def parseReference(self, fpdb, dry_out=None):
flushPrint("parsing " + fpdb + "...")
m = PDBModel(fpdb)
solute_res = m.atom2resMask(logical_not(m.maskSolvent()))
self.lenres = self.lenres or sum(solute_res)
self.lenatoms = len(m) - sum(m.maskH2O())
if dry_out:
m.remove(m.maskH2O())
m.writePdb(dry_out)
flushPrint('done.\n')
def parseReference(self, fpdb, dry_out=None ):
flushPrint("parsing "+fpdb+"...")
m = PDBModel( fpdb )
solute_res = m.atom2resMask( logical_not( m.maskSolvent() ) )
self.lenres = self.lenres or sum( solute_res )
self.lenatoms = len( m ) - sum( m.maskH2O() )
if dry_out:
m.remove( m.maskH2O() )
m.writePdb( dry_out )
flushPrint('done.\n')
class Test(BT.BiskitTest):
"""Test class"""
def test_reduce(self):
"""AtomCharger test"""
if self.local: self.log.add('\nLoading PDB...')
self.m1 = PDBModel(T.testRoot('lig/1A19_dry.model'))
self.m2 = T.load(T.testRoot('com/ref.complex'))
self.m2 = self.m2.model()
if self.local: self.log.add('\nRunning Reduce...')
self.x = Reduce(self.m1,
debug=self.DEBUG,
verbose=self.local,
log=self.log,
autocap=True)
self.m1 = self.x.run()
if self.local:
self.log.add('\nReduce protein complex')
self.x = Reduce(self.m2,
debug=self.DEBUG,
verbose=self.local,
log=self.log,
autocap=True)
self.m2 = self.x.run()
if self.local:
self.log.add('\nSetup Residue Library\n')
ac = AtomCharger(log=self.log, verbose=self.local)
if self.local:
self.log.add('match residues to Amber topology')
ac.charge(self.m1)
ac.charge(self.m2)
self.assertAlmostEqual(N.sum(self.m1['partial_charge']), -6, 2)
self.assertAlmostEqual(N.sum(self.m2['partial_charge']), -4, 2)
self.assert_(N.all(self.m1['partial_charge'] != 0),
'unmatched atoms 1')
self.assert_(N.all(self.m2['partial_charge'] != 0),
'unmatched atoms 2')
if self.local:
self.log.add('\nNow test handling of atom miss-matches:\n')
self.m3 = PDBModel(self.m1.clone())
self.m3.remove([0, 3, 100, 101, 102, 200])
ac.charge(self.m3)
self.assertAlmostEqual(N.sum(self.m3['partial_charge']), -8.21, 2)
class Test(BT.BiskitTest):
"""Test class"""
def test_reduce( self ):
"""AtomCharger test"""
if self.local: self.log.add('\nLoading PDB...')
self.m1 = PDBModel( T.testRoot( 'lig/1A19_dry.model' ) )
self.m2 = T.load( T.testRoot( 'com/ref.complex' ) )
self.m2 = self.m2.model()
if self.local: self.log.add('\nRunning Reduce...')
self.x = Reduce( self.m1, debug=self.DEBUG, verbose=self.local,
log=self.log,
autocap=True )
self.m1 = self.x.run()
if self.local:
self.log.add('\nReduce protein complex')
self.x = Reduce( self.m2, debug=self.DEBUG, verbose=self.local,
log=self.log,
autocap=True )
self.m2 = self.x.run()
if self.local:
self.log.add('\nSetup Residue Library\n')
ac = AtomCharger(log=self.log, verbose=self.local)
if self.local:
self.log.add('match residues to Amber topology')
ac.charge( self.m1 )
ac.charge( self.m2 )
self.assertAlmostEqual( N.sum(self.m1['partial_charge']), -6, 2 )
self.assertAlmostEqual( N.sum(self.m2['partial_charge']), -4, 2 )
self.assert_(N.all(self.m1['partial_charge'] != 0),'unmatched atoms 1')
self.assert_(N.all(self.m2['partial_charge'] != 0),'unmatched atoms 2')
if self.local:
self.log.add('\nNow test handling of atom miss-matches:\n')
self.m3 = PDBModel(self.m1.clone())
self.m3.remove( [0,3,100,101,102,200] )
ac.charge( self.m3 )
self.assertAlmostEqual( N.sum(self.m3['partial_charge']),-8.21, 2)
errWriteln("loading pdbs...")
m1 = PDBModel(f1)
m2 = PDBModel(f2)
if options.has_key('c1'):
m1 = m1.takeChains(toIntList(options['c1']))
if options.has_key('c2'):
m2 = m2.takeChains(toIntList(options['c2']))
m1.removeRes('TIP3')
m2.removeRes('TIP3')
m1.sort()
m2.sort()
errWriteln("compare atoms of pdbs...")
mask1, mask2 = m1.equalAtoms(m2)
errWriteln("removing %i atoms from %s" % (sum(logical_not(mask1)), f1))
m1.remove(logical_not(mask1))
errWriteln("removing %i atoms from %s" % (sum(logical_not(mask2)), f2))
m2.remove(logical_not(mask2))
errWriteln("writing new pdbs...")
m1.writePdb(o1)
m2.writePdb(o2)
sys.exit(0)
### MAIN ###
############
options = T.cmdDict( {'o':'ref.complex', 'lo':'lig.model', 'ro':'rec.model' } )
if len (sys.argv) < 3:
_use( options )
## create a reference complex
print "Loading..."
ref_com = PDBModel( options['c'] )
print "Removing water..."
ref_com.remove( lambda a: a['residue_name'] in ['TIP3','HOH','WAT'] )
## extract rec and lig chains
rec_chains = T.toIntList( options['r'] )
lig_chains = T.toIntList( options['l'] )
print "Extracting rec and lig..."
ref_rec = ref_com.takeChains( rec_chains )
ref_lig = ref_com.takeChains( lig_chains )
## create Protein complex
com = ProteinComplex( ref_rec, ref_lig )
print "Saving..."
ref_lig.saveAs( T.absfile( options['lo'] ) )
errWriteln("loading pdbs...")
m1 = PDBModel( f1 )
m2 = PDBModel( f2 )
if options.has_key('c1'):
m1 = m1.takeChains( toIntList( options['c1'] ) )
if options.has_key('c2'):
m2 = m2.takeChains( toIntList( options['c2'] ) )
m1.removeRes( 'TIP3' )
m2.removeRes( 'TIP3' )
m1.sort()
m2.sort()
errWriteln("compare atoms of pdbs...")
mask1, mask2 = m1.equalAtoms( m2 )
errWriteln("removing %i atoms from %s" % (sum( logical_not( mask1 ) ), f1))
m1.remove( logical_not( mask1 ) )
errWriteln("removing %i atoms from %s" % (sum( logical_not( mask2 ) ), f2))
m2.remove( logical_not( mask2 ) )
errWriteln("writing new pdbs..." )
m1.writePdb( o1 )
m2.writePdb( o2 )