Source code for cphstats.cestats_run

#!/usr/bin/env python3

"""Module containing the Cestats 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_amber.cphstats.common import check_input_path, check_output_path


[docs]class CestatsRun(BiobbObject): """ | biobb_amber CestatsRun | Wrapper of the `AmberTools (AMBER MD Package) cestats tool <https://ambermd.org/AmberTools.php>`_ module. | Analyzing the results of constant Redox potential MD simulations using cestats tool from the AMBER MD package. Args: input_cein_path (str): Input cein or cpein file (from pmemd or sander) with titrating residue information. File type: input. `Sample file <https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/data/cphstats/structure.cein>`_. Accepted formats: cein (edam:format_2330), cpein (edam:format_2330). input_ceout_path (str): Output ceout file (AMBER ceout). File type: input. `Sample file <https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/data/cphstats/sander.ceout.gz>`_. Accepted formats: ceout (edam:format_2330), zip (edam:format_3987), gzip (edam:format_3987), gz (edam:format_3987). output_dat_path (str): Output file to which the standard calceo-type statistics are written. File type: output. `Sample file <https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/reference/cphstats/cestats.dat>`_. Accepted formats: dat (edam:format_2330), out (edam:format_2330), txt (edam:format_2330), o (edam:format_2330). output_population_path (str) (Optional): Output file where protonation state populations are printed for every state of every residue. File type: output. `Sample file <https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/reference/cphstats/cestats.dat>`_. Accepted formats: dat (edam:format_2330), out (edam:format_2330), txt (edam:format_2330), o (edam:format_2330). output_chunk_path (str) (Optional): Output file where the time series data calculated over chunks of the simulation are printed. File type: output. `Sample file <https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/reference/cphstats/cestats.dat>`_. Accepted formats: dat (edam:format_2330), out (edam:format_2330), txt (edam:format_2330), o (edam:format_2330). output_cumulative_path (str) (Optional): Output file where the cumulative time series data is printed. File type: output. `Sample file <https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/reference/cphstats/cestats.dat>`_. Accepted formats: dat (edam:format_2330), out (edam:format_2330), txt (edam:format_2330), o (edam:format_2330). output_conditional_path (str) (Optional): Output file with requested conditional probabilities. File type: output. `Sample file <https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/reference/cphstats/cestats.dat>`_. Accepted formats: dat (edam:format_2330), out (edam:format_2330), txt (edam:format_2330), o (edam:format_2330). output_chunk_conditional_path (str) (Optional): Output file with a time series of the conditional probabilities over a trajectory split up into chunks. File type: output. `Sample file <https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/reference/cphstats/cestats.dat>`_. Accepted formats: dat (edam:format_2330), out (edam:format_2330), txt (edam:format_2330), o (edam:format_2330). properties (dict - Python dictionary object containing the tool parameters, not input/output files): * **timestep** (*float*) - (0.002) Simulation time step -in ps-, used to print data as a function of time. * **verbose** (*bool*) - (False) Controls how much information is printed to the calceo-style output file. Options are: False - Just print fraction protonated. True - Print everything calceo prints. * **interval** (*int*) - (1000) Interval between which to print out time series data like chunks, cumulative data, and running averages. It is also used as the window of the conditional probability time series. * **reduced** (*bool*) - (True) Print out reduction fraction instead of oxidation fraction in time series data. * **eos** (*bool*) - (False) Print predicted Eos -via Nernst equation- in place of fraction reduced or oxidized. * **calceo** (*bool*) - (True) Triggers the calceo-style output. * **running_avg_window** (*int*) - (100) Defines a window size -in MD steps- for a moving, running average time series. * **chunk_window** (*int*) - (100) Computes the time series data over a chunk of the simulation of this specified size -window- time steps. * **cumulative** (*bool*) - (False) Computes the cumulative average time series data over the course of the trajectory. * **fix_remd** (*str*) - ("") This option will trigger cestats to reassemble the titration data into pH-specific ensembles. This is an exclusive mode of the program, no other analyses will be done. * **conditional** (*str*) - ("") Evaluates conditional probabilities. CONDITIONAL should be a string of the format: <resid>:<state>,<resid>:<state>,... or <resid>:PROT,<resid>:DEPROT,... or <resid>:<state1>;<state2>,<resid>:PROT,... where <resid> is the residue number in the prmtop and <state> is either the state number or -p-rotonated or -d-eprotonated, case-insensitive. * **binary_path** (*str*) - ("cestats") Path to the cestats 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_amber.cestats.cestats_run import cestats_run prop = { 'timestep' : 0.002 } cestats_run(input_cein_path='/path/to/cein.cein', input_ceout_path='/path/to/ceout.cpout', output_dat_path='/path/to/cestats.dat', properties=prop) Info: * wrapped_software: * name: AMBER cestats * version: >=1.5 * license: other * ontology: * name: EDAM * schema: http://edamontology.org/EDAM.owl """ def __init__(self, input_cein_path: str, input_ceout_path: str, output_dat_path: str, output_population_path: str = None, output_chunk_path: str = None, output_cumulative_path: str = None, output_conditional_path: str = None, output_chunk_conditional_path: str = None, properties: dict = 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_cein_path': input_cein_path, 'input_ceout_path': input_ceout_path}, 'out': {'output_dat_path': output_dat_path, 'output_population_path': output_population_path, 'output_chunk_path': output_chunk_path, 'output_cumulative_path': output_cumulative_path, 'output_conditional_path': output_conditional_path, 'output_chunk_conditional_path': output_chunk_conditional_path} } # Properties specific for BB self.properties = properties self.timestep = properties.get('timestep', 0.002) self.verbose = properties.get('verbose', False) self.interval = properties.get('interval', 1000) self.reduced = properties.get('reduced', True) self.eos = properties.get('eos', False) self.calceo = properties.get('calceo', True) self.running_avg_window = properties.get('running_avg_window', 100) self.chunk_window = properties.get('chunk_window', 100) self.cumulative = properties.get('cumulative', False) self.fix_remd = properties.get('fix_remd', "") self.conditional = properties.get('conditional', "") self.binary_path = properties.get('binary_path', 'cestats') # Check the properties self.check_properties(properties) self.check_arguments()
[docs] def check_data_params(self, out_log, err_log): """ Checks input/output paths correctness """ # Check input(s) self.io_dict["in"]["input_cein_path"] = check_input_path(self.io_dict["in"]["input_cein_path"], "input_cein_path", False, out_log, self.__class__.__name__) self.io_dict["in"]["input_ceout_path"] = check_input_path(self.io_dict["in"]["input_ceout_path"], "input_ceout_path", False, out_log, self.__class__.__name__) # Check output(s) self.io_dict["out"]["output_dat_path"] = check_output_path(self.io_dict["out"]["output_dat_path"], "output_dat_path", False, out_log, self.__class__.__name__) self.io_dict["out"]["output_population_path"] = check_output_path(self.io_dict["out"]["output_population_path"], "output_population_path", True, out_log, self.__class__.__name__) self.io_dict["out"]["output_chunk_path"] = check_output_path(self.io_dict["out"]["output_chunk_path"], "output_chunk_path", True, out_log, self.__class__.__name__) self.io_dict["out"]["output_cumulative_path"] = check_output_path(self.io_dict["out"]["output_cumulative_path"], "output_cumulative_path", True, out_log, self.__class__.__name__) self.io_dict["out"]["output_chunk_conditional_path"] = check_output_path(self.io_dict["out"]["output_chunk_conditional_path"], "output_chunk_conditional_path", True, out_log, self.__class__.__name__) self.io_dict["out"]["output_conditional_path"] = check_output_path(self.io_dict["out"]["output_conditional_path"], "output_conditional_path", True, out_log, self.__class__.__name__)
[docs] @launchlogger def launch(self): """Launches the execution of the CestatsRun module.""" # 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() # Command line # cphstats -i 4LYT.equil.cpin 0/4LYT.md1.cpout -o pH0_calcpka.dat --population pH0_populations.dat self.cmd = [self.binary_path, '-O', '-i', self.stage_io_dict['in']['input_cein_path'], '-o', self.stage_io_dict['out']['output_dat_path'], self.stage_io_dict['in']['input_ceout_path'] ] if self.io_dict['out']['output_population_path']: self.cmd.append('--population ') self.cmd.append(self.stage_io_dict['out']['output_population_path']) if self.io_dict['out']['output_chunk_path']: self.cmd.append('--chunk-out ') self.cmd.append(self.stage_io_dict['out']['output_chunk_path']) if self.chunk_window: self.cmd.append('--chunk') self.cmd.append(str(self.chunk_window)) if self.io_dict['out']['output_cumulative_path']: self.cmd.append('--cumulative-out ') self.cmd.append(self.stage_io_dict['out']['output_cumulative_path']) if self.io_dict['out']['output_conditional_path']: self.cmd.append('--conditional-output ') self.cmd.append(self.stage_io_dict['out']['output_conditional_path']) if self.io_dict['out']['output_chunk_conditional_path']: self.cmd.append('--chunk-conditional ') self.cmd.append(self.stage_io_dict['out']['output_chunk_conditional_path']) if self.verbose: self.cmd.append('-v 1') if self.interval: self.cmd.append('-n') self.cmd.append(str(self.interval)) if self.reduced: self.cmd.append('-p') else: self.cmd.append('-d') if self.eos: self.cmd.append('-a') if self.calceo: self.cmd.append('--calceo') else: self.cmd.append('--no-calceo') if self.running_avg_window: self.cmd.append('-r') self.cmd.append(str(self.running_avg_window)) if self.cumulative: self.cmd.append('--cumulative') if self.fix_remd: self.cmd.append('--fix-remd') self.cmd.append(str(self.fix_remd)) if self.conditional: self.cmd.append('-c') self.cmd.append(str(self.conditional)) # Run Biobb block self.run_biobb() # Copy files to host self.copy_to_host() # Remove temporary file(s) self.tmp_files.extend([ self.stage_io_dict.get("unique_dir") ]) self.remove_tmp_files() self.check_arguments(output_files_created=True, raise_exception=False) return self.return_code
[docs]def cestats_run(input_cein_path: str, input_ceout_path: str, output_dat_path: str, output_population_path: str = None, output_chunk_path: str = None, output_conditional_path: str = None, output_chunk_conditional_path: str = None, output_cumulative_path: str = None, properties: dict = None, **kwargs) -> int: """Create :class:`CestatsRun <cestats.chpstats_run.CestatsRun>`cestats.chpstats_run.CestatsRun class and execute :meth:`launch() <cestats.chpstats_run.CestatsRun.launch>` method""" return CestatsRun(input_cein_path=input_cein_path, input_ceout_path=input_ceout_path, output_dat_path=output_dat_path, output_population_path=output_population_path, output_chunk_path=output_chunk_path, output_chunk_conditional_path=output_chunk_conditional_path, output_conditional_path=output_conditional_path, output_cumulative_path=output_cumulative_path, properties=properties).launch()
[docs]def main(): parser = argparse.ArgumentParser(description='Analyzing the results of constant Redox potential MD simulations using cestats tool from the AMBER MD package.', formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999)) parser.add_argument('--config', required=False, help='Configuration file') # Specific args required_args = parser.add_argument_group('required arguments') required_args.add_argument('--input_cein_path', required=True, help='Input cein or cpein file (from pmemd or sander) with titrating residue information. Accepted formats: cein, cpein.') required_args.add_argument('--input_ceout_path', required=True, help='Output ceout file (AMBER ceout). Accepted formats: ceout.') required_args.add_argument('--output_dat_path', required=True, help='Output file to which the standard calceo-type statistics are written. Accepted formats: dat, out, txt, o.') required_args.add_argument('--output_population_path', required=False, help='Output file where protonation state populations are printed for every state of every residue. Accepted formats: dat, out, txt, o.') required_args.add_argument('--output_chunk_path', required=False, help='Output file where the time series data calculated over chunks of the simulation are printed. Accepted formats: dat, out, txt, o.') required_args.add_argument('--output_cumulative_path', required=False, help='Output file where the cumulative time series data is printed. Accepted formats: dat, out, txt, o.') required_args.add_argument('--output_conditional_path', required=False, help='Output file with requested conditional probabilities. Accepted formats: dat, out, txt, o.') required_args.add_argument('--output_chunk_conditional_path', required=False, help='Output file with a time series of the conditional probabilities over a trajectory split up into chunks. Accepted formats: dat, out, txt, o.') args = parser.parse_args() config = args.config if args.config else None properties = settings.ConfReader(config=config).get_prop_dic() # Specific call cestats_run(input_cein_path=args.input_cein_path, input_ceout_path=args.input_ceout_path, output_dat_path=args.output_dat_path, output_population_path=args.output_population_path, output_chunk_path=args.output_chunk_path, output_cumulative_path=args.output_cumulative_path, output_conditional_path=args.output_conditional_path, output_chunk_conditional_path=args.output_chunk_conditional_path, properties=properties)
if __name__ == '__main__': main()