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

Clean up line breaks in protonate.py.

Browse Source 
See https://github.com/jensengroup/propka-3.1/issues/43
This commit is contained in:
Nathan Baker
2020-05-25 20:25:15 -07:00
parent a6016ed827
commit 0ac800333d
1 changed files with 19 additions and 19 deletions
Download Patch File Download Diff File Expand all files Collapse all files

34
propka/protonate.py
View File

@@ -16,23 +16,23 @@ class Protonate:
verbose: True for verbose output verbose: True for verbose output
""" """
self.verbose = verbose self.verbose = verbose
self.valence_electrons = {'H': 1, 'He': 2, 'Li': 1, 'Be': 2, 'B': 3, self.valence_electrons = {
'C': 4, 'N': 5, 'O': 6, 'F': 7, 'Ne': 8, 'H': 1, 'He': 2, 'Li': 1, 'Be': 2, 'B': 3, 'C': 4, 'N': 5,
'Na': 1, 'Mg': 2, 'Al': 3, 'Si': 4, 'P': 5, 'O': 6, 'F': 7, 'Ne': 8, 'Na': 1, 'Mg': 2, 'Al': 3, 'Si': 4,
'S': 6, 'Cl': 7, 'Ar': 8, 'K': 1, 'Ca': 2, 'P': 5, 'S': 6, 'Cl': 7, 'Ar': 8, 'K': 1, 'Ca': 2, 'Sc': 2,
'Sc': 2, 'Ti': 2, 'Va': 2, 'Cr': 1, 'Mn': 2, 'Ti': 2, 'Va': 2, 'Cr': 1, 'Mn': 2, 'Fe': 2, 'Co': 2, 'Ni': 2,
'Fe': 2, 'Co': 2, 'Ni': 2, 'Cu': 1, 'Zn': 2, 'Cu': 1, 'Zn': 2, 'Ga': 3, 'Ge': 4, 'As': 5, 'Se': 6, 'Br': 7,
'Ga': 3, 'Ge': 4, 'As': 5, 'Se': 6, 'Br': 7,
'Kr': 8, 'I': 7} 'Kr': 8, 'I': 7}
# TODO - consider putting charges in a configuration file # TODO - consider putting charges in a configuration file
self.standard_charges = {'ARG-NH1': 1.0, 'ASP-OD2': -1.0, self.standard_charges = {
'GLU-OE2': -1.0, 'HIS-ND1': 1.0, 'ARG-NH1': 1.0, 'ASP-OD2': -1.0, 'GLU-OE2': -1.0, 'HIS-ND1': 1.0,
'LYS-NZ': 1.0, 'N+': 1.0, 'C-': -1.0} 'LYS-NZ': 1.0, 'N+': 1.0, 'C-': -1.0}
self.sybyl_charges = {'N.pl3': 1, 'N.3': 1, 'N.4': 1, 'N.ar': 1, self.sybyl_charges = {
'O.co2-': 1} 'N.pl3': 1, 'N.3': 1, 'N.4': 1, 'N.ar': 1, 'O.co2-': 1}
# TODO - consider putting bond lengths in a configuration file # TODO - consider putting bond lengths in a configuration file
self.bond_lengths = {'C': 1.09, 'N': 1.01, 'O': 0.96, 'F': 0.92, self.bond_lengths = {
'Cl': 1.27, 'Br': 1.41, 'I': 1.61, 'S': 1.35} 'C': 1.09, 'N': 1.01, 'O': 0.96, 'F': 0.92, 'Cl': 1.27,
'Br': 1.41, 'I': 1.61, 'S': 1.35}
self.protonation_methods = {4: self.tetrahedral, 3: self.trigonal} self.protonation_methods = {4: self.tetrahedral, 3: self.trigonal}
def protonate(self, molecules): def protonate(self, molecules):
@@ -217,7 +217,8 @@ class Protonate:
# use other atoms bonded to the neighbour to establish the # use other atoms bonded to the neighbour to establish the
# plane, if possible # plane, if possible
other_atom_indices = [] other_atom_indices = []
for i, bonded_atom in enumerate(atom.bonded_atoms[0].bonded_atoms): for i, bonded_atom in enumerate(
atom.bonded_atoms[0].bonded_atoms):
if bonded_atom != atom: if bonded_atom != atom:
other_atom_indices.append(i) other_atom_indices.append(i)
vec1 = Vector(atom1=atom, atom2=atom.bonded_atoms[0]) vec1 = Vector(atom1=atom, atom2=atom.bonded_atoms[0])
@@ -333,9 +334,8 @@ class Protonate:
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.residue_label = "%-3s%4d%2s" % (
proton.res_num, proton.name, proton.res_num, proton.chain_id)
proton.chain_id)
i += 1 i += 1
debug('added', new_h, 'to', atom) debug('added', new_h, 'to', atom)