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'>}

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

Bases: object

__init__(typer_rule=None)

check_system(filename)

get_trait(filename)

prepare(*arg, **kwarg)