Source code for parmed.parmed_cpinutil

#!/usr/bin/env python3

"""Module containing the ParmedCpinUtil class and the command line interface."""
import argparse
from biobb_common.generic.biobb_object import BiobbObject
from biobb_common.configuration import settings
from import file_utils as fu
from import launchlogger
from biobb_amber.parmed.common import check_input_path, check_output_path

[docs]class ParmedCpinUtil(BiobbObject): """ | biobb_amber ParmedCpinUtil | Wrapper of the `AmberTools (AMBER MD Package) parmed tool <>`_ module. | Creates a cpin file for constant pH simulations from an AMBER topology file using parmed tool from the AmberTools MD package. Args: input_top_path (str): Input AMBER topology file. File type: input. `Sample file <>`_. Accepted formats: top (edam:format_3881), parmtop (edam:format_3881), prmtop (edam:format_3881). output_cpin_path (str): Output AMBER constant pH input (CPin) file. File type: output. `Sample file <>`_. Accepted formats: cpin (edam:format_2330). output_top_path (str) (Optional): Output topology file (AMBER ParmTop). File type: output. `Sample file <>`_. Accepted formats: top (edam:format_3881), parmtop (edam:format_3881), prmtop (edam:format_3881). properties (dic - Python dictionary object containing the tool parameters, not input/output files): * **resnames** (*str*) - ("None") Residue names to include in CPIN file. Values: AS4, GL4, HIP, CYS, LYS, TYR. * **igb** (*int*) - (2) Generalized Born model which you intend to use to evaluate dynamics or protonation state swaps. Values: 1, 2, 5, 7, 8. * **system** (*str*) - ("Unknown") Name of system to titrate. * **binary_path** (*str*) - ("") Path to the executable binary. * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files. * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist. * **container_path** (*str*) - (None) Container path definition. * **container_image** (*str*) - ('afandiadib/ambertools:serial') Container image definition. * **container_volume_path** (*str*) - ('/tmp') Container volume path definition. * **container_working_dir** (*str*) - (None) Container working directory definition. * **container_user_id** (*str*) - (None) Container user_id definition. * **container_shell_path** (*str*) - ('/bin/bash') Path to default shell inside the container. Examples: This is a use example of how to use the building block from Python:: from biobb_amber.parmed.parmed_cpinutil import parmed_cpinutil prop = { 'igb' : 2, 'resnames': 'AS4 GL4', 'system': 'cln025', 'remove_tmp': False } parmed_cpinutil(input_top_path='/path/to/', output_cpin_path='/path/to/newCpin.cpin', output_top_path='/path/to/', properties=prop) Info: * wrapped_software: * name: AmberTools parmed * version: >20.9 * license: LGPL 2.1 * ontology: * name: EDAM * schema: """ def __init__(self, input_top_path, output_cpin_path, output_top_path=None, properties=None, **kwargs) -> None: properties = properties or {} # Call parent class constructor super().__init__(properties) self.locals_var_dict = locals().copy() # Input/Output files self.io_dict = { 'in': {'input_top_path': input_top_path}, 'out': {'output_cpin_path': output_cpin_path, 'output_top_path': output_top_path} } # Properties specific for BB = properties self.resnames = properties.get('resnames') self.igb = properties.get('igb', 2) self.system = properties.get('system', "Unknown") self.binary_path = properties.get('binary_path', '') # Check the properties self.check_properties(properties) self.check_arguments()
[docs] def check_data_params(self, out_log, err_log): """ Checks input/output paths correctness """ # Check input(s) self.io_dict["in"]["input_top_path"] = check_input_path(self.io_dict["in"]["input_top_path"], "input_top_path", False, out_log, self.__class__.__name__) # Check output(s) self.io_dict["out"]["output_cpin_path"] = check_output_path(self.io_dict["out"]["output_cpin_path"], "output_cpin_path", False, out_log, self.__class__.__name__) self.io_dict["out"]["output_top_path"] = check_output_path(self.io_dict["out"]["output_top_path"], "output_top_path", True, out_log, self.__class__.__name__)
[docs] @launchlogger def launch(self): """Launches the execution of the ParmedCpinUtil module.""" # check input/output paths and parameters self.check_data_params(self.out_log, self.err_log) # Setup Biobb if self.check_restart(): return 0 self.stage_files() # Creating temporary folder self.tmp_folder = fu.create_unique_dir() fu.log('Creating %s temporary folder' % self.tmp_folder, self.out_log) # -igb 2 -resname AS4 GL4 -p $1.prmtop -op $1.cpH.prmtop # -p cln025.cpH.prmtop -igb 2 -system "CLN" -o cpin fu.log('Creating command line with instructions and required arguments', self.out_log, self.global_log) self.cmd = [self.binary_path, '-p', self.stage_io_dict['in']['input_top_path'], '-o', self.stage_io_dict['out']['output_cpin_path'] ] if self.igb: self.cmd.append('-igb') self.cmd.append(str(self.igb)) if self.system: self.cmd.append('-system') self.cmd.append(self.system) if self.resnames: self.cmd.append('-resnames') self.cmd.append(self.resnames) if self.io_dict["out"]["output_top_path"]: self.cmd.append('-op') self.cmd.append(self.stage_io_dict["out"]["output_top_path"]) # Run Biobb block self.run_biobb() # Copy files to host self.copy_to_host() # remove temporary folder(s) self.tmp_files.extend([ self.stage_io_dict.get("unique_dir"), self.tmp_folder ]) self.remove_tmp_files() self.check_arguments(output_files_created=True, raise_exception=False) return self.return_code
[docs]def parmed_cpinutil(input_top_path: str, output_cpin_path: str, output_top_path: str = None, properties: dict = None, **kwargs) -> int: """Create :class:`ParmedCpinUtil <parmed.parmed_cpinutil.ParmedCpinUtil>`parmed.parmed_cpinutil.ParmedCpinUtil class and execute :meth:`launch() <parmed.parmed_cpinutil.ParmedCpinUtil.launch>` method""" return ParmedCpinUtil(input_top_path=input_top_path, output_cpin_path=output_cpin_path, output_top_path=output_top_path, properties=properties).launch()
[docs]def main(): parser = argparse.ArgumentParser(description='create a cpin file for constant pH simulations from an AMBER topology file using parmed program from AmberTools MD package.', formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999)) parser.add_argument('--config', required=False, help='Configuration file') # Specific args required_args = parser.add_argument_group('required arguments') required_args.add_argument('--input_top_path', required=True, help='Input AMBER topology file. Accepted formats: top, parmtop, prmtop.') required_args.add_argument('--output_cpin_path', required=True, help='Output AMBER constant pH input (CPin) file. Accepted formats: cpin.') required_args.add_argument('--output_top_path', required=False, help='Output topology file (AMBER ParmTop). Accepted formats: top, parmtop, prmtop.') args = parser.parse_args() config = args.config if args.config else None properties = settings.ConfReader(config=config).get_prop_dic() # Specific call parmed_cpinutil(input_top_path=args.input_top_path, output_cpin_path=args.output_cpin_path, output_top_path=args.output_top_path, properties=properties)
if __name__ == '__main__': main()