#!/usr/bin/env python3
"""Module containing the PCZlindemann class and the command line interface."""
import argparse
import shutil
import json
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 PCZlindemann(BiobbObject):
"""
| biobb_flexserv PCZlindemann
| Extract Lindemann coefficient (an estimate of the solid-liquid behaviour of a protein) 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 Eigen Vectors. File type: output. `Sample file <https://github.com/bioexcel/biobb_flexserv/raw/master/biobb_flexserv/test/reference/pcasuite/pcz_lindemann.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.
* **mask** (*str*) - ("all atoms") Residue mask, in the format ":resnum1, resnum2, resnum3" (e.g. ":10,21,33"). See https://mmb.irbbarcelona.org/software/pcasuite/ for the complete format specification.
* **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
* **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
Examples:
This is a use example of how to use the building block from Python::
from biobb_flexserv.pcasuite.pcz_lindemann import pcz_lindemann
prop = {
'mask': ':10,12,15'
}
pcz_lindemann( input_pcz_path='/path/to/pcazip_input.pcz',
output_json_path='/path/to/lindemann_report.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: 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.mask = properties.get('mask', '')
# Check the properties
self.check_properties(properties)
self.check_arguments()
[docs] @launchlogger
def launch(self):
"""Launches the execution of the FlexServ pcz_lindemann 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 --lindemann -M ":2-86" -o lindemann_report.txt
# self.cmd = [self.binary_path,
# "-i", input_pcz,
# "-o", temp_out,
# "--lindemann"
# ]
self.cmd = ['cd', self.tmp_folder, ';',
self.binary_path,
"-i", PurePath(self.io_dict["in"]["input_pcz_path"]).name,
"-o", temp_out,
"--lindemann"
]
if self.mask:
self.cmd.append("-M {}".format(self.mask))
# Run Biobb block
self.run_biobb()
# Parse output Lindemann
# 0.132891
info_dict = {}
with open(PurePath(self.tmp_folder).joinpath(temp_out), 'r') as file:
for line in file:
info = float(line.strip())
info_dict['lindemann'] = info
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_lindemann(input_pcz_path: str, output_json_path: str,
properties: dict = None, **kwargs) -> int:
"""Create :class:`PCZlindemann <flexserv.pcasuite.pcz_lindemann>`flexserv.pcasuite.PCZlindemann class and
execute :meth:`launch() <flexserv.pcasuite.pcz_lindemann.launch>` method"""
return PCZlindemann(input_pcz_path=input_pcz_path,
output_json_path=output_json_path,
properties=properties).launch()
[docs]def main():
parser = argparse.ArgumentParser(description='Extract Lindemann coefficients 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 Lindemann coefficient report. Accepted formats: json.')
args = parser.parse_args()
args.config = args.config or "{}"
properties = settings.ConfReader(config=args.config).get_prop_dic()
# Specific call
pcz_lindemann(input_pcz_path=args.input_pcz_path,
output_json_path=args.output_json_path,
properties=properties)
if __name__ == '__main__':
main()