Coverage for biobb_analysis/ambertools/cpptraj_rgyr.py: 82%
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« prev ^ index » next coverage.py v7.6.4, created at 2024-11-14 14:38 +0000
1#!/usr/bin/env python3
3"""Module containing the Cpptraj Rgyr class and the command line interface."""
4import argparse
5from typing import Optional
6from pathlib import PurePath
7from biobb_common.generic.biobb_object import BiobbObject
8from biobb_common.configuration import settings
9from biobb_common.tools import file_utils as fu
10from biobb_common.tools.file_utils import launchlogger
11from biobb_analysis.ambertools.common import get_default_value, check_top_path, check_traj_path, check_out_path, get_binary_path, get_in_parameters, get_negative_mask, copy_instructions_file_to_container, setup_structure
14class CpptrajRgyr(BiobbObject):
15 """
16 | biobb_analysis CpptrajRgyr
17 | Wrapper of the Ambertools Cpptraj module for computing the radius of gyration (Rgyr) from a given cpptraj compatible trajectory.
18 | Cpptraj (the successor to ptraj) is the main program in Ambertools for processing coordinate trajectories and data files. The parameter names and defaults are the same as the ones in the official `Cpptraj manual <https://amber-md.github.io/cpptraj/CPPTRAJ.xhtml>`_.
20 Args:
21 input_top_path (str): Path to the input structure or topology file. File type: input. `Sample file <https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/data/ambertools/cpptraj.parm.top>`_. Accepted formats: top (edam:format_3881), pdb (edam:format_1476), prmtop (edam:format_3881), parmtop (edam:format_3881), zip (edam:format_3987).
22 input_traj_path (str): Path to the input trajectory to be processed. File type: input. `Sample file <https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/data/ambertools/cpptraj.traj.dcd>`_. Accepted formats: mdcrd (edam:format_3878), crd (edam:format_3878), cdf (edam:format_3650), netcdf (edam:format_3650), nc (edam:format_3650), restart (edam:format_3886), ncrestart (edam:format_3886), restartnc (edam:format_3886), dcd (edam:format_3878), charmm (edam:format_3887), cor (edam:format_2033), pdb (edam:format_1476), mol2 (edam:format_3816), trr (edam:format_3910), gro (edam:format_2033), binpos (edam:format_3885), xtc (edam:format_3875), cif (edam:format_1477), arc (edam:format_2333), sqm (edam:format_2033), sdf (edam:format_3814), conflib (edam:format_2033).
23 output_cpptraj_path (str): Path to the output analysis. File type: output. `Sample file <https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/reference/ambertools/ref_cpptraj.rgyr.dat>`_. Accepted formats: dat (edam:format_1637), agr (edam:format_2033), xmgr (edam:format_2033), gnu (edam:format_2033).
24 properties (dic - Python dictionary object containing the tool parameters, not input/output files):
25 * **start** (*int*) - (1) [1~100000|1] Starting frame for slicing.
26 * **end** (*int*) - (-1) [-1~100000|1] Ending frame for slicing.
27 * **steps** (*int*) - (1) [1~100000|1] Step for slicing.
28 * **mask** (*str*) - ("all-atoms") Mask definition. Values: c-alpha (All c-alpha atoms; protein only), backbone (Backbone atoms), all-atoms (All system atoms), heavy-atoms (System heavy atoms; not hydrogen), side-chain (All not backbone atoms), solute (All system atoms except solvent atoms), ions (All ion molecules), solvent (All solvent atoms), AnyAmberFromatMask (Amber atom selection syntax like `@*`).
29 * **binary_path** (*str*) - ("cpptraj") Path to the cpptraj executable binary.
30 * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
31 * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
32 * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.
33 * **container_path** (*str*) - (None) Container path definition.
34 * **container_image** (*str*) - ('afandiadib/ambertools:serial') Container image definition.
35 * **container_volume_path** (*str*) - ('/tmp') Container volume path definition.
36 * **container_working_dir** (*str*) - (None) Container working directory definition.
37 * **container_user_id** (*str*) - (None) Container user_id definition.
38 * **container_shell_path** (*str*) - ('/bin/bash') Path to default shell inside the container.
40 Examples:
41 This is a use example of how to use the building block from Python::
43 from biobb_analysis.ambertools.cpptraj_rgyr import cpptraj_rgyr
44 prop = {
45 'start': 1,
46 'end': -1,
47 'steps': 1,
48 'mask': 'c-alpha'
49 }
50 cpptraj_rgyr(input_top_path='/path/to/myTopology.top',
51 input_traj_path='/path/to/myTrajectory.dcd',
52 output_cpptraj_path='/path/to/newAnalysis.dat',
53 properties=prop)
55 Info:
56 * wrapped_software:
57 * name: Ambertools Cpptraj
58 * version: >=20.0
59 * license: GNU
60 * ontology:
61 * name: EDAM
62 * schema: http://edamontology.org/EDAM.owl
64 """
66 def __init__(self, input_top_path, input_traj_path, output_cpptraj_path,
67 properties=None, **kwargs) -> None:
68 properties = properties or {}
70 # Call parent class constructor
71 super().__init__(properties)
72 self.locals_var_dict = locals().copy()
74 # Input/Output files
75 self.io_dict = {
76 "in": {"input_top_path": input_top_path, "input_traj_path": input_traj_path},
77 "out": {"output_cpptraj_path": output_cpptraj_path}
78 }
80 # Properties specific for BB
81 self.instructions_file = get_default_value('instructions_file')
82 self.start = properties.get('start', 1)
83 self.end = properties.get('end', -1)
84 self.steps = properties.get('steps', 1)
85 self.mask = properties.get('mask', 'all-atoms')
86 self.properties = properties
87 self.binary_path = get_binary_path(properties, 'binary_path')
89 # Check the properties
90 self.check_properties(properties)
91 self.check_arguments()
93 def check_data_params(self, out_log, err_log):
94 """ Checks all the input/output paths and parameters """
95 self.io_dict["in"]["input_top_path"], self.input_top_path_orig = check_top_path(self.io_dict["in"]["input_top_path"], out_log, self.__class__.__name__)
96 self.io_dict["in"]["input_traj_path"] = check_traj_path(self.io_dict["in"]["input_traj_path"], out_log, self.__class__.__name__)
97 self.io_dict["out"]["output_cpptraj_path"] = check_out_path(self.io_dict["out"]["output_cpptraj_path"], out_log, self.__class__.__name__)
98 self.in_parameters = {'start': self.start, 'end': self.end, 'step': self.steps, 'mask': self.mask}
100 def create_instructions_file(self, container_io_dict, out_log, err_log):
101 """Creates an input file using the properties file settings"""
102 instructions_list = []
103 # different path if container execution or not
104 if self.container_path:
105 self.instructions_file = str(PurePath(self.container_volume_path).joinpath(self.instructions_file))
106 else:
107 self.instructions_file = str(PurePath(fu.create_unique_dir()).joinpath(self.instructions_file))
108 fu.create_name(prefix=self.prefix, step=self.step, name=self.instructions_file)
110 # parm
111 instructions_list.append('parm ' + container_io_dict["in"]["input_top_path"])
113 # trajin
114 in_params = get_in_parameters(self.in_parameters, out_log)
115 instructions_list.append('trajin ' + container_io_dict["in"]["input_traj_path"] + ' ' + in_params)
117 # Set up
118 instructions_list += setup_structure(self)
120 # mask
121 mask = self.in_parameters.get('mask', '')
122 if mask:
123 strip_mask = get_negative_mask(mask, out_log)
124 instructions_list.append('strip ' + strip_mask)
126 # output
127 instructions_list.append('radgyr time 1 out ' + container_io_dict["out"]["output_cpptraj_path"])
129 # create .in file
130 with open(self.instructions_file, 'w') as mdp:
131 for line in instructions_list:
132 mdp.write(line.strip() + '\n')
134 return self.instructions_file
136 @launchlogger
137 def launch(self) -> int:
138 """Execute the :class:`CpptrajRgyr <ambertools.cpptraj_rgyr.CpptrajRgyr>` ambertools.cpptraj_rgyr.CpptrajRgyr object."""
140 # check input/output paths and parameters
141 self.check_data_params(self.out_log, self.err_log)
143 # Setup Biobb
144 if self.check_restart():
145 return 0
146 self.stage_files()
148 # create instructions file
149 self.create_instructions_file(self.stage_io_dict, self.out_log, self.err_log)
151 # if container execution, copy intructions file to container
152 if self.container_path:
153 copy_instructions_file_to_container(self.instructions_file, self.stage_io_dict['unique_dir'])
155 # create cmd and launch execution
156 self.cmd = [self.binary_path, '-i', self.instructions_file]
158 # Run Biobb block
159 self.run_biobb()
161 # Copy files to host
162 self.copy_to_host()
164 # remove temporary folder(s)
165 self.tmp_files.extend([
166 self.stage_io_dict.get("unique_dir", ""),
167 str(PurePath(self.instructions_file).parent)
168 ])
169 self.remove_tmp_files()
171 self.check_arguments(output_files_created=True, raise_exception=False)
173 return self.return_code
176def cpptraj_rgyr(input_top_path: str, input_traj_path: str, output_cpptraj_path: str, properties: Optional[dict] = None, **kwargs) -> int:
177 """Execute the :class:`CpptrajRgyr <ambertools.cpptraj_rgyr.CpptrajRgyr>` class and
178 execute the :meth:`launch() <ambertools.cpptraj_rgyr.CpptrajRgyr.launch>` method."""
180 return CpptrajRgyr(input_top_path=input_top_path,
181 input_traj_path=input_traj_path,
182 output_cpptraj_path=output_cpptraj_path,
183 properties=properties, **kwargs).launch()
186def main():
187 """Command line execution of this building block. Please check the command line documentation."""
188 parser = argparse.ArgumentParser(description="Computes the radius of gyration (Rgyr) from a given cpptraj compatible trajectory.", formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999))
189 parser.add_argument('--config', required=False, help='Configuration file')
191 # Specific args of each building block
192 required_args = parser.add_argument_group('required arguments')
193 required_args.add_argument('--input_top_path', required=True, help='Path to the input structure or topology file. Accepted formats: top, pdb, prmtop, parmtop, zip.')
194 required_args.add_argument('--input_traj_path', required=True, help='Path to the input trajectory to be processed. Accepted formats: crd, cdf, netcdf, restart, ncrestart, restartnc, dcd, charmm, cor, pdb, mol2, trr, gro, binpos, xtc, cif, arc, sqm, sdf, conflib.')
195 required_args.add_argument('--output_cpptraj_path', required=True, help='Path to the output analysis.')
197 args = parser.parse_args()
198 args.config = args.config or "{}"
199 properties = settings.ConfReader(config=args.config).get_prop_dic()
201 # Specific call of each building block
202 cpptraj_rgyr(input_top_path=args.input_top_path,
203 input_traj_path=args.input_traj_path,
204 output_cpptraj_path=args.output_cpptraj_path,
205 properties=properties)
208if __name__ == '__main__':
209 main()