molecule_list = []
# read all the molecules in a directory and adds them to a list
molecule_list = glob.glob(os.getcwd() + '/*.pdb')
mds.enableDiagnosticOutput() # enable verbose output
for index in molecule_list:
print "start of molecule: " + os.path.basename(index)
ligand = []
chain = []
lig_name = []
pdb_file = open(index, 'r')
basic_info()
sys.stdout.flush()
# read molecule from file do operation on molecule object
mol = mds.readMolecule(index)
mds.addHydrogens(mol) # add hydrogens to molecule object
if len(ligand) == None:
continue
a = 0
for a in range(len(ligand)):
if len(chain[a]) != 1:
print "chain name is not character"
chain[a] = chain[a][0]
if len(ligand[a]) < 3:
print " Ligand name is less than 3 characters"
ligand[a] = ' ' + ligand[a]
ligand_molecule = mds.extractLigand(mol, ligand[a], chain[a])
if ligand_molecule == None:
print "ligand_molecule is none(not present)"
import sys
import mds
import glob
import shutil
molecule_list = []
# read all the molecules in a directory and adds them to a list
molecule_list = glob.glob(os.getcwd() + '/*.pdb')
mds.enableDiagnosticOutput() # enable verbose output
for index in molecule_list:
print "start of molecule: " + os.path.basename(index)
sys.stdout.flush()
# read molecule from file do operation on molecule object
mol = mds.readMolecule(index)
print ">> ADD HYDROGEN"
sys.stdout.flush()
mds.addHydrogens(mol) # add hydrogens to molecule object
print "<< ADD HYDROGEN"
sys.stdout.flush()
print ">> Retain chain "
sys.stdout.flush()
chain_ids = []
chain_ids = mds.getChainIds(mol) # get chain ids from a protein - molecule
print "chains present in pdb:" + str(chain_ids)
if len(chain_ids) == 1:
# if only one chain is present
mds.retainOnlyChainAndGroup(mol, chain_ids[0], [])
print "retained chain :" + chain_ids[0]
else:
# retains chain A and all groups
mds.retainOnlyChainAndGroup(mol, "A", [])