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: ''}¶
- 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 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 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 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:
struc
must have two CTs.The first CT must have a CT-level property
constants.FEP_FRAGNAME
and the value of the property must be “none”.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 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'>}¶