frag_pele/Covalent/pdb_corrector.py
def _join_ligand_and_residue(self, reindexing=True):
        """
        It appends ligand lines onto the residue, and it can reindex atom ids.

        Parameters
        ----------
        reindexing : bool
            if it is true, it will reindex the atom IDs of the joining result
            
        Returns
        -------
        joining_result : list
            lines of the amino-acid with the ligand attached, all in the same residue
        """
        counter = 1
        joining_result = []
        for res_line in self.residue.split('\n')[0:-1]:  # The last line is empty because of the splitting
            res_line = list(res_line)
            if reindexing:
                res_line = list(res_line)
                res_line[6:11] = "{:>5}".format(counter)
                counter = counter + 1
            res_line[17:20] = self._ligand_resname
            res_line = ''.join(res_line)
            joining_result.append(res_line+'\n')
        for lig_line in self._ligand_lines:
            lig_line = list(lig_line)
            if reindexing:
                lig_line = list(lig_line)
                lig_line[6:11] = "{:>5}".format(counter)
                counter = counter + 1
            lig_line[17:20] = self._ligand_resname
            lig_line = ''.join(lig_line)
            joining_result.append(lig_line)
        return joining_result

        It appends ligand lines onto the residue, and it can reindex atom ids.

        Parameters
        ----------
        reindexing : bool
            if it is true, it will reindex the atom IDs of the joining result
            
        Returns
        -------
        joining_result : list
            lines of the amino-acid with the ligand attached, all in the same residue
        
It appends ligand lines onto the residue, and it can reindex atom ids.
Parameters

reindexing : bool
if it is true, it will reindex the atom IDs of the joining result

Returns

joining_result : list
lines of the amino-acid with the ligand attached, all in the same residue
It appends ligand lines onto the residue and it can reindex atom ids . Parameters reindexing : bool if it is true it will reindex the atom IDs of the joining result Returns joining_result : list lines of the amino - acid with the ligand attached all in the same residue
def _join_ligand_and_residue(self, reindexing=True):
        counter = 1
        joining_result = []
        for res_line in self.residue.split('\n')[0:-1]:  
            res_line = list(res_line)
            if reindexing:
                res_line = list(res_line)
                res_line[6:11] = "{:>5}".format(counter)
                counter = counter + 1
            res_line[17:20] = self._ligand_resname
            res_line = ''.join(res_line)
            joining_result.append(res_line+'\n')
        for lig_line in self._ligand_lines:
            lig_line = list(lig_line)
            if reindexing:
                lig_line = list(lig_line)
                lig_line[6:11] = "{:>5}".format(counter)
                counter = counter + 1
            lig_line[17:20] = self._ligand_resname
            lig_line = ''.join(lig_line)
            joining_result.append(lig_line)
        return joining_result
def _join_ligand_and_residue ( self , reindexing = True ) : counter = 1 joining_result = [ ] for res_line in self . residue . split ( '\n' ) [ 0 : - 1 ] : res_line = list ( res_line ) if reindexing : res_line = list ( res_line ) res_line [ 6 : 11 ] = "{:>5}" . format ( counter ) counter = counter + 1 res_line [ 17 : 20 ] = self . _ligand_resname res_line = '' . join ( res_line ) joining_result . append ( res_line + '\n' ) for lig_line in self . _ligand_lines : lig_line = list ( lig_line ) if reindexing : lig_line = list ( lig_line ) lig_line [ 6 : 11 ] = "{:>5}" . format ( counter ) counter = counter + 1 lig_line [ 17 : 20 ] = self . _ligand_resname lig_line = '' . join ( lig_line ) joining_result . append ( lig_line ) return joining_result
It appends ligand lines onto the residue, and it can reindex atom ids.
It appends ligand lines onto the residue and it can reindex atom ids .
"""
        It appends ligand lines onto the residue, and it can reindex atom ids.

        Parameters
        ----------
        reindexing : bool
            if it is true, it will reindex the atom IDs of the joining result
            
        Returns
        -------
        joining_result : list
            lines of the amino-acid with the ligand attached, all in the same residue
        """ # The last line is empty because of the splitting
self
reindexing