transformato.state

Description

Classes

class transformato.state.IntermediateStateFactory(system, configuration, multiple_runs=False)[source]
Parameters:
__init__(system, configuration, multiple_runs=False)[source]

Generate the intermediate directories with for the provided systems with the provided mutations. :param system: definition of the two states for a given system (either waterbox and vacuum or waterbox and complex) :type system: transformato.system :param mutation_list: list of mutations defined by the transformato.ProposeMutationRoute object :type mutation_list: list :param configuration: configuration dictionary :type configuration: dict :param multiple_runs: defines how many runs should be performed per intst state, if not used it is 0 (=False) else give an integer number :type multiple_runs: bool or int

Parameters:
__weakref__

list of weak references to the object

_check_hmr(file)[source]

add hmr if requested in config file

_copy_charmm_files(intermediate_state_file_path)[source]

_copy_charmm_files Copy CHARMM specific files in running directories

Parameters:

intermediate_state_file_path ([type]) – [description]

_copy_files(intermediate_state_file_path)[source]

Copy the files from the original CHARMM-GUI output folder in the intermediate directories.

Parameters:

intermediate_state_file_path (str)

_copy_omm_files(intermediate_state_file_path)[source]

_copy_omm_files Copyies the files needed for the production runs with openMM in the intst* directories

Parameters:

intermediate_state_file_path (str) – [description]

Raises:

RuntimeError – [description]

_init_base_dir()[source]

Generates the base directory in which all intermediate states are located and create the central toppar dir.

_init_intermediate_state_dir(nr)[source]

Generates the intermediate state directory.

Parameters:

nr (int)

_overwrite_simulation_script_parameters(omm_simulation_parameter_source, omm_simulation_parameter_target)[source]

_overwrite_simulation_script_parameters changes parameters that are defined in omm_simulation_parameter_source

Parameters:

  • omm_simulation_parameter_source (str) – key:value pair file that defines parameters to overwrite

  • omm_simulation_parameter_target (str) – new parameter file for simulation

_write_amber_files(psf, output_file_base, tlc, env)[source]

Write a parm7 and rst7 file for each intermediate step, including information about the dummy atoms

Parameters:

  • psf (AmberParm)

  • output_file_base (str)

  • tlc (str)

  • env (str)

static _write_psf(psf, output_file_base, env)[source]

Writes the new psf and pdb file.

Parameters:

  • output_file_base (str)

  • env (str)

_write_rtf_file(psf, output_file_base, tlc)[source]

Generates the dummy atom parameter rtf.

_write_workload_preamble(filepath)[source]

Prepends the preamble of the selected workload manager in the file specified by filepath

The preamble is the *-preamble.sh file found in transformato/bin

Parameters:

filepath (str) – Path to the file (usually _script_target)

write_state(mutation_conf, lambda_value_electrostatic=1.0, lambda_value_vdw=1.0, common_core_transformation=1.0)[source]

write_state Defines everything that is written to the intermediate state directories

Parameters:

  • mutation_conf (List) – [description]

  • lambda_value_electrostatic (float, optional) – [description], by default 1.0

  • lambda_value_vdw (float, optional) – [description], by default 1.0

  • common_core_transformation (float, optional) – [description], by default 1.0