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'>}
class schrodinger.application.desmond.systype.SysType(typer_rule=None)

Bases: object

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