def _cv_kwargs_remapper(dct):
kwargs = dct.pop('kwargs', {})
dct.update(kwargs)
return dct
# MDTraj-specific
MDTRAJ_CV_PLUGIN = CVCompilerPlugin(
builder=Builder(
'openpathsampling.experimental.storage.'
'collective_variables.MDTrajFunctionCV',
remapper=_cv_kwargs_remapper),
parameters=[
Parameter('topology', build_topology),
Parameter('func',
AllowedPackageHandler('mdtraj'),
json_type='string',
description="MDTraj function, e.g., "
"``compute_distances``"),
Parameter('kwargs',
lambda kwargs:
{key: custom_eval(arg)
for key, arg in kwargs.items()},
json_type='object',
default=None,
description="keyword arguments for ``func``"),
Parameter('period_min',
custom_eval_float,
default=None,
from paths_cli.compiling.core import (
InstanceCompilerPlugin, Builder, Parameter
)
from paths_cli.compiling.tools import custom_eval
from paths_cli.compiling.plugins import (
NetworkCompilerPlugin, CategoryPlugin, InterfaceSetPlugin
)
from paths_cli.compiling.root_compiler import compiler_for
from paths_cli.compiling.json_type import (
json_type_ref, json_type_list, json_type_eval
)
INITIAL_STATES_PARAM = Parameter(
'initial_states', compiler_for('volume'),
json_type=json_type_list(json_type_ref('volume')),
description="initial states for this transition",
)
INITIAL_STATE_PARAM = Parameter(
'initial_state', compiler_for('volume'),
json_type=json_type_list(json_type_ref('volume')),
description="initial state for this transition",
)
FINAL_STATES_PARAM = Parameter(
'final_states', compiler_for('volume'),
json_type=json_type_list(json_type_ref('volume')),
description="final states for this transition",
def _openmm_options(dct):
n_steps_per_frame = dct.pop('n_steps_per_frame')
n_frames_max = dct.pop('n_frames_max')
options = {
'n_steps_per_frame': n_steps_per_frame,
'n_frames_max': n_frames_max
}
dct['options'] = options
return dct
OPENMM_PARAMETERS = [
Parameter('topology',
build_topology,
json_type='string',
description=("File describing the topoplogy of this system; "
"PDB recommended")),
Parameter('system',
load_openmm_xml,
json_type='string',
description="XML file with the OpenMM system"),
Parameter('integrator',
load_openmm_xml,
json_type='string',
description="XML file with the OpenMM integrator"),
Parameter('n_steps_per_frame',
custom_eval_int_strict_pos,
json_type=json_type_eval('IntStrictPos'),
description="number of MD steps per saved frame"),
Parameter("n_frames_max",
builder = paths.CVDefinedVolume
if cv.period_min is not None or cv.period_max is not None:
builder = paths.PeriodicCVDefinedVolume
dct['period_min'] = cv.period_min
dct['period_max'] = cv.period_max
dct['collectivevariable'] = dct.pop('cv')
# TODO: wrap this with some logging
return builder(**dct)
CV_VOLUME_PLUGIN = VolumeCompilerPlugin(
builder=cv_volume_build_func,
parameters=[
Parameter('cv',
compiler_for('cv'),
json_type=json_type_ref('cv'),
description="CV that defines this volume"),
Parameter('lambda_min',
custom_eval_float,
json_type=json_type_eval("Float"),
description="Lower bound for this volume"),
Parameter('lambda_max',
custom_eval_float,
json_type=json_type_eval("Float"),
description="Upper bound for this volume")
],
description=("A volume defined by an allowed range of values for the "
"given CV."),
name='cv-volume',
)
def _group_parameter(group_name):
return Parameter('group',
str,
json_type="string",
default=group_name,
description="the group name for these movers")
def _strategy_name(class_name):
return f"openpathsampling.strategies.{class_name}"
def _group_parameter(group_name):
return Parameter('group',
str,
json_type="string",
default=group_name,
description="the group name for these movers")
# TODO: maybe this moves into shooting once we have the metadata?
ENGINE_PARAMETER = Parameter('engine',
compiler_for('engine'),
json_type=json_type_ref('engine'),
description="the engine for moves of this type")
SHOOTING_GROUP_PARAMETER = _group_parameter('shooting')
REPEX_GROUP_PARAMETER = _group_parameter('repex')
MINUS_GROUP_PARAMETER = _group_parameter('minus')
REPLACE_TRUE_PARAMETER = Parameter(
'replace',
bool,
json_type="bool",
default=True,
description=("whether this should replace existing objects (default "
"True)"))
REPLACE_FALSE_PARAMETER = Parameter(
'replace',
from paths_cli.compiling.core import (InstanceCompilerPlugin, CategoryCompiler,
Builder, Parameter)
from paths_cli.compiling.root_compiler import compiler_for
from paths_cli.compiling.tools import custom_eval_float
from paths_cli.compiling.plugins import ShootingPointSelectorPlugin
from paths_cli.compiling.json_type import json_type_ref, json_type_eval
shooting_selector_compiler = compiler_for('shooting-point-selector')
SP_SELECTOR_PARAMETER = Parameter(
'selector',
compiler_for('shooting-point-selector'),
default=None,
json_type=json_type_ref('shooting-point-selector'),
description="shooting point selection algorithm to use.",
)
build_uniform_selector = ShootingPointSelectorPlugin(
builder=Builder('openpathsampling.UniformSelector'),
parameters=[],
name='uniform',
description=("Uniform shooting point selection probability: all frames "
"have equal probability (endpoints excluded)."),
)
def _remapping_gaussian_stddev(dct):
dct['alpha'] = 0.5 / dct.pop('stddev')**2
dct['collectivevariable'] = dct.pop('cv')
dct['l_0'] = dct.pop('mean')
return dct