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__
¶ Initialize self. See help(type(self)) for accurate signature.
-
args
¶
-
with_traceback
()¶ Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.
-
-
exception
schrodinger.application.desmond.systype.
UnknownRuleError
¶ Bases:
Exception
-
__init__
¶ Initialize self. See help(type(self)) for accurate signature.
-
args
¶
-
with_traceback
()¶ Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.
-
-
exception
schrodinger.application.desmond.systype.
FormatError
¶ Bases:
Exception
-
__init__
¶ Initialize self. See help(type(self)) for accurate signature.
-
args
¶
-
with_traceback
()¶ Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.
-
-
exception
schrodinger.application.desmond.systype.
DetectionError
¶ Bases:
Exception
-
__init__
¶ Initialize self. See help(type(self)) for accurate signature.
-
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)¶
-
__init__
¶ Initialize self. See help(type(self)) for accurate signature.
-
-
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)¶
-
__init__
¶ Initialize self. See help(type(self)) for accurate signature.
-
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)¶
-
__init__
¶ Initialize self. See help(type(self)) for accurate signature.
-
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
get_trait
(struc)¶
-
static
prepare
(stage, filename)¶
-
__init__
¶ Initialize self. See help(type(self)) for accurate signature.
-
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'>}¶
-