Coverage for biobb_analysis/ambertools/cpptraj_rmsf.py: 83%
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1#!/usr/bin/env python3
3"""Module containing the Cpptraj Rmsf 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, get_mask, get_reference
13class CpptrajRmsf(BiobbObject):
14 """
15 | biobb_analysis CpptrajRmsf
16 | Wrapper of the Ambertools Cpptraj module for calculating the Root Mean Square fluctuations (RMSf) of 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 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).
23 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).
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 * **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).
30 * **binary_path** (*str*) - ("cpptraj") Path to the cpptraj executable binary.
31 * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
32 * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
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: >=20.0
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_properties(properties)
94 self.check_arguments()
96 def check_data_params(self, out_log, err_log):
97 """ Checks all the input/output paths and parameters """
98 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__)
99 self.io_dict["in"]["input_traj_path"] = check_traj_path(self.io_dict["in"]["input_traj_path"], out_log, self.__class__.__name__)
100 self.io_dict["out"]["output_cpptraj_path"] = check_out_path(self.io_dict["out"]["output_cpptraj_path"], out_log, self.__class__.__name__)
101 self.in_parameters = {'start': self.start, 'end': self.end, 'step': self.steps, 'mask': self.mask, 'reference': self.reference}
103 def create_instructions_file(self, container_io_dict, out_log, err_log):
104 """Creates an input file using the properties file settings"""
105 instructions_list = []
106 # different path if container execution or not
107 if self.container_path:
108 self.instructions_file = str(PurePath(self.container_volume_path).joinpath(self.instructions_file))
109 else:
110 self.instructions_file = str(PurePath(fu.create_unique_dir()).joinpath(self.instructions_file))
111 fu.create_name(prefix=self.prefix, step=self.step, name=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')
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:`CpptrajRmsf <ambertools.cpptraj_rmsf.CpptrajRmsf>` ambertools.cpptraj_rmsf.CpptrajRmsf 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 # if container execution, copy intructions file to container
162 if self.container_path:
163 copy_instructions_file_to_container(self.instructions_file, self.stage_io_dict['unique_dir'])
165 # create cmd and launch execution
166 self.cmd = [self.binary_path, '-i', self.instructions_file]
168 # Run Biobb block
169 self.run_biobb()
171 # Copy files to host
172 self.copy_to_host()
174 # remove temporary folder(s)
175 self.tmp_files.extend([
176 self.stage_io_dict.get("unique_dir"),
177 PurePath(self.instructions_file).parent
178 ])
179 self.remove_tmp_files()
181 self.check_arguments(output_files_created=True, raise_exception=False)
183 return self.return_code
186def cpptraj_rmsf(input_top_path: str, input_traj_path: str, output_cpptraj_path: str, input_exp_path: str = None, properties: dict = None, **kwargs) -> int:
187 """Execute the :class:`CpptrajRmsf <ambertools.cpptraj_rmsf.CpptrajRmsf>` class and
188 execute the :meth:`launch() <ambertools.cpptraj_rmsf.CpptrajRmsf.launch>` method."""
190 return CpptrajRmsf(input_top_path=input_top_path,
191 input_traj_path=input_traj_path,
192 output_cpptraj_path=output_cpptraj_path,
193 input_exp_path=input_exp_path,
194 properties=properties, **kwargs).launch()
197def main():
198 """Command line execution of this building block. Please check the command line documentation."""
199 parser = argparse.ArgumentParser(description="Calculates the Root Mean Square fluctuations (RMSf) of a given cpptraj compatible trajectory.", formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999))
200 parser.add_argument('--config', required=False, help='Configuration file')
202 # Specific args of each building block
203 required_args = parser.add_argument_group('required arguments')
204 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.')
205 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.')
206 parser.add_argument('--input_exp_path', required=False, help='Path to the experimental reference file (required if reference = experimental).')
207 required_args.add_argument('--output_cpptraj_path', required=True, help='Path to the output processed analysis.')
209 args = parser.parse_args()
210 args.config = args.config or "{}"
211 properties = settings.ConfReader(config=args.config).get_prop_dic()
213 # Specific call of each building block
214 cpptraj_rmsf(input_top_path=args.input_top_path,
215 input_traj_path=args.input_traj_path,
216 output_cpptraj_path=args.output_cpptraj_path,
217 input_exp_path=args.input_exp_path,
218 properties=properties)
221if __name__ == '__main__':
222 main()