cl = contact(cl, ref, fout + 'cont.cl', add_hosts=add_hosts)
cl = filter_zero_contacts(cl) ## happened in one case
## cl = cl.filter( 'fnac_10', (0., 0.) )
cl = cl.filter('fnarc_10', (0., 0.))
flushPrint('%i orientations removed because of fnarc > 0.0\n' %
(n_cl - len(cl)))
cg = group(cl, 0.001, 0.0001)
dump(cg, fout + 'grouped.cg')
## final selection
nr_cl = selectClusters(cg, 10)
flushPrint(
'dumping %i non-redundant, non-overlapping, non-native complexes\n'\
% len( nr_cl ) )
dump(nr_cl, fout + 'nr.cl')
flushPrint('Dumping random complexes.')
saveComplexes(nr_cl, com_out)
## for visualisation
flushPrint('\nPreparing trajectory...')
t = Trajectory([c.model() for c in nr_cl])
t.ref.addChainId()
t.ref.writePdb(fout + 'nr_traj_ref.pdb', ter=2)
t.writeCrd(fout + 'nr_traj.crd')
out = absfile( options['o'] )
n = int( options['n'] )
traj= absfile( options.get('traj', None) )
finp= absfile( options.get('debug', None))
debug = ( finp is not None )
except:
print "Missing or wrong option:"
print lastError()
_use()
cr = ComplexRandomizer( rec, lig, ro, lo, debug=debug )
result = ComplexList()
flushPrint('generating...')
for i in range( n ):
result.append( cr.random_complex( inp_mirror=finp ) )
flushPrint('#')
flushPrint('\nDumping result...')
dump( result, out )
if traj:
flushPrint('\nWriting trajectory...')
t = Trajectory( [ c.model() for c in result ] )
t.ref.writePdb( traj + '.pdb' )
t.writeCrd( traj + '.crd' )
flushPrint('done')
lo = absfile(options['lo'])
out = absfile(options['o'])
n = int(options['n'])
traj = absfile(options.get('traj', None))
finp = absfile(options.get('debug', None))
debug = (finp is not None)
except:
print "Missing or wrong option:"
print lastError()
_use()
cr = ComplexRandomizer(rec, lig, ro, lo, debug=debug)
result = ComplexList()
flushPrint('generating...')
for i in range(n):
result.append(cr.random_complex(inp_mirror=finp))
flushPrint('#')
flushPrint('\nDumping result...')
dump(result, out)
if traj:
flushPrint('\nWriting trajectory...')
t = Trajectory([c.model() for c in result])
t.ref.writePdb(traj + '.pdb')
t.writeCrd(traj + '.crd')
flushPrint('done')
cl = contact( cl, ref, fout + 'cont.cl', add_hosts=add_hosts )
cl = filter_zero_contacts( cl ) ## happened in one case
## cl = cl.filter( 'fnac_10', (0., 0.) )
cl = cl.filter( 'fnarc_10', (0., 0.) )
flushPrint('%i orientations removed because of fnarc > 0.0\n' % (n_cl-len(cl)))
cg = group( cl, 0.001, 0.0001 )
dump( cg, fout+'grouped.cg' )
## final selection
nr_cl = selectClusters( cg, 10 )
flushPrint(
'dumping %i non-redundant, non-overlapping, non-native complexes\n'\
% len( nr_cl ) )
dump( nr_cl, fout+'nr.cl')
flushPrint('Dumping random complexes.')
saveComplexes( nr_cl, com_out )
## for visualisation
flushPrint('\nPreparing trajectory...')
t = Trajectory( [ c.model() for c in nr_cl ] )
t.ref.addChainId()
t.ref.writePdb( fout+'nr_traj_ref.pdb', ter=2 )
t.writeCrd( fout+'nr_traj.crd')