Source code for gromacs.gmx_image

#!/usr/bin/env python3

"""Module containing the GMX TrjConvStr class and the command line interface."""
import argparse
from biobb_common.generic.biobb_object import BiobbObject
from biobb_common.configuration import  settings
from biobb_common.tools.file_utils import launchlogger
from biobb_analysis.gromacs.common import *


[docs]class GMXImage(BiobbObject): """ | biobb_analysis GMXImage | Wrapper of the GROMACS trjconv module for correcting periodicity (image) from a given GROMACS compatible trajectory file. | GROMACS trjconv module can convert trajectory files in many ways. See the `GROMACS trjconv <http://manual.gromacs.org/documentation/2018/onlinehelp/gmx-trjconv.html>`_ official documentation for further information. Args: input_traj_path (str): Path to the GROMACS trajectory file. File type: input. `Sample file <https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/data/gromacs/trajectory.trr>`_. Accepted formats: xtc (edam:format_3875), trr (edam:format_3910), cpt (edam:format_2333), gro (edam:format_2033), g96 (edam:format_2033), pdb (edam:format_1476), tng (edam:format_3876). input_top_path (str): Path to the GROMACS input topology file. File type: input. `Sample file <https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/data/gromacs/topology.tpr>`_. Accepted formats: tpr (edam:format_2333), gro (edam:format_2033), g96 (edam:format_2033), pdb (edam:format_1476), brk (edam:format_2033), ent (edam:format_1476). input_index_path (str) (Optional): Path to the GROMACS index file. File type: input. `Sample file <https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/data/gromacs/index.ndx>`_. Accepted formats: ndx (edam:format_2033). output_traj_path (str): Path to the output file. File type: output. `Sample file <https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/reference/gromacs/ref_image.xtc>`_. Accepted formats: xtc (edam:format_3875), trr (edam:format_3910), cpt (edam:format_2333), gro (edam:format_2033), g96 (edam:format_2033), pdb (edam:format_1476), tng (edam:format_3876). properties (dic - Python dictionary object containing the tool parameters, not input/output files): * **fit_selection** (*str*) - ("System") Group where the fitting will be performed. If **input_index_path** provided, check the file for the accepted values. Values: System (all atoms in the system), Protein (all protein atoms), Protein-H (protein atoms excluding hydrogens), C-alpha (C-alpha atoms), Backbone (protein backbone atoms: N; C-alpha and C), MainChain (protein main chain atoms: N; C-alpha; C and O; including oxygens in C-terminus), MainChain+Cb (protein main chain atoms including C-beta), MainChain+H (protein main chain atoms including backbone amide hydrogens and hydrogens on the N-terminus), SideChain (protein side chain atoms: that is all atoms except N; C-alpha; C; O; backbone amide hydrogens and oxygens in C-terminus and hydrogens on the N-terminus), SideChain-H (protein side chain atoms excluding all hydrogens), Prot-Masses (protein atoms excluding dummy masses), non-Protein (all non-protein atoms), Water (water molecules), SOL (water molecules), non-Water (anything not covered by the Water group), Ion (any name matching an Ion entry in residuetypes.dat), NA (all NA atoms), CL (all CL atoms), Water_and_ions (combination of the Water and Ions groups). * **center_selection** (*str*) - ("System") Group where the trjconv will be performed. If **input_index_path** provided, check the file for the accepted values. Values: System (all atoms in the system), Protein (all protein atoms), Protein-H (protein atoms excluding hydrogens), C-alpha (C-alpha atoms), Backbone (protein backbone atoms: N; C-alpha and C), MainChain (protein main chain atoms: N; C-alpha; C and O; including oxygens in C-terminus), MainChain+Cb (protein main chain atoms including C-beta), MainChain+H (protein main chain atoms including backbone amide hydrogens and hydrogens on the N-terminus), SideChain (protein side chain atoms: that is all atoms except N; C-alpha; C; O; backbone amide hydrogens and oxygens in C-terminus and hydrogens on the N-terminus), SideChain-H (protein side chain atoms excluding all hydrogens), Prot-Masses (protein atoms excluding dummy masses), non-Protein (all non-protein atoms), Water (water molecules), SOL (water molecules), non-Water (anything not covered by the Water group), Ion (any name matching an Ion entry in residuetypes.dat), NA (all NA atoms), CL (all CL atoms), Water_and_ions (combination of the Water and Ions groups). * **output_selection** (*str*) - ("System") Group that is going to be written in the output trajectory. If **input_index_path** provided, check the file for the accepted values. Values: System (all atoms in the system), Protein (all protein atoms), Protein-H (protein atoms excluding hydrogens), C-alpha (C-alpha atoms), Backbone (protein backbone atoms: N; C-alpha and C), MainChain (protein main chain atoms: N; C-alpha; C and O; including oxygens in C-terminus), MainChain+Cb (protein main chain atoms including C-beta), MainChain+H (protein main chain atoms including backbone amide hydrogens and hydrogens on the N-terminus), SideChain (protein side chain atoms: that is all atoms except N; C-alpha; C; O; backbone amide hydrogens and oxygens in C-terminus and hydrogens on the N-terminus), SideChain-H (protein side chain atoms excluding all hydrogens), Prot-Masses (protein atoms excluding dummy masses), non-Protein (all non-protein atoms), Water (water molecules), SOL (water molecules), non-Water (anything not covered by the Water group), Ion (any name matching an Ion entry in residuetypes.dat), NA (all NA atoms), CL (all CL atoms), Water_and_ions (combination of the Water and Ions groups). * **pbc** (*str*) - ("mol") PBC treatment (see help text for full description). Values: none (No PBC treatment), mol (Puts the center of mass of molecules in the box), res (Puts the center of mass of residues in the box), atom (Puts all the atoms in the box), nojump (Checks if atoms jump across the box and then puts them back), cluster (Clusters all the atoms in the selected index such that they are all closest to the center of mass of the cluster which is iteratively updated), whole (Only makes broken molecules whole). * **center** (*bool*) - (True) Center atoms in box. * **ur** (*str*) - ("compact") Unit-cell representation. Values: rect (It's the ordinary brick shape), tric (It's the triclinic unit cell), compact (Puts all atoms at the closest distance from the center of the box). * **fit** (*str*) - ("none") Fit molecule to ref structure in the structure file. Values: none, rot+trans, rotxy+transxy, translation, transxy, progressive. * **gmx_path** (*str*) - ("gmx") Path to the GROMACS executable binary. * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files. * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist. * **container_path** (*str*) - (None) Container path definition. * **container_image** (*str*) - ('gromacs/gromacs:latest') Container image definition. * **container_volume_path** (*str*) - ('/tmp') Container volume path definition. * **container_working_dir** (*str*) - (None) Container working directory definition. * **container_user_id** (*str*) - (None) Container user_id definition. * **container_shell_path** (*str*) - ('/bin/bash') Path to default shell inside the container. Examples: This is a use example of how to use the building block from Python:: from biobb_analysis.gromacs.gmx_image import gmx_image prop = { 'fit_selection': 'System', 'center_selection': 'Water_and_ions', 'output_selection': 'System', 'pbc': 'mol' } gmx_image(input_traj_path='/path/to/myTrajectory.trr', input_top_path='/path/to/myTopology.tpr', output_traj_path='/path/to/newTrajectory.xtc', input_index_path='/path/to/myIndex.ndx', properties=prop) Info: * wrapped_software: * name: GROMACS trjconv * version: >=2019.1 * license: LGPL 2.1 * ontology: * name: EDAM * schema: http://edamontology.org/EDAM.owl """ def __init__(self, input_traj_path, input_top_path, output_traj_path, input_index_path=None, properties=None, **kwargs) -> None: properties = properties or {} # Call parent class constructor super().__init__(properties) # Input/Output files self.io_dict = { "in": { "input_traj_path": input_traj_path, "input_top_path": input_top_path, "input_index_path": input_index_path }, "out": { "output_traj_path": output_traj_path } } # Properties specific for BB self.fit_selection = properties.get('fit_selection', "System") self.center_selection = properties.get('center_selection', "System") self.output_selection = properties.get('output_selection', "System") self.pbc = properties.get('pbc', "mol") self.center = properties.get('dista', True) self.ur = properties.get('ur', "compact") self.fit = properties.get('fit', "none") self.properties = properties # Properties common in all GROMACS BB self.gmx_path = get_binary_path(properties, 'gmx_path') # Check the properties self.check_properties(properties)
[docs] def check_data_params(self, out_log, err_log): """ Checks all the input/output paths and parameters """ self.io_dict["in"]["input_traj_path"] = check_traj_path(self.io_dict["in"]["input_traj_path"], out_log, self.__class__.__name__) self.io_dict["in"]["input_top_path"] = check_input_path(self.io_dict["in"]["input_top_path"], out_log, self.__class__.__name__) self.io_dict["in"]["input_index_path"] = check_index_path(self.io_dict["in"]["input_index_path"], out_log, self.__class__.__name__) self.io_dict["out"]["output_traj_path"] = check_out_traj_path(self.io_dict["out"]["output_traj_path"], out_log, self.__class__.__name__) if not self.io_dict["in"]["input_index_path"]: self.fit_selection = get_image_selection(self.properties, 'fit_selection', out_log, self.__class__.__name__) self.center_selection = get_image_selection(self.properties, 'center_selection', out_log, self.__class__.__name__) self.output_selection = get_image_selection(self.properties, 'output_selection', out_log, self.__class__.__name__) else: self.fit_selection = get_selection_index_file(self.properties, self.io_dict["in"]["input_index_path"], 'fit_selection', out_log, self.__class__.__name__) self.center_selection = get_selection_index_file(self.properties, self.io_dict["in"]["input_index_path"], 'center_selection', out_log, self.__class__.__name__) self.output_selection = get_selection_index_file(self.properties, self.io_dict["in"]["input_index_path"], 'output_selection', out_log, self.__class__.__name__) self.pbc = get_pbc(self.properties, out_log, self.__class__.__name__) self.center = get_center(self.properties, out_log, self.__class__.__name__) self.ur = get_ur(self.properties, out_log, self.__class__.__name__) self.fit = get_fit(self.properties, out_log, self.__class__.__name__)
[docs] @launchlogger def launch(self) -> int: """Execute the :class:`GMXImage <gromacs.gmx_image.GMXImage>` gromacs.gmx_image.GMXImage object.""" # check input/output paths and parameters self.check_data_params(self.out_log, self.err_log) # Setup Biobb if self.check_restart(): return 0 self.stage_files() # If fitting provided, echo fit_selection if self.fit == 'none': selections = '\"' + self.center_selection + '\" \"' + self.output_selection + '\"' else: selections = '\"' + self.fit_selection + '\" \"' + self.center_selection + '\" \"' + self.output_selection + '\"' self.cmd = ['echo', selections, '|', self.gmx_path, 'trjconv', '-f', self.stage_io_dict["in"]["input_traj_path"], '-s', self.stage_io_dict["in"]["input_top_path"], '-fit', self.fit, '-o', self.stage_io_dict["out"]["output_traj_path"]] if self.stage_io_dict["in"]["input_index_path"]: self.cmd.extend(['-n', self.stage_io_dict["in"]["input_index_path"]]) # Unit-cell representation, PBC tratment and atoms center are incompatible with fitting if self.fit == 'none': self.cmd.append('-center' if self.center else '-nocenter') self.cmd.append('-pbc') self.cmd.append(self.pbc) self.cmd.append('-ur') self.cmd.append(self.ur) # Run Biobb block self.run_biobb() # Copy files to host self.copy_to_host() # if container execution, remove temporary folder if self.container_path: self.tmp_files.append(self.stage_io_dict.get("unique_dir")) self.remove_tmp_files() return self.return_code
[docs]def gmx_image(input_traj_path: str, input_top_path: str, output_traj_path: str, input_index_path: str = None, properties: dict = None, **kwargs) -> int: """Execute the :class:`GMXImage <gromacs.gmx_image.GMXImage>` class and execute the :meth:`launch() <gromacs.gmx_image.GMXImage.launch>` method.""" return GMXImage(input_traj_path=input_traj_path, input_top_path = input_top_path, output_traj_path=output_traj_path, input_index_path=input_index_path, properties=properties, **kwargs).launch()
[docs]def main(): """Command line execution of this building block. Please check the command line documentation.""" parser = argparse.ArgumentParser(description="Corrects periodicity (image) from a given GROMACS compatible trajectory file.", formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999)) parser.add_argument('--config', required=False, help='Configuration file') #Specific args of each building block required_args = parser.add_argument_group('required arguments') required_args.add_argument('--input_traj_path', required=True, help='Path to the GROMACS trajectory file. Accepted formats: xtc, trr, cpt, gro, g96, pdb, tng.') required_args.add_argument('--input_top_path', required=True, help='Path to the GROMACS input topology file. Accepted formats: tpr, gro, g96, pdb, brk, ent.') parser.add_argument('--input_index_path', required=False, help="Path to the GROMACS index file. Accepted formats: ndx.") required_args.add_argument('--output_traj_path', required=True, help='Path to the output file. Accepted formats: xtc, trr, gro, g96, pdb, tng.') args = parser.parse_args() args.config = args.config or "{}" properties = settings.ConfReader(config=args.config).get_prop_dic() #Specific call of each building block gmx_image(input_traj_path=args.input_traj_path, input_top_path=args.input_top_path, output_traj_path=args.output_traj_path, input_index_path=args.input_index_path, properties=properties)
if __name__ == '__main__': main()