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))
if o in ('-v', '--v'):
verbose = True
if verbose: print 'set verbose to ', True
if o in ('-h', '--'):
usage()
sys.exit()
#read all the docking logs in current directory, one by one
dlg_list = glob.glob('./*.dlg')
dockings = []
#build a list of all atom types in all dlgs
#it is assumed that all the dockings used the same grids
ctr = 0
at_types = {}
for dlg in dlg_list:
d = Docking()
d.readDlg(dlg)
ctr += 1
print ctr, ": read ", dlg
dockings.append(d)
for a in d.ligMol.allAtoms:
at_types[a.autodock_element] = 0
if debug: print 'at_types=', at_types.keys()
d = dockings[0] #get grid info from the first docking
xcen, ycen, zcen = d.dlo_list[0].parser.center_pt
#for the output maps...
# nxgrid=nygrid=nzgrid=npts ??is this required??
nxpts = nypts = nzpts = int(num_pts) / 2 * 2 + 1 #ensure an odd integer
npts = (nxpts, nypts, nzpts)
macroStem = d.dlo_list[0].macroStem
# build list of all atom types
if verbose: print 'set verbose to ', True
if o in ('-h', '--'):
usage()
sys.exit()
if not directory:
print 'summarize_wcg_docking: directory must be specified.'
usage()
sys.exit()
#read all the xml docking logs in as one Docking
xml_list = glob.glob('*.xml')
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()[:]
if not refdirectory:
msg += 'reference directory must be specified!\n'
if not directory:
msg = 'Both reference directory and directory must be specified!\n'
elif not directory:
msg += 'directory must be specified!'
if not refdirectory or not directory:
print(msg)
usage()
sys.exit()
#process docking in reference directory
#read all the docking logs in reference directory as one Docking
ref_dlg_list = glob.glob(refdirectory + '/*.dlg')
ref_d = Docking()
for dlg in ref_dlg_list:
ref_d.readDlg(dlg)
#setup rmsd tool
coords = ref_d.ligMol.allAtoms.coords[:]
ref_d.clusterer.rmsTool = RMSDCalculator(coords)
ref_d.clusterer.make_clustering(rms_tolerance)
clust0 = ref_d.clusterer.clustering_dict[rms_tolerance][0]
c = clust0[0] #lowest energy overall in reference docking
ref_d.ch.set_conformation(c)
ref_LE_coords = ref_d.ligMol.allAtoms.coords[:]
ref_largest = clust0
for clust in ref_d.clusterer.clustering_dict[rms_tolerance]:
if verbose: print("current largest cluster len= ", len(clust))
if len(clust) > len(ref_largest):
if verbose: print("resetting largest clust: now len=", len(clust))
