meeko/writer.py
def remark_index_map(self, order=None, prefix="REMARK INDEX MAP", missing_h=[]):
        """ write mapping of atom indices from input molecule to output PDBQT
            order[ob_index(i.e. 'key')] = smiles_index
        """

        if order is None: order = {key: key for key in self._numbering}
        #max_line_length = 79
        #remark_lines = []
        #line = prefix
        strings = []
        for key in self._numbering:
            if key in self.setup.atom_pseudo: continue
            if key in missing_h: continue
            string = " %d %d" % (order[key], self._numbering[key])
            strings.append(string)
        return self.strings_to_remarks(strings, prefix)
        #    candidate_text = " %d %d" % (order[key], self._numbering[key])
        #    if (len(line) + len(candidate_text)) < max_line_length:
        #        line += candidate_text
        #    else:
        #        remark_lines.append(line)
        #        line = 'REMARK INDEX MAP' + candidate_text
        #remark_lines.append(line)
        #return remark_lines
 write mapping of atom indices from input molecule to output PDBQT
            order[ob_index(i.e. 'key')] = smiles_index
        
write mapping of atom indices from input molecule to output PDBQT
order[ob_index] = smiles_index
write mapping of atom indices from input molecule to output PDBQT order [ ob_index ] = smiles_index
def remark_index_map(self, order=None, prefix="REMARK INDEX MAP", missing_h=[]):
        if order is None: order = {key: key for key in self._numbering}
        strings = []
        for key in self._numbering:
            if key in self.setup.atom_pseudo: continue
            if key in missing_h: continue
            string = " %d %d" % (order[key], self._numbering[key])
            strings.append(string)
        return self.strings_to_remarks(strings, prefix)
def remark_index_map ( self , order = None , prefix = "REMARK INDEX MAP" , missing_h = [ ] ) : if order is None : order = { key : key for key in self . _numbering } strings = [ ] for key in self . _numbering : if key in self . setup . atom_pseudo : continue if key in missing_h : continue string = " %d %d" % ( order [ key ] , self . _numbering [ key ] ) strings . append ( string ) return self . strings_to_remarks ( strings , prefix )
write mapping of atom indices from input molecule to output PDBQT
order[ob_index(i.e.
write mapping of atom indices from input molecule to output PDBQT order [ ob_index ( i . e .
""" write mapping of atom indices from input molecule to output PDBQT
            order[ob_index(i.e. 'key')] = smiles_index
        """ #max_line_length = 79 #remark_lines = [] #line = prefix #    candidate_text = " %d %d" % (order[key], self._numbering[key]) #    if (len(line) + len(candidate_text)) < max_line_length: #        line += candidate_text #    else: #        remark_lines.append(line) #        line = 'REMARK INDEX MAP' + candidate_text #remark_lines.append(line) #return remark_lines
self
order
prefix
missing_h