psamm.mapmaker – Mapmaker Functions

Functions for predicting compound pairs using the MapMaker algorithm.

The MapMaker algorithm is described in [Tervo16].

psamm.mapmaker.default_weight(element)

Return weight of formula element.

This implements the default weight proposed for MapMaker.

exception psamm.mapmaker.UnbalancedReactionError

Raised when an unbalanced reaction is provided.

psamm.mapmaker.predict_compound_pairs(reaction, compound_formula, solver, epsilon=1e-05, alt_elements=None, weight_func=<function default_weight>)

Predict compound pairs of reaction using MapMaker.

Yields all solutions as dictionaries with compound pairs as keys and formula objects as values.

Parameters:
  • reaction – psamm.reaction.Reaction object.
  • compound_formula – Dictionary mapping compound IDs to formulas. Formulas must be flattened.
  • solver – LP solver (MILP).
  • epsilon – Threshold for rounding floating-point values to integers in the predicted transfers.
  • alt_elements – Iterable of elements to consider for alternative solutions. Only alternate solutions that have different transfers of these elements will be returned (default=all elements).
  • weight_func – Optional function that returns a weight for a formula element (should handle specific Atom and Radical objects). By default, the standard MapMaker weights will be used (H=0, R=40, N=0.4, O=0.4, P=0.4, *=1).