cphstats package
Submodules
cphstats.cphstats_run module
Module containing the Cphstats class and the command line interface.
- class cphstats.cphstats_run.CphstatsRun(input_cpin_path: str, input_cpout_path: str, output_dat_path: str, output_population_path: Optional[str] = None, output_chunk_path: Optional[str] = None, output_cumulative_path: Optional[str] = None, output_conditional_path: Optional[str] = None, output_chunk_conditional_path: Optional[str] = None, properties: Optional[dict] = None, **kwargs)[source]
Bases:
BiobbObject
biobb_amber CphstatsRunWrapper of the AmberTools (AMBER MD Package) cphstats tool module.Analyzing the results of constant pH MD simulations using cphstats tool from the AMBER MD package.- Parameters
input_cpin_path (str) – Input constant pH file (AMBER cpin). File type: input. Sample file. Accepted formats: cpin (edam:format_2330).
input_cpout_path (str) –
Output constant pH file (AMBER cpout). File type: input. Sample file. Accepted formats: cpout (edam:format_2330), zip (edam:format_3987), gzip (edam:format_3987).
output_dat_path (str) –
Output file to which the standard calcpka-type statistics are written. File type: output. Sample file. 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. 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. 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. 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. 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. 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 calcpka-style output file. Options are: False - Just print fraction protonated. True - Print everything calcpka 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.
protonated (bool) - (True) Print out protonation fraction instead of deprotonation fraction in time series data.
pka (bool) - (False) Print predicted pKas -via Henderson-Hasselbalch equation- in place of fraction -de-protonated.
calcpka (bool) - (True) Triggers the calcpka-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 cphstats 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) - (“cphstats”) Path to the cphstats 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.cphstats.cphstats_run import cphstats_run prop = { 'timestep' : 0.002 } cphstats_run(input_cpin_path='/path/to/cpin.cpin', input_cpout_path='/path/to/cpout.cpout', output_dat_path='/path/to/cphstats.dat', properties=prop)
- Info:
- wrapped_software:
name: AMBER cphstats
version: >=1.5
license: other
- ontology:
name: EDAM
schema: http://edamontology.org/EDAM.owl
- cphstats.cphstats_run.cphstats_run(input_cpin_path: str, input_cpout_path: str, output_dat_path: str, output_population_path: Optional[str] = None, output_chunk_path: Optional[str] = None, output_conditional_path: Optional[str] = None, output_chunk_conditional_path: Optional[str] = None, output_cumulative_path: Optional[str] = None, properties: Optional[dict] = None, **kwargs) int [source]
Create
CphstatsRun
method
cphstats.cestats_run module
Module containing the Cestats class and the command line interface.
- class cphstats.cestats_run.CestatsRun(input_cein_path: str, input_ceout_path: str, output_dat_path: str, output_population_path: Optional[str] = None, output_chunk_path: Optional[str] = None, output_cumulative_path: Optional[str] = None, output_conditional_path: Optional[str] = None, output_chunk_conditional_path: Optional[str] = None, properties: Optional[dict] = None, **kwargs)[source]
Bases:
BiobbObject
biobb_amber CestatsRunWrapper of the AmberTools (AMBER MD Package) cestats tool module.Analyzing the results of constant Redox potential MD simulations using cestats tool from the AMBER MD package.- Parameters
input_cein_path (str) –
Input cein or cpein file (from pmemd or sander) with titrating residue information. File type: input. Sample file. Accepted formats: cein (edam:format_2330), cpein (edam:format_2330).
input_ceout_path (str) –
Output ceout file (AMBER ceout). File type: input. Sample file. 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. 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. 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. 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. 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. 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. 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
- cphstats.cestats_run.cestats_run(input_cein_path: str, input_ceout_path: str, output_dat_path: str, output_population_path: Optional[str] = None, output_chunk_path: Optional[str] = None, output_conditional_path: Optional[str] = None, output_chunk_conditional_path: Optional[str] = None, output_cumulative_path: Optional[str] = None, properties: Optional[dict] = None, **kwargs) int [source]
Create
CestatsRun
method