localpdb/plugins/utils/MakeMultimer.py
def parseBiomt(self):
        '''
        carve up the file according to biomolecules, which are defined
        in the REMARK 350 lines.
        '''
        bm_lines = [l[10:].strip() for l in self.pdb_lines if l.startswith('REMARK 350')]
        if not bm_lines:    # this file doesn't have any biomt instructions for us.
            raise PdbError('input file does not contain any BIOMT instructions')
        # OK, try to carve up the biomolecules
        biomolecules = []
        in_group = False
        group = []
        bm_marker = 'BIOMOLECULE:'
        for line in bm_lines:
            if line.startswith(bm_marker): # start new group ?
                                           # somehow parsing this again seems redundant.
                                           # need to figure it out some more.
                in_group = True
                if group:
                    biomolecules.append(
                        BioMolecule(group, self.originalchains, self.options))
                    group = []
            if in_group and line.strip():
                group.append(line)
        if group:
            biomolecules.append(BioMolecule(group, self.originalchains, self.options))

        return biomolecules

        carve up the file according to biomolecules, which are defined
        in the REMARK 350 lines.
        
carve up the file according to biomolecules, which are defined
in the REMARK 350 lines.
carve up the file according to biomolecules which are defined in the REMARK 350 lines .
def parseBiomt(self):
        bm_lines = [l[10:].strip() for l in self.pdb_lines if l.startswith('REMARK 350')]
        if not bm_lines:    
            raise PdbError('input file does not contain any BIOMT instructions')
        biomolecules = []
        in_group = False
        group = []
        bm_marker = 'BIOMOLECULE:'
        for line in bm_lines:
            if line.startswith(bm_marker): 
                in_group = True
                if group:
                    biomolecules.append(
                        BioMolecule(group, self.originalchains, self.options))
                    group = []
            if in_group and line.strip():
                group.append(line)
        if group:
            biomolecules.append(BioMolecule(group, self.originalchains, self.options))
        return biomolecules
def parseBiomt ( self ) : bm_lines = [ l [ 10 : ] . strip ( ) for l in self . pdb_lines if l . startswith ( 'REMARK 350' ) ] if not bm_lines : raise PdbError ( 'input file does not contain any BIOMT instructions' ) biomolecules = [ ] in_group = False group = [ ] bm_marker = 'BIOMOLECULE:' for line in bm_lines : if line . startswith ( bm_marker ) : in_group = True if group : biomolecules . append ( BioMolecule ( group , self . originalchains , self . options ) ) group = [ ] if in_group and line . strip ( ) : group . append ( line ) if group : biomolecules . append ( BioMolecule ( group , self . originalchains , self . options ) ) return biomolecules
carve up the file according to biomolecules, which are defined
in the REMARK 350 lines.
carve up the file according to biomolecules which are defined in the REMARK 350 lines .
'''
        carve up the file according to biomolecules, which are defined
        in the REMARK 350 lines.
        ''' # this file doesn't have any biomt instructions for us. # OK, try to carve up the biomolecules # start new group ? # somehow parsing this again seems redundant. # need to figure it out some more.
self