Package schrodinger :: Package application :: Package desmond :: Module config

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Module config

Utilities for handling Desmond config files.

Classes

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_create_when_needed

DEFAULT_SETTING

_FepSchedule

Functions

[hide private]

extract_cfg(cpt_fname, min_size=1048576, return_raw=False)
Extracts the extended ark content from a checkpoint file.

has_plugin(desmond_exec, plugin_name)

add_plugin(desmond_exec, plugin_name, position=None)

remove_plugin(desmond_exec, plugin_name)

get_homebox(box, cpu_top)

is_triclinic_box(box)

optimize_key(msj, cfg, model)
Optimizes the simulation parameters in 'cfg', where 'cfg' must represent a complete config file.

parse_lambda(s)

lambda_type(lambda_)

num_lambda_window(lambda_)

get_fep_lambda_schedule(lambda_, fep_type)

_xchk_check_lambda(map, valid, ev, prefix)

_xchk_check_iwindow(map, valid, ev, prefix)

_xchk_check_annealing(map, valid, ev, prefix)

_xchk_check_remd_temp_generator(map, valid, ev, prefix)

_xchk_check_remd_temp_generator2(map, valid, ev, prefix)

get_default_setting(msj)

tag_md(map, tag='MD')

tag_minimize(map, tag='MINIMIZE')

tag_remd(map, tag='REMD')

tag_meta(map, tag='META')

tag_vrun(map, tag='VRUN')

is_minimize(msj)

is_remd(msj)

is_meta(msj)

is_vrun(msj)

get_exec(msj, cfg)

get_exec_name(msj)

num_replica(msj, model, printer=None)

num_cpu(msj)

__calc_vdw_lambda(n_win)
Given the number of windows, returns a list of lambda values for VDW potentials.

__calc_charge_lambda(n_win)

__calc_bonded_lambda(n_win)

get_fep_lambdas(n_win, fep_type, scheme)
return default lambdas

__get_regular_lambda_schedule_for_core_hopping(n_win=16)
Return _FepSchedule for core-hopping FIXME: Currently, the number of windows is hard coded to 16.

__get_fep_schedule(n_win, fep_type='alchemical', scheme='default')
Returns a FEP schedule, which is calculated for the given FEP type ('fep_type').

__set_fep(msj, cfg, model)

__set_meta(msj, cfg, model)

__set_cutoff_radius(msj, cfg, model)

__set_bigger_rclone(msj, cfg, model)

__set_taper(msj, cfg, model)

__set_coulomb_method(msj, cfg, model)

__set_temperature(msj, cfg, model)

__set_annealing(msj, cfg, model)

__set_pressure(msj, cfg, model)

__set_surface_tension(msj, cfg, model)

get_ensemble_class_method(msj)

__set_ensemble(msj, cfg, model)

__set_time(msj, cfg, model)

__set_elapsed_time(msj, cfg, model)

__set_timestep(msj, cfg, model)

__set_cpu(msj, cfg, model)

__set_glue(msj, cfg, model)

__set_vrun_frameset(msj, cfg, model)

__set_trajectory(msj, cfg, model)

__set_eneseq(msj, cfg, model)

__set_checkpt(msj, cfg, model)

__set_maeff_output(msj, cfg, model)

__set_randomize_velocity(msj, cfg, model)

__set_simbox(msj, cfg, model)

get_simbox_output_filename(msj)
Returns 'None' if the simbox_output plugin is turned off.

__set_energy_group(msj, cfg, model)

get_energy_group_output_filename(msj)
Returns 'None' if the energy_groups plugin is turned off.

get_fep_output_filename(msj)

__set_max_steps(msj, cfg, model)

__set_convergence(msj, cfg, model)

__set_steepest_descent_steps(msj, cfg, model)

__set_num_vector(msj, cfg, model)

__set_backend(msj, cfg, model)

gen_temperature_for_solute_tempering(setting, model, base_temp, asl, printer=None)

gen_replica(msj, model=None)

__set_replica(msj, cfg, model)

get_replica_setting(msj)

__set_model_file(msj, cfg, model)

__attach_msj(msj, cfg, model)

__optimize_cfg(msj, cfg, model)

__clean_cfg(cfg)

__fix_cfg(msj, cfg)

__msj2cfg_helper(msj, cfg, model, macro)

msj2cfg(msj, cfg, model, macro={}, is_gdesmond=False)

translate_output_file_names_helper(msj, macro_dict)

translate_output_file_names(msj, macro_dict, num_replica=1)

__canonicalize_fep(msj)

__canonicalize_temperature(msj)

__canonicalize_pressure(msj)

__canonicalize_ensemble(msj)

__canonicalize_coulomb_method(msj)

canonicalize(msj)

Variables

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FEP_LAMBDA_SCHEMES = ['default', 'flexible', 'quickcharge', 's...

DEFAULT_CONFIG = '{\nDesmond = {\n config_version = 3\n}\n\n...

MD = '\n##################################################\nDA...

MINIMIZE = ['\n###############################################...

REMD = ['\n##################################################\...

META = ['\n##################################################\...

VRUN = ['\n##################################################\...

msj = sea.Map(open(sys.argv [1], "r").read())

cfg = translate_output_file_names(msj, {"$JOBNAME": "test"})

__package__ = 'schrodinger.application.desmond'

Function Details

[hide private]

extract_cfg(cpt_fname, min_size=1048576, return_raw=False)

Extracts the extended ark content from a checkpoint file. This function returns a `sea.Map' object or None if parsing fails.

The ark as represented by the string contains the following values:

argv : the argument vector
boot_timestamp : the boot time for the program
chemical_time : chemical time in pico seconds
config : the ark file
threader_size : the number of threads
version : the desmond version
world_size : the number of processors

__get_fep_schedule(n_win, fep_type=`'alchemical'`, scheme=`'default'`)

Returns a FEP schedule, which is calculated for the given FEP type ('fep_type').

Parameters:

fep_type - Can take the following values: "alchemical", "binding".

Variables Details

[hide private]

FEP_LAMBDA_SCHEMES

Value:

['default', 'flexible', 'quickcharge', 'superquickcharge']

DEFAULT_CONFIG

Value:

'''{
Desmond = {
   config_version = 3
}

app       = "mdsim"
boot.file = ""

...

MD

Value:

'''
##################################################
DATA = {
fep = {
   lambda   = "default:12"
   i_window = ?
   output   = {
      name     = "$JOBNAME$[_replica$REPLICA$].dE"
...

MINIMIZE

Value:

['''
##################################################
DATA = {
fep = {
   lambda   = "default:12"
   i_window = ?
   output   = {
      name     = "$JOBNAME$[_replica$REPLICA$].dE"
...

REMD

Value:

['''
##################################################
DATA = {
fep = {
   lambda   = "default:12"
   i_window = ?
   output   = {
      name     = "$JOBNAME$[_replica$REPLICA$].dE"
...

VRUN

Value:

['''
##################################################
DATA = {
fep = {
   lambda   = "default:12"
   i_window = ?
   output   = {
      name     = "$JOBNAME$[_replica$REPLICA$].dE"
...

Module config

extract_cfg(cpt_fname, min_size=1048576, return_raw=False)

__get_fep_schedule(n_win, fep_type='alchemical', scheme='default')

FEP_LAMBDA_SCHEMES

DEFAULT_CONFIG

MD

MINIMIZE

REMD

META

VRUN

__get_fep_schedule(n_win, fep_type=`'alchemical'`, scheme=`'default'`)