#!/usr/bin/env python3
"""Module containing the AmberToPDB 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.file_utils import launchlogger
from biobb_amber.ambpdb.common import check_input_path, check_output_path
[docs]class AmberToPDB(BiobbObject):
"""
| biobb_amber AmberToPDB
| Wrapper of the `AmberTools (AMBER MD Package) ambpdb tool <https://ambermd.org/AmberTools.php>`_ module.
| Generates a PDB structure from AMBER topology (parmtop) and coordinates (crd) files, using the ambpdb tool from the AmberTools MD package.
Args:
input_top_path (str): AMBER topology file. File type: input. `Sample file <https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/data/ambpdb/structure.leap.top>`_. Accepted formats: top (edam:format_3881), parmtop (edam:format_3881), prmtop (edam:format_3881).
input_crd_path (str): AMBER coordinates file. File type: input. `Sample file <https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/data/ambpdb/structure.leap.crd>`_. Accepted formats: crd (edam:format_3878), mdcrd (edam:format_3878), inpcrd (edam:format_3878), rst (edam:format_3886).
output_pdb_path (str): Structure PDB file. File type: output. `Sample file <https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/reference/ambpdb/structure.ambpdb.pdb>`_. Accepted formats: pdb (edam:format_1476).
properties (dic - Python dictionary object containing the tool parameters, not input/output files):
* **binary_path** (*str*) - ("ambpdb") Path to the ambpdb 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.ambpdb.amber_to_pdb import amber_to_pdb
prop = {
'remove_tmp': True
}
amber_to_pdb(input_top_path='/path/to/topology.top',
input_crd_path='/path/to/coordinates.crd',
output_pdb_path='/path/to/newStructure.pdb',
properties=prop)
Info:
* wrapped_software:
* name: AmberTools ambpdb
* version: >20.9
* license: LGPL 2.1
* ontology:
* name: EDAM
* schema: http://edamontology.org/EDAM.owl
"""
def __init__(self, input_top_path, input_crd_path, output_pdb_path, properties: dict = None, **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_top_path': input_top_path,
'input_crd_path': input_crd_path},
'out': {'output_pdb_path': output_pdb_path}
}
# Properties specific for BB
self.properties = properties
self.binary_path = properties.get('binary_path', 'ambpdb')
# 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__)
self.io_dict["in"]["input_crd_path"] = check_input_path(self.io_dict["in"]["input_crd_path"], "input_crd_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):
# 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()
# Command line
self.cmd = [self.binary_path,
'-p', self.stage_io_dict['in']['input_top_path'],
'-c', self.stage_io_dict['in']['input_crd_path'],
'> ', self.stage_io_dict['out']['output_pdb_path']
]
# Run Biobb block
self.run_biobb()
# Copy files to host
self.copy_to_host()
# Remove temporary file(s)
self.tmp_files.extend([
self.stage_io_dict.get("unique_dir")
])
self.remove_tmp_files()
self.check_arguments(output_files_created=True, raise_exception=False)
return self.return_code
[docs]def amber_to_pdb(input_top_path: str, input_crd_path: str, output_pdb_path: str,
properties: dict = None, **kwargs) -> int:
"""Create :class:`AmberToPDB <amber.amber_to_pdb.AmberToPDB>`amber.amber_to_pdb.AmberToPDB class and
execute :meth:`launch() <amber.amber_to_pdb.AmberToPDB.launch>` method"""
return AmberToPDB(input_top_path=input_top_path,
input_crd_path=input_crd_path,
output_pdb_path=output_pdb_path,
properties=properties).launch()
[docs]def main():
"""Command line execution of this building block. Please check the command line documentation."""
parser = argparse.ArgumentParser(description='Generates a PDB structure from AMBER topology (parmtop) and coordinates (crd) files, using the ambpdb 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_top_path', required=True, help='AMBER topology file. Accepted formats: top, parmtop, prmtop.')
required_args.add_argument('--input_crd_path', required=True, help='AMBER coordinates file. Accepted formats: crd, mdcrd, inpcrd.')
required_args.add_argument('--output_pdb_path', required=True, help='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
amber_to_pdb(input_top_path=args.input_top_path,
input_crd_path=args.input_crd_path,
output_pdb_path=args.output_pdb_path,
properties=properties)
if __name__ == '__main__':
main()