schrodinger.application.desmond.systype module

Facilities for detecting type of model systems.

Copyright Schrodinger, LLC. All rights reserved.

class schrodinger.application.desmond.systype.DesmondTyper

Bases: schrodinger.application.desmond.systype.TyperBase

MATURE_AFEP = 103

MATURE_FEP = 102

MATURE_REGULAR = 101

NAME = 'desmond'

RAW_AFEP = 203

RAW_FEP = 202

RAW_REGULAR = 201

RULE = {'raw_regular': [201, 203], 'mature_fep': [102, 103], 'auto': [101, 102, 103, 201, 202, 203], 'afep': [103, 203], 'raw': [201, 202, 203], 'mature_afep': [103], 'regular': [101, 103, 201, 203], 'mature_regular': [101, 103], 'raw_fep': [202, 203], 'fep': [102, 103, 202, 203], 'raw_afep': [203], 'mature': [101, 102, 103]}

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'}

UNKNOWN = 0

static check_rule(systype, rule)

static check_system(struc, filename, rule)

static detect(struc, filename)

static get_trait(struc)

static has_rule(rule)

exception schrodinger.application.desmond.systype.DetectionError

Bases: exceptions.Exception

exception schrodinger.application.desmond.systype.FormatError

Bases: exceptions.Exception

class schrodinger.application.desmond.systype.McproTyper

Bases: schrodinger.application.desmond.systype.TyperBase

NAME = 'mcpro'

RAW_FEP = 202

RAW_REGULAR = 201

RULE = {'raw_fep': [202], 'raw_regular': [201], 'auto': [202, 201], 'raw': [202, 201], 'regular': [201], 'fep': [202]}

STRING = {201: 'a raw geometry for regular monte carlo simulations', 202: 'raw geometries created for FEP calculations'}

UNKNOWN = 0

static check_rule(systype, rule)

static check_system(struc, filename, rule)

static detect(struc, filename)

static get_trait(struc)

static has_rule(rule)

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

Bases: object

check_system(filename)

get_trait(filename)

prepare(*arg, **kwarg)

class schrodinger.application.desmond.systype.TyperBase

Bases: object

NAME = 'generic'

RULE = {}

STRING = {None: ''}

static check_rule(systype, rule)

static detect(struc, filename)

static get_trait(struc)

static has_rule(rule)

static prepare(*arg, **kwarg)

typer_cls = {'generic': <class 'schrodinger.application.desmond.systype.TyperBase'>, 'desmond': <class 'schrodinger.application.desmond.systype.DesmondTyper'>, 'mcpro': <class 'schrodinger.application.desmond.systype.McproTyper'>, 'watermap': <class 'schrodinger.application.desmond.systype.WatermapTyper'>}

exception schrodinger.application.desmond.systype.UnknownAppError

Bases: exceptions.Exception

exception schrodinger.application.desmond.systype.UnknownRuleError

Bases: exceptions.Exception

class schrodinger.application.desmond.systype.WatermapTyper

Bases: schrodinger.application.desmond.systype.TyperBase

NAME = 'watermap'

RAW_REGULAR = 201

RULE = {'': [201], 'regular': [201]}

STRING = {201: 'a raw geometry for regular watermap jobs'}

static check_rule(systype, rule)

static check_system(struc, filename, rule)

static detect(struc, filename)

static get_trait(struc)

static has_rule(rule)

static prepare(stage, filename)