localpdb/plugins/utils/MakeMultimer.py
def output(self, filename='stuff'):
        '''
        return our collected results in one big string. This will
        be the main part of the output pdb file.
        '''
        self.collate()
        header = [self.title_template % filename]
        header.append('by MakeMultimer.py (%s)' % url)
        header.append('')
        if self.overflow_warnings:
            header.append('The following errors occurred with naming and numbering:')
            header.extend(sorted(list(self.overflow_warnings)))
            header.append('')
        atoms_out = []
        chain_data_lines = []
        for old, new, first_res, last_res, first_atom, last_atom, atoms \
                                                       in self.collected_chains:
            chain_data_lines.append((new, old, first_res, last_res, first_atom, last_atom))
            atoms_out.extend(atoms)
        formatted = tableFormat(self.chain_titles, chain_data_lines)
        header.extend(formatted)
        header.append('')
        header.append('BIOMT instructions applied:')
        header.extend(self.bm_lines)
        header.append('')

        out = ['REMARK  ' + h for h in header] + atoms_out

        return '\n'.join(out)

        return our collected results in one big string. This will
        be the main part of the output pdb file.
        
return our collected results in one big string. This will
be the main part of the output pdb file.
return our collected results in one big string . This will be the main part of the output pdb file .
def output(self, filename='stuff'):
        self.collate()
        header = [self.title_template % filename]
        header.append('by MakeMultimer.py (%s)' % url)
        header.append('')
        if self.overflow_warnings:
            header.append('The following errors occurred with naming and numbering:')
            header.extend(sorted(list(self.overflow_warnings)))
            header.append('')
        atoms_out = []
        chain_data_lines = []
        for old, new, first_res, last_res, first_atom, last_atom, atoms \
                                                       in self.collected_chains:
            chain_data_lines.append((new, old, first_res, last_res, first_atom, last_atom))
            atoms_out.extend(atoms)
        formatted = tableFormat(self.chain_titles, chain_data_lines)
        header.extend(formatted)
        header.append('')
        header.append('BIOMT instructions applied:')
        header.extend(self.bm_lines)
        header.append('')
        out = ['REMARK  ' + h for h in header] + atoms_out
        return '\n'.join(out)
def output ( self , filename = 'stuff' ) : self . collate ( ) header = [ self . title_template % filename ] header . append ( 'by MakeMultimer.py (%s)' % url ) header . append ( '' ) if self . overflow_warnings : header . append ( 'The following errors occurred with naming and numbering:' ) header . extend ( sorted ( list ( self . overflow_warnings ) ) ) header . append ( '' ) atoms_out = [ ] chain_data_lines = [ ] for old , new , first_res , last_res , first_atom , last_atom , atoms in self . collected_chains : chain_data_lines . append ( ( new , old , first_res , last_res , first_atom , last_atom ) ) atoms_out . extend ( atoms ) formatted = tableFormat ( self . chain_titles , chain_data_lines ) header . extend ( formatted ) header . append ( '' ) header . append ( 'BIOMT instructions applied:' ) header . extend ( self . bm_lines ) header . append ( '' ) out = [ 'REMARK  ' + h for h in header ] + atoms_out return '\n' . join ( out )
return our collected results in one big string.
return our collected results in one big string .
'''
        return our collected results in one big string. This will
        be the main part of the output pdb file.
        '''
self
filename