#!/usr/bin/env python3
"""Module containing the Curves class and the command line interface."""
import os
import zipfile
from typing import Optional
import shutil
from pathlib import Path
from biobb_common.generic.biobb_object import BiobbObject
from biobb_common.tools import file_utils as fu
from biobb_common.tools.file_utils import launchlogger
[docs]
class Curves(BiobbObject):
"""
| biobb_dna Curves
| Wrapper for the Cur+ executable that is part of the Curves+ software suite.
| The Cur+ program is used to analyze the structure of nucleic acids and their complexes.
Args:
input_struc_path (str): Trajectory or PDB input file. File type: input. `Sample file <https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/curvesplus/structure.stripped.trj>`_. Accepted formats: trj (edam:format_3910), pdb (edam:format_1476), netcdf (edam:format_3650), nc (edam:format_3650).
input_top_path (str) (Optional): Topology file, needed along with .trj file (optional). File type: input. `Sample file <https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/curvesplus/structure.stripped.top>`_. Accepted formats: top (edam:format_3881), pdb (edam:format_1476).
output_cda_path (str): Filename for Curves+ output .cda file. File type: output. `Sample file <https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/reference/curvesplus/curves_trj_output.cda>`_. Accepted formats: cda (edam:format_2330).
output_lis_path (str): Filename for Curves+ output .lis file. File type: output. `Sample file <https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/reference/curvesplus/curves_trj_output.lis>`_. Accepted formats: lis (edam:format_2330).
output_zip_path (str) (Optional): Filename for .zip files containing Curves+ output that is not .cda or .lis files. File type: output. `Sample file <https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/reference/curvesplus/curves_trj_output.zip>`_. Accepted formats: zip (edam:format_3987).
properties (dict):
* **s1range** (*str*) - (None) Range of first strand. Must be specified in the form "start:end".
* **s2range** (*str*) - (None) Range of second strand. Must be specified in the form "start:end".
* **stdlib_path** (*str*) - ('standard') Path to Curves' standard library files for nucleotides. If not specified will look for 'standard' files in current directory.
* **itst** (*int*) - (0) Iteration start index.
* **itnd** (*int*) - (0) Iteration end index.
* **itdel** (*int*) - (1) Iteration delimiter.
* **ions** (*bool*) - (False) If True, helicoidal analysis of ions (or solvent molecules) around solute is carried out.
* **test** (*bool*) - (False) If True, provide addition output in .lis file on fitting and axis generation.
* **line** (*bool*) - (False) if True, find the best linear helical axis.
* **fit** (*bool*) - (True) if True, fit a standard bases to the input coordinates (important for MD snapshots to avoid base distortions leading to noisy helical parameters).
* **axfrm** (*bool*) - (False) if True, generates closely spaced helical axis frames as input for Canal and Canion.
* **binary_path** (*str*) - (Cur+) Path to Curves+ executable, otherwise the program wil look for Cur+ executable in the binaries folder.
* **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_dna.curvesplus.biobb_curves import biobb_curves
prop = {
's1range': '1:12',
's2range': '24:13',
}
biobb_curves(
input_struc_path='/path/to/structure/file.trj',
input_top_path='/path/to/topology/file.top',
output_cda_path='/path/to/output/file.cda',
output_lis_path='/path/to/output/file.lis',
properties=prop)
Info:
* wrapped_software:
* name: Curves
* version: >=2.6
* license: BSD 3-Clause
* ontology:
* name: EDAM
* schema: http://edamontology.org/EDAM.owl
"""
def __init__(
self, input_struc_path, output_lis_path,
output_cda_path, output_zip_path=None,
input_top_path=None, properties=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_struc_path': input_struc_path,
'input_top_path': input_top_path
},
'out': {
'output_lis_path': output_lis_path,
'output_cda_path': output_cda_path,
'output_zip_path': output_zip_path
}
}
# Properties specific for BB
self.s1range = properties.get('s1range', None)
self.binary_path = properties.get('binary_path', 'Cur+')
self.stdlib_path = properties.get('stdlib_path', None)
self.s2range = properties.get('s2range', None)
self.itst = properties.get('itst', 0)
self.itnd = properties.get('itnd', 0)
self.itdel = properties.get('itdel', 1)
self.ions = ".t." if properties.get('ions', False) else ".f."
self.test = ".t." if properties.get('test', False) else ".f."
self.line = ".t." if properties.get('line', False) else ".f."
self.fit = ".t." if properties.get('fit', True) else ".f."
self.axfrm = ".t." if properties.get('axfrm', False) else ".f."
self.properties = properties
# Check the properties
self.check_properties(properties)
self.check_arguments()
[docs]
def create_curvesplus_folder(self):
"""Create .curvesplus folder in the current temporal folder and copy the lib files inside."""
# Create .curvesplus directory in temporary folder
dst_dir = self.stage_io_dict.get("unique_dir", "") + '/.curvesplus'
os.makedirs(dst_dir, exist_ok=True)
# Get lib files from stdlib_path
lib_files = list(Path(os.path.dirname(self.stdlib_path)).glob("*.lib"))
# Copy each lib file to the .curvesplus directory in temporary folder
for file in lib_files:
shutil.copy(file, dst_dir)
[docs]
@launchlogger
def launch(self) -> int:
"""Execute the :class:`Curves <biobb_dna.curvesplus.biobb_curves.Curves>` object."""
# Setup Biobb
if self.check_restart():
return 0
self.stage_files()
if self.s1range is None:
raise ValueError("property 's1range' must be specified!")
if self.s2range is None:
# compute s2range if not provided
range1_end = int(self.s1range.split(":")[1])
s2start = range1_end + 1
s2end = 2 * range1_end
self.s2range = f"{s2end}:{s2start}"
# check standard library files location if not provided
if self.stdlib_path is None:
if os.getenv("CONDA_PREFIX", False):
curves_aux_path = Path(
os.getenv("CONDA_PREFIX", "")) / ".curvesplus"
# check if .curvesplus directory is in $CONDA_PREFIX
if curves_aux_path.exists():
if len(list(curves_aux_path.glob("standard_*.lib"))) != 3:
raise FileNotFoundError(
"One or all standard library files "
f"missing from {curves_aux_path}! "
"Check files standard_b.lib, "
"standard_s.lib and standard_i.lib exist.")
self.stdlib_path = curves_aux_path / "standard"
else:
raise FileNotFoundError(
".curvesplus directory not found in "
f"{os.getenv('CONDA_PREFIX')} !"
"Please indicate where standard_*.lib files are "
"located with the stdlib_path property.")
# copy standard library files to temporary folder
shutil.copytree(curves_aux_path, self.stage_io_dict.get("unique_dir", "") + '/.curvesplus')
relative_lib_path = '.curvesplus/standard'
else:
# CONDA_PREFIX undefined
fu.log('CONDA_PREFIX undefined, please put the standard_b.lib, standard_s.lib and standard_i.lib files in the current working directory', self.out_log)
self.stdlib_path = Path.cwd() / "standard"
# create .curvesplus folder in the current temporal folder and copy the lib files inside
self.create_curvesplus_folder()
# set relative path
relative_lib_path = '.curvesplus/standard'
else:
# create .curvesplus folder in the current temporal folder and copy the lib files inside
self.create_curvesplus_folder()
# set relative path
path_parts = str(self.stdlib_path).split(os.sep)
relative_lib_path = '.curvesplus/' + os.sep.join(path_parts[-1:])
# change directory to temporary folder
original_directory = os.getcwd()
os.chdir(self.stage_io_dict.get("unique_dir", ""))
# define temporary file names
tmp_struc_input = Path(self.stage_io_dict['in']['input_struc_path']).name
if self.stage_io_dict['in']['input_top_path'] is not None:
tmp_top_input = Path(self.stage_io_dict['in']['input_top_path']).name
# create intructions
instructions = [
f"{self.binary_path} <<! ",
"&inp",
f" file={tmp_struc_input},"]
if self.stage_io_dict['in']['input_top_path'] is not None:
# add topology file if needed
fu.log('Appending provided topology to command',
self.out_log, self.global_log)
instructions.append(
f" ftop={tmp_top_input},")
# create intructions
instructions = instructions + [
" lis='curves_output',",
f" lib={relative_lib_path},",
f" ions={self.ions},",
f" test={self.test},",
f" line={self.line},",
f" fit={self.fit},",
f" axfrm={self.axfrm},",
f" itst={self.itst},itnd={self.itnd},itdel={self.itdel},",
"&end",
"2 1 -1 0 0",
f"{self.s1range}",
f"{self.s2range}",
"!"
]
self.cmd = ["\n".join(instructions)]
fu.log('Creating command line with instructions and required arguments',
self.out_log, self.global_log)
# Run Biobb block
self.run_biobb()
# change back to original directory
os.chdir(original_directory)
# create zipfile and write output inside
if self.stage_io_dict.get("out", {}).get("output_zip_path") is not None:
zf = zipfile.ZipFile(
Path(self.stage_io_dict["out"]["output_zip_path"]),
"w")
for curves_outfile in Path(self.stage_io_dict.get("unique_dir", "")).glob("curves_output*"):
if curves_outfile.suffix not in (".cda", ".lis", ".zip"):
zf.write(
curves_outfile,
arcname=curves_outfile.name)
zf.close()
# rename cda and lis files
(Path(self.stage_io_dict.get("unique_dir", "")) / "curves_output.cda").rename(
self.stage_io_dict["out"]["output_cda_path"])
(Path(self.stage_io_dict.get("unique_dir", "")) / "curves_output.lis").rename(
self.stage_io_dict["out"]["output_lis_path"])
# Copy files to host
self.copy_to_host()
# Remove temporary file(s)
self.remove_tmp_files()
self.check_arguments(output_files_created=True, raise_exception=False)
return self.return_code
[docs]
def biobb_curves(
input_struc_path: str, output_lis_path: str, output_cda_path: str,
input_top_path: Optional[str] = None, output_zip_path: Optional[str] = None,
properties: Optional[dict] = None, **kwargs) -> int:
"""Create :class:`Curves <biobb_dna.curvesplus.biobb_curves.Curves>` class and
execute the :meth:`launch() <biobb_dna.curvesplus.biobb_curves.Curves.launch>` method."""
return Curves(**dict(locals())).launch()
biobb_curves.__doc__ = Curves.__doc__
main = Curves.get_main(biobb_curves, "Execute Cur+ form the Curves+ software suite.")
if __name__ == '__main__':
main()