<no title>

Defines MacroModel optimizers.

exception MacroModelConversionError¶

Bases: Exception

__init__(self, /, *args, **kwargs)¶: 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 MacroModelForceField(macromodel_path, output_dir=None, restricted=False, timeout=None, force_field=16, maximum_iterations=2500, minimum_gradient=0.05, use_cache=False)¶

Bases: stk.calculators.optimization.macromodel._MacroModel

Uses MacroModel force fields to optimize molecules.

Methods

`add_to_cache`(self, mol[, value])	Add a molecule to the cache.
`get_cached_value`(self, mol)	Return the value stored in the cache for mol.
`is_caching`(self)	`True` if the calculator has caching turned on.
`is_in_cache`(self, mol)	Return `True` if mol is cached.
`optimize`(self, mol)	Optimize a molecule.
`set_cache_use`(self, use_cache)	Set cache use on or off.

__init__(self, macromodel_path, output_dir=None, restricted=False, timeout=None, force_field=16, maximum_iterations=2500, minimum_gradient=0.05, use_cache=False)¶

Initialize a MacroModelForceField object.

Parameters

macromodel_path (str) – The full path of the Schrodinger suite within the user’s machine. For example, on a Linux machine this may be something like '/opt/schrodinger2017-2'.
output_dir (str, optional) – The name of the directory into which files generated during the optimization are written, if None then uuid.uuid4() is used.
restricted (bool, optional) – If True then an optimization is performed only on the bonds added by construct(). If False then all bonds are optimized.
timeout (float, optional) – The amount in seconds the optimization is allowed to run before being terminated. None means there is no timeout.
force_field (int, optional) – The number of the force field to be used.
maximum_iterations (int, optional) – The maximum number of iterations done during the optimization. Cannot be more than 999999.
minimum_gradient (float, optional) – The gradient at which optimization is stopped. Cannot be less than 0.0001.
use_cache (bool, optional) – If True optimize() will not run twice on the same molecule.

add_to_cache(self, mol, value=None)¶

Add a molecule to the cache.

Parameters

mol (Molecule) – The molecule to be added to the cache.
value (class:object, optional) – The cached value associated with the molecule.

Returns

The calculator.

Return type

MoleculeCalculator

get_cached_value(self, mol)¶

Return the value stored in the cache for mol.

Parameters: mol (Molecule) – The molecule whose cached value is to be returned.
Returns: The cached value.
Return type: object

is_caching(self)¶

True if the calculator has caching turned on.

Returns: True if the calculator has caching turned on.
Return type: bool

is_in_cache(self, mol)¶

Return True if mol is cached.

Parameters: mol (Molecule) – The molecule being checked.
Returns: True if mol is cached.
Return type: bool

optimize(self, mol)¶

Optimize a molecule.

Parameters: mol (Molecule) – The molecule to be optimized.
Returns: None
Return type: NoneType

set_cache_use(self, use_cache)¶

Set cache use on or off.

Parameters: use_cache (bool) – True if the cache is to be used.
Returns: The calculator.
Return type: MoleculeCalculator

exception MacroModelForceFieldError¶

Bases: Exception

__init__(self, /, *args, **kwargs)¶: 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 MacroModelInputError¶

Bases: Exception

__init__(self, /, *args, **kwargs)¶: 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 MacroModelLewisStructureError¶

Bases: Exception

__init__(self, /, *args, **kwargs)¶: 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 MacroModelMD(macromodel_path, output_dir=None, timeout=None, force_field=16, temperature=750, conformers=50, time_step=1, eq_time=10, simulation_time=200, maximum_iterations=2500, minimum_gradient=0.05, restricted_bonds=None, restricted_bond_angles=None, restricted_torsional_angles=None, use_cache=False)¶

Bases: stk.calculators.optimization.macromodel._MacroModel

Runs a molecular dynamics conformer search using MacroModel.

Methods

`add_to_cache`(self, mol[, value])	Add a molecule to the cache.
`get_cached_value`(self, mol)	Return the value stored in the cache for mol.
`is_caching`(self)	`True` if the calculator has caching turned on.
`is_in_cache`(self, mol)	Return `True` if mol is cached.
`optimize`(self, mol)	Optimize a molecule.
`set_cache_use`(self, use_cache)	Set cache use on or off.

__init__(self, macromodel_path, output_dir=None, timeout=None, force_field=16, temperature=750, conformers=50, time_step=1, eq_time=10, simulation_time=200, maximum_iterations=2500, minimum_gradient=0.05, restricted_bonds=None, restricted_bond_angles=None, restricted_torsional_angles=None, use_cache=False)¶

Initialize a MacroModelMD instance.

Parameters

macromodel_path (str) – The full path of the Schrodinger suite within the user’s machine. For example, on a Linux machine this may be something like '/opt/schrodinger2017-2'.
output_dir (str, optional) – The name of the directory into which files generated during the optimization are written, if None then uuid.uuid4() is used.
timeout (float, optional) – The amount in seconds the MD is allowed to run before being terminated. None means there is no timeout.
force_field (int, optional) – The number of the force field to be used.
temperature (float, optional) – The temperature in Kelvin at which the MD is run. Cannot be more than 99999.99.
conformers' (int, optional) – The number of conformers sampled and optimized from the MD. Cannot be more than 9999.
simulation_time (float, optional) – The simulation time in ps of the MD. Cannot be more than 999999.99.
time_step (float, optional) – The time step in fs for the MD. Cannot be more than 99999.99.
eq_time (float, optional) – The equilibriation time in ps before the MD is run. Cannot be more than 999999.99.
maximum_iterations (int, optional) – The maximum number of iterations done during the optimization. Cannot be more than 999999.
minimum_gradient (float, optional) – The gradient at which optimization is stopped. Cannot be less than 0.0001.
restricted_bonds (set, optional) –
A set of the form
```
restricted_bonds = {
    frozenset((0, 10)),
    frozenset((3, 14)),
    frozenset((5, 6))
}
```
Where each frozenset defines which bonds should have a fixed length via the atom ids of atoms in the bond.
restricted_bond_angles (set, optional) –
A set of the form
```
restricted_bonds = {
    frozenset((0, 10, 12)),
    frozenset((3, 14, 7)),
    frozenset((5, 8, 2))
}
```
Where each frozenset defines which bond angles should have a fixed size via the atom ids of atoms in the bond angle.
restricted_torsional_angles (set, optional) –
A set of the form
```
restricted_bonds = {
    frozenset((0, 10, 12, 3)),
    frozenset((3, 14, 7, 4)),
    frozenset((5, 8, 2, 9))
}
```
Where each frozenset defines which torsional angles should have a fixed size via the atom ids of atoms in the torsional angle.
use_cache (bool, optional) – If True optimize() will not run twice on the same molecule.

add_to_cache(self, mol, value=None)¶

Add a molecule to the cache.

Parameters

mol (Molecule) – The molecule to be added to the cache.
value (class:object, optional) – The cached value associated with the molecule.

Returns

The calculator.

Return type

MoleculeCalculator

get_cached_value(self, mol)¶

Return the value stored in the cache for mol.

Parameters: mol (Molecule) – The molecule whose cached value is to be returned.
Returns: The cached value.
Return type: object

is_caching(self)¶

True if the calculator has caching turned on.

Returns: True if the calculator has caching turned on.
Return type: bool

is_in_cache(self, mol)¶

Return True if mol is cached.

Parameters: mol (Molecule) – The molecule being checked.
Returns: True if mol is cached.
Return type: bool

optimize(self, mol)¶

Optimize a molecule.

Parameters: mol (Molecule) – The molecule to be optimized.
Returns: None
Return type: NoneType

set_cache_use(self, use_cache)¶

Set cache use on or off.

Parameters: use_cache (bool) – True if the cache is to be used.
Returns: The calculator.
Return type: MoleculeCalculator

exception MacroModelOptimizationError¶

Bases: Exception

__init__(self, /, *args, **kwargs)¶: 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 MacroModelPathError¶

Bases: Exception

__init__(self, /, *args, **kwargs)¶: Initialize self. See help(type(self)) for accurate signature.

args¶

with_traceback()¶: Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.