Coverage for biobb_analysis/ambertools/cpptraj_bfactor.py: 94%
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« prev ^ index » next coverage.py v7.14.1, created at 2026-06-02 08:53 +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.stage_io_dict['unique_dir']).joinpath("cpptraj.in"))
110 self.instructions_file_path = str(PurePath(self.container_volume_path).joinpath("cpptraj.in"))
111 else:
112 self.instructions_file = self.create_tmp_file(self.instructions_file)
113 self.instructions_file_path = self.instructions_file
115 # parm
116 instructions_list.append('parm ' + container_io_dict["in"]["input_top_path"])
118 # trajin
119 in_params = get_in_parameters(self.in_parameters, out_log)
120 instructions_list.append('trajin ' + container_io_dict["in"]["input_traj_path"] + ' ' + in_params)
122 # Set up
123 instructions_list += setup_structure(self)
125 # mask
126 mask = self.in_parameters.get('mask', '')
127 ref_mask = ''
128 if mask:
129 strip_mask = get_negative_mask(mask, out_log)
130 ref_mask = get_mask(mask, out_log)
131 instructions_list.append('strip ' + strip_mask)
133 # reference
134 reference = self.in_parameters.get('reference', '')
135 inp_exp_pth = None
136 if "input_exp_path" in container_io_dict["in"]:
137 inp_exp_pth = container_io_dict["in"]["input_exp_path"]
138 instructions_list += get_reference(reference, container_io_dict["out"]["output_cpptraj_path"], inp_exp_pth, ref_mask, False, self.__class__.__name__, out_log)
139 instructions_list.append('atomicfluct out ' + container_io_dict["out"]["output_cpptraj_path"] + ' byres bfactor')
141 # create .in file
142 with open(self.instructions_file, 'w') as mdp:
143 for line in instructions_list:
144 mdp.write(line.strip() + '\n')
146 return self.instructions_file_path
148 @launchlogger
149 def launch(self) -> int:
150 """Execute the :class:`CpptrajBfactor <ambertools.cpptraj_bfactor.CpptrajBfactor>` object."""
152 # check input/output paths and parameters
153 self.check_data_params(self.out_log, self.err_log)
155 # Setup Biobb
156 if self.check_restart():
157 return 0
158 self.stage_files()
160 # Create instructions file
161 self.create_instructions_file(self.stage_io_dict, self.out_log, self.err_log)
163 # Create cmd and launch execution
164 self.cmd = [self.binary_path, '-i', self.instructions_file_path]
166 # Run Biobb block
167 self.run_biobb()
168 # Copy files to host
169 self.copy_to_host()
170 # Remove temporary folder
171 self.remove_tmp_files()
172 self.check_arguments(output_files_created=True, raise_exception=False)
174 return self.return_code
177def cpptraj_bfactor(input_top_path: str,
178 input_traj_path: str,
179 output_cpptraj_path: str,
180 input_exp_path: Optional[str] = None,
181 properties: Optional[dict] = None, **kwargs) -> int:
182 """Create the :class:`CpptrajBfactor <ambertools.cpptraj_bfactor.CpptrajBfactor>` class and
183 execute the :meth:`launch() <ambertools.cpptraj_bfactor.CpptrajBfactor.launch>` method."""
184 return CpptrajBfactor(**dict(locals())).launch()
187cpptraj_bfactor.__doc__ = CpptrajBfactor.__doc__
188main = CpptrajBfactor.get_main(
189 cpptraj_bfactor,
190 "Calculates the Bfactor fluctuations of a given cpptraj compatible trajectory."
191)
193if __name__ == '__main__':
194 main()