process package

Submodules

process.process_minout module

Module containing the ProcessMinOut class and the command line interface.

class process.process_minout.ProcessMinOut(input_log_path: str, output_dat_path: str, properties, **kwargs)[source]

Bases: BiobbObject

biobb_amber.process.process_minout ProcessMinOut
Wrapper of the AmberTools (AMBER MD Package) process_minout tool module.
Parses the AMBER (sander) minimization output file (log) and dumps statistics that can then be plotted. Using the process_minout.pl tool from the AmberTools MD package.
Parameters:

  • input_log_path (str) – AMBER (sander) Minimization output (log) file. File type: input. Sample file. Accepted formats: log (edam:format_2330), out (edam:format_2330), txt (edam:format_2330), o (edam:format_2330).

  • output_dat_path (str) –

    Dat output file containing data from the specified terms along the minimization process. File type: output. Sample file. Accepted formats: dat (edam:format_1637), txt (edam:format_2330), csv (edam:format_3752).

  • properties (dic - Python dictionary object containing the tool parameters, not input/output files) –

    • terms (list) - ([“ENERGY”]) Statistics descriptors. Values: ANGLE, BOND, DIHEDRAL, EEL, EEL14, ENERGY, GMAX, HBOND, NAME, NSTEP, NUMBER, RESTRAINT, RMS, VDW14, VDWAALS.

    • binary_path (str) - (“process_minout.perl”) Path to the process_minout.perl executable binary.

    • remove_tmp (bool) - (True) [WF property] Remove temporal files.

    • restart (bool) - (False) [WF property] Do not execute if output files exist.

    • sandbox_path (str) - (“./”) [WF property] Parent path to the sandbox directory.

    • 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.process.process_minout import process_minout
prop = {
    'terms' : ['ENERGY','RMS']
}
process_minout(input_log_path='/path/to/ambermin.log',
              output_dat_path='/path/to/newFeature.dat',
              properties=prop)
Info:
check_data_params(out_log, out_err)[source]

Checks input/output paths correctness

launch()[source]

Launches the execution of the ProcessMinOut module.

process.process_minout.main()[source]
process.process_minout.process_minout(input_log_path: str, output_dat_path: str, properties: dict | None = None, **kwargs) → int[source]

Create ProcessMinOut method

process.process_mdout module

Module containing the ProcessMDOut class and the command line interface.

class process.process_mdout.ProcessMDOut(input_log_path: str, output_dat_path: str, properties, **kwargs)[source]

Bases: BiobbObject

biobb_amber.process.process_mdout ProcessMDOut
Wrapper of the AmberTools (AMBER MD Package) process_mdout tool module.
Parses the AMBER (sander) md output file (log) and dumps statistics that can then be plotted. Using the process_mdout.pl tool from the AmberTools MD package.
Parameters:

  • input_log_path (str) –

    AMBER (sander) MD output (log) file. File type: input. Sample file. Accepted formats: log (edam:format_2330), out (edam:format_2330), txt (edam:format_2330), o (edam:format_2330).

  • output_dat_path (str) –

    Dat output file containing data from the specified terms along the minimization process. File type: output. Sample file. Accepted formats: dat (edam:format_1637), txt (edam:format_2330), csv (edam:format_3752).

  • properties (dic - Python dictionary object containing the tool parameters, not input/output files) –

    • terms (list) - ([“ETOT”]) Statistics descriptors. Values: VOLUME, TSOLVENT, TSOLUTE, TEMP, PRES, ETOT, ESCF, EPTOT, EKTOT, EKCMT, DENSITY.

    • binary_path (str) - (“process_mdout.perl”) Path to the process_mdout.perl executable binary.

    • remove_tmp (bool) - (True) [WF property] Remove temporal files.

    • restart (bool) - (False) [WF property] Do not execute if output files exist.

    • sandbox_path (str) - (“./”) [WF property] Parent path to the sandbox directory.

    • 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.process.process_mdout import process_mdout
prop = {
    'terms' : ['TEMP','VOLUME','DENSITY']
}
process_mdout(input_log_path='/path/to/ambermd.log',
              output_dat_path='/path/to/newFeature.dat',
              properties=prop)
Info:
check_data_params(out_log, err_log)[source]

Checks input/output paths correctness

launch()[source]

Launches the execution of the ProcessMDOut module.

process.process_mdout.main()[source]
process.process_mdout.process_mdout(input_log_path: str, output_dat_path: str, properties: dict | None = None, **kwargs) → int[source]

Create ProcessMDOut method