chain.append(column[2])
if column[0] == "HETNAM":
if column[1].isdigit() == False:
lig_name.append(column[2])
if column[0] == 'REMARK':
if column[1] == '2':
if len(column) > 2:
if column[2] == 'RESOLUTION.':
resolution = column[3]
print "RESOLUTION of pdb is " + str(resolution) + " Angstroms"
print "list of ligands present:" + str(ligand)
print "corresponding chains are:" + str(chain)
print "Ligand name is " + str(lig_name)
sys.stdout.flush()
mol = mds.readMolecule(
index) # read molecule from file do operation on molecule object
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)"
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 "The score is " + str(score)
logfile.write("The best pose is: " + str(pose))
logfile.write("The score is " + str(score))
print "XXXXXXXXXXXXXXXXXX"
logfile.close()
# read all the molecules in a directory and adds them to a list
base_address = os.getcwd() + '/output/'
receptor_address = os.getcwd() + '/pdb/'
folder = []
folder = os.listdir(base_address)
for x in folder:
# read molecule from file do operation on molecule object
receptor = mds.readMolecule(receptor_address + x + '_cleaned.mol2')
os.chdir(base_address + '/' + x + '/')
logfile = []
logfile = glob.glob(os.getcwd() + '/*.log')
wb = xl.Workbook('best_poses.xlsx')
ws = wb.add_worksheet()
counter = 0
inter = xl.Workbook('interactions.xlsx')
row = 1
col = 1
worksheet = inter.add_worksheet()
counter2 = 0
interrow = 0
intercol = 0
for index in logfile:
#worksheet = inter.add_worksheet()