#!/usr/bin/env python3
"""Module containing the Pdb4amber 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.pdb4amber.common import check_input_path, check_output_path
[docs]class Pdb4amberRun(BiobbObject):
"""
| biobb_amber.pdb4amber.pdb4amber_run Pdb4amberRun
| Wrapper of the `AmberTools (AMBER MD Package) pdb4amber tool <https://ambermd.org/AmberTools.php>`_ module.
| Analyse PDB files and clean them for further usage, especially with the LEaP programs of Amber, using pdb4amber tool from the AmberTools MD package.
Args:
input_pdb_path (str): Input 3D structure PDB file. File type: input. `Sample file <https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/data/pdb4amber/1aki_fixed.pdb>`_. Accepted formats: pdb (edam:format_1476).
output_pdb_path (str): Output 3D structure PDB file. File type: output. `Sample file <https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/reference/pdb4amber/structure.pdb4amber.pdb>`_. Accepted formats: pdb (edam:format_1476).
properties (dict - Python dictionary object containing the tool parameters, not input/output files):
* **remove_hydrogens** (*bool*) - (False) Remove hydrogen atoms from the PDB file.
* **remove_waters** (*bool*) - (False) Remove water molecules from the PDB file.
* **constant_pH** (*bool*) - (False) Rename ionizable residues e.g. GLU,ASP,HIS for constant pH simulation.
* **binary_path** (*str*) - ("pdb4amber") Path to the pdb4amber 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.pdb4amber.pdb4amber_run import pdb4amber_run
prop = {
'remove_tmp': True
}
pdb4amber_run(input_pdb_path='/path/to/structure.pdb',
output_pdb_path='/path/to/newStructure.pdb',
properties=prop)
Info:
* wrapped_software:
* name: AmberTools pdb4amber
* version: >20.9
* license: LGPL 2.1
* ontology:
* name: EDAM
* schema: http://edamontology.org/EDAM.owl
"""
def __init__(self, input_pdb_path: str, output_pdb_path: str,
properties: dict, **kwargs):
properties = properties or {}
# Call parent class constructor
super().__init__(properties)
self.locals_var_dict = locals().copy()
# Input/Output files
self.io_dict = {
'in': {'input_pdb_path': input_pdb_path},
'out': {'output_pdb_path': output_pdb_path}
}
# Properties specific for BB
self.properties = properties
self.remove_hydrogens = properties.get('remove_hydrogens', False)
self.remove_waters = properties.get('remove_waters', False)
self.constant_pH = properties.get('constant_pH', False)
self.binary_path = properties.get('binary_path', 'pdb4amber')
# 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_pdb_path"] = check_input_path(self.io_dict["in"]["input_pdb_path"], "input_pdb_path", False, out_log, self.__class__.__name__)
# Check output(s)
self.io_dict["out"]["output_pdb_path"] = check_output_path(self.io_dict["out"]["output_pdb_path"], "output_pdb_path", False, out_log, self.__class__.__name__)
[docs] @launchlogger
def launch(self):
"""Launches the execution of the Pdb4amberRun 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)
# Command line
# sander -O -i mdin/min.mdin -p $1.cpH.prmtop -c ph$i/$1.inpcrd -r ph$i/$1.min.rst7 -o ph$i/$1.min.o
self.cmd = [self.binary_path,
'-i', self.stage_io_dict['in']['input_pdb_path'],
'-o', self.stage_io_dict['out']['output_pdb_path']
]
if self.remove_hydrogens:
self.cmd.append("-y ")
if self.remove_waters:
self.cmd.append("-d ")
if self.constant_pH:
self.cmd.append("--constantph ")
# 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 pdb4amber_run(input_pdb_path: str, output_pdb_path: str,
properties: dict = None, **kwargs) -> int:
"""Create :class:`Pdb4amberRun <pdb4amber.pdb4amber_run.Pdb4amberRun>`pdb4amber.pdb4amber_run.Pdb4amberRun class and
execute :meth:`launch() <pdb4amber.pdb4amber_run.Pdb4amberRun.launch>` method"""
return Pdb4amberRun(input_pdb_path=input_pdb_path,
output_pdb_path=output_pdb_path,
properties=properties).launch()
[docs]def main():
parser = argparse.ArgumentParser(description='Analyse PDB files and clean them for further usage, especially with the LEaP programs of Amber, using pdb4amber tool from the 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_pdb_path', required=True, help='Input 3D structure PDB file. Accepted formats: pdb.')
required_args.add_argument('--output_pdb_path', required=True, help='Output 3D structure PDB file. Accepted formats: pdb.')
args = parser.parse_args()
config = args.config if args.config else None
properties = settings.ConfReader(config=config).get_prop_dic()
# Specific call
pdb4amber_run(input_pdb_path=args.input_pdb_path,
output_pdb_path=args.output_pdb_path,
properties=properties)
if __name__ == '__main__':
main()