#!/usr/bin/env python3
"""Module containing the ProcessMinOut class and the command line interface."""
import argparse
import shutil
from pathlib import Path, PurePath
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.process.common import check_input_path, check_output_path
[docs]class ProcessMinOut(BiobbObject):
"""
| biobb_amber.process.process_minout ProcessMinOut
| Wrapper of the `AmberTools (AMBER MD Package) process_minout tool <https://ambermd.org/AmberTools.php>`_ module.
| Parses the AMBER (sander) minimization output file (log) and dumps statistics that can then be plotted. Using the process_minout.pl tool from the AmberTools MD package.
Args:
input_log_path (str): AMBER (sander) Minimization output (log) file. File type: input. `Sample file <https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/data/process/sander.min.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.min.energy.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*) - (["ENERGY"]) Statistics descriptors. Values: ANGLE, BOND, DIHEDRAL, EEL, EEL14, ENERGY, GMAX, HBOND, NAME, NSTEP, NUMBER, RESTRAINT, RMS, VDW14, VDWAALS.
* **binary_path** (*str*) - ("process_minout.perl") Path to the process_minout.perl 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.process.process_minout import process_minout
prop = {
'terms' : ['ENERGY','RMS']
}
process_minout(input_log_path='/path/to/ambermin.log',
output_dat_path='/path/to/newFeature.dat',
properties=prop)
Info:
* wrapped_software:
* name: AmberTools process_minout
* 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 = properties.get('terms', ["ENERGY"])
self.binary_path = properties.get('binary_path', 'process_minout.perl')
# 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_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 ProcessMinOut 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(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(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"),
list(Path().glob('summary*')),
self.tmp_folder
])
self.remove_tmp_files()
self.check_arguments(output_files_created=True, raise_exception=False)
return self.return_code
[docs]def process_minout(input_log_path: str, output_dat_path: str,
properties: dict = None, **kwargs) -> int:
"""Create :class:`ProcessMinOut <process.process_mdout.ProcessMinOut>`process.process_mdout.ProcessMinOut class and
execute :meth:`launch() <process.process_mdout.ProcessMinOut.launch>` method"""
return ProcessMinOut(input_log_path=input_log_path,
output_dat_path=output_dat_path,
properties=properties).launch()
[docs]def main():
parser = argparse.ArgumentParser(description='Parses the AMBER (sander) minimization output file (log) and dumps statistics that can then be plotted. Using the process_minout.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) minimization 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 minimization 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_minout(input_log_path=args.input_log_path,
output_dat_path=args.output_dat_path,
properties=properties)
if __name__ == '__main__':
main()