API reference

API reference#

This reference documents the public interface re-exported from the top-level molfoundry package – everything listed in molfoundry.__all__. It is generated directly from the source and its type hints, so it always matches the installed version.

Building molecules and graphs#

Constructors that turn a textual description into a Graph, plus the graph data structure itself.

`smiles`
`inchi`
`molfile`
`graphGMLString`
`Graph`
`Vertex`
`Edge`
`VertexRange`
`EdgeRange`
`VertexFilter`

Chemical attributes#

Value types used to label and describe atoms, bonds, and graphs.

`GraphType`
`BondType`
`Charge`	Representation of the charge of an atom.
`Isotope`	Representation of the isotope of an atom.
`AtomId`	Identifies a chemical element and exposes its data from the shared `Atom` table.
`LabelType`
`LabelRelation`
`LabelSettings`
`Conformer`
`GraphPrinter`

Rules and rule composition#

Transformation rules and the algebra for combining them.

`ruleGMLString`
`ruleGML`
`ruleMolFoundry`
`Rule`
`RCEvaluator`	Evaluates rule-composition expressions.
`RCExp`	A rule-composition expression.
`rcCommon`
`rcParallel`
`rcSub`
`rcSuper`

Derivation graphs#

Reaction networks built by applying rules, and the objects that describe how each derivation maps atoms.

`DG`
`Derivation`
`Derivations`
`DGVertexMapper`	Enumerates the atom-atom maps of a hyperedge.
`VertexMap`	An atom-atom map of a hyperedge, as a sequence of `VertexMapEntry`.
`VertexMapEntry`	One atom of an atom-atom map.
`AutGroup`
`Aut`

Strategies#

The strategy DSL that drives network expansion.

`DGStrat`
`GraphState`
`addUniverse`
`addSubset`
`leftPredicate`
`rightPredicate`
`repeat`
`execute`
`filterUniverse`
`filterSubset`
`revive`

Stochastic simulation#

Rule-based Gillespie simulation with on-demand network expansion.

`Stochsim`	Rule-based Gillespie stochastic simulation with on-demand network expansion.
`MultiPhaseStochsim`	Exact multiphase (multi-compartment) stochastic simulation.

Post-processing and global state#

Summary output and the implicit global input collections.

`enable_post`
`disable_post`
`postSection`
`postChapter`
`inputRules`	Built-in mutable sequence.
`inputGraphs`	Built-in mutable sequence.

Exceptions#

LogicError

Subpackages#

molfoundry.atomtracing