API Reference

Identify catalytic sites in protein structures by matching templates derived from the Mechanism and Catalytic Site Atlas with the Enzyme Motif Miner!

See also

Investigating Enzyme Function by Geometric Matching of Catalytic Motifs Raymund E. Hackett, Ioannis Riziotis, Martin Larralde, Antonio J. M. Ribeiro, Janet M. Thornton bioRxiv 2026.02.10.705182 doi:10.64898/2026.02.10.705182

Input

jess_run.load_molecules	Load query molecules from a list of paths to PDB or CIF/mmCIF structure files.
template.load_templates	Load templates from a given directory, recursively.

Templates

template.load_templates	Load templates from a given directory, recursively.
template.Vec3	Class for storing 3D vectors in XYZ.
template.Residue	Class for storing template residues (defined as 3 atoms) with relevant information.
template.AnnotatedResidue	Child class inheriting from Residue for M-CSA annotated template residues.
template.Cluster	Class for storing template cluster information.
template.Template	Class for storing templates and associated information.
template.AnnotatedTemplate	Child class inheriting from Template for M-CSA annotated catalytic site templates.

Matching

jess_run.Matcher	Class from which a query Molecule is matched to a list of Template.
jess_run.Match	Class for storing annotated PyJess hits.
jess_run.ModelEnsemble	Ensemble of Models which each produce a binary prediction.
jess_run.LogisticRegressionModel	Class for storing a Logistc Regression Model for predicting if a match is correct.

M-CSA

mcsa_info.HomologousPDB	Class for a PDB Entry homologous to or identical to the structure from which a template was generated.
mcsa_info.HomologousResidue	Base class for a PDB residue identical or homologous to a template residue.
mcsa_info.NonReferenceCatalyticResidue	Child Class of HomologousResidue for a non-reference PDB residue for a template residue.
mcsa_info.ReferenceCatalyticResidue	Child Class of HomologousResidue for a reference PDB residue for a template residue.

Output

output.BaseTable	A base class for different types of output styles.
output.FullMatchTable	A class for representing the full information associated with EnzyMM matches.
output.SimpleMatchTable	A class for representing the simpler information associated with EnzyMM matches.
output.MatchResidueTable	A class for representing residue mappings between query, template and reference from EnzyMM matches.
output.Tables	A class for creating instances of children of BaseTable of the selected kind