#!/usr/bin/env python3
"""Module containing the ProcessMDOut class and the command line interface."""
import argparse
import shutil
from pathlib import Path, PurePath
from typing import Optional
from biobb_common.configuration import settings
from biobb_common.generic.biobb_object import BiobbObject
from biobb_common.tools import file_utils as fu
from biobb_common.tools.file_utils import launchlogger
from biobb_amber.process.common import (
_from_string_to_list,
check_input_path,
check_output_path,
)
[docs]
class ProcessMDOut(BiobbObject):
"""
| biobb_amber.process.process_mdout ProcessMDOut
| Wrapper of the `AmberTools (AMBER MD Package) process_mdout tool <https://ambermd.org/AmberTools.php>`_ module.
| Parses the AMBER (sander) md output file (log) and dumps statistics that can then be plotted. Using the process_mdout.pl tool from the AmberTools MD package.
Args:
input_log_path (str): AMBER (sander) MD output (log) file. File type: input. `Sample file <https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/data/process/sander.heat.log>`_. Accepted formats: log (edam:format_2330), out (edam:format_2330), txt (edam:format_2330), o (edam:format_2330).
output_dat_path (str): Dat output file containing data from the specified terms along the minimization process. File type: output. `Sample file <https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/reference/process/sander.md.temp.dat>`_. Accepted formats: dat (edam:format_1637), txt (edam:format_2330), csv (edam:format_3752).
properties (dic - Python dictionary object containing the tool parameters, not input/output files):
* **terms** (*list*) - (["ETOT"]) Statistics descriptors. Values: VOLUME, TSOLVENT, TSOLUTE, TEMP, PRES, ETOT, ESCF, EPTOT, EKTOT, EKCMT, DENSITY.
* **binary_path** (*str*) - ("process_mdout.perl") Path to the process_mdout.perl executable binary.
* **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
* **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
* **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.
* **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.process.process_mdout import process_mdout
prop = {
'terms' : ['TEMP','VOLUME','DENSITY']
}
process_mdout(input_log_path='/path/to/ambermd.log',
output_dat_path='/path/to/newFeature.dat',
properties=prop)
Info:
* wrapped_software:
* name: AmberTools process_mdout
* version: >20.9
* license: LGPL 2.1
* ontology:
* name: EDAM
* schema: http://edamontology.org/EDAM.owl
"""
def __init__(self, input_log_path: str, output_dat_path: str, properties, **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_log_path": input_log_path},
"out": {"output_dat_path": output_dat_path},
}
# Properties specific for BB
self.properties = properties
self.terms = _from_string_to_list(properties.get("terms", ["ETOT"]))
self.binary_path = properties.get("binary_path", "process_mdout.perl")
# 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_log_path"] = check_input_path(
self.io_dict["in"]["input_log_path"],
"input_log_path",
False,
out_log,
self.__class__.__name__,
)
# Check output(s)
self.io_dict["out"]["output_dat_path"] = check_output_path(
self.io_dict["out"]["output_dat_path"],
"output_dat_path",
False,
out_log,
self.__class__.__name__,
)
[docs]
@launchlogger
def launch(self):
"""Launches the execution of the ProcessMDOut 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()
if not self.container_path:
self.tmp_folder = fu.create_unique_dir()
fu.log("Creating %s temporary folder" % self.tmp_folder, self.out_log)
self.cmd = [
"cd",
self.tmp_folder,
";",
self.binary_path,
str(Path(self.stage_io_dict["in"]["input_log_path"]).resolve()),
]
else:
self.tmp_folder = None
self.cmd = [self.binary_path, self.stage_io_dict["in"]["input_log_path"]]
# Run Biobb block
self.run_biobb()
# Copy files to host
self.copy_to_host()
if len(self.terms) == 1:
if self.container_path:
shutil.copy(
PurePath(self.stage_io_dict["unique_dir"]).joinpath(
"summary." + self.terms[0]
),
self.io_dict["out"]["output_dat_path"],
)
else:
shutil.copy(
PurePath(str(self.tmp_folder)).joinpath("summary." + self.terms[0]),
self.io_dict["out"]["output_dat_path"],
)
else:
if self.container_path:
tmp = self.stage_io_dict["unique_dir"]
else:
tmp = self.tmp_folder
ene_dict = {}
for term in self.terms:
with open(str(tmp) + "/summary." + term) as fp:
for line in fp:
x = line.split()
if x:
if len(x) > 1:
ene_dict.setdefault(float(x[0]), {})[term] = x[1]
else:
ene_dict.setdefault(float(x[0]), {})[term] = "-"
with open(self.io_dict["out"]["output_dat_path"], "w") as fp_out:
fp_out.write("# TIME ")
for term in self.terms:
fp_out.write(term + " ")
fp_out.write("\n")
for key in sorted(ene_dict.keys()):
fp_out.write(str(key) + " ")
for term in self.terms:
fp_out.write(ene_dict[key][term] + " ")
fp_out.write("\n")
# remove temporary folder(s)
self.tmp_files.extend([
# self.stage_io_dict.get("unique_dir", ""),
str(self.tmp_folder)
] + list(Path().glob("summary*"))
)
self.remove_tmp_files()
self.check_arguments(output_files_created=True, raise_exception=False)
return self.return_code
[docs]
def process_mdout(
input_log_path: str,
output_dat_path: str,
properties: Optional[dict] = None,
**kwargs,
) -> int:
"""Create :class:`ProcessMDOut <process.process_mdout.ProcessMDOut>`process.process_mdout.ProcessMDOut class and
execute :meth:`launch() <process.process_mdout.ProcessMDOut.launch>` method"""
return ProcessMDOut(
input_log_path=input_log_path,
output_dat_path=output_dat_path,
properties=properties,
).launch()
process_mdout.__doc__ = ProcessMDOut.__doc__
[docs]
def main():
parser = argparse.ArgumentParser(
description="Parses the AMBER (sander) MD output file (log) and dumps statistics that can then be plotted. Using the process_mdout.pl 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_log_path",
required=True,
help="AMBER (sander) MD output (log) file. Accepted formats: log, out, txt, o.",
)
required_args.add_argument(
"--output_dat_path",
required=True,
help="Dat output file containing data from the specified terms along the MD process. File type: output. Accepted formats: dat, txt, csv.",
)
args = parser.parse_args()
config = args.config if args.config else None
properties = settings.ConfReader(config=config).get_prop_dic()
# Specific call
process_mdout(
input_log_path=args.input_log_path,
output_dat_path=args.output_dat_path,
properties=properties,
)
if __name__ == "__main__":
main()