indexers module

Full Documentation for hippynn.layers.indexers module. Click here for a summary page.

Layers for encoding, decoding, index states, besides pairs

class AtomDeIndexer(*args, **kwargs)

Bases: Module

forward(features, mol_index, atom_index, n_molecules, n_atoms_max)

Define the computation performed at every call.

Should be overridden by all subclasses.

Note

Although the recipe for forward pass needs to be defined within this function, one should call the Module instance afterwards instead of this since the former takes care of running the registered hooks while the latter silently ignores them.

class AtomReIndexer(*args, **kwargs)

Bases: Module

forward(molatom_thing, real_atoms)

Define the computation performed at every call.

Should be overridden by all subclasses.

Note

Although the recipe for forward pass needs to be defined within this function, one should call the Module instance afterwards instead of this since the former takes care of running the registered hooks while the latter silently ignores them.

class CellScaleInducer(*args, **kwargs)

Bases: Module

forward(coordinates, cell)

Define the computation performed at every call.

Should be overridden by all subclasses.

Note

Although the recipe for forward pass needs to be defined within this function, one should call the Module instance afterwards instead of this since the former takes care of running the registered hooks while the latter silently ignores them.

class FilterBondsOneway(*args, **kwargs)

Bases: Module

forward(bonds, pair_first, pair_second)

Define the computation performed at every call.

Should be overridden by all subclasses.

Note

Although the recipe for forward pass needs to be defined within this function, one should call the Module instance afterwards instead of this since the former takes care of running the registered hooks while the latter silently ignores them.

class FuzzyHistogram(length, vmin, vmax)

Bases: Module

Transforms a scalar feature into a vectorized feature via the fuzzy/soft histogram method.

Parameters:

length – length of vectorized feature

:returns FuzzyHistogram

forward(values)

Define the computation performed at every call.

Should be overridden by all subclasses.

Note

Although the recipe for forward pass needs to be defined within this function, one should call the Module instance afterwards instead of this since the former takes care of running the registered hooks while the latter silently ignores them.

class MolSummer(*args, **kwargs)

Bases: Module

Molecule Summer

Description:

This sums (flatatom) things into (mol) things. It actually works similarly to the interaction layer

forward(features, mol_index, n_molecules)

Define the computation performed at every call.

Should be overridden by all subclasses.

Note

Although the recipe for forward pass needs to be defined within this function, one should call the Module instance afterwards instead of this since the former takes care of running the registered hooks while the latter silently ignores them.

class OneHotSpecies(species_set)

Bases: Module

Encodes species as one-hot map using species_set :param species_set iterable of species types. Typically this will be the Z-value of the elemeent. Note: 0 denotes a ‘blank atom’ used only for padding purposes

:returns OneHotSpecies

forward(species)

Parameters:

species

Returns:

Initial one-hotted features, nonblank atoms

class PaddingIndexer(*args, **kwargs)

Bases: Module

Hipnn’s indexer

Description:

This indexer allows us to go from rectangular (mol,atom) representations To (flatatom) representations and a corresponding molecule index for those atoms. The ‘real_index’ allows us to take _values_ from a flattened rectangular representation (mol*atom) And select only the real ones. The ‘inv_real_index’, when indexed, converts a (mol*atom) index set into a (flatatom) index set

forward(features, nonblank)

Pytorch Enforced Forward function

Parameters:

• features

• nonblank

Returns:

real atoms, amd inverse atoms mappings

class QuadPack

Bases: Module

Converts quadrupoles flattened form to packed triangular, assumes symmmetric. Packed form: (molecule) XX, YY, ZZ, XY, XZ, YZ Index 0, 4, 8, 1, 2, 5 Unpacked form: (molecule) XX, XY, XZ, YX, YY, YZ , ZX, ZY, ZZ Index 00 01 02, 10, 11, 12, 20, 21, 22

forward(quadrupoles)

Define the computation performed at every call.

Should be overridden by all subclasses.

Note

Although the recipe for forward pass needs to be defined within this function, one should call the Module instance afterwards instead of this since the former takes care of running the registered hooks while the latter silently ignores them.

class QuadUnpack

Bases: Module

Converts quadrupoles from packed triangular form to flattened molecule form. Packed form: (molecule) XX, YY, ZZ, XY, XZ, YZ Index 0, 1, 2, 3, 4, 5 Unpacked form: (molecule) XX, XY, XZ, YX, YY, YZ , ZX, ZY, ZZ Index 0, 3, 4, 3, 1, 5, 4, 5, 2

forward(packed_quadrupoles)

Define the computation performed at every call.

Should be overridden by all subclasses.

Note

Although the recipe for forward pass needs to be defined within this function, one should call the Module instance afterwards instead of this since the former takes care of running the registered hooks while the latter silently ignores them.

class SysMaxOfAtoms(*args, **kwargs)

Bases: Module

Take maximum over atom dimension.

forward(features, mol_index, n_molecules)

Define the computation performed at every call.

Should be overridden by all subclasses.

Note

Although the recipe for forward pass needs to be defined within this function, one should call the Module instance afterwards instead of this since the former takes care of running the registered hooks while the latter silently ignores them.