Module input

Facilities for reading and writing simplified MacroModel input files.

It can also be used to write MacroModel *.com files.

Classes

[hide private]

_MacroModel
Class for reading and writing simplified MacroModel input files.

ConfSearch
A special class for dealing with Conformation Search jobs.

EnergyListing
A special class for dealing with Energy Listing jobs.

RCE
A special class for dealing with RCE jobs.

Minta
A special class for dealing with Minta jobs.

Minimization
A special class for dealing with Minimization jobs.

EmbraceMinimization
A special class for dealing with Enbrace Minimization jobs.

EmbraceConfSearch
A special class for dealing with Embrace Conformation Search jobs.

Variables

[hide private]

SUPPORTED_FFLD = ['OPLS2.0', 'OPLS2.1', 'OPLS_2005', 'OPLS3']

VALID_FORCEFIELD_LIST = ('OPLS_2005', 'OPLS3')

VALID_FORCEFIELD_NAME = '"OPLS2.0", "OPLS2.1", "OPLS_2005", "O...

GENERAL_SPECS = ['', 'JOB_TYPE = option(\'ENERG...

MINIMIZER_SPECS = ['', 'MINI_METHOD = option(\'PRC...

EMBRACE_SPECS = ['', 'COMPLEX_MINI_METHOD = option(\...

MINTA_SPECS = ['', 'MINTA_ITERATIONS = integer(de...

RCE_SPECS = ['', 'CONF_ELIM_USE_JAGUAR_ENERGIES = boolean(de...

CONFSEARCH_SPECS = ['', 'CONFSEARCH_METHOD = option(\'MC...

ENERGY_LISTING_SPECS = ['', 'ENERGY_REPORT_OPTION = option(...

FORCEFIELD = 'OPLS3'

__package__ = 'schrodinger.application.macromodel'

i = ''

Variables Details

[hide private]

VALID_FORCEFIELD_NAME

Value:

'"OPLS2.0", "OPLS2.1", "OPLS_2005", "OPLS3"'

GENERAL_SPECS

Value:

['',
 'JOB_TYPE                = option(\'ENERGY_LISTING\', \'MINIMIZATION\
', \'EMBRACE_MINIMIZATION\', \'EMBRACE_CONFSEARCH\', \'MINTA\', \'RCE\
', default=\'CONFSEARCH\')',
 'INPUT_STRUCTURE_FILE    = string()',
 'OUTPUT_STRUCTURE_FILE   = string()',
 'FORCE_FIELD             = option("MM2*", "MM3*", "AMBER*", "AMBER94"
, "OPLS", "MMFF", "MMFFs", "OPLS2.0", "OPLS2.1", "OPLS_2005", "OPLS3",
...

MINIMIZER_SPECS

Value:

['',
 'MINI_METHOD             = option(\'PRCG\', \'TNCG\', \'OSVM\', \'SD\
', \'FMNR\', \'LBFGS\', \'Optimal\', default=\'PRCG\')',
 'MAXIMUM_ITERATION       = integer(default=5000)',
 'CONVERGE_ON             = option(\'Gradient\', \'Energy\', \'Movemen
t\', \'Nothing\', default=\'Gradient\')',
 'CONVERGENCE_THRESHOLD   = float(default=0.05)',
 '']

EMBRACE_SPECS

Value:

['',
 'COMPLEX_MINI_METHOD           = option(\'PRCG\', \'TNCG\', \'OSVM\',
 \'SD\', \'FMNR\', \'LBFGS\', \'Optimal\', default=\'PRCG\')',
 'COMPLEX_MAXIMUM_ITERATION     = integer(default=5000)',
 'COMPLEX_CONVERGE_ON           = option(\'Gradient\', \'Energy\', \'M
ovement\', \'Nothing\', default=\'Gradient\')',
 'COMPLEX_CONVERGENCE_THRESHOLD = float(default=0.05)',
 'MODE                          = option(\'EnergyDifference\', \'Inter
...

MINTA_SPECS

Value:

['',
 'MINTA_ITERATIONS              = integer(default=5)',
 'MINTA_ENERGY_EVALUATIONS      = integer(default=2000)',
 'MINTA_TEMPERATURE             = float(default=300.0)',
 '']

RCE_SPECS

Value:

['',
 'CONF_ELIM_USE_JAGUAR_ENERGIES   = boolean(default=False)',
 'CONF_ELIM_MAX_STRUCT_RETAIN     = integer(default=0) #  In bmin defa
ult becomes 10,000',
 '']

CONFSEARCH_SPECS

Value:

['',
 'CONFSEARCH_METHOD       = option(\'MCMM\', \'Confgen\', \'Lowmode\',
 \'Mixed\', \'mcmm\', \'cgen\', \'lmod\', \'lmcs\', \'mixed\', default
=\'MCMM\')',
 'INCONFS_PER_SEARCH      = integer()',
 'OUTCONFS_PER_SEARCH     = integer(default=1, min=1)',
 'CONFSEARCH_STEPS        = integer(default=200)',
 'CONFSEARCH_SEED         = integer(default=0, max=78593)',
...

ENERGY_LISTING_SPECS

Value:

['',
 'ENERGY_REPORT_OPTION    = option("LOGFILE", "MMOFILE", "FULLREPORT")
 # FIXME come up with better names',
 '']