conformers

class isicle.conformers.ConformationalEnsemble(*args)[source]

Collection of Geometry, or related subclass, instances.

_abc_impl = <_abc._abc_data object>
_apply_function(func, **kwargs)[source]

Process conformational ensemble members according to supplied function.

Parameters:

  • func (function) – Function by which ensemble members will be processed.

  • kwargs – Keyword arguments passed to func.

Returns:

Result of operation, type depends on func return type.

Return type:

ConformationalEnsemble or list

_apply_method(method, **kwargs)[source]

Process conformational ensemble members according to supplied method.

Parameters:

  • method (str) – Method by which ensemble members will be processed.

  • kwargs – Keyword arguments passed to method.

Returns:

Result of operation, type depends on method return type.

Return type:

ConformationalEnsemble or list

_check_attributes(attr)[source]

Check if all ensemble members have the supplied attribute.

Parameters:

attr (str) – Attribute to check.

Raises:

AttributeError – If all members do not have attr.

apply(func=None, method=None, **kwargs)[source]

Process conformational ensemble members according to supplied function or method.

Parameters:

  • func (function) – Function by which ensemble members will be processed.

  • method (str) – Method by which ensemble members will be processed.

  • kwargs – Keyword arguments passed to method.

Returns:

Result of operation, type depends on method return type.

Return type:

ConformationalEnsemble or list

Raises:

ValueError – If neither func nor method is supplied.

get_structures()[source]

Extract all structures from containing object as a conformational ensemble.

Returns:

Conformational ensemble.

Return type:

ConformationalEnsemble

reduce(attr, func='boltzmann', **kwargs)[source]

Combine attribute values according to indicated function.

Parameters:

  • attr (str) – Attribute that will be combined.

  • func (str) – Alias for function selection (one of “boltzmann”, “simple”, “lowest”, or “threshold”).

  • kwargs – Additional keyword arguments passed to func.

Returns:

Result of reduction operation.

Return type:

DataFrame

isicle.conformers._energy_based(func)[source]

Checks whether function employs an energy-based reduction operation.

Parameters:

func (function) – Conformer reduction function.

Returns:

True if energy based, otherwise False.

Return type:

bool

isicle.conformers._function_selector(func)[source]

Selects a supported reduction function for reducing a set of conformers.

Parameters:

func (str) – Alias for function selection (one of “boltzmann”, “simple”, “lowest”, or “threshold”).

Returns:

Conformer reduction function.

Return type:

func

isicle.conformers.boltzmann(value, energy, index=None, atom=None)[source]

Combine values according to a Boltzmann-weighted average.

Parameters:

  • value (array) – Array containing values that will be combined.

  • energy (array) – Array containing energy values that correspond to entries in value.

  • index (None or array) – Index by which to group values for averaging.

  • atom (None or array) – Atom by which to group values for averaging.

Returns:

Result of reduction operation.

Return type:

DataFrame

isicle.conformers.build_conformational_ensemble(geometries)[source]

Create a conformational ensemble from a collection of geometries.

Parameters:

geometries (list of Geometry or related subclass) – Collection of geometry instances.

Returns:

Conformational ensemble.

Return type:

ConformationalEnsemble

isicle.conformers.energy_threshold(value, energy, threshold=5, index=None, atom=None)[source]

Combine values with energy below a given threshold according to a simple average.

Parameters:

  • value (array) – Array containing values that will be combined.

  • energy (array) – Array containing energy values that correspond to entries in value.

  • index (None or array) – Index by which to group values for averaging.

  • atom (None or array) – Atom by which to group values for averaging.

Returns:

Result of reduction operation.

Return type:

DataFrame

isicle.conformers.lowest_energy(value, energy, index=None, atom=None)[source]

Combine values according to lowest energy.

Parameters:

  • value (array) – Array containing values that will be combined.

  • energy (array) – Array containing energy values that correspond to entries in value.

  • index (None or array) – Index by which to group values for averaging.

  • atom (None or array) – Atom by which to group values for averaging.

Returns:

Result of reduction operation.

Return type:

DataFrame

isicle.conformers.reduce(value, func='boltzmann', **kwargs)[source]

Combine values according to indicated function.

Parameters:

  • value (array) – Array containing values that will be combined.

  • func (str) – Alias for function selection (one of “boltzmann”, “simple”, “lowest”, or “threshold”).

  • kwargs – Additional keyword arguments passed to func.

Returns:

Result of reduction operation.

Return type:

DataFrame

isicle.conformers.simple_average(value, index=None, atom=None)[source]

Combine values according to a simple average.

Parameters:

  • value (array) – Array containing values that will be combined.

  • index (None or array) – Index by which to group values for averaging.

  • atom (None or array) – Atom by which to group values for averaging.

Returns:

Result of reduction operation.

Return type:

DataFrame

isicle.conformers.transform(value, m={'C': 1.0, 'H': 1.0}, b={'C': 0.0, 'H': 0.0}, index=None, atom=None)[source]

Perform linear transformation with values using provided parameters.

Parameters:

  • value – Array containing vales that will be transformed.

  • m (float or dict) – Slope value

  • b (float or dict) – Y-intercept value

  • index (None or :obj: ~numpy.array) – Index by which to group values for transforming.

  • atom (None or :obj: ~numpy.array) – Atom by which to group values for transforming.

Returns:

Result of transformation operation.

Return type:

obj: ~pandas.DataFrame