Coverage for biobb_analysis/ambertools/cpptraj_bfactor.py: 96%
69 statements
« prev ^ index » next coverage.py v7.10.6, created at 2025-09-08 10:47 +0000
1#!/usr/bin/env python3
3"""Module containing the Cpptraj Bfactor class and the command line interface."""
5from typing import Optional
6from pathlib import PurePath
7from biobb_common.generic.biobb_object import BiobbObject
8from biobb_common.tools.file_utils import launchlogger
9from biobb_analysis.ambertools.common import get_default_value, check_top_path, check_traj_path, check_out_path, get_binary_path, get_in_parameters, setup_structure, get_negative_mask, get_mask, get_reference
12class CpptrajBfactor(BiobbObject):
13 """
14 | biobb_analysis CpptrajBfactor
15 | Wrapper of the Ambertools Cpptraj module for calculating the Bfactor fluctuations of a given cpptraj compatible trajectory.
16 | 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://raw.githubusercontent.com/Amber-MD/cpptraj/master/doc/CpptrajManual.pdf>`_.
18 Args:
19 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).
20 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).
21 input_exp_path (str) (Optional): Path to the experimental reference file (required if reference = experimental). File type: input. `Sample file <https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/data/ambertools/experimental.1e5t.pdb>`_. Accepted formats: pdb (edam:format_1476).
22 output_cpptraj_path (str): Path to the output processed analysis. File type: output. `Sample file <https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/reference/ambertools/ref_cpptraj.bfactor.first.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 * **reference** (*str*) - ("first") Reference definition. Values: first (Use the first trajectory frame as reference), average (Use the average of all trajectory frames as reference), experimental (Use the experimental structure as reference).
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_bfactor import cpptraj_bfactor
44 prop = {
45 'start': 1,
46 'end': -1,
47 'steps': 1,
48 'mask': 'c-alpha',
49 'reference': 'first'
50 }
51 cpptraj_bfactor(input_top_path='/path/to/myTopology.top',
52 input_traj_path='/path/to/myTrajectory.dcd',
53 output_cpptraj_path='/path/to/newAnalysis.dat',
54 input_exp_path= '/path/to/myExpStructure.pdb',
55 properties=prop)
57 Info:
58 * wrapped_software:
59 * name: Ambertools Cpptraj
60 * version: >=22.5
61 * license: GNU
62 * ontology:
63 * name: EDAM
64 * schema: http://edamontology.org/EDAM.owl
66 """
68 def __init__(self, input_top_path, input_traj_path, output_cpptraj_path,
69 input_exp_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": {"input_top_path": input_top_path,
79 "input_traj_path": input_traj_path,
80 "input_exp_path": input_exp_path},
81 "out": {"output_cpptraj_path": output_cpptraj_path}
82 }
84 # Properties specific for BB
85 self.instructions_file = get_default_value('instructions_file')
86 self.start = properties.get('start', 1)
87 self.end = properties.get('end', -1)
88 self.steps = properties.get('steps', 1)
89 self.mask = properties.get('mask', 'all-atoms')
90 self.reference = properties.get('reference', 'first')
91 self.properties = properties
92 self.binary_path = get_binary_path(properties, 'binary_path')
94 # Check the properties
95 self.check_init(properties)
97 def check_data_params(self, out_log, err_log):
98 """ Checks all the input/output paths and parameters """
99 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__)
100 self.io_dict["in"]["input_traj_path"] = check_traj_path(self.io_dict["in"]["input_traj_path"], out_log, self.__class__.__name__)
101 self.io_dict["out"]["output_cpptraj_path"] = check_out_path(self.io_dict["out"]["output_cpptraj_path"], out_log, self.__class__.__name__)
102 self.in_parameters = {'start': self.start, 'end': self.end, 'step': self.steps, 'mask': self.mask, 'reference': self.reference}
104 def create_instructions_file(self, container_io_dict, out_log, err_log):
105 """Creates an input file using the properties file settings"""
106 instructions_list = []
107 # Different path if container execution or not
108 if self.container_path:
109 self.instructions_file = str(PurePath(self.container_volume_path).joinpath(self.instructions_file))
110 else:
111 self.instructions_file = self.create_tmp_file(self.instructions_file)
113 # parm
114 instructions_list.append('parm ' + container_io_dict["in"]["input_top_path"])
116 # trajin
117 in_params = get_in_parameters(self.in_parameters, out_log)
118 instructions_list.append('trajin ' + container_io_dict["in"]["input_traj_path"] + ' ' + in_params)
120 # Set up
121 instructions_list += setup_structure(self)
123 # mask
124 mask = self.in_parameters.get('mask', '')
125 ref_mask = ''
126 if mask:
127 strip_mask = get_negative_mask(mask, out_log)
128 ref_mask = get_mask(mask, out_log)
129 instructions_list.append('strip ' + strip_mask)
131 # reference
132 reference = self.in_parameters.get('reference', '')
133 inp_exp_pth = None
134 if "input_exp_path" in container_io_dict["in"]:
135 inp_exp_pth = container_io_dict["in"]["input_exp_path"]
136 instructions_list += get_reference(reference, container_io_dict["out"]["output_cpptraj_path"], inp_exp_pth, ref_mask, False, self.__class__.__name__, out_log)
137 instructions_list.append('atomicfluct out ' + container_io_dict["out"]["output_cpptraj_path"] + ' byres bfactor')
139 # create .in file
140 with open(self.instructions_file, 'w') as mdp:
141 for line in instructions_list:
142 mdp.write(line.strip() + '\n')
144 return self.instructions_file
146 @launchlogger
147 def launch(self) -> int:
148 """Execute the :class:`CpptrajBfactor <ambertools.cpptraj_bfactor.CpptrajBfactor>` object."""
150 # check input/output paths and parameters
151 self.check_data_params(self.out_log, self.err_log)
153 # Setup Biobb
154 if self.check_restart():
155 return 0
156 self.stage_files()
158 # Create instructions file
159 self.create_instructions_file(self.stage_io_dict, self.out_log, self.err_log)
161 # Create cmd and launch execution
162 self.cmd = [self.binary_path, '-i', self.instructions_file]
164 # Run Biobb block
165 self.run_biobb()
166 # Copy files to host
167 self.copy_to_host()
168 # Remove temporary folder
169 self.remove_tmp_files()
170 self.check_arguments(output_files_created=True, raise_exception=False)
172 return self.return_code
175def cpptraj_bfactor(input_top_path: str,
176 input_traj_path: str,
177 output_cpptraj_path: str,
178 input_exp_path: Optional[str] = None,
179 properties: Optional[dict] = None, **kwargs) -> int:
180 """Execute the :class:`CpptrajBfactor <ambertools.cpptraj_bfactor.CpptrajBfactor>` class and
181 execute the :meth:`launch() <ambertools.cpptraj_bfactor.CpptrajBfactor.launch>` method."""
182 return CpptrajBfactor(**dict(locals())).launch()
185cpptraj_bfactor.__doc__ = CpptrajBfactor.__doc__
186main = CpptrajBfactor.get_main(
187 cpptraj_bfactor,
188 "Calculates the Bfactor fluctuations of a given cpptraj compatible trajectory."
189)
191if __name__ == '__main__':
192 main()