Class ProteinFactory

Class serving for creation of coarse-grained proteins

Hierarchy

ProteinFactory

Index

Constructors

constructor

Properties

Methods

Constructors

constructor

new ProteinFactory(): ProteinFactory

- Defined in backend/src/catana/nanomodeling/protein-factory.ts:14
Returns ProteinFactory

Properties

Private _aaToHelixPref

_aaToHelixPref: Map<AminoAcidType, number>

Private _aaToSheetPref

_aaToSheetPref: Map<AminoAcidType, number>

Methods

Private appendAsHelix

appendAsHelix(chain: CgAminoAcidChain, startPos: Vector3, initDir: Vector3, seq: AminoAcidType[]): void

- Defined in backend/src/catana/nanomodeling/protein-factory.ts:69
Appends amino acids forming an alpha-helical structure

Parameters
- chain: CgAminoAcidChain
  
  chain to append to
- startPos: Vector3
  
  starting position of the helix
- initDir: Vector3
  
  initial direction of the helix
- seq: AminoAcidType[]
  
  sequence of amino acids in the helix
Returns void

Private appendAsSheet

appendAsSheet(chain: CgAminoAcidChain, startPos: Vector3, initDir: Vector3, seq: AminoAcidType[]): void

- Defined in backend/src/catana/nanomodeling/protein-factory.ts:101
Appends amino acids forming a very simplistic antiparallel beta sheet-like structure

Parameters
- chain: CgAminoAcidChain
  
  chain to append to
- startPos: Vector3
  
  starting position of the sheet
- initDir: Vector3
  
  initial direction of the sheet
- seq: AminoAcidType[]
  
  sequence of amino acids in the sheet
Returns void

buildPeptide

buildPeptide(startPosition: Vector3, initialDirection: Vector3, sequence: AminoAcidType[]): CgAminoAcidChain | null

- Defined in backend/src/catana/nanomodeling/protein-factory.ts:44
Builds coarse-grained peptide at the desired location in space

Parameters
- startPosition: Vector3
  
  starting position of the peptide chain
- initialDirection: Vector3
  
  initial direction in which the peptide should start
- sequence: AminoAcidType[]
  
  sequence of the peptide
Returns CgAminoAcidChain | null

coarse-grained amino acid chain with the given sequence

buildPeptideFromSequence

buildPeptideFromSequence(fastaSequence: string): CgAminoAcidChain | null

- Defined in backend/src/catana/nanomodeling/protein-factory.ts:27
Builds coarse-grained peptide from the given FASTA sequence

Parameters
- fastaSequence: string
  
  one-letter sequence determining the structure to be built
Returns CgAminoAcidChain | null

coarse-grained amino acid chain with the given sequence

Private getAaToHelixMap

getAaToHelixMap(): Map<AminoAcidType, number>

- Defined in backend/src/catana/nanomodeling/protein-factory.ts:160
Returns Map<AminoAcidType, number>

map storing preferences of individual amino acids to alpha helix conformation

Private getAaToSheetMap

getAaToSheetMap(): Map<AminoAcidType, number>

- Defined in backend/src/catana/nanomodeling/protein-factory.ts:195
Returns Map<AminoAcidType, number>

map storing preferences of individual amino acids to beta sheet conformation

Private shouldFormHelix

shouldFormHelix(sequence: AminoAcidType[]): boolean

- Defined in backend/src/catana/nanomodeling/protein-factory.ts:140
Checks if the given amino acid sequence should form an alpha helix or not

Parameters
- sequence: AminoAcidType[]
  
  sequence to check for
Returns boolean

true if this sequence tends to form an alpha helix

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