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"]

VALID_FORCEFIELD_LIST = pymmlibs.mmcommon_get_valid_forcefield...

VALID_FORCEFIELD_NAME = '"%s"' %('", "'.join(SUPPORTED_FFLD))

GENERAL_SPECS = [i for i in ...

MINIMIZER_SPECS = [i for i in ...

EMBRACE_SPECS = [i for i in ...

MINTA_SPECS = [i for i in ...

RCE_SPECS = [i for i in ...

CONFSEARCH_SPECS = [i for i in ...

ENERGY_LISTING_SPECS = [i for i in ...

Variables Details

[hide private]

VALID_FORCEFIELD_LIST

Value:

pymmlibs.mmcommon_get_valid_forcefields_names()

GENERAL_SPECS

Value:

[i for i in """
JOB_TYPE                = option('ENERGY_LISTING', 'MINIMIZATION', 'EM
BRACE_MINIMIZATION', 'EMBRACE_CONFSEARCH', 'MINTA', 'RCE', default='CO
NFSEARCH')
INPUT_STRUCTURE_FILE    = string()
OUTPUT_STRUCTURE_FILE   = string()
FORCE_FIELD             = option("MM2*", "MM3*", "AMBER*", "AMBER94", 
"OPLS", "MMFF", "MMFFs", VALID_FORCEFIELD_NAME, default='OPLS_2005')
...

MINIMIZER_SPECS

Value:

[i for i in """
MINI_METHOD             = option('PRCG', 'TNCG', 'OSVM', 'SD', 'FMNR',
 'LBFGS', 'Optimal', default='PRCG')
MAXIMUM_ITERATION       = integer(default=5000)
CONVERGE_ON             = option('Gradient', 'Energy', 'Movement', 'No
thing', default='Gradient')
CONVERGENCE_THRESHOLD   = float(default=0.05)
""".split('\n')]

EMBRACE_SPECS

Value:

[i for i in """
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', 'Movement
', 'Nothing', default='Gradient')
COMPLEX_CONVERGENCE_THRESHOLD = float(default=0.05)
MODE                          = option('EnergyDifference', 'Interactio
...

MINTA_SPECS

Value:

[i for i in """
MINTA_ITERATIONS              = integer(default=5)
MINTA_ENERGY_EVALUATIONS      = integer(default=2000)
MINTA_TEMPERATURE             = float(default=300.0)
""".split('\n')]

RCE_SPECS

Value:

[i for i in """
CONF_ELIM_USE_JAGUAR_ENERGIES   = boolean(default=False)
CONF_ELIM_MAX_STRUCT_RETAIN     = integer(default=0) #  In bmin defaul
t becomes 10,000
""".split('\n')]

CONFSEARCH_SPECS

Value:

[i for i in """
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)
CONFSEARCH_STEPS_PER_ROTATABLE = integer(default=50)
...

ENERGY_LISTING_SPECS

Value:

[i for i in """
ENERGY_REPORT_OPTION    = option("LOGFILE", "MMOFILE", "FULLREPORT") #
 FIXME come up with better names
""".split('\n')]