class

Kamae::ProteinEnsemble

Inherits Indexable < Enumerable < Iterable < Reference < Object

One ChainGroup per input structure (ensemble[i]), the family of each protein chain, and the family ids that form the ligand site.

Constructors

new(structures : Array(Chem::Structure)) : self

Groups protein chains into families (see assign_family_ids) and picks each structure's site chains (see find_site_candidates). The site families are those most often contacted by a structure's main ligand (most protein contacts). A structure's site chains are those of its main ligand among ligands contacting those families, or nil if none does. Aborts if no structure has a ligand. Several chains of one family are copies of the same protein at the site.

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Instance methods

family_id(chain : Chem::Chain) : Int32

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find_chain(chains : Array(Chem::Chain), family_id : Int32) : Chem::Chain | Nil

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find_chain!(chains : Array(Chem::Chain), family_id : Int32) : Chem::Chain

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find_family_chain(group : ChainGroup, family_id : Int32) : Chem::Chain | Nil

The site chain of family_id, or any protein chain of that family.

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select_chains(chains : Array(Chem::Chain), family_id : Int32) : Array(Chem::Chain)

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select_family_chains(group : ChainGroup, family_id : Int32) : Array(Chem::Chain)

Site chains of family_id, or every protein chain of that family when group has no ligand site.

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site_family_ids

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size

Returns the number of elements in this container.

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unsafe_fetch(index : Int) : ChainGroup

Indexable checks the bounds, then calls this.

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