smamp.charges_to_rtp module

Transfer Charges from CSV table to .rft file

Copyright 2019 Simulation Lab

University of Freiburg

Author : Lukas Elflein elfleinl@cs.uni-freiburg.de

 

""" Transfer Charges from CSV table to .rft file
Copyright 2019 Simulation Lab
University of Freiburg
Author: Lukas Elflein <elfleinl@cs.uni-freiburg.de>
"""

import pandas as pd
import argparse
import shutil


def import_charges(csv_path):
        """
        Read and filter the best-fit charges.

        Args:
        csv_path: path to the charge table
        
        Return:
        charges: pandas DataFrame with atom names, residue names, charges
        """
        charges = pd.read_csv(csv_path)

        # select atom names, the residue and q column
        charges = charges[['atom', 'residue', 'q']]
        print('Charge table sucessfully imported.')

        return charges

def parse_rft(rtp_path, charges=None):
        """
        Substitute the fitted charges for the original charges in the RTF file.

        Args:
        rtp_path: A string containing the original GROMACS topology file path
        charges: A pandas DataFrame containing the best fit charges

        Returns:
        fitted_rtp_text: The original topoly file, but with updated charges
        """

        with open(rtp_path, 'r') as rtp_file:
                print('Successfully loaded topolgy file {}'.format(rtp_path))
                rtp_text = rtp_file.readlines()

                # save all possible atom names
                atom_names = charges.atom.unique()
                # and residuum names
                residuum_names = charges.residue.unique()
                
                # We will append all modified lines to sub_text
                sub_text = ''
                
                # Keep track of how often we substituted for debugging
                nr_substitutions = 0

                current_residuum = None         
                for line in rtp_text:
                        # Atom names are only unique inside one residuum
                        # Thus, specify which res we are currently in
                        for residuum in residuum_names:
                                if residuum in line:
                                        current_residuum = residuum
                                        break
                        # Now, we can look up the atom name in the charge table.
                        # First, select the lines with exactly one atom name
                        for atom_name in atom_names:
                                # Select lines with at least one atom name
                                if atom_name in line[0:7]:
                                        second_entry = line[8:18].replace('+', '')
                                        second_entry = second_entry.replace('-', '').strip()
                                        # Select lines with no atom name in second column
                                        if not second_entry in atom_names:
                                                # Now we can substitute the charge with the fitted one
                                                line = substitute(line, charges, current_residuum)
                                                nr_substitutions += 1
                                                break

                        # We substituted the charge, if applicable.
                        # Now we can append the line to the text file
                        sub_text += line

        # Make sure that all substitutions were executed
        assert len(charges.index) == nr_substitutions
        print('{} of {} charges substituted.'.format(nr_substitutions, len(charges.index)))

        return sub_text

def substitute(line, charges, current_residuum):
        """
        Look up the charge for an atom, and write into a string.

        Args:
        line: String containing an atom name, residuum name, and original charge.
        charges: DataFrame containing atom name, residuum names, new charges.

        Returns:
        line: the original line, with the charge updated from the `charges` table.
        """
        current_atom = line[0:7].strip()

        # look up the current atom name in the residuum we are currently in
        mask = (charges.atom == current_atom) & (charges.residue == current_residuum)
        # Exract the charge q
        new_charge = charges[mask].q.values[0]
        charge_string = '{: 1.6f}'.format(new_charge) + '  '
        modified_line = line[:24] + charge_string + line[34:]

        return modified_line

def export_rft(text, out_path):
        """
        Write the modified text to a file.
        """
        with open(out_path, 'w') as outfile:
                outfile.write(text)
        print('Modified topoly file written to {}'.format(out_path))

def cmd_parser():
        parser = argparse.ArgumentParser(prog='',
                                         description='Transfer charges from a csv file to an .rtp file')
        parser.add_argument('-rtp',
        help='The location of the GROMACS topology file (.rtp)',
        default='./n7nh2.rtp', metavar='./n7nh2.rtp')

        parser.add_argument('-csv', metavar='./charges.csv',
        help='The location of the atomname-charge table, in the .csv format.', 
        default='./average_cost_function_check/fitted_points_charges.csv')
        
        parser.add_argument('-out', metavar='./modified.rtp',
        help='The location where the modified rtp file should be saved.',
        default='modified.rtp')

        args = parser.parse_args()

        return args.rtp, args.csv, args.out
        
        
def main():
        """
        Run the script.
        """
        rtp_path, csv_path, out_path = cmd_parser()
        charges = import_charges(csv_path)
        sub_text = parse_rft(rtp_path=rtp_path, charges=charges) 
        export_rft(text=sub_text, out_path=out_path)
        print('Done.')

if __name__ == '__main__':
        main()

Functions

def cmd_parser()

Source code

def cmd_parser():
        parser = argparse.ArgumentParser(prog='',
                                         description='Transfer charges from a csv file to an .rtp file')
        parser.add_argument('-rtp',
        help='The location of the GROMACS topology file (.rtp)',
        default='./n7nh2.rtp', metavar='./n7nh2.rtp')

        parser.add_argument('-csv', metavar='./charges.csv',
        help='The location of the atomname-charge table, in the .csv format.', 
        default='./average_cost_function_check/fitted_points_charges.csv')
        
        parser.add_argument('-out', metavar='./modified.rtp',
        help='The location where the modified rtp file should be saved.',
        default='modified.rtp')

        args = parser.parse_args()

        return args.rtp, args.csv, args.out

def export_rft(text, out_path)

Write the modified text to a file.

Source code

def export_rft(text, out_path):
        """
        Write the modified text to a file.
        """
        with open(out_path, 'w') as outfile:
                outfile.write(text)
        print('Modified topoly file written to {}'.format(out_path))

def import_charges(csv_path)

Read and filter the best-fit charges.

Args:

csv_path : path to the charge table

 

Return:

charges : pandas DataFrame with atom names, residue names, charges

 

Source code

def import_charges(csv_path):
        """
        Read and filter the best-fit charges.

        Args:
        csv_path: path to the charge table
        
        Return:
        charges: pandas DataFrame with atom names, residue names, charges
        """
        charges = pd.read_csv(csv_path)

        # select atom names, the residue and q column
        charges = charges[['atom', 'residue', 'q']]
        print('Charge table sucessfully imported.')

        return charges

def main()

Run the script.

Source code

def main():
        """
        Run the script.
        """
        rtp_path, csv_path, out_path = cmd_parser()
        charges = import_charges(csv_path)
        sub_text = parse_rft(rtp_path=rtp_path, charges=charges) 
        export_rft(text=sub_text, out_path=out_path)
        print('Done.')

def parse_rft(rtp_path, charges=None)

Substitute the fitted charges for the original charges in the RTF file.

Args:

rtp_path : A string containing the original GROMACS topology file path

 

charges : A pandas DataFrame containing the best fit charges

 

Returns:

fitted_rtp_text : The original topoly file, but with updated charges

 

Source code

def parse_rft(rtp_path, charges=None):
        """
        Substitute the fitted charges for the original charges in the RTF file.

        Args:
        rtp_path: A string containing the original GROMACS topology file path
        charges: A pandas DataFrame containing the best fit charges

        Returns:
        fitted_rtp_text: The original topoly file, but with updated charges
        """

        with open(rtp_path, 'r') as rtp_file:
                print('Successfully loaded topolgy file {}'.format(rtp_path))
                rtp_text = rtp_file.readlines()

                # save all possible atom names
                atom_names = charges.atom.unique()
                # and residuum names
                residuum_names = charges.residue.unique()
                
                # We will append all modified lines to sub_text
                sub_text = ''
                
                # Keep track of how often we substituted for debugging
                nr_substitutions = 0

                current_residuum = None         
                for line in rtp_text:
                        # Atom names are only unique inside one residuum
                        # Thus, specify which res we are currently in
                        for residuum in residuum_names:
                                if residuum in line:
                                        current_residuum = residuum
                                        break
                        # Now, we can look up the atom name in the charge table.
                        # First, select the lines with exactly one atom name
                        for atom_name in atom_names:
                                # Select lines with at least one atom name
                                if atom_name in line[0:7]:
                                        second_entry = line[8:18].replace('+', '')
                                        second_entry = second_entry.replace('-', '').strip()
                                        # Select lines with no atom name in second column
                                        if not second_entry in atom_names:
                                                # Now we can substitute the charge with the fitted one
                                                line = substitute(line, charges, current_residuum)
                                                nr_substitutions += 1
                                                break

                        # We substituted the charge, if applicable.
                        # Now we can append the line to the text file
                        sub_text += line

        # Make sure that all substitutions were executed
        assert len(charges.index) == nr_substitutions
        print('{} of {} charges substituted.'.format(nr_substitutions, len(charges.index)))

        return sub_text

def substitute(line, charges, current_residuum)

Look up the charge for an atom, and write into a string.

Args: line: String containing an atom name, residuum name, and original charge. charges: DataFrame containing atom name, residuum names, new charges.

Returns: line: the original line, with the charge updated from the charges table.

Source code

def substitute(line, charges, current_residuum):
        """
        Look up the charge for an atom, and write into a string.

        Args:
        line: String containing an atom name, residuum name, and original charge.
        charges: DataFrame containing atom name, residuum names, new charges.

        Returns:
        line: the original line, with the charge updated from the `charges` table.
        """
        current_atom = line[0:7].strip()

        # look up the current atom name in the residuum we are currently in
        mask = (charges.atom == current_atom) & (charges.residue == current_residuum)
        # Exract the charge q
        new_charge = charges[mask].q.values[0]
        charge_string = '{: 1.6f}'.format(new_charge) + '  '
        modified_line = line[:24] + charge_string + line[34:]

        return modified_line