#!/usr/bin/env python3
"""Module containing the Cpptraj Rgyr class and the command line interface."""
import argparse
from pathlib import PurePath
from biobb_common.generic.biobb_object import BiobbObject
from biobb_common.configuration import settings
from biobb_common.tools import file_utils as fu
from biobb_common.tools.file_utils import launchlogger
from 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
[docs]class CpptrajRgyr(BiobbObject):
"""
| biobb_analysis CpptrajRgyr
| Wrapper of the Ambertools Cpptraj module for computing the radius of gyration (Rgyr) from a given cpptraj compatible trajectory.
| 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>`_.
Args:
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).
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).
output_cpptraj_path (str): Path to the output analysis. File type: output. `Sample file <https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/reference/ambertools/ref_cpptraj.rgyr.dat>`_. Accepted formats: dat (edam:format_1637), agr (edam:format_2033), xmgr (edam:format_2033), gnu (edam:format_2033).
properties (dic - Python dictionary object containing the tool parameters, not input/output files):
* **start** (*int*) - (1) [1~100000|1] Starting frame for slicing.
* **end** (*int*) - (-1) [-1~100000|1] Ending frame for slicing.
* **steps** (*int*) - (1) [1~100000|1] Step for slicing.
* **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 `@*`).
* **binary_path** (*str*) - ("cpptraj") Path to the cpptraj 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*) - ('afandiadib/ambertools:serial') 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.ambertools.cpptraj_rgyr import cpptraj_rgyr
prop = {
'start': 1,
'end': -1,
'steps': 1,
'mask': 'c-alpha'
}
cpptraj_rgyr(input_top_path='/path/to/myTopology.top',
input_traj_path='/path/to/myTrajectory.dcd',
output_cpptraj_path='/path/to/newAnalysis.dat',
properties=prop)
Info:
* wrapped_software:
* name: Ambertools Cpptraj
* version: >=20.0
* license: GNU
* ontology:
* name: EDAM
* schema: http://edamontology.org/EDAM.owl
"""
def __init__(self, input_top_path, input_traj_path, output_cpptraj_path,
properties=None, **kwargs) -> None:
properties = properties or {}
# Call parent class constructor
super().__init__(properties)
self.locals_var_dict = locals().copy()
# Input/Output files
self.io_dict = {
"in": {"input_top_path": input_top_path, "input_traj_path": input_traj_path},
"out": {"output_cpptraj_path": output_cpptraj_path}
}
# Properties specific for BB
self.instructions_file = get_default_value('instructions_file')
self.start = properties.get('start', 1)
self.end = properties.get('end', -1)
self.steps = properties.get('steps', 1)
self.mask = properties.get('mask', 'all-atoms')
self.properties = properties
self.binary_path = get_binary_path(properties, 'binary_path')
# Check the properties
self.check_properties(properties)
self.check_arguments()
[docs] def check_data_params(self, out_log, err_log):
""" Checks all the input/output paths and parameters """
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__)
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["out"]["output_cpptraj_path"] = check_out_path(self.io_dict["out"]["output_cpptraj_path"], out_log, self.__class__.__name__)
self.in_parameters = {'start': self.start, 'end': self.end, 'step': self.steps, 'mask': self.mask}
[docs] def create_instructions_file(self, container_io_dict, out_log, err_log):
"""Creates an input file using the properties file settings"""
instructions_list = []
# different path if container execution or not
if self.container_path:
self.instructions_file = str(PurePath(self.container_volume_path).joinpath(self.instructions_file))
else:
self.instructions_file = str(PurePath(fu.create_unique_dir()).joinpath(self.instructions_file))
fu.create_name(prefix=self.prefix, step=self.step, name=self.instructions_file)
# parm
instructions_list.append('parm ' + container_io_dict["in"]["input_top_path"])
# trajin
in_params = get_in_parameters(self.in_parameters, out_log)
instructions_list.append('trajin ' + container_io_dict["in"]["input_traj_path"] + ' ' + in_params)
# Set up
instructions_list += setup_structure(self)
# mask
mask = self.in_parameters.get('mask', '')
if mask:
strip_mask = get_negative_mask(mask, out_log)
instructions_list.append('strip ' + strip_mask)
# output
instructions_list.append('radgyr time 1 out ' + container_io_dict["out"]["output_cpptraj_path"])
# create .in file
with open(self.instructions_file, 'w') as mdp:
for line in instructions_list:
mdp.write(line.strip() + '\n')
return self.instructions_file
[docs] @launchlogger
def launch(self) -> int:
"""Execute the :class:`CpptrajRgyr <ambertools.cpptraj_rgyr.CpptrajRgyr>` ambertools.cpptraj_rgyr.CpptrajRgyr 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()
# create instructions file
self.create_instructions_file(self.stage_io_dict, self.out_log, self.err_log)
# if container execution, copy intructions file to container
if self.container_path:
copy_instructions_file_to_container(self.instructions_file, self.stage_io_dict['unique_dir'])
# create cmd and launch execution
self.cmd = [self.binary_path, '-i', self.instructions_file]
# Run Biobb block
self.run_biobb()
# Copy files to host
self.copy_to_host()
# remove temporary folder(s)
self.tmp_files.extend([
self.stage_io_dict.get("unique_dir"),
PurePath(self.instructions_file).parent
])
self.remove_tmp_files()
self.check_arguments(output_files_created=True, raise_exception=False)
return self.return_code
[docs]def cpptraj_rgyr(input_top_path: str, input_traj_path: str, output_cpptraj_path: str, properties: dict = None, **kwargs) -> int:
"""Execute the :class:`CpptrajRgyr <ambertools.cpptraj_rgyr.CpptrajRgyr>` class and
execute the :meth:`launch() <ambertools.cpptraj_rgyr.CpptrajRgyr.launch>` method."""
return CpptrajRgyr(input_top_path=input_top_path,
input_traj_path=input_traj_path,
output_cpptraj_path=output_cpptraj_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="Computes the radius of gyration (Rgyr) from a given cpptraj compatible trajectory.", 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_top_path', required=True, help='Path to the input structure or topology file. Accepted formats: top, pdb, prmtop, parmtop, zip.')
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.')
required_args.add_argument('--output_cpptraj_path', required=True, help='Path to the output analysis.')
args = parser.parse_args()
args.config = args.config or "{}"
properties = settings.ConfReader(config=args.config).get_prop_dic()
# Specific call of each building block
cpptraj_rgyr(input_top_path=args.input_top_path,
input_traj_path=args.input_traj_path,
output_cpptraj_path=args.output_cpptraj_path,
properties=properties)
if __name__ == '__main__':
main()