if key in list(self.number_of_pi_electrons_in_bonds_in_sidechains.keys()): if key in list(self.number_of_pi_electrons_in_bonds_in_sidechains.keys()):
atom1.number_of_pi_electrons_in_double_and_triple_bonds = self.number_of_pi_electrons_in_bonds_in_sidechains[key] atom1.num_pi_elec_2_3_bonds = self.number_of_pi_electrons_in_bonds_in_sidechains[key]
if key in list(self.number_of_pi_electrons_in_conjugate_bonds_in_sidechains.keys()): if key in list(self.number_of_pi_electrons_in_conjugate_bonds_in_sidechains.keys()):
atom1.number_of_pi_electrons_in_conjugate_double_and_triple_bonds = self.number_of_pi_electrons_in_conjugate_bonds_in_sidechains[key] atom1.num_pi_elec_conj_2_3_bonds = self.number_of_pi_electrons_in_conjugate_bonds_in_sidechains[key]
if not atom1.name in self.backbone_atoms: if not atom1.name in self.backbone_atoms:
if not atom1.name in self.terminal_oxygen_names: if not atom1.name in self.terminal_oxygen_names:
for atom2 in atoms: for atom2 in atoms:
if atom2.name in self.protein_bonds[atom1.resName][atom1.name]: if atom2.name in self.protein_bonds[atom1.res_name][atom1.name]:
self.make_bond(atom1,atom2) self.make_bond(atom1,atom2)
return return
@@ -225,22 +225,22 @@ class bondmaker:
# for ligands # for ligands
if atom.type == 'hetatm': if atom.type == 'hetatm':
if atom.sybyl_type in self.number_of_pi_electrons_in_bonds_ligands.keys(): if atom.sybyl_type in self.number_of_pi_electrons_in_bonds_ligands.keys():
atom.number_of_pi_electrons_in_double_and_triple_bonds = self.number_of_pi_electrons_in_bonds_ligands[atom.sybyl_type] atom.num_pi_elec_2_3_bonds = self.number_of_pi_electrons_in_bonds_ligands[atom.sybyl_type]
if atom.sybyl_type in self.number_of_pi_electrons_in_conjugate_bonds_in_ligands.keys(): if atom.sybyl_type in self.number_of_pi_electrons_in_conjugate_bonds_in_ligands.keys():
atom.number_of_pi_electrons_in_conjugate_double_and_triple_bonds = self.number_of_pi_electrons_in_conjugate_bonds_in_ligands[atom.sybyl_type] atom.num_pi_elec_conj_2_3_bonds = self.number_of_pi_electrons_in_conjugate_bonds_in_ligands[atom.sybyl_type]
# for protein # for protein
if atom.type == 'atom': if atom.type == 'atom':
key = '%s-%s'%(atom.resName,atom.name) key = '%s-%s'%(atom.res_name,atom.name)
if key in list(self.number_of_pi_electrons_in_bonds_in_sidechains.keys()): if key in list(self.number_of_pi_electrons_in_bonds_in_sidechains.keys()):
atom.number_of_pi_electrons_in_double_and_triple_bonds = self.number_of_pi_electrons_in_bonds_in_sidechains[key] atom.num_pi_elec_2_3_bonds = self.number_of_pi_electrons_in_bonds_in_sidechains[key]
if key in list(self.number_of_pi_electrons_in_conjugate_bonds_in_sidechains.keys()): if key in list(self.number_of_pi_electrons_in_conjugate_bonds_in_sidechains.keys()):
atom.number_of_pi_electrons_in_conjugate_double_and_triple_bonds = self.number_of_pi_electrons_in_conjugate_bonds_in_sidechains[key] atom.num_pi_elec_conj_2_3_bonds = self.number_of_pi_electrons_in_conjugate_bonds_in_sidechains[key]
if atom.name in list(self.number_of_pi_electrons_in_bonds_in_backbone.keys()): if atom.name in list(self.number_of_pi_electrons_in_bonds_in_backbone.keys()):
atom.number_of_pi_electrons_in_double_and_triple_bonds = self.number_of_pi_electrons_in_bonds_in_backbone[atom.name] atom.num_pi_elec_2_3_bonds = self.number_of_pi_electrons_in_bonds_in_backbone[atom.name]
if atom.name in list(self.number_of_pi_electrons_in_conjugate_bonds_in_backbone.keys()) and len(atom.bonded_atoms)>1: # last part to avoid including N-term if atom.name in list(self.number_of_pi_electrons_in_conjugate_bonds_in_backbone.keys()) and len(atom.bonded_atoms)>1: # last part to avoid including N-term
atom.number_of_pi_electrons_in_conjugate_double_and_triple_bonds = self.number_of_pi_electrons_in_conjugate_bonds_in_backbone[atom.name] atom.num_pi_elec_conj_2_3_bonds = self.number_of_pi_electrons_in_conjugate_bonds_in_backbone[atom.name]
return return
@@ -251,7 +251,7 @@ class bondmaker:
atoms = [] atoms = []
for chain in molecule.chains: for chain in molecule.chains:
for residue in chain.residues: for residue in chain.residues:
if residue.resName.replace(' ','') not in ['N+','C-']: if residue.res_name.replace(' ','') not in ['N+','C-']:
for atom in residue.atoms: for atom in residue.atoms:
atoms.append(atom) atoms.append(atom)
@@ -423,9 +423,9 @@ class bondmaker:
for atom in atoms: for atom in atoms:
for bonded_atom in atom.bonded_atoms: for bonded_atom in atom.bonded_atoms:
resi_i = atom.resName resi_i = atom.res_name
name_i = atom.name name_i = atom.name
resi_j = bonded_atom.resName resi_j = bonded_atom.res_name
name_j = bonded_atom.name name_j = bonded_atom.name
if not name_i in self.backbone_atoms or\ if not name_i in self.backbone_atoms or\

42
propka/calculations.py
View File

@@ -68,22 +68,22 @@ def protonate_30_style(molecular_container):
O=None O=None
C=None C=None
for atom in molecular_container.conformations[name].atoms: for atom in molecular_container.conformations[name].atoms:
if atom.resNumb != curres: if atom.res_num != curres:
curres = atom.resNumb curres = atom.res_num
if len(residue)>0: if len(residue)>0:
#backbone #backbone
[O, C]= addBackBoneHydrogen(residue,O,C) [O, C]= addBackBoneHydrogen(residue,O,C)
#arginine #arginine
if residue[0].resName == 'ARG': if residue[0].res_name == 'ARG':
addArgHydrogen(residue) addArgHydrogen(residue)
#histidine #histidine
if residue[0].resName == 'HIS': if residue[0].res_name == 'HIS':
addHisHydrogen(residue) addHisHydrogen(residue)
#tryptophan #tryptophan
if residue[0].resName == 'TRP': if residue[0].res_name == 'TRP':
addTrpHydrogen(residue) addTrpHydrogen(residue)
#amides #amides
if residue[0].resName in ['GLN','ASN']: if residue[0].res_name in ['GLN','ASN']:
addAmdHydrogen(residue) addAmdHydrogen(residue)
@@ -159,7 +159,7 @@ def addTrpHydrogen(residue):
elif atom.name == "CE2": elif atom.name == "CE2":
CE = atom CE = atom
if CD == None or NE == None or CE == None: if CD == None or NE == None or CE == None:
str = "Did not find all atoms in %s%4d - in %s" % (self.resName, self.resNumb, "addTrpHydrogen()") str = "Did not find all atoms in %s%4d - in %s" % (self.res_name, self.res_num, "addTrpHydrogen()")
info(str) info(str)
sys.exit(0) sys.exit(0)
@@ -176,15 +176,15 @@ def addAmdHydrogen(residue):
O = None O = None
N = None N = None
for atom in residue: for atom in residue:
if (atom.resName == "GLN" and atom.name == "CD") or (atom.resName == "ASN" and atom.name == "CG"): if (atom.res_name == "GLN" and atom.name == "CD") or (atom.res_name == "ASN" and atom.name == "CG"):
C = atom C = atom
elif (atom.resName == "GLN" and atom.name == "OE1") or (atom.resName == "ASN" and atom.name == "OD1"): elif (atom.res_name == "GLN" and atom.name == "OE1") or (atom.res_name == "ASN" and atom.name == "OD1"):
O = atom O = atom
elif (atom.resName == "GLN" and atom.name == "NE2") or (atom.resName == "ASN" and atom.name == "ND2"): elif (atom.res_name == "GLN" and atom.name == "NE2") or (atom.res_name == "ASN" and atom.name == "ND2"):
N = atom N = atom
if C == None or O == None or N == None: if C == None or O == None or N == None:
str = "Did not find N, C and/or O in %s%4d - in %s" % (atom.resName, atom.resNumb, "addAmdHydrogen()") str = "Did not find N, C and/or O in %s%4d - in %s" % (atom.res_name, atom.res_num, "addAmdHydrogen()")
info(str) info(str)
sys.exit(0) sys.exit(0)
@@ -222,7 +222,7 @@ def addBackBoneHydrogen(residue, O, C):
return [new_O,new_C] return [new_O,new_C]
if N.resName == "PRO": if N.res_name == "PRO":
""" PRO doesn't have an H-atom; do nothing """ """ PRO doesn't have an H-atom; do nothing """
else: else:
H = protonateDirection([N, O, C]) H = protonateDirection([N, O, C])
@@ -311,11 +311,11 @@ def protonateSP2(list):
def make_new_H(atom, x,y,z): def make_new_H(atom, x,y,z):
new_H = propka.atom.Atom() new_H = propka.atom.Atom()
new_H.setProperty(numb = None, new_H.set_property(numb = None,
name = 'H%s'%atom.name[1:], name = 'H%s'%atom.name[1:],
resName = atom.resName, res_name = atom.res_name,
chainID = atom.chainID, chain_id = atom.chain_id,
resNumb = atom.resNumb, res_num = atom.res_num,
x = x, x = x,
y = y, y = y,
z = z, z = z,
@@ -329,7 +329,7 @@ def make_new_H(atom, x,y,z):
new_H.steric_number = 0 new_H.steric_number = 0
new_H.number_of_lone_pairs = 0 new_H.number_of_lone_pairs = 0
new_H.number_of_protons_to_add = 0 new_H.number_of_protons_to_add = 0
new_H.number_of_pi_electrons_in_double_and_triple_bonds = 0 new_H.num_pi_elec_2_3_bonds = 0
atom.bonded_atoms.append(new_H) atom.bonded_atoms.append(new_H)
atom.conformation_container.add_atom(new_H) atom.conformation_container.add_atom(new_H)
@@ -357,7 +357,7 @@ def radial_volume_desolvation(parameters, group):
for atom in all_atoms: for atom in all_atoms:
# ignore atoms in the same residue # ignore atoms in the same residue
if atom.resNumb == group.atom.resNumb and atom.chainID == group.atom.chainID: if atom.res_num == group.atom.res_num and atom.chain_id == group.atom.chain_id:
continue continue
sq_dist = squared_distance(group, atom) sq_dist = squared_distance(group, atom)
@@ -409,15 +409,15 @@ def contactDesolvation(parameters, group):
'N+': 4.5} 'N+': 4.5}
all_atoms = group.atom.conformation_container.get_non_hydrogen_atoms() all_atoms = group.atom.conformation_container.get_non_hydrogen_atoms()
if residue.resName in version.desolvationRadii: if residue.res_name in version.desolvationRadii:
local_cutoff = version.desolvationRadii[residue.resName] local_cutoff = version.desolvationRadii[residue.res_name]
else: else:
local_cutoff = 0.00 local_cutoff = 0.00
residue.Nmass = 0 residue.Nmass = 0
residue.Nlocl = 0 residue.Nlocl = 0
for atom in all_atoms: for atom in all_atoms:
if atom.resNumb != group.atom.resNumb or atom.chainID != group.atom.chainID: if atom.res_num != group.atom.res_num or atom.chain_id != group.atom.chain_id:
dX = atom.x - residue.x dX = atom.x - residue.x
dY = atom.y - residue.y dY = atom.y - residue.y
dZ = atom.z - residue.z dZ = atom.z - residue.z

14
propka/conformation_container.py
View File

@@ -158,7 +158,7 @@ class Conformation_container:
titrate_only = self.molecular_container.options.titrate_only titrate_only = self.molecular_container.options.titrate_only
if titrate_only is not None: if titrate_only is not None:
at = group.atom at = group.atom
if not (at.chainID, at.resNumb, at.icode) in titrate_only: if not (at.chain_id, at.res_num, at.icode) in titrate_only:
group.titratable = False group.titratable = False
if group.residue_type == 'CYS': if group.residue_type == 'CYS':
group.exclude_cys_from_results = True group.exclude_cys_from_results = True
@@ -376,7 +376,7 @@ class Conformation_container:
return [atom for atom in self.atoms if atom.type=='hetatm' and atom.element != 'H'] return [atom for atom in self.atoms if atom.type=='hetatm' and atom.element != 'H']
def get_chain(self,chain): def get_chain(self,chain):
return [atom for atom in self.atoms if atom.chainID != chain] return [atom for atom in self.atoms if atom.chain_id != chain]
def add_atom(self, atom): def add_atom(self, atom):
@@ -388,13 +388,13 @@ class Conformation_container:
atom.molecular_container = self.molecular_container atom.molecular_container = self.molecular_container
# store chain id for bookkeeping # store chain id for bookkeeping
if not atom.chainID in self.chains: if not atom.chain_id in self.chains:
self.chains.append(atom.chainID) self.chains.append(atom.chain_id)
return return
def copy_atom(self, atom): def copy_atom(self, atom):
new_atom = atom.makeCopy() new_atom = atom.make_copy()
self.atoms.append(new_atom) self.atoms.append(new_atom)
new_atom.conformation_container = self new_atom.conformation_container = self
@@ -443,8 +443,8 @@ class Conformation_container:
return return
def sort_atoms_key(self, atom): def sort_atoms_key(self, atom):
key = ord(atom.chainID)*1e7 key = ord(atom.chain_id)*1e7
key += atom.resNumb*1000 key += atom.res_num*1000
if len(atom.name) > len(atom.element): if len(atom.name) > len(atom.element):
key += ord(atom.name[len(atom.element)]) key += ord(atom.name[len(atom.element)])
#info(atom,ord(atom.name[len(atom.element)]), '|%s||%s|'%(atom.name,atom.element)) #info(atom,ord(atom.name[len(atom.element)]), '|%s||%s|'%(atom.name,atom.element))

2
propka/determinants.py
View File

@@ -54,7 +54,7 @@ def addDeterminants(group1, group2, distance, version):
def addSidechainDeterminants(group1, group2, version=None): def addSidechainDeterminants(group1, group2, version=None):
""" """
adding side-chain determinants/perturbations adding side-chain determinants/perturbations
Note, resNumb1 > resNumb2 Note, res_num1 > res_num2
""" """
hbond_interaction = version.hydrogen_bond_interaction(group1, group2) hbond_interaction = version.hydrogen_bond_interaction(group1, group2)

26
propka/group.py
View File

@@ -111,22 +111,22 @@ class Group:
self.common_charge_centre = False self.common_charge_centre = False
self.residue_type = self.atom.resName self.residue_type = self.atom.res_name
if self.atom.terminal: if self.atom.terminal:
self.residue_type = self.atom.terminal self.residue_type = self.atom.terminal
if self.atom.type=='atom': if self.atom.type=='atom':
self.label = '%-3s%4d%2s'%(self.residue_type, atom.resNumb, atom.chainID) self.label = '%-3s%4d%2s'%(self.residue_type, atom.res_num, atom.chain_id)
elif self.atom.resName in ['DA ','DC ','DG ','DT ']: elif self.atom.res_name in ['DA ','DC ','DG ','DT ']:
self.label = '%1s%1s%1s%4d%2s'%(self.residue_type[1], self.label = '%1s%1s%1s%4d%2s'%(self.residue_type[1],
atom.element, atom.element,
atom.name.replace('\'','')[-1], atom.name.replace('\'','')[-1],
atom.resNumb, atom.res_num,
atom.chainID) atom.chain_id)
# self.label = '%1s%1s%1s%4d%2s'%(self.residue_type[1], atom.element,atom.name[-1], atom.resNumb, atom.chainID) # self.label = '%1s%1s%1s%4d%2s'%(self.residue_type[1], atom.element,atom.name[-1], atom.res_num, atom.chain_id)
else: else:
self.label = '%-3s%4s%2s'%(self.residue_type, atom.name, atom.chainID) self.label = '%-3s%4s%2s'%(self.residue_type, atom.name, atom.chain_id)
# container for squared distances # container for squared distances
@@ -253,7 +253,7 @@ class Group:
return self.label==other.label return self.label==other.label
else: else:
# For heterogene atoms we also need to check the residue number # For heterogene atoms we also need to check the residue number
return self.label==other.label and self.atom.resNumb == other.atom.resNumb return self.label==other.label and self.atom.res_num == other.atom.res_num
def __hash__(self): def __hash__(self):
""" Needed together with __eq__ - otherwise we can't make sets of groups """ """ Needed together with __eq__ - otherwise we can't make sets of groups """
@@ -361,7 +361,7 @@ class Group:
if not self.model_pka_set: if not self.model_pka_set:
self.model_pka = self.parameters.model_pkas[self.residue_type] self.model_pka = self.parameters.model_pkas[self.residue_type]
# check if we should apply a custom model pka # check if we should apply a custom model pka
key = '%s-%s'%(self.atom.resName.strip(), self.atom.name.strip()) key = '%s-%s'%(self.atom.res_name.strip(), self.atom.name.strip())
if key in self.parameters.custom_model_pkas.keys(): if key in self.parameters.custom_model_pkas.keys():
self.model_pka = self.parameters.custom_model_pkas[key] self.model_pka = self.parameters.custom_model_pkas[key]
@@ -1122,7 +1122,7 @@ class Ion_group(Group):
def __init__(self, atom): def __init__(self, atom):
Group.__init__(self,atom) Group.__init__(self,atom)
self.type = 'ION' self.type = 'ION'
self.residue_type = atom.resName.strip() self.residue_type = atom.res_name.strip()
info('Found ion group:', atom) info('Found ion group:', atom)
return return
@@ -1201,7 +1201,7 @@ def is_protein_group(parameters,atom):
### Backbone ### Backbone
if atom.type == 'atom' and atom.name == 'N': if atom.type == 'atom' and atom.name == 'N':
# ignore proline backbone nitrogens # ignore proline backbone nitrogens
if atom.resName != 'PRO': if atom.res_name != 'PRO':
return BBN_group(atom) return BBN_group(atom)
if atom.type == 'atom' and atom.name == 'C': if atom.type == 'atom' and atom.name == 'C':
# ignore C- carboxyl # ignore C- carboxyl
@@ -1209,7 +1209,7 @@ def is_protein_group(parameters,atom):
return BBC_group(atom) return BBC_group(atom)
### Filters for side chains based on PDB protein atom names ### Filters for side chains based on PDB protein atom names
key = '%s-%s'%(atom.resName, atom.name) key = '%s-%s'%(atom.res_name, atom.name)
if key in parameters.protein_group_mapping.keys(): if key in parameters.protein_group_mapping.keys():
return eval('%s_group(atom)'%parameters.protein_group_mapping[key]) return eval('%s_group(atom)'%parameters.protein_group_mapping[key])
@@ -1342,7 +1342,7 @@ def is_ligand_group_by_marvin_pkas(parameters, atom):
def is_ion_group(parameters, atom): def is_ion_group(parameters, atom):
if atom.resName.strip() in parameters.ions.keys(): if atom.res_name.strip() in parameters.ions.keys():
return Ion_group(atom) return Ion_group(atom)
return None return None

12
propka/iterative.py
View File

@@ -124,9 +124,9 @@ def addIterativeIonPair(object1, object2, interaction, version):
Q2 = object2.Q Q2 = object2.Q
comp1 = object1.pKa_old + annihilation[0] + Q1*coulomb_value comp1 = object1.pKa_old + annihilation[0] + Q1*coulomb_value
comp2 = object2.pKa_old + annihilation[1] + Q2*coulomb_value comp2 = object2.pKa_old + annihilation[1] + Q2*coulomb_value
if object1.resName not in version.parameters.exclude_sidechain_interactions: if object1.res_name not in version.parameters.exclude_sidechain_interactions:
comp1 += Q1*hbond_value comp1 += Q1*hbond_value
if object2.resName not in version.parameters.exclude_sidechain_interactions: if object2.res_name not in version.parameters.exclude_sidechain_interactions:
comp2 += Q2*hbond_value comp2 += Q2*hbond_value
if Q1 == -1.0 and comp1 < comp2: if Q1 == -1.0 and comp1 < comp2:
@@ -155,12 +155,12 @@ def addIterativeIonPair(object1, object2, interaction, version):
# Side-chain # Side-chain
if hbond_value > 0.005: if hbond_value > 0.005:
# residue1 # residue1
if object1.resName not in version.parameters.exclude_sidechain_interactions: if object1.res_name not in version.parameters.exclude_sidechain_interactions:
interaction = [object2, Q1*hbond_value] interaction = [object2, Q1*hbond_value]
annihilation[0] += -Q1*hbond_value annihilation[0] += -Q1*hbond_value
object1.determinants['sidechain'].append(interaction) object1.determinants['sidechain'].append(interaction)
# residue2 # residue2
if object2.resName not in version.parameters.exclude_sidechain_interactions: if object2.res_name not in version.parameters.exclude_sidechain_interactions:
interaction = [object1, Q2*hbond_value] interaction = [object1, Q2*hbond_value]
annihilation[1] += -Q2*hbond_value annihilation[1] += -Q2*hbond_value
object2.determinants['sidechain'].append(interaction) object2.determinants['sidechain'].append(interaction)
@@ -309,7 +309,7 @@ class Iterative:
self.label = group.label self.label = group.label
self.atom = group.atom self.atom = group.atom
self.resName = group.residue_type self.res_name = group.residue_type
self.Q = group.charge self.Q = group.charge
self.pKa_old = None self.pKa_old = None
self.pKa_new = None self.pKa_new = None
@@ -357,7 +357,7 @@ class Iterative:
return self.label==other.label return self.label==other.label
else: else:
# For heterogene atoms we also need to check the residue number # For heterogene atoms we also need to check the residue number
return self.label==other.label and self.atom.resNumb == other.atom.resNumb return self.label==other.label and self.atom.res_num == other.atom.res_num
def __hash__(self): def __hash__(self):
""" Needed together with __eq__ - otherwise we can't make sets of groups """ """ Needed together with __eq__ - otherwise we can't make sets of groups """

10
propka/output.py
View File

@@ -38,13 +38,13 @@ def writePDB(protein, file=None, filename=None, include_hydrogens=False, options
numb = 0 numb = 0
for chain in protein.chains: for chain in protein.chains:
for residue in chain.residues: for residue in chain.residues:
if residue.resName not in ["N+ ", "C- "]: if residue.res_name not in ["N+ ", "C- "]:
for atom in residue.atoms: for atom in residue.atoms:
if include_hydrogens == False and atom.name[0] == "H": if include_hydrogens == False and atom.name[0] == "H":
""" don't print """ """ don't print """
else: else:
numb += 1 numb += 1
line = atom.makePDBLine(numb=numb) line = atom.make_pdb_line2(numb=numb)
line += "\n" line += "\n"
file.write(line) file.write(line)
@@ -130,7 +130,7 @@ def getDeterminantSection(protein, conformation, parameters):
# printing determinants # printing determinants
for chain in protein.conformations[conformation].chains: for chain in protein.conformations[conformation].chains:
for residue_type in parameters.write_out_order: for residue_type in parameters.write_out_order:
groups = [g for g in protein.conformations[conformation].groups if g.atom.chainID == chain] groups = [g for g in protein.conformations[conformation].groups if g.atom.chain_id == chain]
for group in groups: for group in groups:
if group.residue_type == residue_type: if group.residue_type == residue_type:
str += "%s" % ( group.getDeterminantString(parameters.remove_penalised_group) ) str += "%s" % ( group.getDeterminantString(parameters.remove_penalised_group) )
@@ -226,8 +226,8 @@ def writeJackalScapFile(mutationData=None, filename="1xxx_scap.list", options=No
""" """
file = open(filename, 'w') file = open(filename, 'w')
for chainID, code1, resNumb, code2 in mutationData: for chain_id, code1, res_num, code2 in mutationData:
str = "%s, %d, %s\n" % (chainID, resNumb, code2) str = "%s, %d, %s\n" % (chain_id, res_num, code2)
file.write(str) file.write(str)
file.close() file.close()

18
propka/pdb.py
View File

@@ -63,27 +63,27 @@ def protein_precheck(conformations, names):
atoms_by_residue[res_id] = [a] atoms_by_residue[res_id] = [a]
for res_id, res_atoms in atoms_by_residue.items(): for res_id, res_atoms in atoms_by_residue.items():
resname = res_atoms[0].resName res_name = res_atoms[0].res_name
residue_label = '%3s%5s'%(resname, res_id) residue_label = '%3s%5s'%(res_name, res_id)
# ignore ligand residues # ignore ligand residues
if resname not in expected_atom_numbers: if res_name not in expected_atom_numbers:
continue continue
# check for c-terminal # check for c-terminal
if 'C-' in [a.terminal for a in res_atoms]: if 'C-' in [a.terminal for a in res_atoms]:
if len(res_atoms) != expected_atom_numbers[resname]+1: if len(res_atoms) != expected_atom_numbers[res_name]+1:
warning('Unexpected number (%d) of atoms in residue %s in conformation %s' % (len(res_atoms), residue_label, name)) warning('Unexpected number (%d) of atoms in residue %s in conformation %s' % (len(res_atoms), residue_label, name))
continue continue
# check number of atoms in residue # check number of atoms in residue
if len(res_atoms) != expected_atom_numbers[resname]: if len(res_atoms) != expected_atom_numbers[res_name]:
warning('Unexpected number (%d) of atoms in residue %s in conformation %s' % (len(res_atoms), residue_label, name)) warning('Unexpected number (%d) of atoms in residue %s in conformation %s' % (len(res_atoms), residue_label, name))
return return
def resid_from_atom(a): def resid_from_atom(a):
return '%4d %s %s'%(a.resNumb,a.chainID,a.icode) return '%4d %s %s'%(a.res_num,a.chain_id,a.icode)
def get_atom_lines_from_pdb(pdb_file, ignore_residues = [], keep_protons=False, tags = ['ATOM ', 'HETATM'], chains=None): def get_atom_lines_from_pdb(pdb_file, ignore_residues = [], keep_protons=False, tags = ['ATOM ', 'HETATM'], chains=None):
@@ -197,7 +197,7 @@ def write_mol2_for_atoms(atoms, filename):
substructure_section = '@<TRIPOS>SUBSTRUCTURE\n\n' substructure_section = '@<TRIPOS>SUBSTRUCTURE\n\n'
if len(atoms)>0: if len(atoms)>0:
substructure_section = '@<TRIPOS>SUBSTRUCTURE\n%-7d %10s %7d\n'%(atoms[0].resNumb,atoms[0].resName,atoms[0].numb) substructure_section = '@<TRIPOS>SUBSTRUCTURE\n%-7d %10s %7d\n'%(atoms[0].res_num,atoms[0].res_name,atoms[0].numb)
out = propka.lib.open_file_for_writing(filename) out = propka.lib.open_file_for_writing(filename)
out.write(header%(len(atoms),id-1)) out.write(header%(len(atoms),id-1))
@@ -210,8 +210,8 @@ def write_mol2_for_atoms(atoms, filename):
def get_bond_order(atom1, atom2): def get_bond_order(atom1, atom2):
type = '1' type = '1'
pi_electrons1 = atom1.number_of_pi_electrons_in_double_and_triple_bonds pi_electrons1 = atom1.num_pi_elec_2_3_bonds
pi_electrons2 = atom2.number_of_pi_electrons_in_double_and_triple_bonds pi_electrons2 = atom2.num_pi_elec_2_3_bonds
if '.ar' in atom1.sybyl_type: if '.ar' in atom1.sybyl_type:
pi_electrons1 -=1 pi_electrons1 -=1

32
propka/protonate.py
View File

@@ -121,7 +121,7 @@ class Protonate:
def set_charge(self, atom): def set_charge(self, atom):
# atom is a protein atom # atom is a protein atom
if atom.type=='atom': if atom.type=='atom':
key = '%3s-%s'%(atom.resName, atom.name) key = '%3s-%s'%(atom.res_name, atom.name)
if atom.terminal: if atom.terminal:
debug(atom.terminal) debug(atom.terminal)
key=atom.terminal key=atom.terminal
@@ -172,8 +172,8 @@ class Protonate:
debug('Valence eletrons: %4d'%-self.valence_electrons[atom.element]) debug('Valence eletrons: %4d'%-self.valence_electrons[atom.element])
atom.number_of_protons_to_add -= len(atom.bonded_atoms) atom.number_of_protons_to_add -= len(atom.bonded_atoms)
debug('Number of bonds: %4d'%- len(atom.bonded_atoms)) debug('Number of bonds: %4d'%- len(atom.bonded_atoms))
atom.number_of_protons_to_add -= atom.number_of_pi_electrons_in_double_and_triple_bonds atom.number_of_protons_to_add -= atom.num_pi_elec_2_3_bonds
debug('Pi electrons: %4d'%-atom.number_of_pi_electrons_in_double_and_triple_bonds) debug('Pi electrons: %4d'%-atom.num_pi_elec_2_3_bonds)
atom.number_of_protons_to_add += int(atom.charge) atom.number_of_protons_to_add += int(atom.charge)
debug('Charge: %4.1f'%atom.charge) debug('Charge: %4.1f'%atom.charge)
@@ -185,7 +185,7 @@ class Protonate:
def set_steric_number_and_lone_pairs(self, atom): def set_steric_number_and_lone_pairs(self, atom):
# If we already did this, there is no reason to do it again # If we already did this, there is no reason to do it again
if atom.steric_number_and_lone_pairs_set: if atom.steric_num_lone_pairs_set:
return return
debug('='*10) debug('='*10)
@@ -211,11 +211,11 @@ class Protonate:
debug('%65s: %4d'%('Number of hydrogen atoms to add',atom.number_of_protons_to_add)) debug('%65s: %4d'%('Number of hydrogen atoms to add',atom.number_of_protons_to_add))
atom.steric_number += atom.number_of_protons_to_add atom.steric_number += atom.number_of_protons_to_add
debug('%65s: %4d'%('Number of pi-electrons in double and triple bonds(-)',atom.number_of_pi_electrons_in_double_and_triple_bonds)) debug('%65s: %4d'%('Number of pi-electrons in double and triple bonds(-)',atom.num_pi_elec_2_3_bonds))
atom.steric_number -= atom.number_of_pi_electrons_in_double_and_triple_bonds atom.steric_number -= atom.num_pi_elec_2_3_bonds
debug('%65s: %4d'%('Number of pi-electrons in conjugated double and triple bonds(-)',atom.number_of_pi_electrons_in_conjugate_double_and_triple_bonds)) debug('%65s: %4d'%('Number of pi-electrons in conjugated double and triple bonds(-)',atom.num_pi_elec_conj_2_3_bonds))
atom.steric_number -= atom.number_of_pi_electrons_in_conjugate_double_and_triple_bonds atom.steric_number -= atom.num_pi_elec_conj_2_3_bonds
debug('%65s: %4d'%('Number of donated co-ordinated bonds',0)) debug('%65s: %4d'%('Number of donated co-ordinated bonds',0))
atom.steric_number += 0 atom.steric_number += 0
@@ -231,7 +231,7 @@ class Protonate:
debug('%65s: %4d'%('Steric number',atom.steric_number)) debug('%65s: %4d'%('Steric number',atom.steric_number))
debug('%65s: %4d'%('Number of lone pairs',atom.number_of_lone_pairs)) debug('%65s: %4d'%('Number of lone pairs',atom.number_of_lone_pairs))
atom.steric_number_and_lone_pairs_set = True atom.steric_num_lone_pairs_set = True
return return
@@ -364,11 +364,11 @@ class Protonate:
def add_proton(self, atom, position): def add_proton(self, atom, position):
# Create the new proton # Create the new proton
new_H = propka.atom.Atom() new_H = propka.atom.Atom()
new_H.setProperty(numb = None, new_H.set_property(numb = None,
name = 'H%s'%atom.name[1:], name = 'H%s'%atom.name[1:],
resName = atom.resName, res_name = atom.res_name,
chainID = atom.chainID, chain_id = atom.chain_id,
resNumb = atom.resNumb, res_num = atom.res_num,
x = round(position.x,3), # round of to three digimal points x = round(position.x,3), # round of to three digimal points
y = round(position.y,3), # to avoid round-off differences y = round(position.y,3), # to avoid round-off differences
z = round(position.z,3), # when input file z = round(position.z,3), # when input file
@@ -382,7 +382,7 @@ class Protonate:
new_H.steric_number = 0 new_H.steric_number = 0
new_H.number_of_lone_pairs = 0 new_H.number_of_lone_pairs = 0
new_H.number_of_protons_to_add = 0 new_H.number_of_protons_to_add = 0
new_H.number_of_pi_electrons_in_double_and_triple_bonds = 0 new_H.num_pi_elec_2_3_bonds = 0
new_H.is_protonates = True new_H.is_protonates = True
atom.bonded_atoms.append(new_H) atom.bonded_atoms.append(new_H)
@@ -390,13 +390,13 @@ class Protonate:
atom.conformation_container.add_atom(new_H) atom.conformation_container.add_atom(new_H)
# update names of all protons on this atom # update names of all protons on this atom
new_H.residue_label = "%-3s%4d%2s" % (new_H.name,new_H.resNumb, new_H.chainID) new_H.residue_label = "%-3s%4d%2s" % (new_H.name,new_H.res_num, new_H.chain_id)
no_protons = atom.count_bonded_elements('H') no_protons = atom.count_bonded_elements('H')
if no_protons > 1: if no_protons > 1:
i = 1 i = 1
for proton in atom.get_bonded_elements('H'): for proton in atom.get_bonded_elements('H'):
proton.name = 'H%s%d'%(atom.name[1:],i) proton.name = 'H%s%d'%(atom.name[1:],i)
proton.residue_label = "%-3s%4d%2s" % (proton.name,proton.resNumb, proton.chainID) proton.residue_label = "%-3s%4d%2s" % (proton.name,proton.res_num, proton.chain_id)
i+=1 i+=1