class Fix_PQR:
'''
Add metal atom to PDB2PQR output
'''
def __init__(self, original_pdb, pqr_file, metal):
self.ori_pdb = Read(original_pdb)[0]
self.pqr = Read(pqr_file)[0]
self.metal = metal
self.new_pdb = pqr_file.split('.')[0] + '.pdb'
if self.metal:
zn = self.ori_pdb.allAtoms.get(lambda x: x.element == 'Zn')
# remove hydrogens added to HYS residues near ZN atoms
close_atoms = self.pqr.closerThan(zn[0].coords, self.pqr.allAtoms,
2.3)
# FIXME: only take the first atoms in list
for a in close_atoms:
if a.element == 'H':
# print a.name
for b in a.bonds:
at2 = b.atom1
if at2 == a: at2 = b.atom2
at2.bonds.remove(b)
a.bonds.remove(b)
a.parent.remove(a)
del a
self.pqr.allAtoms = self.pqr.chains.residues.atoms + zn
writer = PdbWriter()
writer.write(self.new_pdb,
self.pqr.allAtoms,
records=['ATOM', 'HETATM'])
class Fix_PQR:
'''
Add metal atom to PDB2PQR output
'''
def __init__(self, original_pdb, pqr_file, metals):
self.ori_pdb = Read(original_pdb)[0]
self.pqr = Read(pqr_file)[0]
self.metals = metals
self.new_pdb = pqr_file.split('.')[0] + '.pdb'
uniq_list = {} # to avoid redundancy
if self.metals:
for met in self.metals:
ele = met[1][:3].strip().lower()
if ele not in uniq_list.keys():
uniq_list[ele] = met[2]
else:
continue
met_atoms = self.ori_pdb.allAtoms.get(
lambda x: x.element.lower() in uniq_list)
for atm in met_atoms:
atm.charge = uniq_list[atm.element.lower()]
print 'atoms charge', atm.element, uniq_list[
atm.element.lower()]
for met_atm in met_atoms:
close_atoms = self.pqr.closerThan(met_atm.coords,
self.pqr.allAtoms, 2.8)
for a in close_atoms:
if a.element == 'H':
for b in a.bonds:
at2 = b.atom1
if at2 == a: at2 = b.atom2
at2.bonds.remove(b)
a.bonds.remove(b)
a.parent.remove(a)
del a
self.pqr.allAtoms = self.pqr.chains.residues.atoms
self.pqr.allAtoms = self.pqr.chains.residues.atoms + met_atoms
writer = PdbWriter()
writer.write(self.new_pdb,
self.pqr.allAtoms,
records=['ATOM', 'HETATM'])
