Source code for process.process_minout

#!/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 import file_utils as fu
from 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 <>`_ module. | Parses the AMBER (sander) minimization output file (log) and dumps statistics that can then be plotted. Using the tool from the AmberTools MD package. Args: input_log_path (str): AMBER (sander) Minimization output (log) file. File type: input. `Sample file <>`_. 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 <>`_. 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: """ 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 = 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 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()