#!/usr/bin/env python3
"""Module containing the PCZhinges class and the command line interface."""
import argparse
import shutil
import json
import re
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 PCZhinges(BiobbObject):
"""
| biobb_flexserv PCZhinges
| Compute possible hinge regions (residues around which large protein movements are organized) of a molecule 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 hinge regions x PCA mode file. File type: output. `Sample file <https://github.com/bioexcel/biobb_flexserv/raw/master/biobb_flexserv/test/reference/pcasuite/hinges.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 bfactor values per residue (0 means average over all modes).
* **method** (*str*) - ("Dynamic_domain") Method to compute the hinge regions (Options: Bfactor_slope, Force_constant, Dynamic_domain)
* **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_hinges import pcz_hinges
prop = {
'eigenvector': 1,
'pdb': True
}
pcz_hinges( input_pcz_path='/path/to/pcazip_input.pcz',
output_json_path='/path/to/hinges.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.eigenvector = properties.get('eigenvector', 1)
self.method = properties.get('method', "Bfactor_slope")
# Check the properties
self.check_properties(properties)
self.check_arguments()
[docs] def parse_output(self, output_file):
""" Parses FlexServ hinges methods output file report """
method = ''
if self.method == "Bfactor_slope":
method = "#### Distance variation method"
elif self.method == "Force_constant":
method = "#### Force constant"
elif self.method == "Dynamic_domain":
method = "#### Lavery method"
else:
print("Method not recognised ({}), please check it and try again. ".format(self.method))
start = False
out_data = ''
with open(output_file, 'r') as file:
for line in file:
if method in line:
start = True
elif "####" in line:
start = False
if start:
out_data += line
dict_out = {}
dict_out["method"] = self.method
if self.method == "Force_constant":
dict_out["values_per_residue"] = []
for line in out_data.split("\n"):
if line and "#" not in line:
dict_out["values_per_residue"].append(float(line.strip()))
if "possible hinge" in line: # Peak constant (possible hinge): residue 64 (16.740)
residue = int(line.split(' ')[6])
dict_out["hinge_residues"] = residue
elif self.method == "Bfactor_slope":
dict_out["hinge_residues"] = []
for line in out_data.split("\n"):
if "Window" in line: # Window 28: residue 54 seems a downhill hinge point
residue = int(re.split(r'\s+', line)[3])
dict_out["hinge_residues"].append(residue)
if "Consensus" in line: # Consensus Downhill hinge point : 23.7 ( 64.965)
hinge_point = float(line.split(':')[1].split('(')[0])
dict_out["consensus_hinge"] = hinge_point
elif self.method == "Dynamic_domain":
start = 0
dict_out["clusters"] = []
for line in out_data.split("\n"):
if "threshold" not in line and "nClusters" in line: # nClusters: 2
nclusters = int(line.split(':')[1])
dict_out["nClusters"] = nclusters
if "Threshold" in line: # *** Threshold defined: 0.300000
threshold = float(line.split(':')[1])
dict_out["threshold"] = threshold
if "Min. drij" in line: # *** Min. drij: 0.000322
minValue = float(line.split(':')[1])
dict_out["minValue"] = minValue
if "Max. drij" in line: # *** Max. drij: 6.385425
maxValue = float(line.split(':')[1])
dict_out["maxValue"] = maxValue
if "threshold" in line: # nClusters: 2 threshold: 3.192873
final_threshold = float(line.split(':')[2])
dict_out["final_threshold"] = final_threshold
if "Cluster" in line and "elements" in line: # Cluster 0 (74 elements)
clusterLine = line.split()
clusterNum = int(clusterLine[1])
clusterElems = int(clusterLine[2].replace('(', ''))
cluster = {"clusterNum": clusterNum, "clusterElems": clusterElems}
dict_out["clusters"].append(cluster)
start = start + 1
if start and "[" in line:
# dict_out["clusters"][start-1]["residues"] = list(map(int,list(line.replace(", ]", "").replace(" [","").split(', '))))
dict_out["clusters"][start-1]["residues"] = eval(line)
# Interacting regions: 13 14 30 31 69 70 84 85 112 113 114 115 116 166 167 199 200
if "Interacting regions" in line:
nums = line.split(':')[1]
dict_out["interacting_regions"] = list(map(int, nums.split()))
# Hinge residues: 13 14 30 31 69 70 84 85 112 113 114 115 116 166 167 199 200
if "Hinge residues" in line:
nums = line.split(':')[1]
dict_out["hinge_residues"] = list(map(int, nums.split()))
return dict_out
[docs] @launchlogger
def launch(self):
"""Launches the execution of the FlexServ pcz_hinges 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_log = "output.log"
temp_json = "output.json"
# Command line (1: dat file)
# pczdump -i structure.ca.std.pcz --fluc=1 -o bfactor_1.dat
# self.cmd = [self.binary_path,
# "-i", input_pcz,
# "-o", temp_out,
# "-t", "0.3",
# "--hinge={}".format(self.eigenvector),
# ">&", "pcz_dump.hinges.log"
# ]
self.cmd = ['cd', self.tmp_folder, ';',
self.binary_path,
'-i', PurePath(self.io_dict["in"]["input_pcz_path"]).name,
'-o', temp_out,
"-t", "0.3",
"--hinge={}".format(self.eigenvector),
">&", temp_log
]
# Run Biobb block
self.run_biobb()
# Parsing output file and extracting results for the given method
dict_out = self.parse_output(PurePath(self.tmp_folder).joinpath(temp_out))
with open(PurePath(self.tmp_folder).joinpath(temp_json), 'w') as out_file:
out_file.write(json.dumps(dict_out, 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_hinges(input_pcz_path: str, output_json_path: str,
properties: dict = None, **kwargs) -> int:
"""Create :class:`PCZhinges <flexserv.pcasuite.pcz_hinges>`flexserv.pcasuite.PCZhinges class and
execute :meth:`launch() <flexserv.pcasuite.pcz_hinges.launch>` method"""
return PCZhinges(input_pcz_path=input_pcz_path,
output_json_path=output_json_path,
properties=properties).launch()
[docs]def main():
parser = argparse.ArgumentParser(description='Compute possible hinge regions (residues around which large protein movements are organized) of a molecule 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 hinge regions x PCA mode file. Accepted formats: json.')
args = parser.parse_args()
args.config = args.config or "{}"
properties = settings.ConfReader(config=args.config).get_prop_dic()
# Specific call
pcz_hinges(input_pcz_path=args.input_pcz_path,
output_json_path=args.output_json_path,
properties=properties)
if __name__ == '__main__':
main()