#!/usr/bin/env python3
"""Module containing the PMX analyse class and the command line interface."""
import argparse
from pathlib import Path
import shutil
from typing import Mapping
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
[docs]class Pmxanalyse(BiobbObject):
"""
| biobb_pmx Pmxanalyse
| Wrapper class for the `PMX analyse <https://github.com/deGrootLab/pmx>`_ module.
Args:
input_a_xvg_zip_path (str): Path the zip file containing the dgdl.xvg files of the A state. File type: input. `Sample file <https://github.com/bioexcel/biobb_pmx/raw/master/biobb_pmx/test/data/pmx/xvg_A.zip>`_. Accepted formats: zip (edam:format_3987).
input_b_xvg_zip_path (str): Path the zip file containing the dgdl.xvg files of the B state. File type: input. `Sample file <https://github.com/bioexcel/biobb_pmx/raw/master/biobb_pmx/test/data/pmx/xvg_B.zip>`_. Accepted formats: zip (edam:format_3987).
output_result_path (str): Path to the TXT results file. File type: output. `Sample file <https://github.com/bioexcel/biobb_pmx/raw/master/biobb_pmx/test/reference/pmx/ref_result.txt>`_. Accepted formats: txt (edam:format_2330).
output_work_plot_path (str): Path to the PNG plot results file. File type: output. `Sample file <https://github.com/bioexcel/biobb_pmx/raw/master/biobb_pmx/test/reference/pmx/ref_plot.png>`_. Accepted formats: png (edam:format_3603).
properties (dic):
* **method** (*str*) - ("CGI BAR JARZ") Choose one or more estimators to use. Values: CGI (Crooks Gaussian Intersection), BAR (Bennet Acceptance Ratio), JARZ (Jarzynski's estimator).
* **temperature** (*float*) - (298.15) [0~1000|0.05] Temperature in Kelvin.
* **nboots** (*int*) - (0) [0~1000|1] Number of bootstrap samples to use for the bootstrap estimate of the standard errors.
* **nblocks** (*int*) - (1) [0~1000|1] Number of blocks to divide the data into for an estimate of the standard error.
* **integ_only** (*bool*) - (False) Whether to do integration only.
* **reverseB** (*bool*) - (False) Whether to reverse the work values for the backward (B->A) transformation.
* **skip** (*int*) - (1) [0~1000|1] Skip files.
* **slice** (*str*) - (None) Subset of trajectories to analyze. Provide list slice, e.g. "10 50" will result in selecting dhdl_files[10:50].
* **rand** (*int*) - (None) [0~1000|1] Take a random subset of trajectories. Default is None (do not take random subset).
* **index** (*str*) - (None) Zero-based index of files to analyze (e.g. "0 10 20 50 60"). It keeps the dhdl.xvg files according to their position in the list, sorted according to the filenames.
* **prec** (*int*) - (2) [0~100|1] The decimal precision of the screen/file output.
* **units** (*str*) - ("kJ") The units of the output. Values: kJ (Kilojoules), kcal (Kilocalories), kT (the product of the Boltzmann constant k and the temperature).
* **no_ks** (*bool*) - (False) Whether to do a Kolmogorov-Smirnov test to check whether the Gaussian assumption for CGI holds.
* **nbins** (*int*) - (20) [0~1000|1] Number of histograms bins for the plot.
* **dpi** (*int*) - (300) [72~2048|1] Resolution of the plot.
* **binary_path** (*str*) - ("pmx") Path to the PMX command line interface.
* **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) Path to the binary executable of your container.
* **container_image** (*str*) - ("gromacs/gromacs:latest") Container Image identifier.
* **container_volume_path** (*str*) - ("/data") Path to an internal directory in the container.
* **container_working_dir** (*str*) - (None) Path to the internal CWD in the container.
* **container_user_id** (*str*) - (None) User number id to be mapped inside the container.
* **container_shell_path** (*str*) - ("/bin/bash") Path to the binary executable of the container shell.
Examples:
This is a use example of how to use the building block from Python::
from biobb_pmx.pmxbiobb.pmxanalyse import pmxanalyse
prop = {
'method': 'CGI BAR JARZ',
'temperature': 298.15,
'dpi': 600
}
pmxanalyse(input_a_xvg_zip_path='/path/to/myAStateFiles.zip',
input_b_xvg_zip_path='/path/to/myBStateFiles.zip',
output_result_path='/path/to/newResults.txt',
output_work_plot_path='/path/to/newResults.png',
properties=prop)
Info:
* wrapped_software:
* name: PMX analyse
* version: >=1.0.1
* license: GNU
* ontology:
* name: EDAM
* schema: http://edamontology.org/EDAM.owl
"""
def __init__(self, input_a_xvg_zip_path: str, input_b_xvg_zip_path: str, output_result_path: str, output_work_plot_path: str,
properties: Mapping = 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": {},
"out": {"output_result_path": output_result_path, "output_work_plot_path": output_work_plot_path}
}
# Should not be copied inside container
self.input_a_xvg_zip_path = input_a_xvg_zip_path
self.input_b_xvg_zip_path = input_b_xvg_zip_path
# Properties specific for BB
self.method = properties.get('method', "CGI BAR JARZ")
self.temperature = properties.get('temperature', 298.15)
self.nboots = properties.get('nboots', 0)
self.nblocks = properties.get('nblocks', 1)
self.integ_only = properties.get('integ_only', False)
self.reverseB = properties.get('reverseB', False)
self.skip = properties.get('skip', 1)
self.slice = properties.get('slice', None)
self.rand = properties.get('rand', None)
self.index = properties.get('index', None)
self.prec = properties.get('prec', 2)
self.units = properties.get('units', "kJ")
self.no_ks = properties.get('no_ks', False)
self.nbins = properties.get('nbins', 20)
self.dpi = properties.get('dpi', 300)
# Properties common in all PMX BB
self.binary_path = properties.get('binary_path', 'pmx')
# Check the properties
self.check_properties(properties)
self.check_arguments()
[docs] @launchlogger
def launch(self) -> int:
"""Execute the :class:`Pmxanalyse <pmx.pmxanalyse.Pmxanalyse>` pmx.pmxanalyse.Pmxanalyse object."""
# Setup Biobb
if self.check_restart():
return 0
self.stage_files()
# Check if executable is exists
if not self.container_path:
if not Path(self.binary_path).is_file():
if not shutil.which(self.binary_path):
raise FileNotFoundError(
'Executable %s not found. Check if it is installed in your system and correctly defined in the properties' % self.binary_path)
list_a_dir = fu.create_unique_dir()
list_b_dir = fu.create_unique_dir()
list_a = list(filter(lambda f: Path(f).exists() and Path(f).stat().st_size > 10, fu.unzip_list(self.input_a_xvg_zip_path, list_a_dir, self.out_log)))
list_b = list(filter(lambda f: Path(f).exists() and Path(f).stat().st_size > 10, fu.unzip_list(self.input_b_xvg_zip_path, list_b_dir, self.out_log)))
string_a = " ".join(list_a)
string_b = " ".join(list_b)
# Copy extra files to container: two directories containing the xvg files
if self.container_path:
shutil.copytree(list_a_dir, Path(self.stage_io_dict.get("unique_dir")).joinpath(Path(list_a_dir).name))
shutil.copytree(list_b_dir, Path(self.stage_io_dict.get("unique_dir")).joinpath(Path(list_b_dir).name))
container_volume = " " + self.container_volume_path + "/"
string_a = self.container_volume_path + "/" + container_volume.join(list_a)
string_b = self.container_volume_path + "/" + container_volume.join(list_b)
self.cmd = [self.binary_path, 'analyse',
'-fA', string_a,
'-fB', string_b,
'-o', self.stage_io_dict["out"]["output_result_path"],
'-w', self.stage_io_dict["out"]["output_work_plot_path"]]
if self.method:
self.cmd.append('-m')
self.cmd.append(self.method)
if self.temperature:
self.cmd.append('-t')
self.cmd.append(str(self.temperature))
if self.nboots:
self.cmd.append('-b')
self.cmd.append(str(self.nboots))
if self.nblocks:
self.cmd.append('-n')
self.cmd.append(str(self.nblocks))
if self.integ_only:
self.cmd.append('--integ_only')
if self.reverseB:
self.cmd.append('--reverseB')
if self.skip:
self.cmd.append('--skip')
self.cmd.append(str(self.skip))
if self.slice:
self.cmd.append('--slice')
self.cmd.append(self.slice)
if self.rand:
self.cmd.append('--rand')
if self.index:
self.cmd.append('--index')
self.cmd.append(self.index)
if self.prec:
self.cmd.append('--prec')
self.cmd.append(str(self.prec))
if self.units:
self.cmd.append('--units')
self.cmd.append(self.units)
if self.no_ks:
self.cmd.append('--no_ks')
if self.nbins:
self.cmd.append('--nbins')
self.cmd.append(str(self.nbins))
if self.dpi:
self.cmd.append('--dpi')
self.cmd.append(str(self.dpi))
# Run Biobb block
self.run_biobb()
# Copy files to host
self.copy_to_host()
self.tmp_files.extend([self.stage_io_dict.get("unique_dir"), list_a_dir, list_b_dir])
self.remove_tmp_files()
self.check_arguments(output_files_created=True, raise_exception=False)
return self.return_code
[docs]def pmxanalyse(input_a_xvg_zip_path: str, input_b_xvg_zip_path: str,
output_result_path: str, output_work_plot_path: str,
properties: dict = None, **kwargs) -> int:
"""Execute the :class:`Pmxanalyse <pmx.pmxanalyse.Pmxanalyse>` class and
execute the :meth:`launch() <pmx.pmxanalyse.Pmxanalyse.launch> method."""
return Pmxanalyse(input_a_xvg_zip_path=input_a_xvg_zip_path,
input_b_xvg_zip_path=input_b_xvg_zip_path,
output_result_path=output_result_path,
output_work_plot_path=output_work_plot_path,
properties=properties).launch()
[docs]def main():
"""Command line execution of this building block. Please check the command line documentation."""
parser = argparse.ArgumentParser(description="Wrapper class for the PMX analyse module.",
formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999))
parser.add_argument('-c', '--config', required=False,
help="This file can be a YAML file, JSON file or JSON string")
# Specific args of each building block
required_args = parser.add_argument_group('required arguments')
required_args.add_argument('--input_a_xvg_zip_path', required=True,
help="Path the zip file containing the dgdl.xvg files of the A state. Accepted formats: zip.")
required_args.add_argument('--input_b_xvg_zip_path', required=True,
help="Path the zip file containing the dgdl.xvg files of the B state. Accepted formats: zip.")
required_args.add_argument('--output_result_path', required=True, help="Path to the TXT results file. Accepted formats: txt.")
required_args.add_argument('--output_work_plot_path', required=True, help="Path to the PNG plot results file. Accepted formats: png.")
args = parser.parse_args()
config = args.config if args.config else None
properties = settings.ConfReader(config=config).get_prop_dic()
# Specific call of each building block
pmxanalyse(input_a_xvg_zip_path=args.input_a_xvg_zip_path,
input_b_xvg_zip_path=args.input_b_xvg_zip_path,
output_result_path=args.output_result_path,
output_work_plot_path=args.output_work_plot_path,
properties=properties)
if __name__ == '__main__':
main()