schrodinger.application.desmond.systype module

Facilities for detecting type of model systems.

Copyright Schrodinger, LLC. All rights reserved.

exception schrodinger.application.desmond.systype.UnknownAppError[source]

Bases: Exception

__init__(*args, **kwargs)
args
with_traceback()

Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception schrodinger.application.desmond.systype.UnknownRuleError[source]

Bases: Exception

__init__(*args, **kwargs)
args
with_traceback()

Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception schrodinger.application.desmond.systype.FormatError[source]

Bases: Exception

__init__(*args, **kwargs)
args
with_traceback()

Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception schrodinger.application.desmond.systype.DetectionError[source]

Bases: Exception

__init__(*args, **kwargs)
args
with_traceback()

Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

class schrodinger.application.desmond.systype.TyperBase[source]

Bases: object

typer_cls = {'desmond': <class 'schrodinger.application.desmond.systype.DesmondTyper'>, 'fep_binding_pose': <class 'schrodinger.application.desmond.systype.FepBindingPoseTyper'>, 'generic': <class 'schrodinger.application.desmond.systype.TyperBase'>, 'mcpro': <class 'schrodinger.application.desmond.systype.McproTyper'>, 'watermap': <class 'schrodinger.application.desmond.systype.WatermapTyper'>}
NAME = 'generic'
RULE = {}
STRING = {None: ''}
static prepare(*arg, **kwarg)[source]
static check_rule(systype, rule)[source]
static detect(struc, filename)[source]
static has_rule(rule)[source]
static get_trait(struc)[source]
class schrodinger.application.desmond.systype.DesmondTyper[source]

Bases: schrodinger.application.desmond.systype.TyperBase

NAME = 'desmond'
UNKNOWN = 0
MATURE_REGULAR = 101
MATURE_FEP = 102
MATURE_AFEP = 103
RAW_REGULAR = 201
RAW_FEP = 202
RAW_AFEP = 203
STRING = {101: 'a mature model system created for regular molecular dynamics simulations', 102: 'a mature model system created for FEP calculations', 103: 'a mature model system created for absolute FEP calculations', 201: 'a raw geometry for regular molecular dynamics simulations', 202: 'raw geometries created for FEP calculations', 203: 'raw geometries created for absolute FEP calculations'}
RULE = {'afep': [103, 203], 'auto': [101, 102, 103, 201, 202, 203], 'fep': [102, 103, 202, 203], 'mature': [101, 102, 103], 'mature_afep': [103], 'mature_fep': [102, 103], 'mature_regular': [101, 103], 'raw': [201, 202, 203], 'raw_afep': [203], 'raw_fep': [202, 203], 'raw_regular': [201, 203], 'regular': [101, 103, 201, 203]}
static detect(struc, filename)[source]
static has_rule(rule)[source]
static check_rule(systype, rule)[source]
static check_system(struc, filename, rule)[source]
static get_trait(struc)[source]
static prepare(*arg, **kwarg)
typer_cls = {'desmond': <class 'schrodinger.application.desmond.systype.DesmondTyper'>, 'fep_binding_pose': <class 'schrodinger.application.desmond.systype.FepBindingPoseTyper'>, 'generic': <class 'schrodinger.application.desmond.systype.TyperBase'>, 'mcpro': <class 'schrodinger.application.desmond.systype.McproTyper'>, 'watermap': <class 'schrodinger.application.desmond.systype.WatermapTyper'>}
class schrodinger.application.desmond.systype.McproTyper[source]

Bases: schrodinger.application.desmond.systype.TyperBase

NAME = 'mcpro'
UNKNOWN = 0
RAW_REGULAR = 201
RAW_FEP = 202
STRING = {201: 'a raw geometry for regular monte carlo simulations', 202: 'raw geometries created for FEP calculations'}
RULE = {'auto': [202, 201], 'fep': [202], 'raw': [202, 201], 'raw_fep': [202], 'raw_regular': [201], 'regular': [201]}
static detect(struc, filename)[source]
static has_rule(rule)[source]
static check_rule(systype, rule)[source]
static check_system(struc, filename, rule)[source]
static get_trait(struc)
static prepare(*arg, **kwarg)
typer_cls = {'desmond': <class 'schrodinger.application.desmond.systype.DesmondTyper'>, 'fep_binding_pose': <class 'schrodinger.application.desmond.systype.FepBindingPoseTyper'>, 'generic': <class 'schrodinger.application.desmond.systype.TyperBase'>, 'mcpro': <class 'schrodinger.application.desmond.systype.McproTyper'>, 'watermap': <class 'schrodinger.application.desmond.systype.WatermapTyper'>}
class schrodinger.application.desmond.systype.WatermapTyper[source]

Bases: schrodinger.application.desmond.systype.TyperBase

NAME = 'watermap'
RAW_REGULAR = 201
STRING = {201: 'a raw geometry for regular watermap jobs'}
RULE = {'': [201], 'regular': [201]}
static detect(struc, filename)[source]
static has_rule(rule)[source]
static check_rule(systype, rule)[source]
static check_system(struc, filename, rule)[source]
static prepare(stage, filename)[source]
static get_trait(struc)
typer_cls = {'desmond': <class 'schrodinger.application.desmond.systype.DesmondTyper'>, 'fep_binding_pose': <class 'schrodinger.application.desmond.systype.FepBindingPoseTyper'>, 'generic': <class 'schrodinger.application.desmond.systype.TyperBase'>, 'mcpro': <class 'schrodinger.application.desmond.systype.McproTyper'>, 'watermap': <class 'schrodinger.application.desmond.systype.WatermapTyper'>}
class schrodinger.application.desmond.systype.FepBindingPoseTyper[source]

Bases: schrodinger.application.desmond.systype.TyperBase

NAME = 'fep_binding_pose'
RAW_REGULAR = 100
STRING = {100: 'a raw geometry for FEP-binding-pose workflow'}
RULE = {'': [100], 'regular': [100]}
static detect(struc: List[schrodinger.structure._structure.Structure], *_) int[source]

Mininum requirements:

  1. struc must have two CTs.

  2. The first CT must have a CT-level property constants.FEP_FRAGNAME and the value of the property must be “none”.

  3. The second CT must have the same property and the value must be not “none”.

If the requirements are not met, this function will raise exceptions. This function will return FepBindingPoseTyper.RAW_REGULAR on success.

static has_rule(rule)[source]
static check_rule(systype, rule)[source]
static get_trait(struc)
static prepare(*arg, **kwarg)
typer_cls = {'desmond': <class 'schrodinger.application.desmond.systype.DesmondTyper'>, 'fep_binding_pose': <class 'schrodinger.application.desmond.systype.FepBindingPoseTyper'>, 'generic': <class 'schrodinger.application.desmond.systype.TyperBase'>, 'mcpro': <class 'schrodinger.application.desmond.systype.McproTyper'>, 'watermap': <class 'schrodinger.application.desmond.systype.WatermapTyper'>}
class schrodinger.application.desmond.systype.SysType(typer_rule=None)[source]

Bases: object

__init__(typer_rule=None)[source]
check_system(filename)[source]
get_trait(filename)[source]
prepare(*arg, **kwarg)[source]