def main():
dlgs = glob('*.dlg')
if len(dlgs) == 0:
sys.exit(1)
if os.path.exists('target') is False:
os.mkdir('target')
ligands = []
receptors = []
for filename in dlgs:
dlg=filename[:-4]
(lig, rec) = dlg.split('--____--')
if not lig in ligands:
ligands.append(lig)
if not rec in receptors:
receptors.append(rec)
res = [[] for i in ligands]
for i in range(len(res)):
res[i] = ['' for j in receptors]
for filename in dlgs:
dlg=filename[:-4]
(lig, rec) = dlg.split('--____--')
d = Docking()
d.readDlg(filename)
lines = d.ligMol.parser.allLines
for i in range(len(lines)):
line = lines[i]
if line.find("\n") == -1:
d.ligMol.parser.allLines[i] = line + "\n"
if not hasattr(d, 'clusterer'):
d.clusterer = Clusterer(d.ch.conformations, sort="binding_energy")
clist = [d.clusterer.data[int(i)] for i in d.clusterer.argsort]
energy = clist[0].binding_energy
res[ligands.index(lig)][receptors.index(rec)] = "%.2f" % energy
d.ligMol.parser.allLines = d.ligMol.parser.write_with_new_coords(clist[0].getCoords())
write_pdb(d.ligMol.parser.parse(), 'target/%s.pdb' % dlg)
res_file = open('target/result.txt', 'w')
print>>res_file, ",%s" % ",".join(receptors)
for i in range(len(res)):
print>>res_file, "%s,%s" % (ligands[i], ",".join(res[i]))
res_file.close()
def parse_dlg(dlgfilename, num, result):
global VERBOSE
d = Docking()
d.readDlg(dlgfilename)
if num > 1:
workdir = outdir + '/' + d.ligMol.name
if os.path.exists(workdir) is False:
os.mkdir(workdir)
if num == 1:
workdir = outdir
if num > 1:
log = {'name': d.ligMol.name, 'num': num, 'target': workdir}
if VERBOSE:
print log
#print>>result, log
lines = d.ligMol.parser.allLines
for i in range(len(lines)):
line = lines[i]
if line.find("\n") == -1:
d.ligMol.parser.allLines[i] = line + "\n"
if not hasattr(d, 'clusterer'):
d.clusterer = Clusterer(d.ch.conformations, sort='binding_energy')
clist = []
for i in d.clusterer.argsort:
clist.append(d.clusterer.data[int(i)])
energy_list = []
for i in range(0, num):
conf = clist[i]
outfile = workdir + '/' + d.ligMol.name + '_' + str(i + 1) + '.pdb'
energy = conf.binding_energy
energy_list.append("%.2f" % energy)
mylog = {'name': outfile, 'energy': energy}
if VERBOSE:
print mylog
d.ligMol.parser.allLines = d.ligMol.parser.write_with_new_coords(
conf.getCoords())
write_pdb(d.ligMol.parser.parse(), outfile)
print >> result, "%s,%s" % (d.ligMol.name, ','.join(energy_list))
print "xml_list =", xml_list
p = XMLParser()
d = Docking(parser=p)
for xml_file in xml_list:
print "calling readXMLResults with", xml_file
d.readXMLResults(xml_file, dpf = dpf_fn)
ligMol = d.ligMol
ligAts = ligMol.allAtoms
#setup rmsd tool
coords = ligAts.coords[:]
atom_ct = len(ligAts)
torsion_ct = len(ligMol.torTree.torsionMap)
tors_penalty = torsion_ct * 0.2744
cl = Clusterer(d.ch.conformations)
d.clusterer = cl
cl.make_clustering(rms_tolerance)
ref_coords = cl.clustering_dict[rms_tolerance][0][0].getCoords()[:]
# for building hydrogen bonds or reporting energy breakdown
# setup receptor:
if build_hydrogen_bonds or report_energy_breakdown:
ligMol.buildBondsByDistance()
receptor = Read(receptor_filename)[0]
receptor.buildBondsByDistance()
if build_hydrogen_bonds:
hbondBuilder = HydrogenBondBuilder()
if report_energy_breakdown:
ms = MolecularSystem()
ms.add_entities(receptor.allAtoms)
ms.add_entities(ligMol.allAtoms)