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2017-2 Schrodinger Python API
Package schrodinger :: Package application :: Package desmond :: Module config
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Module config

Utilities for handling Desmond config files.

Copyright Schrodinger, LLC. All rights reserved.

Classes [hide private]
  _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')
 
tag_concat(map, tag='CONCAT')
 
is_minimize(msj)
 
is_remd(msj)
 
is_meta(msj)
 
is_vrun(msj)
 
is_concat(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_file(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)
 
__set_restrain(msj, cfg, model)
restrain only used in gconfig.py for concatenator
 
__optimize_cfg(msj, cfg, model)
 
__clean_cfg(cfg)
 
__fix_cfg(msj, cfg)
 
__msj2cfg_helper(msj, cfg, model, macro)
 
msj2cfg(msj, cfg, model, macro=None, 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 [hide private]
  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##################################################\...
  CONCAT = ['\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"
...

META

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"
...

CONCAT

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

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2017-2 Schrodinger Python API
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