schrodinger.application.desmond.systype module¶
Facilities for detecting type of model systems.
Copyright Schrodinger, LLC. All rights reserved.
- exception schrodinger.application.desmond.systype.UnknownAppError¶
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¶
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¶
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¶
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¶
Bases:
object- typer_cls = {'desmond': <class 'schrodinger.application.desmond.systype.DesmondTyper'>, '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)¶
- static check_rule(systype, rule)¶
- static detect(struc, filename)¶
- static has_rule(rule)¶
- static get_trait(struc)¶
- class schrodinger.application.desmond.systype.DesmondTyper¶
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)¶
- static has_rule(rule)¶
- static check_rule(systype, rule)¶
- static check_system(struc, filename, rule)¶
- static get_trait(struc)¶
- static prepare(*arg, **kwarg)¶
- typer_cls = {'desmond': <class 'schrodinger.application.desmond.systype.DesmondTyper'>, '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¶
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)¶
- static has_rule(rule)¶
- static check_rule(systype, rule)¶
- static check_system(struc, filename, rule)¶
- static get_trait(struc)¶
- static prepare(*arg, **kwarg)¶
- typer_cls = {'desmond': <class 'schrodinger.application.desmond.systype.DesmondTyper'>, '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¶
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)¶
- static has_rule(rule)¶
- static check_rule(systype, rule)¶
- static check_system(struc, filename, rule)¶
- static prepare(stage, filename)¶
- static get_trait(struc)¶
- typer_cls = {'desmond': <class 'schrodinger.application.desmond.systype.DesmondTyper'>, 'generic': <class 'schrodinger.application.desmond.systype.TyperBase'>, 'mcpro': <class 'schrodinger.application.desmond.systype.McproTyper'>, 'watermap': <class 'schrodinger.application.desmond.systype.WatermapTyper'>}¶