Coverage for biobb_analysis/ambertools/cpptraj_rgyr.py: 82%
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« prev ^ index » next coverage.py v7.5.1, created at 2024-05-06 15:22 +0000
1#!/usr/bin/env python3
3"""Module containing the Cpptraj Rgyr class and the command line interface."""
4import argparse
5from pathlib import PurePath
6from biobb_common.generic.biobb_object import BiobbObject
7from biobb_common.configuration import settings
8from biobb_common.tools import file_utils as fu
9from biobb_common.tools.file_utils import launchlogger
10from 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
13class CpptrajRgyr(BiobbObject):
14 """
15 | biobb_analysis CpptrajRgyr
16 | Wrapper of the Ambertools Cpptraj module for computing the radius of gyration (Rgyr) from a given cpptraj compatible trajectory.
17 | 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>`_.
19 Args:
20 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).
21 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).
22 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).
23 properties (dic - Python dictionary object containing the tool parameters, not input/output files):
24 * **start** (*int*) - (1) [1~100000|1] Starting frame for slicing.
25 * **end** (*int*) - (-1) [-1~100000|1] Ending frame for slicing.
26 * **steps** (*int*) - (1) [1~100000|1] Step for slicing.
27 * **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 `@*`).
28 * **binary_path** (*str*) - ("cpptraj") Path to the cpptraj executable binary.
29 * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
30 * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
31 * **container_path** (*str*) - (None) Container path definition.
32 * **container_image** (*str*) - ('afandiadib/ambertools:serial') Container image definition.
33 * **container_volume_path** (*str*) - ('/tmp') Container volume path definition.
34 * **container_working_dir** (*str*) - (None) Container working directory definition.
35 * **container_user_id** (*str*) - (None) Container user_id definition.
36 * **container_shell_path** (*str*) - ('/bin/bash') Path to default shell inside the container.
38 Examples:
39 This is a use example of how to use the building block from Python::
41 from biobb_analysis.ambertools.cpptraj_rgyr import cpptraj_rgyr
42 prop = {
43 'start': 1,
44 'end': -1,
45 'steps': 1,
46 'mask': 'c-alpha'
47 }
48 cpptraj_rgyr(input_top_path='/path/to/myTopology.top',
49 input_traj_path='/path/to/myTrajectory.dcd',
50 output_cpptraj_path='/path/to/newAnalysis.dat',
51 properties=prop)
53 Info:
54 * wrapped_software:
55 * name: Ambertools Cpptraj
56 * version: >=20.0
57 * license: GNU
58 * ontology:
59 * name: EDAM
60 * schema: http://edamontology.org/EDAM.owl
62 """
64 def __init__(self, input_top_path, input_traj_path, output_cpptraj_path,
65 properties=None, **kwargs) -> None:
66 properties = properties or {}
68 # Call parent class constructor
69 super().__init__(properties)
70 self.locals_var_dict = locals().copy()
72 # Input/Output files
73 self.io_dict = {
74 "in": {"input_top_path": input_top_path, "input_traj_path": input_traj_path},
75 "out": {"output_cpptraj_path": output_cpptraj_path}
76 }
78 # Properties specific for BB
79 self.instructions_file = get_default_value('instructions_file')
80 self.start = properties.get('start', 1)
81 self.end = properties.get('end', -1)
82 self.steps = properties.get('steps', 1)
83 self.mask = properties.get('mask', 'all-atoms')
84 self.properties = properties
85 self.binary_path = get_binary_path(properties, 'binary_path')
87 # Check the properties
88 self.check_properties(properties)
89 self.check_arguments()
91 def check_data_params(self, out_log, err_log):
92 """ Checks all the input/output paths and parameters """
93 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__)
94 self.io_dict["in"]["input_traj_path"] = check_traj_path(self.io_dict["in"]["input_traj_path"], out_log, self.__class__.__name__)
95 self.io_dict["out"]["output_cpptraj_path"] = check_out_path(self.io_dict["out"]["output_cpptraj_path"], out_log, self.__class__.__name__)
96 self.in_parameters = {'start': self.start, 'end': self.end, 'step': self.steps, 'mask': self.mask}
98 def create_instructions_file(self, container_io_dict, out_log, err_log):
99 """Creates an input file using the properties file settings"""
100 instructions_list = []
101 # different path if container execution or not
102 if self.container_path:
103 self.instructions_file = str(PurePath(self.container_volume_path).joinpath(self.instructions_file))
104 else:
105 self.instructions_file = str(PurePath(fu.create_unique_dir()).joinpath(self.instructions_file))
106 fu.create_name(prefix=self.prefix, step=self.step, name=self.instructions_file)
108 # parm
109 instructions_list.append('parm ' + container_io_dict["in"]["input_top_path"])
111 # trajin
112 in_params = get_in_parameters(self.in_parameters, out_log)
113 instructions_list.append('trajin ' + container_io_dict["in"]["input_traj_path"] + ' ' + in_params)
115 # Set up
116 instructions_list += setup_structure(self)
118 # mask
119 mask = self.in_parameters.get('mask', '')
120 if mask:
121 strip_mask = get_negative_mask(mask, out_log)
122 instructions_list.append('strip ' + strip_mask)
124 # output
125 instructions_list.append('radgyr time 1 out ' + container_io_dict["out"]["output_cpptraj_path"])
127 # create .in file
128 with open(self.instructions_file, 'w') as mdp:
129 for line in instructions_list:
130 mdp.write(line.strip() + '\n')
132 return self.instructions_file
134 @launchlogger
135 def launch(self) -> int:
136 """Execute the :class:`CpptrajRgyr <ambertools.cpptraj_rgyr.CpptrajRgyr>` ambertools.cpptraj_rgyr.CpptrajRgyr object."""
138 # check input/output paths and parameters
139 self.check_data_params(self.out_log, self.err_log)
141 # Setup Biobb
142 if self.check_restart():
143 return 0
144 self.stage_files()
146 # create instructions file
147 self.create_instructions_file(self.stage_io_dict, self.out_log, self.err_log)
149 # if container execution, copy intructions file to container
150 if self.container_path:
151 copy_instructions_file_to_container(self.instructions_file, self.stage_io_dict['unique_dir'])
153 # create cmd and launch execution
154 self.cmd = [self.binary_path, '-i', self.instructions_file]
156 # Run Biobb block
157 self.run_biobb()
159 # Copy files to host
160 self.copy_to_host()
162 # remove temporary folder(s)
163 self.tmp_files.extend([
164 self.stage_io_dict.get("unique_dir"),
165 PurePath(self.instructions_file).parent
166 ])
167 self.remove_tmp_files()
169 self.check_arguments(output_files_created=True, raise_exception=False)
171 return self.return_code
174def cpptraj_rgyr(input_top_path: str, input_traj_path: str, output_cpptraj_path: str, properties: dict = None, **kwargs) -> int:
175 """Execute the :class:`CpptrajRgyr <ambertools.cpptraj_rgyr.CpptrajRgyr>` class and
176 execute the :meth:`launch() <ambertools.cpptraj_rgyr.CpptrajRgyr.launch>` method."""
178 return CpptrajRgyr(input_top_path=input_top_path,
179 input_traj_path=input_traj_path,
180 output_cpptraj_path=output_cpptraj_path,
181 properties=properties, **kwargs).launch()
184def main():
185 """Command line execution of this building block. Please check the command line documentation."""
186 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))
187 parser.add_argument('--config', required=False, help='Configuration file')
189 # Specific args of each building block
190 required_args = parser.add_argument_group('required arguments')
191 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.')
192 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.')
193 required_args.add_argument('--output_cpptraj_path', required=True, help='Path to the output analysis.')
195 args = parser.parse_args()
196 args.config = args.config or "{}"
197 properties = settings.ConfReader(config=args.config).get_prop_dic()
199 # Specific call of each building block
200 cpptraj_rgyr(input_top_path=args.input_top_path,
201 input_traj_path=args.input_traj_path,
202 output_cpptraj_path=args.output_cpptraj_path,
203 properties=properties)
206if __name__ == '__main__':
207 main()