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')
if __name__ == '__main__':
options = cmdDict( {'ter':1} )
if len( options ) < 2:
_use( options )
skip = None
if options.has_key('wat'):
skip = ['TIP3', 'WAT', 'HOH', 'H2O', 'Na+', 'Cl-']
fin = [ absfile(f) for f in toList( options['i'] ) ]
ter = int( options['ter'] )
codeprefix = options.has_key( 'codeprefix' )
for f in fin:
fout= options.get('o', None) or stripSuffix( f ) + '.pdb'
m = PDBModel( f )
if codeprefix:
code = m.pdbCode or ''
fpath, fname = osp.split( fout )
fout = osp.join( fpath, code + fname )
m.writePdb( fout, ter=ter )
errWriteln('dumped ' + fout )
def process_all( self, file_dic, keep_hetatoms=0 ):
"""
Process PDB files in file_dic.
The PDB is read from:
- L{TemplateSearcher.F_NR}
and cleaned files are written to:
- L{F_CLEANED}
- L{F_COFFEE}
- L{F_MODELLER}
If the file L{F_CLEANED} already exists, this file is
used to write modeller and t-coffee pdbs.
@param file_dic: dictionary mapping filenames of pdb files to
the chains of interest, e.g. { fname : chain_id, }
@type file_dic: {str:str}
@param keep_hetatoms: keep hetatoms (default: 0)
@type keep_hetatoms: 0|1
"""
fasta = ""
c = None
for f, id in file_dic.items():
self.logWrite( '\nCLEANING ' + f + '...')
try:
code = string.split(f, '/')[-1][:4]
## clean to standard PDB
c = PDBCleaner( f, self.log )
## if /templates/nr_cleaned/pfb-file exists
if os.path.exists(
self.outFolder+self.F_CLEANED + code + '.pdb' ):
model = PDBModel( self.outFolder+self.F_CLEANED \
+ code + '.pdb' )
## read pdb from /templates/nr
else:
model = c.process( keep_hetatoms=keep_hetatoms )
## write complete cleaned PDB
model.writePdb( self.outFolder+self.F_CLEANED \
+ code + '.pdb')
code = model.pdbCode
title = code + '_' + id
## extract needed chain
if len( id ) > 0:
model = self.__chain_by_id( model, id )
fname = "%s%s.pdb" % (self.outFolder + self.F_MODELLER, title)
self.write_modeller_pdb( model, fname )
## write T_coffee CA trace with res sequence
fname = "%s%s.alpha"%(self.outFolder + self.F_COFFEE, title)
self.write_tcoffee_pdb( model, fname )
## append fasta
fasta += self.fasta_sequence( title, model.sequence() )
except:
self.logWrite( 'Error cleaning ' + f)
self.logWrite( T.lastError() )
self.err_cleaner = c
self.err_file = f
fasta_out = open( self.outFolder + self.F_FASTA, 'w' )
fasta_out.write( fasta )
fasta_out.close()
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)
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 )
