module

Kamae

Constants

BACKBONE_NAMES = {"N", "CA", "C", "O"}
Log = ::Log.for("kamae")
PROTEIN_CHAIN_MIN = 20
RARE_FLOOR = 0.05

Frequency floor for rare vs frequent states / joint fingerprints (5%).

SITE_RADIUS = 5.0
UNKNOWN_CODE = '?'

Missing residues are X in an aligned sequence, so an unknown residue code must be a different character.

VERSION = {{ (`shards version \"/tmp/tmp.emaGmk/src/src/..\"`).chomp.stringify }}

shard.yml is the only copy of the version (shards version at compile time).

Class methods

align_on_site(structures : Array(Chem::Structure), site : Array(ResId), frame : Chem::Structure | Nil = nil) : Nil

Superimposes structures on the CA atoms of the site residues resolved in all of them (see Chem.align_ensemble). frame, when given, is the coordinate frame (placed first in the fit); an external frame is not moved.

Source
detect_binding_site(structures : Array(Chem::Structure)) : Array(ResId)
Source
renumber_ensemble(structures : Array(Chem::Structure), sequence : String, reference : Chem::Structure) : Nil

Renumbers structures in place after the positions (from 1) of sequence. Chain ids follow reference, which must have a ligand site and may be one of structures. Structures that cannot be renumbered are removed and reported.

Source
renumber_ensemble(structures : Array(Chem::Structure), reference : Chem::Structure) : Nil

Renumbers structures in place after the author numbering and chain ids of reference, which may be one of them. Structures that cannot be renumbered are removed and reported.

Source
select_medoids(structures : Array(Chem::Structure), matrix : StateMatrix) : Array(Chem::Structure)

Medoids of matrix, then pin frequent codes, drop structurally redundant medoids, and restore any per-column state that drop lost. Writes nothing.

Source
select_receptors(structures : Array(Chem::Structure), residues : Array(ResId), frame : Chem::Structure) : Array(Chem::Structure)

Fingerprint residues of an already superimposed ensemble and select representatives. frame is the secondary-structure reference. Writes nothing.

Source
state_matrix(structures : Array(Chem::Structure), residues : Array(ResId), frame : Chem::Structure) : StateMatrix

Conformational states of an already superimposed ensemble. frame is the secondary-structure reference. Rows are StateMatrix#fingerprints. Writes nothing.

Source

Nested types