Index

_

__add__() (enzymm.template.Vec3 method) __call__() (enzymm.jess_run.LogisticRegressionModel method) (enzymm.jess_run.ModelEnsemble method) __init__() (enzymm.jess_run.LogisticRegressionModel method) (enzymm.jess_run.Match method) (enzymm.jess_run.Matcher method) (enzymm.jess_run.ModelEnsemble method) (enzymm.mcsa_info.HomologousPDB method) (enzymm.mcsa_info.HomologousResidue method) (enzymm.mcsa_info.NonReferenceCatalyticResidue method) (enzymm.mcsa_info.ReferenceCatalyticResidue method) (enzymm.template.AnnotatedResidue method) (enzymm.template.AnnotatedTemplate method) (enzymm.template.Cluster method) (enzymm.template.Residue method) (enzymm.template.Template method) (enzymm.template.Vec3 method)

__matmul__() (enzymm.template.Vec3 method) __sub__() (enzymm.template.Vec3 method) __truediv__() (enzymm.template.Vec3 method)

A

allowed_residues (enzymm.template.Residue property) angle_to() (enzymm.template.Vec3 method) AnnotatedResidue (class in enzymm.template) AnnotatedTemplate (class in enzymm.template)

assembly (enzymm.mcsa_info.HomologousPDB attribute) assembly_chain_id (enzymm.mcsa_info.HomologousPDB attribute) atom_triplets (enzymm.jess_run.Match property) atoms (enzymm.template.Residue property) auth_number (enzymm.mcsa_info.HomologousResidue attribute)

B

backbone (enzymm.template.Residue property)

C

calc_residue_orientation() (enzymm.template.Residue static method) chain_id (enzymm.mcsa_info.HomologousPDB attribute) (enzymm.template.Residue property) Cluster (class in enzymm.template)

coef (enzymm.jess_run.LogisticRegressionModel attribute) complete (enzymm.jess_run.Match attribute) construct_residues_from_atoms() (enzymm.template.Residue class method) copy() (enzymm.template.AnnotatedTemplate method) (enzymm.template.Template method)

D

dump() (enzymm.jess_run.Match method) (enzymm.template.Template method) dump2pdb() (enzymm.jess_run.Match method)

dump_query() (enzymm.jess_run.Match method) dump_template() (enzymm.jess_run.Match method) dumps() (enzymm.jess_run.Match method) (enzymm.template.Template method)

E

effective_size (enzymm.template.Template property) ensemble (enzymm.jess_run.ModelEnsemble attribute) enzymm module enzymm.jess_run module

enzymm.mcsa_info module enzymm.template module

F

from_json() (enzymm.jess_run.ModelEnsemble class method) from_molecule() (enzymm.template.Template class method) from_molecule_residue() (enzymm.template.Residue class method)

from_structure_file() (enzymm.template.Template class method) from_xyz() (enzymm.template.Vec3 class method) function_location_abv (enzymm.mcsa_info.ReferenceCatalyticResidue attribute)

G

get_identifying_attributes() (enzymm.jess_run.Match method)

H

has_ptm (enzymm.template.AnnotatedResidue property) hit (enzymm.jess_run.Match attribute)

HomologousPDB (class in enzymm.mcsa_info) HomologousResidue (class in enzymm.mcsa_info)

I

id (enzymm.template.Cluster attribute) index (enzymm.jess_run.Match attribute) intercept (enzymm.jess_run.LogisticRegressionModel attribute)

is_metal_ligand (enzymm.template.AnnotatedResidue property) is_mutated (enzymm.template.AnnotatedResidue property) is_reference (enzymm.mcsa_info.HomologousPDB attribute)

L

load() (enzymm.template.AnnotatedTemplate class method) (enzymm.template.Template class method) load_templates() (in module enzymm.template)

loads() (enzymm.template.AnnotatedTemplate class method) (enzymm.template.Template class method) LogisticRegressionModel (class in enzymm.jess_run) logit_threshold (enzymm.jess_run.LogisticRegressionModel property)

M

Match (class in enzymm.jess_run) match_vector_list (enzymm.jess_run.Match property) matched_residues (enzymm.jess_run.Match property) Matcher (class in enzymm.jess_run) mcsa_id (enzymm.mcsa_info.HomologousPDB attribute) member (enzymm.template.Cluster attribute) min_true_template_size (enzymm.jess_run.ModelEnsemble attribute) minimum_effective_size (enzymm.jess_run.ModelEnsemble attribute)

ModelEnsemble (class in enzymm.jess_run) module enzymm enzymm.jess_run enzymm.mcsa_info enzymm.template multimeric (enzymm.jess_run.Match property) (enzymm.template.Template property)

N

name (enzymm.mcsa_info.HomologousResidue attribute) (enzymm.template.Residue property) NonReferenceCatalyticResidue (class in enzymm.mcsa_info) norm (enzymm.template.Vec3 property)

normalize() (enzymm.template.Vec3 method) number (enzymm.mcsa_info.HomologousResidue attribute) (enzymm.template.Residue property) number_of_models() (enzymm.jess_run.ModelEnsemble method)

O

orientation (enzymm.jess_run.Match property)

orientation_vector (enzymm.template.Residue property) orientation_vector_indices (enzymm.template.Residue property)

P

pairwise_distance (enzymm.jess_run.Match attribute) pdb_id (enzymm.mcsa_info.HomologousPDB attribute)

predicted_correct (enzymm.jess_run.Match property) preserved_resid_order (enzymm.jess_run.Match property) ptm (enzymm.mcsa_info.ReferenceCatalyticResidue attribute)

Q

query_atom_count (enzymm.jess_run.Match property)

query_residue_count (enzymm.jess_run.Match property)

R

reference (enzymm.mcsa_info.NonReferenceCatalyticResidue attribute) reference_idx (enzymm.template.AnnotatedResidue attribute) reference_pdb (enzymm.template.AnnotatedResidue attribute) reference_pdbchain (enzymm.mcsa_info.HomologousPDB attribute) reference_residue (enzymm.template.AnnotatedResidue attribute) ReferenceCatalyticResidue (class in enzymm.mcsa_info) relative_order (enzymm.template.Template property)

Residue (class in enzymm.template) residues (enzymm.mcsa_info.HomologousPDB attribute) roles (enzymm.mcsa_info.ReferenceCatalyticResidue attribute) (enzymm.template.AnnotatedResidue property) roles_summary (enzymm.mcsa_info.ReferenceCatalyticResidue attribute) (enzymm.template.AnnotatedResidue property) run() (enzymm.jess_run.Matcher method) run_single() (enzymm.jess_run.Matcher method)

S

size (enzymm.template.Cluster attribute)

specific (enzymm.template.Residue property)

T

Template (class in enzymm.template)

template_vector_list (enzymm.jess_run.Match property) threshold (enzymm.jess_run.LogisticRegressionModel attribute)

V

Vec3 (class in enzymm.template)

verbose_print() (enzymm.jess_run.Matcher method)

X

x (enzymm.template.Vec3 attribute)

Y

y (enzymm.template.Vec3 attribute)

Z

z (enzymm.template.Vec3 attribute)