def prepare( self ):
"""
"""
mrec = self.com.rec()
mlig = self.com.lig()
m = mrec.concat( mlig )
if self.protonate:
if self.verbose:
self.log.add( '\nRe-building hydrogen atoms...' )
tempdir = self.tempdir
if tempdir:
tempdir += '/0_reduce'
r = Reduce( m, tempdir=tempdir, log=self.log,
autocap=False,
debug=self.debug, verbose=self.verbose )
m = r.run()
if self.addcharge:
if self.verbose:
self.log.add( '\nAssigning charges from Amber topologies...')
ac = AtomCharger( log=self.log, verbose=self.verbose )
ac.charge( m )
mrec = m.takeChains( range( mrec.lenChains() ) )
mlig = m.takeChains( range( mrec.lenChains(), m.lenChains() ) )
self.delphicom = Complex( mrec, mlig )
def prepare(self):
"""
"""
mrec = self.com.rec()
mlig = self.com.lig()
m = mrec.concat(mlig)
if self.protonate:
if self.verbose:
self.log.add('\nRe-building hydrogen atoms...')
tempdir = self.tempdir
if tempdir:
tempdir += '/0_reduce'
r = Reduce(m,
tempdir=tempdir,
log=self.log,
autocap=False,
debug=self.debug,
verbose=self.verbose)
m = r.run()
if self.addcharge:
if self.verbose:
self.log.add('\nAssigning charges from Amber topologies...')
ac = AtomCharger(log=self.log, verbose=self.verbose)
ac.charge(m)
mrec = m.takeChains(range(mrec.lenChains()))
mlig = m.takeChains(range(mrec.lenChains(), m.lenChains()))
self.delphicom = Complex(mrec, mlig)
def test_delphiCharges2(self):
"""
PDB2DelphiCharges test
"""
if self.local:
T.errWrite('loading PDB...')
self.m1 = self.MODEL or PDBModel(T.testRoot('lig/1A19_dry.model'))
Test.MODEL = self.m1
if self.local:
T.errWriteln('Done.')
if self.local:
T.errWrite('Adding hydrogens to model (reduce)...')
self.rmodel = Reduce(self.m1, verbose=self.local).run()
self.rmodel.xplor2amber()
if self.local:
T.errWriteln('Done.')
ac = AtomCharger()
ac.charge(self.rmodel)
self.rmodel.addChainFromSegid()
self.dc = PDB2DelphiCharges(self.rmodel)
self.dc.prepare()
self.assertEqual(len(self.dc.resmap['LYS']), 2) # normal and N'
self.assertEqual(len(self.dc.resmap['SER']), 2) # normal and C'
if self.local:
T.errWriteln('writing delphi charge file to %s' % self.fcrg)
self.dc.tofile(self.fcrg)
self.assertTrue(os.path.exists(self.fcrg))
def test_delphiCharges2( self ):
"""
PDB2DelphiCharges test
"""
if self.local:
T.errWrite( 'loading PDB...' )
self.m1 = self.MODEL or PDBModel( T.testRoot( 'lig/1A19_dry.model' ) )
Test.MODEL = self.m1
if self.local:
T.errWriteln( 'Done.' )
if self.local:
T.errWrite( 'Adding hydrogens to model (reduce)...' )
self.rmodel = Reduce( self.m1, verbose=self.local ).run()
self.rmodel.xplor2amber()
if self.local:
T.errWriteln( 'Done.' )
ac = AtomCharger()
ac.charge(self.rmodel)
self.rmodel.addChainFromSegid()
self.dc = PDB2DelphiCharges( self.rmodel )
self.dc.prepare()
self.assertEqual( len(self.dc.resmap['LYS']), 2 ) # normal and N'
self.assertEqual( len(self.dc.resmap['SER']), 2 ) # normal and C'
if self.local:
T.errWriteln( 'writing delphi charge file to %s' % self.fcrg )
self.dc.tofile( self.fcrg )
self.assertTrue( os.path.exists( self.fcrg ) )
def __prepareCharges(self, f_out):
try:
if self.addcharge:
if self.verbose:
self.log.add(
'\nAssigning atomic charges with AtomCharger...')
if self.topologies is None:
reslib = None
else:
reslib = AmberResidueLibrary(self.topologies,
log=self.log,
verbose=self.verbose)
ac = AtomCharger(reslibrary=reslib,
log=self.log,
verbose=self.verbose)
ac.charge(self.delphimodel)
if self.verbose:
self.log.add('Creating Delphi charge file %s' % f_out)
dc = PDB2DelphiCharges(self.delphimodel)
dc.prepare()
dc.tofile(f_out)
if self.verbose:
qmissing = self.delphimodel['partial_charge'] == 0
self.log.add('\nAtoms without charges: %i' % N.sum(qmissing))
if N.sum(qmissing) > 0:
self.log.add('Warning: there are atoms without charge:')
m = self.delphimodel.compress(qmissing)
for a in m:
self.log.add(
'%(serial_number)4i %(name)-4s %(residue_name)3s %(residue_number)3i %(chain_id)s'\
% a)
except IOError as why:
raise IOError('Error creating custom delphi charge file '+f_out+\
'( '+str(why)+' )')
def __prepareCharges(self, f_out ):
try:
if self.addcharge:
if self.verbose:
self.log.add(
'\nAssigning atomic charges with AtomCharger...')
if self.topologies is None:
reslib = None
else:
reslib = AmberResidueLibrary(self.topologies,log=self.log,
verbose=self.verbose)
ac = AtomCharger( reslibrary=reslib,
log=self.log, verbose=self.verbose )
ac.charge( self.delphimodel )
if self.verbose:
self.log.add('Creating Delphi charge file %s'%f_out)
dc = PDB2DelphiCharges( self.delphimodel )
dc.prepare()
dc.tofile( f_out )
if self.verbose:
qmissing = self.delphimodel['partial_charge']==0
self.log.add('\nAtoms without charges: %i' % N.sum(qmissing))
if N.sum(qmissing) > 0:
self.log.add('Warning: there are atoms without charge:')
m = self.delphimodel.compress( qmissing )
for a in m:
self.log.add(
'%(serial_number)4i %(name)-4s %(residue_name)3s %(residue_number)3i %(chain_id)s'\
% a)
except IOError as why:
raise IOError('Error creating custom delphi charge file '+f_out+\
'( '+str(why)+' )')
def prepare(self):
if not 'partial_charge' in self.model.atoms:
ac = AtomCharger()
ac.charge(self.model)
self.resmap = self.mapResidues()
def prepare( self ):
if not 'partial_charge' in self.model.atoms:
ac = AtomCharger()
ac.charge( self.model )
self.resmap = self.mapResidues()