Source code for pcasuite.pcz_stiffness

#!/usr/bin/env python3

"""Module containing the PCZstiffness class and the command line interface."""
import argparse
from typing import Optional
import shutil
import json
import math
from pathlib import PurePath
from biobb_common.tools import file_utils as fu
from biobb_common.generic.biobb_object import BiobbObject
from biobb_common.configuration import settings
from biobb_common.tools.file_utils import launchlogger


[docs] class PCZstiffness(BiobbObject): """ | biobb_flexserv PCZstiffness | Extract PCA stiffness from a compressed PCZ file. | Wrapper of the pczdump tool from the PCAsuite FlexServ module. Args: input_pcz_path (str): Input compressed trajectory file. File type: input. `Sample file <https://github.com/bioexcel/biobb_flexserv/raw/master/biobb_flexserv/test/data/pcasuite/pcazip.pcz>`_. Accepted formats: pcz (edam:format_3874). output_json_path (str): Output json file with PCA Stiffness. File type: output. `Sample file <https://github.com/bioexcel/biobb_flexserv/raw/master/biobb_flexserv/test/reference/pcasuite/pcz_stiffness.json>`_. Accepted formats: json (edam:format_3464). properties (dict - Python dictionary object containing the tool parameters, not input/output files): * **binary_path** (*str*) - ("pczdump") pczdump binary path to be used. * **eigenvector** (*int*) - (0) PCA mode (eigenvector) from which to extract stiffness. * **temperature** (*int*) - (300) Temperature with which compute the apparent stiffness. * **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. Examples: This is a use example of how to use the building block from Python:: from biobb_flexserv.pcasuite.pcz_stiffness import pcz_stiffness prop = { 'eigenvector': 1 } pcz_stiffness( input_pcz_path='/path/to/pcazip_input.pcz', output_json_path='/path/to/pcz_stiffness.json', properties=prop) Info: * wrapped_software: * name: FlexServ PCAsuite * version: >=1.0 * license: Apache-2.0 * ontology: * name: EDAM * schema: http://edamontology.org/EDAM.owl """ def __init__(self, input_pcz_path: str, output_json_path: str, properties: Optional[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_pcz_path': input_pcz_path}, 'out': {'output_json_path': output_json_path} } # Properties specific for BB self.properties = properties self.binary_path = properties.get('binary_path', 'pczdump') self.eigenvector = properties.get('eigenvector', 0) self.temperature = properties.get('temperature', 300) # Check the properties self.check_properties(properties) self.check_arguments()
[docs] @launchlogger def launch(self): """Launches the execution of the FlexServ pcz_stiffness module.""" # Setup Biobb if self.check_restart(): return 0 # self.stage_files() # Internal file paths # try: # # Using rel paths to shorten the amount of characters due to fortran path length limitations # input_pcz = str(Path(self.stage_io_dict["in"]["input_pcz_path"]).relative_to(Path.cwd())) # output_json = str(Path(self.stage_io_dict["out"]["output_json_path"]).relative_to(Path.cwd())) # except ValueError: # # Container or remote case # input_pcz = self.stage_io_dict["in"]["input_pcz_path"] # output_json = self.stage_io_dict["out"]["output_json_path"] # Manually creating a Sandbox to avoid issues with input parameters buffer overflow: # Long strings defining a file path makes Fortran or C compiled programs crash if the string # declared is shorter than the input parameter path (string) length. # Generating a temporary folder and working inside this folder (sandbox) fixes this problem. # The problem was found in Galaxy executions, launching Singularity containers (May 2023). # Creating temporary folder self.tmp_folder = fu.create_unique_dir() fu.log('Creating %s temporary folder' % self.tmp_folder, self.out_log) shutil.copy2(self.io_dict["in"]["input_pcz_path"], self.tmp_folder) # Temporary output # temp_out = str(Path(self.stage_io_dict.get("unique_dir", "")).joinpath("output.dat")) temp_out = "output.dat" temp_json = "output.json" # Command line # pczdump -i structure.ca.std.pcz --stiffness -o pcz.stiffness # self.cmd = [self.binary_path, # "-i", input_pcz, # "-o", temp_out, # "--stiff={}".format(self.eigenvector), # "--temperature={}".format(self.temperature) # ] self.cmd = ['cd', self.tmp_folder, ';', self.binary_path, "-i", PurePath(self.io_dict["in"]["input_pcz_path"]).name, "-o", temp_out, "--stiff={}".format(self.eigenvector), "--temperature={}".format(self.temperature) ] # Run Biobb block self.run_biobb() # Parse output stiffness info_dict = {} info_dict['stiffness'] = [] info_dict['stiffness_log'] = [] row = 0 with open(PurePath(self.tmp_folder).joinpath(temp_out), 'r') as file: for line in file: info = line.strip().split(',') line_array = [] line_array_log = [] for nums in info: if nums: line_array.append(float(nums)) if float(nums) != 0: line_array_log.append(math.log10(float(nums))) else: line_array_log.append(float(nums)) info_dict['stiffness'].append(line_array) info_dict['stiffness'][row][row] = float('inf') info_dict['stiffness_log'].append(line_array_log) info_dict['stiffness_log'][row][row] = float('inf') row += 1 with open(PurePath(self.tmp_folder).joinpath(temp_json), 'w') as out_file: out_file.write(json.dumps(info_dict, indent=4)) # Copy outputs from temporary folder to output path shutil.copy2(PurePath(self.tmp_folder).joinpath(temp_json), PurePath(self.io_dict["out"]["output_json_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.tmp_folder ]) self.remove_tmp_files() self.check_arguments(output_files_created=True, raise_exception=False) return self.return_code
[docs] def pcz_stiffness(input_pcz_path: str, output_json_path: str, properties: Optional[dict] = None, **kwargs) -> int: """Create :class:`PCZstiffness <flexserv.pcasuite.pcz_stiffness>`flexserv.pcasuite.PCZstiffness class and execute :meth:`launch() <flexserv.pcasuite.pcz_stiffness.launch>` method""" return PCZstiffness(input_pcz_path=input_pcz_path, output_json_path=output_json_path, properties=properties).launch()
[docs] def main(): parser = argparse.ArgumentParser(description='Extract PCA Stiffness from a compressed PCZ file.', 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_pcz_path', required=True, help='Input compressed trajectory file. Accepted formats: pcz.') required_args.add_argument('--output_json_path', required=True, help='Output json file with PCA stiffness. Accepted formats: json.') args = parser.parse_args() args.config = args.config or "{}" properties = settings.ConfReader(config=args.config).get_prop_dic() # Specific call pcz_stiffness(input_pcz_path=args.input_pcz_path, output_json_path=args.output_json_path, properties=properties)
if __name__ == '__main__': main()