Coverage for biobb_analysis/ambertools/cpptraj_rmsf.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 Rmsf 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, get_negative_mask, setup_structure, get_mask, get_reference
12class CpptrajRmsf(BiobbObject):
13 """
14 | biobb_analysis CpptrajRmsf
15 | Wrapper of the Ambertools Cpptraj module for calculating the Root Mean Square fluctuations (RMSf) 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.rmsf.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_rmsf import cpptraj_rmsf
44 prop = {
45 'start': 1,
46 'end': -1,
47 'steps': 1,
48 'mask': 'c-alpha',
49 'reference': 'first'
50 }
51 cpptraj_rmsf(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, "input_traj_path": input_traj_path, "input_exp_path": input_exp_path},
79 "out": {"output_cpptraj_path": output_cpptraj_path}
80 }
82 # Properties specific for BB
83 self.instructions_file = get_default_value('instructions_file')
84 self.start = properties.get('start', 1)
85 self.end = properties.get('end', -1)
86 self.steps = properties.get('steps', 1)
87 self.mask = properties.get('mask', 'all-atoms')
88 self.reference = properties.get('reference', 'first')
89 self.properties = properties
90 self.binary_path = get_binary_path(properties, 'binary_path')
92 # Check the properties
93 self.check_init(properties)
95 def check_data_params(self, out_log, err_log):
96 """ Checks all the input/output paths and parameters """
97 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__)
98 self.io_dict["in"]["input_traj_path"] = check_traj_path(self.io_dict["in"]["input_traj_path"], out_log, self.__class__.__name__)
99 self.io_dict["out"]["output_cpptraj_path"] = check_out_path(self.io_dict["out"]["output_cpptraj_path"], out_log, self.__class__.__name__)
100 self.in_parameters = {'start': self.start, 'end': self.end, 'step': self.steps, 'mask': self.mask, 'reference': self.reference}
102 def create_instructions_file(self, container_io_dict, out_log, err_log):
103 """Creates an input file using the properties file settings"""
104 instructions_list = []
105 # different path if container execution or not
106 if self.container_path:
107 self.instructions_file = str(PurePath(self.container_volume_path).joinpath(self.instructions_file))
108 else:
109 self.instructions_file = self.create_tmp_file(self.instructions_file)
111 # parm
112 instructions_list.append('parm ' + container_io_dict["in"]["input_top_path"])
114 # trajin
115 in_params = get_in_parameters(self.in_parameters, out_log)
116 instructions_list.append('trajin ' + container_io_dict["in"]["input_traj_path"] + ' ' + in_params)
118 # Set up
119 instructions_list += setup_structure(self)
121 # mask
122 mask = self.in_parameters.get('mask', '')
123 ref_mask = ''
124 if mask:
125 strip_mask = get_negative_mask(mask, out_log)
126 ref_mask = get_mask(mask, out_log)
127 instructions_list.append('strip ' + strip_mask)
129 # reference
130 reference = self.in_parameters.get('reference', '')
131 inp_exp_pth = None
132 if "input_exp_path" in container_io_dict["in"]:
133 inp_exp_pth = container_io_dict["in"]["input_exp_path"]
134 instructions_list += get_reference(reference, container_io_dict["out"]["output_cpptraj_path"], inp_exp_pth, ref_mask, False, self.__class__.__name__, out_log)
135 instructions_list.append('atomicfluct out ' + container_io_dict["out"]["output_cpptraj_path"] + ' byres')
137 # create .in file
138 with open(self.instructions_file, 'w') as mdp:
139 for line in instructions_list:
140 mdp.write(line.strip() + '\n')
142 return self.instructions_file
144 @launchlogger
145 def launch(self) -> int:
146 """Execute the :class:`CpptrajRmsf <ambertools.cpptraj_rmsf.CpptrajRmsf>` object."""
148 # check input/output paths and parameters
149 self.check_data_params(self.out_log, self.err_log)
151 # Setup Biobb
152 if self.check_restart():
153 return 0
154 self.stage_files()
156 # create instructions file
157 self.create_instructions_file(self.stage_io_dict, self.out_log, self.err_log)
159 # create cmd and launch execution
160 self.cmd = [self.binary_path, '-i', self.instructions_file]
162 # Run Biobb block
163 self.run_biobb()
165 # Copy files to host
166 self.copy_to_host()
168 # remove temporary folder(s)
169 self.remove_tmp_files()
170 self.check_arguments(output_files_created=True, raise_exception=False)
172 return self.return_code
175def cpptraj_rmsf(input_top_path: str, input_traj_path: str, output_cpptraj_path: str, input_exp_path: Optional[str] = None, properties: Optional[dict] = None, **kwargs) -> int:
176 """Execute the :class:`CpptrajRmsf <ambertools.cpptraj_rmsf.CpptrajRmsf>` class and
177 execute the :meth:`launch() <ambertools.cpptraj_rmsf.CpptrajRmsf.launch>` method."""
178 return CpptrajRmsf(**dict(locals())).launch()
181cpptraj_rmsf.__doc__ = CpptrajRmsf.__doc__
182main = CpptrajRmsf.get_main(cpptraj_rmsf, "Calculates the Root Mean Square fluctuations (RMSf) of a given cpptraj compatible trajectory.")
184if __name__ == '__main__':
185 main()