#!/usr/bin/env python3
"""Module containing the Cpptraj Rms 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, get_mask, get_reference_rms
[docs]class CpptrajRms(BiobbObject):
"""
| biobb_analysis CpptrajRms
| Wrapper of the Ambertools Cpptraj module for calculating the Root Mean Square deviation (RMSd) of 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).
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).
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.rms.first.dat>`_. Accepted formats: dat (edam:format_1637), agr (edam:format_2033), xmgr (edam:format_2033), gnu (edam:format_2033).
output_traj_path (str) (Optional): Path to the output processed trajectory. File type: output. `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).
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 `@*`).
* **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).
* **nofit** (*bool*) - (False) Do not perform best-fit RMSD
* **norotate** (*bool*) - (False) Translate but do not rotate coordinates
* **nomod** (*bool*) - (False) Do not modify coordinates
* **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_rms import cpptraj_rms
prop = {
'start': 1,
'end': -1,
'steps': 1,
'mask': 'c-alpha',
'reference': 'first'
}
cpptraj_rms(input_top_path='/path/to/myTopology.top',
input_traj_path='/path/to/myTrajectory.dcd',
output_cpptraj_path='/path/to/newAnalysis.dat',
input_exp_path= '/path/to/myExpStructure.pdb',
output_traj_path='/path/to/newTrajectory.netcdf',
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,
input_exp_path=None, output_traj_path=None, 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, "input_exp_path": input_exp_path},
"out": {"output_cpptraj_path": output_cpptraj_path, "output_traj_path": output_traj_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.reference = properties.get('reference', 'first')
self.nofit = properties.get('nofit', False)
self.norotate = properties.get('norotate', False)
self.nomod = properties.get('nomod', False)
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__)
if self.io_dict["out"]["output_traj_path"]:
self.io_dict["out"]["output_traj_path"] = check_out_path(self.io_dict["out"]["output_traj_path"], out_log, self.__class__.__name__)
self.in_parameters = {'start': self.start, 'end': self.end, 'step': self.steps, 'mask': self.mask, 'reference': self.reference}
[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', '')
ref_mask = ''
if mask:
strip_mask = get_negative_mask(mask, out_log)
ref_mask = get_mask(mask, out_log)
instructions_list.append('strip ' + strip_mask)
# reference
reference = self.in_parameters.get('reference', '')
inp_exp_pth = None
if "input_exp_path" in container_io_dict["in"]:
inp_exp_pth = container_io_dict["in"]["input_exp_path"]
instructions_list += get_reference_rms(reference, container_io_dict["out"]["output_cpptraj_path"], inp_exp_pth, ref_mask, True,
self.__class__.__name__, out_log, self.nofit, self.norotate, self.nomod)
# trajout
if ("output_traj_path" in container_io_dict["out"]):
instructions_list.append('trajout ' + container_io_dict["out"]["output_traj_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:`CpptrajRms <ambertools.cpptraj_rms.CpptrajRms>` ambertools.cpptraj_rms.CpptrajRms 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_rms(input_top_path: str, input_traj_path: str, output_cpptraj_path: str, input_exp_path: str = None, output_traj_path: str = None, properties: dict = None, **kwargs) -> int:
"""Execute the :class:`CpptrajRms <ambertools.cpptraj_rms.CpptrajRms>` class and
execute the :meth:`launch() <ambertools.cpptraj_rms.CpptrajRms.launch>` method."""
return CpptrajRms(input_top_path=input_top_path,
input_traj_path=input_traj_path,
output_cpptraj_path=output_cpptraj_path,
input_exp_path=input_exp_path,
output_traj_path=output_traj_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="Calculates the Root Mean Square deviation (RMSd) of 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.')
parser.add_argument('--input_exp_path', required=False, help='Path to the experimental reference file (required if reference = experimental).')
required_args.add_argument('--output_cpptraj_path', required=True, help='Path to the output processed analysis.')
parser.add_argument('--output_traj_path', required=False, help='Path to the output processed trajectory.')
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_rms(input_top_path=args.input_top_path,
input_traj_path=args.input_traj_path,
output_cpptraj_path=args.output_cpptraj_path,
input_exp_path=args.input_exp_path,
output_traj_path=args.output_traj_path,
properties=properties)
if __name__ == '__main__':
main()