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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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42
propka/bonds.py
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@@ -105,15 +105,15 @@ class bondmaker:
# side chains
for chain in protein.chains:
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)
info('++++ Backbones ++++')
# backbone
last_residues = []
for chain in protein.chains:
for i in range(1, len(chain.residues)):
if chain.residues[i-1].resName.replace(' ', '') not in ['N+', 'C-']:
if chain.residues[i].resName.replace(' ', '') not in ['N+', 'C-']:
if chain.residues[i-1].res_name.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])
last_residues.append(chain.residues[i])
info('++++ terminal oxygen ++++')
@@ -124,9 +124,9 @@ class bondmaker:
# Cysteines
for chain in protein.chains:
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)):
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],
chain.residues[j])
@@ -180,9 +180,9 @@ class bondmaker:
def find_bonds_for_residue_backbone(self, residue):
for atom1 in residue.atoms:
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
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:
for atom2 in residue.atoms:
@@ -196,16 +196,16 @@ class bondmaker:
""" Finds bonds for a side chain """
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()):
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()):
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.terminal_oxygen_names:
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)
return
@@ -225,22 +225,22 @@ class bondmaker:
# for ligands
if atom.type == 'hetatm':
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():
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
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()):
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()):
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()):
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
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
@@ -251,7 +251,7 @@ class bondmaker:
atoms = []
for chain in molecule.chains:
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:
atoms.append(atom)
@@ -423,9 +423,9 @@ class bondmaker:
for atom in atoms:
for bonded_atom in atom.bonded_atoms:
resi_i = atom.resName
resi_i = atom.res_name
name_i = atom.name
resi_j = bonded_atom.resName
resi_j = bonded_atom.res_name
name_j = bonded_atom.name
if not name_i in self.backbone_atoms or\