if atm_type == 0:
atm_type = a.babel_type
atm_type = converter.clean_atom_type(atm_type)
a.babel_cov_rad = babel_elements[atm_type]['cov_rad']
a.babel_bond_ord_rad = babel_elements[atm_type]['bond_ord_rad']
a.babel_max_bonds = babel_elements[atm_type]['max_bonds']
if __name__ == '__main__':
import pdb, sys
from atomTypes import AtomHybridization
from cycle import RingFinder
from MolKit.pdbParser import NewPdbParser
parser = NewPdbParser("/tsri/pdb/struct/%s.pdb"%sys.argv[1])
mols = parser.parse()
mol = mols[0]
mol.buildBondsByDistance()
allAtoms = mol.chains.residues.atoms
bonds = allAtoms.bonds[0]
print "assigning atom types"
babel = AtomHybridization()
babel.assignHybridization(allAtoms)
print "looking for rings"
rings = RingFinder()
rings.findRings(allAtoms, bonds)
print "assigning bond order"
if not hasattr(self, 'rings'):
return
i = 0
for r in self.rings:
print 'RING ',i
for j in range(len(r['atoms'])):
a = r['atoms'][j]
b = r['bonds'][j]
print '%10s %4d %s'%(a.name, a.number, repr(b))
i = i + 1
if __name__ == '__main__':
import pdb, sys
from MolKit.pdbParser import NewPdbParser
parser = NewPdbParser("/tsri/pdb/struct/%s.pdb"%sys.argv[1])
mols = parser.parse()
mol = mols[0]
mol.buildBondsByDistance()
allAtoms = mol.chains.residues.atoms
print 'Looking for rings'
r = RingFinder()
bonds = (allAtoms.bonds)[0]
r.findRings(allAtoms, bonds)
r.printRings()
from MolKit.pdbParser import NewPdbqParser
parser = NewPdbqParser("./txp.pdbq")
mols = parser.parse()