#!/usr/bin/env python3
"""Module containing the GOdMDRun class and the command line interface."""
import argparse
import shutil
from pathlib import Path
from pathlib import PurePath
from biobb_common.generic.biobb_object import BiobbObject
from biobb_common.configuration import settings
from biobb_common.tools.file_utils import launchlogger
from biobb_godmd.godmd.common import check_input_path, check_output_path
[docs]class GOdMDRun(BiobbObject):
"""
| biobb_godmd GOdMDRun
| Wrapper of the `GOdMD tool <http://mmb.irbbarcelona.org/GOdMD/>`_ module.
| Computes conformational transition trajectories for proteins using GOdMD tool.
Args:
input_pdb_orig_path (str): Input PDB file to be used as origin in the conformational transition. File type: input. `Sample file <https://github.com/bioexcel/biobb_godmd/raw/master/biobb_godmd/test/data/godmd/1ake_A.pdb>`_. Accepted formats: pdb (edam:format_1476).
input_pdb_target_path (str): Input PDB file to be used as target in the conformational transition. File type: input. `Sample file <https://github.com/bioexcel/biobb_godmd/raw/master/biobb_godmd/test/data/godmd/4ake_A.pdb>`_. Accepted formats: pdb (edam:format_1476).
input_aln_orig_path (str): Input GOdMD alignment file corresponding to the origin structure of the conformational transition. File type: input. `Sample file <https://github.com/bioexcel/biobb_godmd/raw/master/biobb_godmd/test/data/godmd/1ake_A.aln>`_. Accepted formats: aln (edam:format_2330), txt (edam:format_2330).
input_aln_target_path (str): Input GOdMD alignment file corresponding to the target structure of the conformational transition. File type: input. `Sample file <https://github.com/bioexcel/biobb_godmd/raw/master/biobb_godmd/test/data/godmd/4ake_A.aln>`_. Accepted formats: aln (edam:format_2330), txt (edam:format_2330).
input_config_path (str) (Optional): Input GOdMD configuration file. File type: input. `Sample file <https://github.com/bioexcel/biobb_godmd/raw/master/biobb_godmd/test/data/godmd/params.in>`_. Accepted formats: in (edam:format_2330), txt (edam:format_2330).
output_log_path (str): Output log file. File type: output. `Sample file <https://github.com/bioexcel/biobb_godmd/raw/master/biobb_godmd/test/reference/godmd/godmd.log>`_. Accepted formats: log (edam:format_2330), out (edam:format_2330), txt (edam:format_2330), o (edam:format_2330).
output_ene_path (str): Output energy file. File type: output. `Sample file <https://github.com/bioexcel/biobb_godmd/raw/master/biobb_godmd/test/reference/godmd/godmd_ene.out>`_. Accepted formats: log (edam:format_2330), out (edam:format_2330), txt (edam:format_2330), o (edam:format_2330).
output_trj_path (str): Output trajectory file. File type: output. `Sample file <https://github.com/bioexcel/biobb_godmd/raw/master/biobb_godmd/test/reference/godmd/godmd_trj.mdcrd>`_. Accepted formats: trj (edam:format_3878), crd (edam:format_3878), mdcrd (edam:format_3878), x (edam:format_3878).
output_pdb_path (str): Output structure file. File type: output. `Sample file <https://github.com/bioexcel/biobb_godmd/raw/master/biobb_godmd/test/reference/godmd/godmd_pdb.pdb>`_. Accepted formats: pdb (edam:format_1476).
properties (dict - Python dictionary object containing the tool parameters, not input/output files):
* **godmdin** (*dict*) - ({}) GOdMD options specification.
* **binary_path** (*str*) - ("discrete") Binary path.
* **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
* **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
Examples:
This is a use example of how to use the building block from Python::
from biobb_godmd.godmd.godmd_run import godmd_run
prop = {
'remove_tmp': True
}
godmd_run( input_pdb_orig_path='/path/to/pdb_orig.pdb',
input_pdb_target_path='/path/to/pdb_target.pdb',
input_aln_orig_path='/path/to/aln_orig.aln',
input_aln_target_path='/path/to/aln_target.aln',
output_log_path='/path/to/godmd_log.log',
output_ene_path='/path/to/godmd_ene.txt',
output_trj_path='/path/to/godmd_trj.mdcrd',
output_pdb_path='/path/to/godmd_pdb.pdb',
properties=prop)
Info:
* wrapped_software:
* name: GOdMD
* version: >=1.0
* license: Apache-2.0
* ontology:
* name: EDAM
* schema: http://edamontology.org/EDAM.owl
"""
def __init__(self, input_pdb_orig_path: str, input_pdb_target_path: str,
input_aln_orig_path: str, input_aln_target_path: str, input_config_path: str,
output_log_path: str, output_ene_path: str, output_trj_path: str, output_pdb_path: str,
properties: dict = 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_pdb_orig_path': input_pdb_orig_path,
'input_pdb_target_path': input_pdb_target_path,
'input_aln_orig_path': input_aln_orig_path,
'input_aln_target_path': input_aln_target_path,
'input_config_path': input_config_path},
'out': {'output_log_path': output_log_path,
'output_ene_path': output_ene_path,
'output_trj_path': output_trj_path,
'output_pdb_path': output_pdb_path}
}
# Properties specific for BB
self.properties = properties
self.godmdin = {k: str(v) for k, v in properties.get('godmdin', dict()).items()}
self.binary_path = properties.get('binary_path', "discrete")
# Check the properties
self.check_properties(properties)
# self.check_arguments()
[docs] def check_data_params(self, out_log, out_err):
""" Checks input/output paths correctness """
# Check input(s)
self.io_dict["in"]["input_pdb_orig_path"] = check_input_path(self.io_dict["in"]["input_pdb_orig_path"], "input_pdb_orig_path", False, out_log, self.__class__.__name__)
self.io_dict["in"]["input_pdb_target_path"] = check_input_path(self.io_dict["in"]["input_pdb_target_path"], "input_pdb_target_path", False, out_log, self.__class__.__name__)
self.io_dict["in"]["input_aln_orig_path"] = check_input_path(self.io_dict["in"]["input_aln_orig_path"], "input_aln_orig_path", False, out_log, self.__class__.__name__)
self.io_dict["in"]["input_aln_target_path"] = check_input_path(self.io_dict["in"]["input_aln_target_path"], "input_aln_target_path", False, out_log, self.__class__.__name__)
self.io_dict["in"]["input_config_path"] = check_input_path(self.io_dict["in"]["input_config_path"], "input_config_path", True, out_log, self.__class__.__name__)
# Check output(s)
self.io_dict["out"]["output_log_path"] = check_output_path(self.io_dict["out"]["output_log_path"], "output_log_path", False, out_log, self.__class__.__name__)
self.io_dict["out"]["output_ene_path"] = check_output_path(self.io_dict["out"]["output_ene_path"], "output_ene_path", False, out_log, self.__class__.__name__)
self.io_dict["out"]["output_trj_path"] = check_output_path(self.io_dict["out"]["output_trj_path"], "output_trj_path", False, out_log, self.__class__.__name__)
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] def create_godmdin(self, path: str = None) -> str:
"""Creates a GOdMD configuration file (godmdin) using the properties file settings"""
godmdin_list = []
self.output_godmdin_path = path
if self.io_dict['in']['input_config_path']:
# GOdMD input parameters read from an input godmdin file
with open(self.io_dict['in']['input_config_path']) as input_params:
for line in input_params:
if '=' in line:
godmdin_list.append(line.upper())
else:
# Pre-configured simulation type parameters
godmdin_list.append(" TSNAP = 500 ! BioBB GOdMD default params \n")
godmdin_list.append(" TEMP = 300 ! BioBB GOdMD default params \n")
godmdin_list.append(" SEED = 2525 ! BioBB GOdMD default params \n")
godmdin_list.append(" ENER_EVO_SIZE = 20 ! BioBB GOdMD default params \n")
godmdin_list.append(" NBLOC = 10000 ! BioBB GOdMD default params \n")
godmdin_list.append(" ERRORACCEPTABLE = 1.5 ! BioBB GOdMD default params \n")
# Adding the rest of parameters in the config file to the mdin file
# if the parameter has already been added replace the value
parameter_keys = [parameter.split('=')[0].strip() for parameter in godmdin_list]
for k, v in self.godmdin.items():
config_parameter_key = str(k).strip().upper()
if config_parameter_key in parameter_keys:
godmdin_list[parameter_keys.index(config_parameter_key)] = '\t' + config_parameter_key + ' = ' + str(v) + ' ! BioBB property \n'
else:
godmdin_list.append('\t' + config_parameter_key + ' = '+str(v) + ' ! BioBB property \n')
# Writing MD configuration file (mdin)
with open(self.output_godmdin_path, 'w') as godmdin:
# GOdMDIN parameters added by the biobb_godmd module
godmdin.write("!This godmdin file has been created by the biobb_godmd module from the BioBB library \n\n")
godmdin.write("&INPUT\n")
# MD config parameters
for line in godmdin_list:
godmdin.write(line)
godmdin.write("&END\n")
return self.output_godmdin_path
[docs] @launchlogger
def launch(self):
"""Launches the execution of the GOdMDRun 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 GOdMD input file
self.output_godmdin_path = self.create_godmdin(path=str(Path(self.stage_io_dict["unique_dir"]).joinpath("godmd.in")))
# Command line
# discrete -i $fileName.in -pdbin $pdbch1 -pdbtarg $pdbch2 -ener $fileName.ene -trj $fileName.crd -p1 $alignFile1 -p2 $alignFile2 -o $fileName.log >& $fileName.out
self.cmd = ['cd', self.stage_io_dict["unique_dir"], ';', self.binary_path,
'-i', "godmd.in",
'-pdbin', PurePath(self.stage_io_dict["in"]["input_pdb_orig_path"]).name,
'-pdbtarg', PurePath(self.stage_io_dict["in"]["input_pdb_target_path"]).name,
'-p1', PurePath(self.stage_io_dict["in"]["input_aln_orig_path"]).name,
'-p2', PurePath(self.stage_io_dict["in"]["input_aln_target_path"]).name,
'-o', PurePath(self.stage_io_dict["out"]["output_log_path"]).name,
'-ener', PurePath(self.stage_io_dict["out"]["output_ene_path"]).name,
'-trj', PurePath(self.stage_io_dict["out"]["output_trj_path"]).name
]
# Run Biobb block
self.run_biobb()
# Copy outputs from temporary folder to output path
shutil.copy2(str(Path(self.stage_io_dict["unique_dir"]).joinpath("reference.pdb")), PurePath(self.io_dict["out"]["output_pdb_path"]))
# Copy files to host
self.copy_to_host()
# remove temporary folder(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 godmd_run(input_pdb_orig_path: str, input_pdb_target_path: str,
input_aln_orig_path: str, input_aln_target_path: str,
output_log_path: str, output_ene_path: str, output_trj_path: str, output_pdb_path: str,
input_config_path: str = None, properties: dict = None, **kwargs) -> int:
"""Create :class:`GOdMDRun <godmd.godmd_run.GOdMDRun>`godmd.godmd_run.GOdMDRun class and
execute :meth:`launch() <godmd.godmd_run.GOdMDRun.launch>` method"""
return GOdMDRun(input_pdb_orig_path=input_pdb_orig_path,
input_pdb_target_path=input_pdb_target_path,
input_aln_orig_path=input_aln_orig_path,
input_aln_target_path=input_aln_target_path,
input_config_path=input_config_path,
output_log_path=output_log_path,
output_ene_path=output_ene_path,
output_trj_path=output_trj_path,
output_pdb_path=output_pdb_path,
properties=properties).launch()
[docs]def main():
parser = argparse.ArgumentParser(description='Computing conformational transition trajectories for proteins using GOdMD tool.', 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_orig_path', required=True, help='Input PDB file to be used as origin in the conformational transition. Accepted formats: pdb.')
required_args.add_argument('--input_pdb_target_path', required=True, help='Input PDB file to be used as target in the conformational transition. Accepted formats: pdb.')
required_args.add_argument('--input_aln_orig_path', required=True, help='Input GOdMD alignment file corresponding to the origin structure of the conformational transition. Accepted formats: aln, txt.')
required_args.add_argument('--input_aln_target_path', required=True, help='Input GOdMD alignment file corresponding to the target structure of the conformational transition. Accepted formats: aln, txt.')
required_args.add_argument('--input_config_path', required=False, help='Input configuration file (GOdMD run options). Accepted formats: in, txt.')
required_args.add_argument('--output_log_path', required=True, help='Output log file. Accepted formats: log, out, txt.')
required_args.add_argument('--output_ene_path', required=True, help='Output energy file. Accepted formats: log, out, txt.')
required_args.add_argument('--output_trj_path', required=True, help='Output trajectory file. Accepted formats: mdcrd.')
required_args.add_argument('--output_pdb_path', required=True, help='Output structure file. Accepted formats: pdb.')
args = parser.parse_args()
# config = args.config if args.config else None
args.config = args.config or "{}"
# properties = settings.ConfReader(config=config).get_prop_dic()
properties = settings.ConfReader(config=args.config).get_prop_dic()
# Specific call
godmd_run(input_pdb_orig_path=args.input_pdb_orig_path,
input_pdb_target_path=args.input_pdb_target_path,
input_aln_orig_path=args.input_aln_orig_path,
input_aln_target_path=args.input_aln_target_path,
input_config_path=args.input_config_path,
output_log_path=args.output_log_path,
output_ene_path=args.output_ene_path,
output_trj_path=args.output_trj_path,
output_pdb_path=args.output_pdb_path,
properties=properties)
if __name__ == '__main__':
main()