stk

Module attributes

BatchKey

A unique key for a Batch.

Functions

get_acute_vector
normalize_vector	Normalizes the given vector.
rotation_matrix_arbitrary_axis	Returns a rotation matrix of angle radians about axis.
vector_angle	Returns the angle between two vectors in radians.

Classes

AboveAverage	Yields above average batches of molecules.
Ac	Initialize an Atom.
Add	Adds a number to the fitness values.
Ag	Initialize an Atom.
Al	Initialize an Atom.
Alcohol	Represents an alcohol functional group.
AlcoholFactory	Creates Alcohol instances.
Aldehyde	Represents an aldehyde functional group.
AldehydeFactory	Creates Aldehyde instances.
Alkene	Represents an alkene functional group.
Alkyne	Represents an alkyne functional group.
Am	Initialize an Atom.
Amide	Represents an amide functional group.
AmideFactory	Creates Amide instances.
Ar	Initialize an Atom.
As	Initialize an Atom.
At	Initialize an Atom.
Atom	An abstract base class for atoms.
AtomInfo	Holds additional info about ConstructedMolecule atoms.
Au	Initialize an Atom.
B	Initialize an Atom.
Ba	Initialize an Atom.
Batch	Represents a batch of molecule records.
Be	Initialize an Atom.
Best	Selects batches of molecules, highest fitness value first.
Bh	Initialize an Atom.
Bi	Initialize an Atom.
Bk	Initialize an Atom.
Bond	Represents an atomic bond.
BondInfo	Holds additional info about ConstructedMolecule bonds.
BoronicAcid	Represents a boronic acid functional group.
BoronicAcidFactory	Creates BoronicAcid instances.
Br	Initialize an Atom.
Bromo	Represents a bromo functional group.
BromoFactory	Creates Bromo instances.
BuildingBlock	Represents a building block of a ConstructedMolecule.
C	Initialize an Atom.
Ca	Initialize an Atom.
CarboxylicAcid	Represents a carboxylic acid functional group.
CarboxylicAcidFactory	Creates CarboxylicAcid instances.
Cd	Initialize an Atom.
Ce	Initialize an Atom.
Cf	Initialize an Atom.
Cl	Initialize an Atom.
Cm	Initialize an Atom.
Cn	Initialize an Atom.
Co	Initialize an Atom.
Collapser	Performs rigid-body collapse of molecules.
ConstructedMolecule	Represents constructed molecules.
ConstructedMoleculeDatabase	Abstract base class for storing constructed molecules.
ConstructedMoleculeDejsonizer	Abstract base class for creating constructed molecules from JSONs.
ConstructedMoleculeJsonizer	Abstract base class for creating JSONs of constructed molecules.
ConstructedMoleculeMongoDb	Uses MongoDB to store and retrieve constructed molecules.
ConstructionResult	The result of TopologyGraph.construct().
ConstructionState	The state of the molecule and topology graph under construction.
Cr	Initialize an Atom.
CrossoverRecord	Abstract base class for a record of a crossover operation.
Cs	Initialize an Atom.
Cu	Initialize an Atom.
DativeReaction	A reaction between two functional groups.
DativeReactionFactory	Create DativeReaction instances.
Db	Initialize an Atom.
Dibromo	Represents a dibromo functional group.
DibromoFactory	Creates Dibromo instances.
Difluoro	Represents a difluoro functional group.
DifluoroFactory	Creates Difluoro instances.
Diol	Represents a diol functional group.
DiolFactory	Creates Diol instances.
DivideByMean	Divides fitness values by the population mean.
Ds	Initialize an Atom.
Dy	Initialize an Atom.
Edge	Represents an edge in a topology graph.
EdgeGroup	Represents a group of edges.
Er	Initialize an Atom.
Es	Initialize an Atom.
Eu	Initialize an Atom.
EvolutionaryAlgorithm	An abstract base class for evolutionary algorithms.
F	Initialize an Atom.
Fe	Initialize an Atom.
FilterBatches	Allows a Selector to select only some batches.
FilterMolecules	Allows a Selector to select only some molecules.
FitnessCalculator	Abstract base class for fitness value calculators.
FitnessFunction	Takes a function and uses it as a fitness calculator.
FitnessNormalizer	Abstract base class for fitness normalizers.
FitnessValues	Fitness values of a molecule.
Fl	Initialize an Atom.
Fluoro	Represents a fluoro functional group.
FluoroFactory	Creates Fluoro instances.
Fm	Initialize an Atom.
Fr	Initialize an Atom.
FunctionalGroup	An abstract base class for functional groups.
FunctionalGroupFactory	An abstract base class for functional group factories.
Ga	Initialize an Atom.
Gd	Initialize an Atom.
Ge	Initialize an Atom.
Generation	An abstract base class for EA generations.
GenericFunctionalGroup	A functional group which defines general atomic classes.
GenericReactionFactory	Create reactions for GenericFunctionalGroup instances.
GeneticRecombination	Recombine building blocks using biological systems as a model.
GraphState	The topology graph of a molecule under construction.
H	Initialize an Atom.
He	Initialize an Atom.
Hf	Initialize an Atom.
Hg	Initialize an Atom.
Ho	Initialize an Atom.
Hs	Initialize an Atom.
I	Initialize an Atom.
In	Initialize an Atom.
Inchi	Used to get the InChI of molecules.
InchiKey	Used to get the InChIKey of molecules.
Iodo	Represents an iodo functional group.
IodoFactory	Creates Iodo instances.
Ir	Initialize an Atom.
K	Initialize an Atom.
Kr	Initialize an Atom.
La	Initialize an Atom.
Li	Initialize an Atom.
Lr	Initialize an Atom.
Lu	Initialize an Atom.
Lv	Initialize an Atom.
MCHammer	Performs Monte Carlo optimisation of long-bonds in molecules.
Mc	Initialize an Atom.
Md	Initialize an Atom.
Mg	Initialize an Atom.
Mn	Initialize an Atom.
Mo	Initialize an Atom.
MolWriter	A writer class for V3000 .mol files.
Molecule	An abstract base class for molecules.
MoleculeCrosser	Performs crossover operations.
MoleculeDatabase	An abstract base class for storing and retrieving molecules.
MoleculeDejsonizer	Abstract base class for creating molecules from JSONs.
MoleculeJsonizer	Abstract base class for creating JSONs of molecules.
MoleculeKeyMaker	An abstract base class for making Molecule keys.
MoleculeMongoDb	Uses MongoDB to store and retrieve molecules.
MoleculeMutator	Performs mutation operations.
MoleculeRecord	An abstract base class for molecular records used by the EA.
MoleculeState	Represents the state of a molecule under construction.
Mt	Initialize an Atom.
Multiply	Multiplies the fitness values by some coefficient.
MutationRecord	Abstract base class for a record of a mutation operation.
N	Initialize an Atom.
Na	Initialize an Atom.
Nb	Initialize an Atom.
Nd	Initialize an Atom.
Ne	Initialize an Atom.
Nh	Initialize an Atom.
Ni	Initialize an Atom.
No	Initialize an Atom.
NormalizerSequence	Applies other normalizers in sequence.
Np	Initialize an Atom.
NullFitnessNormalizer	Does nothing.
NullOptimizer	Does not perform an optimization.
O	Initialize an Atom.
Og	Initialize an Atom.
OneOneReaction	A reaction between two functional groups, each with 1 bonder atom.
OneTwoReaction	A reaction between two functional groups.
Optimizer	An abstract base class for optimizers.
Os	Initialize an Atom.
P	Initialize an Atom.
Pa	Initialize an Atom.
Pb	Initialize an Atom.
Pd	Initialize an Atom.
PdbWriter	A writer class for .pdb files.
PeriodicCollapser	Performs rigid-body collapse of molecules.
PeriodicInfo	Periodic cell information for periodic systems.
Pm	Initialize an Atom.
Po	Initialize an Atom.
Power	Raises fitness values to some power.
Pr	Initialize an Atom.
PrimaryAmino	Represents a primary amino functional group.
PrimaryAminoFactory	Creates PrimaryAmino instances.
ProgressPlotter	Plots how a property changes during an EA run.
PropertyVector	Uses multiple molecular properties as a fitness value.
Pt	Initialize an Atom.
Pu	Initialize an Atom.
Ra	Initialize an Atom.
RandomBuildingBlock	Substitutes random building blocks.
RandomCrosser	Use some other crosser at random.
RandomMutator	Use some other mutator at random.
RandomTopologyGraph	Changes topology graphs at random.
Rb	Initialize an Atom.
Re	Initialize an Atom.
Reaction	An abstract base class for reactions.
ReactionFactory	An abstract base class for reaction factories.
ReactionResult	The result of a reaction.
RemoveBatches	Prevents a Selector from selecting some batches.
RemoveMolecules	Prevents a Selector from selecting some molecules.
ReplaceFitness	Replaces fitness values of a certain value with a new value.
Rf	Initialize an Atom.
Rg	Initialize an Atom.
Rh	Initialize an Atom.
RingAmine	Represents an amine bonded to a ring.
RingAmineFactory	Creates RingAmine functional groups.
RingAmineReaction	Performs a reaction between two RingAmine groups.
Rn	Initialize an Atom.
Roulette	Uses roulette selection to select batches of molecules.
Ru	Initialize an Atom.
S	Initialize an Atom.
Sb	Initialize an Atom.
Sc	Initialize an Atom.
Se	Initialize an Atom.
SecondaryAmino	Represents a secondary amino functional group.
SecondaryAminoFactory	Creates SecondaryAmino instances.
SelectionPlotter	Plots which molecule records a Selector selects.
Selector	An abstract base class for selectors.
Sg	Initialize an Atom.
ShiftUp	Shifts negative fitness values to be positive.
Si	Initialize an Atom.
SimilarBuildingBlock	Substitutes similar building blocks.
SingleAtom	Represents an abstract single atom functional group.
Sm	Initialize an Atom.
SmartsFunctionalGroupFactory	Creates GenericFunctionalGroup instances.
Smiles	Used to get the SMILES of molecules.
Sn	Initialize an Atom.
Spinner	Performs Monte Carlo optimisation of host-guest complexes.
Sr	Initialize an Atom.
StochasticUniversalSampling	Yields batches of molecules through stochastic universal sampling.
Sum	Combines fitness value components into a single fitness value.
Ta	Initialize an Atom.
Tb	Initialize an Atom.
Tc	Initialize an Atom.
Te	Initialize an Atom.
TerminalAlkeneFactory	Creates Alkene instances.
TerminalAlkyneFactory	Creates Alkyne instances.
Th	Initialize an Atom.
Thioacid	Represents a thioacid functional group.
ThioacidFactory	Creates Thioacid instances.
Thiol	Represents a thiol functional group.
ThiolFactory	Creates Thiol instances.
Ti	Initialize an Atom.
Tl	Initialize an Atom.
Tm	Initialize an Atom.
TopologyGraph	An abstract base class for topology graphs.
Tournament	Yields batches of molecules through tournament selection.
Ts	Initialize an Atom.
TurbomoleWriter	A writer class for Turbomole files.
TwoTwoReaction	A reaction between two functional groups, each with 2 bonder atoms.
U	Initialize an Atom.
V	Initialize an Atom.
ValueDatabase	Abstract base class for storing of molecular property values.
ValueMongoDb	Use MongoDB to store and retrieve molecular property values.
Vertex	An abstract base class for TopologyGraph vertices.
W	Initialize an Atom.
Worst	Selects batches of molecules, lowest fitness value first.
Xe	Initialize an Atom.
XyzWriter	A writer class for .xyz files.
Y	Initialize an Atom.
Yb	Initialize an Atom.
Zn	Initialize an Atom.
Zr	Initialize an Atom.

Modules

stk.cage
stk.cof
stk.host_guest
stk.macrocycle
stk.metal_complex
stk.polymer
stk.rotaxane
stk.small