Package schrodinger :: Package application :: Package desmond :: Module gconfig

Module gconfig

Utilities for handling gDesmond config files.

Functions

real_to_int(val)
round up to the closest integer when the difference is less than 1e-7

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

__get_epsilon_lambda_schedule(n_win=16, B=False)
generate lambda schedule for epsilons in soft-core potentials n_win: number of windows B: final state

__get_flexible_lambda_schedule()
Return sea.List object for flexible lambda schedules FIXME: the number of windowns is hardcoded to 16

__set_fep(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)

sea.Map

concatenate_cfgs(simulate_cfgs, base_cfg)
Create a single backend config file from a list of simulate configs created from the simulate block of a concatenate front-end config and the backend config created from the rest of the concatenate front-end config.

set_relative_restrain_scaling(first_restrain, restrain, this_integrator)
Set each integrator's posre_scaling attribute to the ratio between the desired restraint force constant and the first force constant.

_restrain_force_constant(restrain)
Get the force constant for a restrain parameter

_check_restrain_diffs(restrain, first_restrain)
Check that the restrain parameters do not differ in any way except the force constant.

__optimize_cfg(msj, cfg, model)

__clean_cfg(cfg)

__fix_cfg(msj, cfg)

__msj2cfg_helper(msj, cfg, model, macro)

msj2cfg(msj, cfg, model, macro=None)

Variables

[hide private]

DEFAULT_CONFIG = '{\napp = mdsim # mdsim | remd |\nbo...

default_flex_vdw = ' {\n vdwA = "@*.*.weights.v...

default_flex_bond = ' {\n A = "@*.*.weights.bon...

default_flex_dihe = ' {\n A = "@*.*.flexible[0]...

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

model = cms.Cms(file= sys.argv [2])

cfg = msj2cfg(msj, None, model, {"$JOBNAME": "test",})

__package__ = 'schrodinger.application.desmond'

Function Details

[hide private]

concatenate_cfgs(simulate_cfgs, base_cfg)

Create a single backend config file from a list of simulate configs created from the simulate block of a concatenate front-end config and the backend config created from the rest of the concatenate front-end config.

Parameters:

simulate_cfgs (list of sea.Map) - The list of backend config files created from the simulate block of a concatenate front-end config
base_cfg (sea.Map) - The backend config file created from a concatenate front-end config, with its simulate block removed.

Returns: sea.Map

A copy of the base concatenate config with the information from the simulate configs merged in.

set_relative_restrain_scaling(first_restrain, restrain, this_integrator)

Set each integrator's posre_scaling attribute to the ratio between the desired restraint force constant and the first force constant. This allows us to modulate the restraint force constant between concatenate stages.

Parameters:

first_restrain (sea.Map) - the restrain parameter from the first stage's config, or None if updating the first stage
restrain (sea.Map) - this stage's restrain parameter
this_integrator (sea.Map) - this stage's integrator

Returns:

the first restrain parameter and the first force constant

Variables Details

[hide private]

DEFAULT_CONFIG

Value:

'''{
app       = mdsim    # mdsim | remd |
boot.file = filename

global_cell = {
   reference_time       = 0.0
   topology             = periodic
   n_replica            = 1
...

default_flex_vdw

Value:

''' {
                vdwA = "@*.*.weights.vdwA"
                vdwB = "@*.*.weights.vdwB"
                qA   = "@*.*.weights.qA"
                qB   = "@*.*.weights.qB"
                name = "%s"} '''

default_flex_bond

Value:

''' {
                A = "@*.*.weights.bondA"
                B = "@*.*.weights.bondB"
                name = "%s" } '''

default_flex_dihe

Value:

''' {
                A = "@*.*.flexible[0].A"
                B = "@*.*.flexible[0].B"
                name = "%s"} '''