Coverage for biobb_dna / curvesplus / biobb_curves.py: 82%
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« prev ^ index » next coverage.py v7.13.0, created at 2025-12-15 18:49 +0000
1#!/usr/bin/env python3
3"""Module containing the Curves class and the command line interface."""
4import os
5import zipfile
6from typing import Optional
7import shutil
8from pathlib import Path
9from biobb_common.generic.biobb_object import BiobbObject
10from biobb_common.tools import file_utils as fu
11from biobb_common.tools.file_utils import launchlogger
14class Curves(BiobbObject):
15 """
16 | biobb_dna Curves
17 | Wrapper for the Cur+ executable that is part of the Curves+ software suite.
18 | The Cur+ program is used to analyze the structure of nucleic acids and their complexes.
20 Args:
21 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).
22 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).
23 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).
24 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).
25 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).
26 properties (dict):
27 * **s1range** (*str*) - (None) Range of first strand. Must be specified in the form "start:end".
28 * **s2range** (*str*) - (None) Range of second strand. Must be specified in the form "start:end".
29 * **stdlib_path** (*str*) - ('standard') Path to Curves' standard library files for nucleotides. If not specified will look for 'standard' files in current directory.
30 * **itst** (*int*) - (0) Iteration start index.
31 * **itnd** (*int*) - (0) Iteration end index.
32 * **itdel** (*int*) - (1) Iteration delimiter.
33 * **ions** (*bool*) - (False) If True, helicoidal analysis of ions (or solvent molecules) around solute is carried out.
34 * **test** (*bool*) - (False) If True, provide addition output in .lis file on fitting and axis generation.
35 * **line** (*bool*) - (False) if True, find the best linear helical axis.
36 * **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).
37 * **axfrm** (*bool*) - (False) if True, generates closely spaced helical axis frames as input for Canal and Canion.
38 * **binary_path** (*str*) - (Cur+) Path to Curves+ executable, otherwise the program wil look for Cur+ executable in the binaries folder.
39 * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
40 * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
41 * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.
42 Examples:
43 This is a use example of how to use the building block from Python::
45 from biobb_dna.curvesplus.biobb_curves import biobb_curves
46 prop = {
47 's1range': '1:12',
48 's2range': '24:13',
49 }
50 biobb_curves(
51 input_struc_path='/path/to/structure/file.trj',
52 input_top_path='/path/to/topology/file.top',
53 output_cda_path='/path/to/output/file.cda',
54 output_lis_path='/path/to/output/file.lis',
55 properties=prop)
56 Info:
57 * wrapped_software:
58 * name: Curves
59 * version: >=2.6
60 * license: BSD 3-Clause
61 * ontology:
62 * name: EDAM
63 * schema: http://edamontology.org/EDAM.owl
64 """
66 def __init__(
67 self, input_struc_path, output_lis_path,
68 output_cda_path, output_zip_path=None,
69 input_top_path=None, properties=None, **kwargs) -> None:
70 properties = properties or {}
72 # Call parent class constructor
73 super().__init__(properties)
74 self.locals_var_dict = locals().copy()
76 # Input/Output files
77 self.io_dict = {
78 'in': {
79 'input_struc_path': input_struc_path,
80 'input_top_path': input_top_path
81 },
82 'out': {
83 'output_lis_path': output_lis_path,
84 'output_cda_path': output_cda_path,
85 'output_zip_path': output_zip_path
86 }
87 }
89 # Properties specific for BB
90 self.s1range = properties.get('s1range', None)
91 self.binary_path = properties.get('binary_path', 'Cur+')
92 self.stdlib_path = properties.get('stdlib_path', None)
93 self.s2range = properties.get('s2range', None)
94 self.itst = properties.get('itst', 0)
95 self.itnd = properties.get('itnd', 0)
96 self.itdel = properties.get('itdel', 1)
97 self.ions = ".t." if properties.get('ions', False) else ".f."
98 self.test = ".t." if properties.get('test', False) else ".f."
99 self.line = ".t." if properties.get('line', False) else ".f."
100 self.fit = ".t." if properties.get('fit', True) else ".f."
101 self.axfrm = ".t." if properties.get('axfrm', False) else ".f."
102 self.properties = properties
104 # Check the properties
105 self.check_properties(properties)
106 self.check_arguments()
108 def create_curvesplus_folder(self):
109 """Create .curvesplus folder in the current temporal folder and copy the lib files inside."""
110 # Create .curvesplus directory in temporary folder
111 dst_dir = self.stage_io_dict.get("unique_dir", "") + '/.curvesplus'
112 os.makedirs(dst_dir, exist_ok=True)
113 # Get lib files from stdlib_path
114 lib_files = list(Path(os.path.dirname(self.stdlib_path)).glob("*.lib"))
115 # Copy each lib file to the .curvesplus directory in temporary folder
116 for file in lib_files:
117 shutil.copy(file, dst_dir)
119 @launchlogger
120 def launch(self) -> int:
121 """Execute the :class:`Curves <biobb_dna.curvesplus.biobb_curves.Curves>` object."""
123 # Setup Biobb
124 if self.check_restart():
125 return 0
126 self.stage_files()
128 if self.s1range is None:
129 raise ValueError("property 's1range' must be specified!")
130 if self.s2range is None:
131 # compute s2range if not provided
132 range1_end = int(self.s1range.split(":")[1])
133 s2start = range1_end + 1
134 s2end = 2 * range1_end
135 self.s2range = f"{s2end}:{s2start}"
137 # check standard library files location if not provided
138 if self.stdlib_path is None:
139 if os.getenv("CONDA_PREFIX", False):
140 curves_aux_path = Path(
141 os.getenv("CONDA_PREFIX", "")) / ".curvesplus"
142 # check if .curvesplus directory is in $CONDA_PREFIX
143 if curves_aux_path.exists():
144 if len(list(curves_aux_path.glob("standard_*.lib"))) != 3:
145 raise FileNotFoundError(
146 "One or all standard library files "
147 f"missing from {curves_aux_path}! "
148 "Check files standard_b.lib, "
149 "standard_s.lib and standard_i.lib exist.")
150 self.stdlib_path = curves_aux_path / "standard"
151 else:
152 raise FileNotFoundError(
153 ".curvesplus directory not found in "
154 f"{os.getenv('CONDA_PREFIX')} !"
155 "Please indicate where standard_*.lib files are "
156 "located with the stdlib_path property.")
157 # copy standard library files to temporary folder
158 shutil.copytree(curves_aux_path, self.stage_io_dict.get("unique_dir", "") + '/.curvesplus')
159 relative_lib_path = '.curvesplus/standard'
160 else:
161 # CONDA_PREFIX undefined
162 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)
163 self.stdlib_path = Path.cwd() / "standard"
164 # create .curvesplus folder in the current temporal folder and copy the lib files inside
165 self.create_curvesplus_folder()
166 # set relative path
167 relative_lib_path = '.curvesplus/standard'
168 else:
169 # create .curvesplus folder in the current temporal folder and copy the lib files inside
170 self.create_curvesplus_folder()
171 # set relative path
172 path_parts = str(self.stdlib_path).split(os.sep)
173 relative_lib_path = '.curvesplus/' + os.sep.join(path_parts[-1:])
175 # change directory to temporary folder
176 original_directory = os.getcwd()
177 os.chdir(self.stage_io_dict.get("unique_dir", ""))
179 # define temporary file names
180 tmp_struc_input = Path(self.stage_io_dict['in']['input_struc_path']).name
181 if self.stage_io_dict['in']['input_top_path'] is not None:
182 tmp_top_input = Path(self.stage_io_dict['in']['input_top_path']).name
184 # create intructions
185 instructions = [
186 f"{self.binary_path} <<! ",
187 "&inp",
188 f" file={tmp_struc_input},"]
189 if self.stage_io_dict['in']['input_top_path'] is not None:
190 # add topology file if needed
191 fu.log('Appending provided topology to command',
192 self.out_log, self.global_log)
193 instructions.append(
194 f" ftop={tmp_top_input},")
196 # create intructions
197 instructions = instructions + [
198 " lis='curves_output',",
199 f" lib={relative_lib_path},",
200 f" ions={self.ions},",
201 f" test={self.test},",
202 f" line={self.line},",
203 f" fit={self.fit},",
204 f" axfrm={self.axfrm},",
205 f" itst={self.itst},itnd={self.itnd},itdel={self.itdel},",
206 "&end",
207 "2 1 -1 0 0",
208 f"{self.s1range}",
209 f"{self.s2range}",
210 "!"
211 ]
212 self.cmd = ["\n".join(instructions)]
213 fu.log('Creating command line with instructions and required arguments',
214 self.out_log, self.global_log)
216 # Run Biobb block
217 self.run_biobb()
219 # change back to original directory
220 os.chdir(original_directory)
222 # create zipfile and write output inside
223 if self.stage_io_dict.get("out", {}).get("output_zip_path") is not None:
224 zf = zipfile.ZipFile(
225 Path(self.stage_io_dict["out"]["output_zip_path"]),
226 "w")
227 for curves_outfile in Path(self.stage_io_dict.get("unique_dir", "")).glob("curves_output*"):
228 if curves_outfile.suffix not in (".cda", ".lis", ".zip"):
229 zf.write(
230 curves_outfile,
231 arcname=curves_outfile.name)
232 zf.close()
234 # rename cda and lis files
235 (Path(self.stage_io_dict.get("unique_dir", "")) / "curves_output.cda").rename(
236 self.stage_io_dict["out"]["output_cda_path"])
237 (Path(self.stage_io_dict.get("unique_dir", "")) / "curves_output.lis").rename(
238 self.stage_io_dict["out"]["output_lis_path"])
240 # Copy files to host
241 self.copy_to_host()
243 # Remove temporary file(s)
244 self.remove_tmp_files()
246 self.check_arguments(output_files_created=True, raise_exception=False)
248 return self.return_code
251def biobb_curves(
252 input_struc_path: str, output_lis_path: str, output_cda_path: str,
253 input_top_path: Optional[str] = None, output_zip_path: Optional[str] = None,
254 properties: Optional[dict] = None, **kwargs) -> int:
255 """Create :class:`Curves <biobb_dna.curvesplus.biobb_curves.Curves>` class and
256 execute the :meth:`launch() <biobb_dna.curvesplus.biobb_curves.Curves.launch>` method."""
257 return Curves(**dict(locals())).launch()
260biobb_curves.__doc__ = Curves.__doc__
261main = Curves.get_main(biobb_curves, "Execute Cur+ form the Curves+ software suite.")
263if __name__ == '__main__':
264 main()