#!/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 biobb_common.tools import file_utils as fu
from biobb_common.tools.file_utils 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 <https://ambermd.org/AmberTools.php>`_ 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 <https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/data/parmed/structure.solv.top>`_. 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 <https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/reference/parmed/cln025.cpin>`_. Accepted formats: cpin (edam:format_2330).
output_top_path (str) (Optional): Output topology file (AMBER ParmTop). File type: output. `Sample file <https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/reference/parmed/cln025.cpH.prmtop>`_. 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*) - ("cpinutil.py") Path to the cpinutil.py 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/topology.top',
output_cpin_path='/path/to/newCpin.cpin',
output_top_path='/path/to/newTopology.top',
properties=prop)
Info:
* wrapped_software:
* name: AmberTools parmed
* version: >20.9
* license: LGPL 2.1
* ontology:
* name: EDAM
* schema: http://edamontology.org/EDAM.owl
"""
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
self.properties = 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', 'cpinutil.py')
# 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)
# cpinutil.py -igb 2 -resname AS4 GL4 -p $1.prmtop -op $1.cpH.prmtop
# cpinutil.py -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()