Coverage for biobb_dna/curvesplus/biobb_curves.py: 82%
100 statements
« prev ^ index » next coverage.py v7.14.1, created at 2026-05-28 06:38 +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 * **container_path** (*str*) - (None) Path to the binary executable of your container.
43 * **container_image** (*str*) - ("cmip/cmip:latest") Container Image identifier.
44 * **container_volume_path** (*str*) - ("/data") Path to an internal directory in the container.
45 * **container_working_dir** (*str*) - (None) Path to the internal CWD in the container.
46 * **container_user_id** (*str*) - (None) User number id to be mapped inside the container.
47 * **container_shell_path** (*str*) - ("/bin/bash") Path to the binary executable of the container shell.
48 Examples:
49 This is a use example of how to use the building block from Python::
51 from biobb_dna.curvesplus.biobb_curves import biobb_curves
52 prop = {
53 's1range': '1:12',
54 's2range': '24:13',
55 }
56 biobb_curves(
57 input_struc_path='/path/to/structure/file.trj',
58 input_top_path='/path/to/topology/file.top',
59 output_cda_path='/path/to/output/file.cda',
60 output_lis_path='/path/to/output/file.lis',
61 properties=prop)
62 Info:
63 * wrapped_software:
64 * name: Curves
65 * version: >=2.6
66 * license: BSD 3-Clause
67 * ontology:
68 * name: EDAM
69 * schema: http://edamontology.org/EDAM.owl
70 """
72 def __init__(
73 self, input_struc_path, output_lis_path,
74 output_cda_path, output_zip_path=None,
75 input_top_path=None, properties=None, **kwargs) -> None:
76 properties = properties or {}
78 # Call parent class constructor
79 super().__init__(properties)
80 self.locals_var_dict = locals().copy()
82 # Input/Output files
83 self.io_dict = {
84 'in': {
85 'input_struc_path': input_struc_path,
86 'input_top_path': input_top_path
87 },
88 'out': {
89 'output_lis_path': output_lis_path,
90 'output_cda_path': output_cda_path,
91 'output_zip_path': output_zip_path
92 }
93 }
95 # Properties specific for BB
96 self.s1range = properties.get('s1range', None)
97 self.binary_path = properties.get('binary_path', 'Cur+')
98 self.stdlib_path = properties.get('stdlib_path', None)
99 self.s2range = properties.get('s2range', None)
100 self.itst = properties.get('itst', 0)
101 self.itnd = properties.get('itnd', 0)
102 self.itdel = properties.get('itdel', 1)
103 self.ions = ".t." if properties.get('ions', False) else ".f."
104 self.test = ".t." if properties.get('test', False) else ".f."
105 self.line = ".t." if properties.get('line', False) else ".f."
106 self.fit = ".t." if properties.get('fit', True) else ".f."
107 self.axfrm = ".t." if properties.get('axfrm', False) else ".f."
108 self.properties = properties
110 # Check the properties
111 self.check_properties(properties)
112 self.check_arguments()
114 def create_curvesplus_folder(self):
115 """Create .curvesplus folder in the current temporal folder and copy the lib files inside."""
116 # Create .curvesplus directory in temporary folder
117 dst_dir = self.stage_io_dict.get("unique_dir", "") + '/.curvesplus'
118 os.makedirs(dst_dir, exist_ok=True)
119 # Get lib files from stdlib_path
120 lib_files = list(Path(os.path.dirname(self.stdlib_path)).glob("*.lib"))
121 # Copy each lib file to the .curvesplus directory in temporary folder
122 for file in lib_files:
123 shutil.copy(file, dst_dir)
125 @launchlogger
126 def launch(self) -> int:
127 """Execute the :class:`Curves <biobb_dna.curvesplus.biobb_curves.Curves>` object."""
129 # Setup Biobb
130 if self.check_restart():
131 return 0
132 self.stage_files()
134 if self.s1range is None:
135 raise ValueError("property 's1range' must be specified!")
136 if self.s2range is None:
137 # compute s2range if not provided
138 range1_end = int(self.s1range.split(":")[1])
139 s2start = range1_end + 1
140 s2end = 2 * range1_end
141 self.s2range = f"{s2end}:{s2start}"
143 # check standard library files location if not provided
144 if self.stdlib_path is None:
145 if os.getenv("CONDA_PREFIX", False):
146 curves_aux_path = Path(
147 os.getenv("CONDA_PREFIX", "")) / ".curvesplus"
148 # check if .curvesplus directory is in $CONDA_PREFIX
149 if curves_aux_path.exists():
150 if len(list(curves_aux_path.glob("standard_*.lib"))) != 3:
151 raise FileNotFoundError(
152 "One or all standard library files "
153 f"missing from {curves_aux_path}! "
154 "Check files standard_b.lib, "
155 "standard_s.lib and standard_i.lib exist.")
156 self.stdlib_path = curves_aux_path / "standard"
157 else:
158 raise FileNotFoundError(
159 ".curvesplus directory not found in "
160 f"{os.getenv('CONDA_PREFIX')} !"
161 "Please indicate where standard_*.lib files are "
162 "located with the stdlib_path property.")
163 # copy standard library files to temporary folder
164 shutil.copytree(curves_aux_path, self.stage_io_dict.get("unique_dir", "") + '/.curvesplus')
165 relative_lib_path = '.curvesplus/standard'
166 else:
167 # CONDA_PREFIX undefined
168 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)
169 self.stdlib_path = Path.cwd() / "standard"
170 # create .curvesplus folder in the current temporal folder and copy the lib files inside
171 self.create_curvesplus_folder()
172 # set relative path
173 relative_lib_path = '.curvesplus/standard'
174 else:
175 # create .curvesplus folder in the current temporal folder and copy the lib files inside
176 self.create_curvesplus_folder()
177 # set relative path
178 path_parts = str(self.stdlib_path).split(os.sep)
179 relative_lib_path = '.curvesplus/' + os.sep.join(path_parts[-1:])
181 # change directory to temporary folder
182 original_directory = os.getcwd()
184 if self.container_path:
185 os.chdir(self.container_working_dir)
186 else:
187 os.chdir(self.stage_io_dict.get("unique_dir", ""))
189 # define temporary file names
190 tmp_struc_input = Path(self.stage_io_dict['in']['input_struc_path']).name
191 if self.stage_io_dict['in']['input_top_path'] is not None:
192 tmp_top_input = Path(self.stage_io_dict['in']['input_top_path']).name
194 # create intructions
195 instructions = [
196 f"{self.binary_path} <<! ",
197 "&inp",
198 f" file={tmp_struc_input},"]
199 if self.stage_io_dict['in']['input_top_path'] is not None:
200 # add topology file if needed
201 fu.log('Appending provided topology to command',
202 self.out_log, self.global_log)
203 instructions.append(
204 f" ftop={tmp_top_input},")
206 # create intructions
207 instructions = instructions + [
208 " lis='curves_output',",
209 f" lib={relative_lib_path},",
210 f" ions={self.ions},",
211 f" test={self.test},",
212 f" line={self.line},",
213 f" fit={self.fit},",
214 f" axfrm={self.axfrm},",
215 f" itst={self.itst},itnd={self.itnd},itdel={self.itdel},",
216 "&end",
217 "2 1 -1 0 0",
218 f"{self.s1range}",
219 f"{self.s2range}",
220 "!"
221 ]
222 self.cmd = ["\n".join(instructions)]
223 fu.log('Creating command line with instructions and required arguments',
224 self.out_log, self.global_log)
226 # Run Biobb block
227 self.run_biobb()
229 # change back to original directory
230 os.chdir(original_directory)
232 workdir = self.stage_io_dict.get("unique_dir", "")
233 zip_host_path = Path(workdir) / Path(self.io_dict["out"]["output_zip_path"]).name
235 # create zipfile and write output inside
236 with zipfile.ZipFile(zip_host_path, "w") as zf:
237 for curves_outfile in Path(workdir).glob("curves_output*"):
238 fu.log(f"Adding {curves_outfile} to zip file", self.out_log, self.global_log)
239 if curves_outfile.suffix not in (".cda", ".lis", ".zip"):
240 zf.write(
241 curves_outfile,
242 arcname=curves_outfile.name)
244 # rename cda and lis files
245 # In container mode stage_io_dict["out"] paths are container-internal
246 # (e.g. /data/file.cda), not host paths. Always rename within unique_dir
247 # so that copy_to_host() can find them by filename.
248 unique_dir = Path(self.stage_io_dict.get("unique_dir", ""))
249 (unique_dir / "curves_output.cda").rename(
250 unique_dir / Path(self.stage_io_dict["out"]["output_cda_path"]).name)
251 (unique_dir / "curves_output.lis").rename(
252 unique_dir / Path(self.stage_io_dict["out"]["output_lis_path"]).name)
254 # Copy files to host
255 self.copy_to_host()
257 # Remove temporary file(s)
258 self.remove_tmp_files()
260 self.check_arguments(output_files_created=True, raise_exception=False)
262 return self.return_code
265def biobb_curves(
266 input_struc_path: str, output_lis_path: str, output_cda_path: str,
267 input_top_path: Optional[str] = None, output_zip_path: Optional[str] = None,
268 properties: Optional[dict] = None, **kwargs) -> int:
269 """Create :class:`Curves <biobb_dna.curvesplus.biobb_curves.Curves>` class and
270 execute the :meth:`launch() <biobb_dna.curvesplus.biobb_curves.Curves.launch>` method."""
271 return Curves(**dict(locals())).launch()
274biobb_curves.__doc__ = Curves.__doc__
275main = Curves.get_main(biobb_curves, "Execute Cur+ form the Curves+ software suite.")
277if __name__ == '__main__':
278 main()