frag_pele/Covalent/pdb_corrector.py
def run(input_pdb, residue_chain, residue_number, out_pdb, ligand_resname='UNK', ligand_chain=' ', 
        verbose=False, extract_ligand=True):
    """
    It process PDB files putting the ligand part of a covalent ligand into the residue that it is attached with.

    Parameters
        ----------
        input_pdb : str
            path to input PDB file
        residue_chain : str
            chain of the residue that has the ligand covalently attached
        residue_number : int
            number of the residue that has the ligand covalently attached
        out_pdb : str
            path of the output PDB file
        ligand_resname : str
            residue name of the ligand that is covalently attached to the previous residue
        ligand_chain : str
            chain of the ligand that is covalently attached to the previous residue
        verbose : bool
            if true it will activate all the prints
        extract_ligand : bool
            if true it extracts the ligand in a separated PDB file
    """
    corrector = CovCorrector(input_pdb=input_pdb, residue_chain=residue_chain, residue_number=residue_number,
                             ligand_resname=ligand_resname, ligand_chain=ligand_chain, verbose=verbose)
    corrector.correct()
    corrector.write_file(output_file=out_pdb, extract_ligand=extract_ligand)

    It process PDB files putting the ligand part of a covalent ligand into the residue that it is attached with.

    Parameters
        ----------
        input_pdb : str
            path to input PDB file
        residue_chain : str
            chain of the residue that has the ligand covalently attached
        residue_number : int
            number of the residue that has the ligand covalently attached
        out_pdb : str
            path of the output PDB file
        ligand_resname : str
            residue name of the ligand that is covalently attached to the previous residue
        ligand_chain : str
            chain of the ligand that is covalently attached to the previous residue
        verbose : bool
            if true it will activate all the prints
        extract_ligand : bool
            if true it extracts the ligand in a separated PDB file
    
It process PDB files putting the ligand part of a covalent ligand into the residue that it is attached with.
Parameters


It process PDB files putting the ligand part of a covalent ligand into the residue that it is attached with . Parameters
def run(input_pdb, residue_chain, residue_number, out_pdb, ligand_resname='UNK', ligand_chain=' ', 
        verbose=False, extract_ligand=True):
    corrector = CovCorrector(input_pdb=input_pdb, residue_chain=residue_chain, residue_number=residue_number,
                             ligand_resname=ligand_resname, ligand_chain=ligand_chain, verbose=verbose)
    corrector.correct()
    corrector.write_file(output_file=out_pdb, extract_ligand=extract_ligand)
def run ( input_pdb , residue_chain , residue_number , out_pdb , ligand_resname = 'UNK' , ligand_chain = ' ' , verbose = False , extract_ligand = True ) : corrector = CovCorrector ( input_pdb = input_pdb , residue_chain = residue_chain , residue_number = residue_number , ligand_resname = ligand_resname , ligand_chain = ligand_chain , verbose = verbose ) corrector . correct ( ) corrector . write_file ( output_file = out_pdb , extract_ligand = extract_ligand )
It process PDB files putting the ligand part of a covalent ligand into the residue that it is attached with.
It process PDB files putting the ligand part of a covalent ligand into the residue that it is attached with .
"""
    It process PDB files putting the ligand part of a covalent ligand into the residue that it is attached with.

    Parameters
        ----------
        input_pdb : str
            path to input PDB file
        residue_chain : str
            chain of the residue that has the ligand covalently attached
        residue_number : int
            number of the residue that has the ligand covalently attached
        out_pdb : str
            path of the output PDB file
        ligand_resname : str
            residue name of the ligand that is covalently attached to the previous residue
        ligand_chain : str
            chain of the ligand that is covalently attached to the previous residue
        verbose : bool
            if true it will activate all the prints
        extract_ligand : bool
            if true it extracts the ligand in a separated PDB file
    """
input_pdb
residue_chain
residue_number
out_pdb
ligand_resname
ligand_chain
verbose
extract_ligand