CgPolymer | catana-backend

Class storing data of single coarse-grained polymer/chain

Hierarchy

CgPolymer
- CgAminoAcidChain
- CgNucleicAcidStrand

Index

Constructors

constructor

Properties

Accessors

Constructors

constructor

new CgPolymer(globalId: number, name: string, parentStructure: CgStructure | undefined, monStore: CgMonomerStore): CgPolymer

- Defined in backend/src/catana/data_model/cg-polymer.ts:20
Parameters
- globalId: number
  
  global ID of this polymer
- name: string
  
  name of this polymer
- parentStructure: CgStructure | undefined
  
  parent structure of this polymer
- monStore: CgMonomerStore
  
  instance of monomer store where the polymer data should be stored
Returns CgPolymer

Properties

Private _customColor

_customColor: Color | undefined = undefined

Private _globalId

_globalId: number

Protected _monomerStore

_monomerStore: CgMonomerStore

Private _name

_name: string

Private _parentStructure

_parentStructure: CgStructure | undefined = undefined

Accessors

customColor

get customColor(): Color | undefined
set customColor(val: Color | undefined): void

- Defined in backend/src/catana/data_model/cg-polymer.ts:162
Sets new custom color for this polymer

Returns Color | undefined

Custom user-defined color of this polymer (or undefined if none set)
- Defined in backend/src/catana/data_model/cg-polymer.ts:169
Sets new custom color for this polymer

Parameters
- val: Color | undefined
Returns void

Custom user-defined color of this polymer (or undefined if none set)

globalId

get globalId(): number
set globalId(val: number): void

- Defined in backend/src/catana/data_model/cg-polymer.ts:134
Sets new global ID for this polymer

Returns number

Global ID of this polymer
- Defined in backend/src/catana/data_model/cg-polymer.ts:141
Sets new global ID for this polymer

Parameters
- val: number
Returns void

Global ID of this polymer

length

get length(): number

- Defined in backend/src/catana/data_model/cg-polymer.ts:190
Returns number

Length of this polymer (i.e., number of monomers)

monomerStore

get monomerStore(): CgMonomerStore

- Defined in backend/src/catana/data_model/cg-polymer.ts:114
Returns CgMonomerStore

reference to the underlying monomer store

name

get name(): string
set name(val: string): void

- Defined in backend/src/catana/data_model/cg-polymer.ts:148
Sets new name for this polymer

Returns string

Name of this polymer
- Defined in backend/src/catana/data_model/cg-polymer.ts:155
Sets new name for this polymer

Parameters
- val: string
Returns void

Name of this polymer

parentStructure

get parentStructure(): CgStructure | undefined
set parentStructure(newPar: CgStructure | undefined): void

- Defined in backend/src/catana/data_model/cg-polymer.ts:176
Sets new parent structure of this polymer

Returns CgStructure | undefined

reference to parent structure of this polymer (or undefined if none exists)
- Defined in backend/src/catana/data_model/cg-polymer.ts:183
Sets new parent structure of this polymer

Parameters
- newPar: CgStructure | undefined
Returns void

reference to parent structure of this polymer (or undefined if none exists)

sequence

get sequence(): MonomerType[]

- Defined in backend/src/catana/data_model/cg-polymer.ts:121
Returns MonomerType[]

an array of monomer types describing the sequence of this polymer

Methods

Abstract applyMatrixTransformation

applyMatrixTransformation(matrix: Matrix4): void

- Defined in backend/src/catana/data_model/cg-polymer.ts:199
Applies matrix transformation to all polymer's monomers

Parameters
- matrix: Matrix4
  
  transformation matrix
Returns void

Protected commonFindIndex

commonFindIndex(pred: (a: CgMonomerProxy, i: number) => boolean): number

- Defined in backend/src/catana/data_model/cg-polymer.ts:242
Returns index of first monomer meeting the given predicate

Parameters
- pred: (a: CgMonomerProxy, i: number) => boolean
  
  boolean predicate function (accepting monomer proxy and its index as parameters)
  - - (a: CgMonomerProxy, i: number): boolean
    - Parameters
      - a: CgMonomerProxy
      - i: number
      Returns boolean
Returns number

index of the first monomer for which the predicate returns "true"

Protected commonForEach

commonForEach(callback: (a: CgMonomerProxy, i: number) => void): void

- Defined in backend/src/catana/data_model/cg-polymer.ts:228
Executes a given callback on each monomer (going from start of the polymer to its end)

Parameters
- callback: (a: CgMonomerProxy, i: number) => void
  
  function to be executed on each monomer, accepting monomer proxy and its index in the polymer as parameters
  - - (a: CgMonomerProxy, i: number): void
    - Parameters
      - a: CgMonomerProxy
      - i: number
      Returns void
Returns void

Protected commonForEachReverse

commonForEachReverse(callback: (a: CgMonomerProxy, i: number) => void): void

- Defined in backend/src/catana/data_model/cg-polymer.ts:258
Executes a given callback on each monomer (going from end of the polymer to its start, i.e., in reverse)

Parameters
- callback: (a: CgMonomerProxy, i: number) => void
  
  function to be executed on each monomer, accepting monomer proxy and its index in the polymer as parameters
  - - (a: CgMonomerProxy, i: number): void
    - Parameters
      - a: CgMonomerProxy
      - i: number
      Returns void
Returns void

copyFrom

copyFrom(other: CgPolymer, startIdx: number, endIdxExcl: number): void

- Defined in backend/src/catana/data_model/cg-polymer.ts:45
Copies data from the particular section of the other polymer to this one. If this polymer carried some data, they will be replaced/removed.

Parameters
- other: CgPolymer
  
  polymer to copy data from
- startIdx: number
  
  index to start copy from (inclusive)
- endIdxExcl: number
  
  index identifying the end of section to copy from (exclusive)
Returns void

dispose

dispose(): void

- Defined in backend/src/catana/data_model/cg-polymer.ts:219
Disposes of this polymer

Returns void

forEachMonomer

forEachMonomer(callback: (mp: CgMonomerProxy, i: number) => void): void

- Defined in backend/src/catana/data_model/cg-polymer.ts:54
Parameters
- callback: (mp: CgMonomerProxy, i: number) => void
  - - (mp: CgMonomerProxy, i: number): void
    - Parameters
      - mp: CgMonomerProxy
      - i: number
      Returns void
Returns void

getIndexForGlobalId

getIndexForGlobalId(globalId: number): number

- Defined in backend/src/catana/data_model/cg-polymer.ts:65
Returns monomer store index corresponding to the monomer with the given global ID.

Parameters
- globalId: number
  
  global ID to search for
Returns number

store index of monomer with given global ID or -1 if no such monomer exists.

Abstract getMonomerProxyTemplate

getMonomerProxyTemplate(): CgMonomerProxy

- Defined in backend/src/catana/data_model/cg-polymer.ts:370
Returns instance of a monomer proxy object with the index being set to -1. It is expected that the index will be manually set by the user later on.

Returns CgMonomerProxy

monomer proxy instance pointing to invalid data

getViews

getViews(filter: Filter): CgPolymerView[]

- Defined in backend/src/catana/data_model/cg-polymer.ts:81
Returns an array of polymer views determined by the provided filter

Parameters
- filter: Filter
  
  filter string determining which monomers to include
Returns CgPolymerView[]

array storing continuous views with monomers passing the filter test

Abstract isCyclic

isCyclic(): boolean

- Defined in backend/src/catana/data_model/cg-polymer.ts:362
Returns boolean

true if this polymer is cyclic/circular

Abstract isDna

isDna(): boolean

- Defined in backend/src/catana/data_model/cg-polymer.ts:357
Returns boolean

true if this polymer is DNA strand

Abstract isNucleic

isNucleic(): boolean

- Defined in backend/src/catana/data_model/cg-polymer.ts:347
Returns boolean

true if this polymer is nucleic acid chain

Abstract isProtein

isProtein(): boolean

- Defined in backend/src/catana/data_model/cg-polymer.ts:342
Returns boolean

true if this polymer is a protein chain

Abstract isRna

isRna(): boolean

- Defined in backend/src/catana/data_model/cg-polymer.ts:352
Returns boolean

true if this polymer is RNA strand

Abstract proxyAtIndex

proxyAtIndex(index: number): CgMonomerProxy | null

- Defined in backend/src/catana/data_model/cg-polymer.ts:337
Returns instance of monomer proxy at given index

Parameters
- index: number
  
  index of the desired monomer
Returns CgMonomerProxy | null

monomer proxy instance at the given index or null if index is not valid

Protected removeMonomer

removeMonomer(proxy: CgMonomerProxy): void

- Defined in backend/src/catana/data_model/cg-polymer.ts:301
Removes given monomer. If the polymer is empty after the removal, it is also removed from the parent structure.

Parameters
- proxy: CgMonomerProxy
  
  monomer to remove
Returns void

Protected removeMonomerAtIndex

removeMonomerAtIndex(index: number): void

- Defined in backend/src/catana/data_model/cg-polymer.ts:273
Removes monomer at given index. If the polymer is empty after the removal, it is also removed from the parent structure.

Parameters
- index: number
  
  index of the monomer to remove
Returns void

Protected removeMonomers

removeMonomers(proxies: CgMonomerProxy[]): void

- Defined in backend/src/catana/data_model/cg-polymer.ts:311
Removes given monomers. If the polymer is empty after the removal, it is also removed from the parent structure.

Parameters
- proxies: CgMonomerProxy[]
  
  monomers to remove
Returns void

Protected removeMonomersAtIndices

removeMonomersAtIndices(indices: number[]): void

- Defined in backend/src/catana/data_model/cg-polymer.ts:287
Removes monomers stored at given indices. If the polymer is empty after the removal, it is also removed from the parent structure.

Parameters
- indices: number[]
  
  an array of indices of monomers to remove
Returns void

renumberMonomerGlobalIds

renumberMonomerGlobalIds(renameMap?: Map<number, number>): void

- Defined in backend/src/catana/data_model/cg-polymer.ts:206
Changes global IDs of all included monomers (using the GlobalIdGenerator)

Parameters
- Optional renameMap: Map<number, number>
  
  if provided, it will store the old id -> new id records for each monomer
Returns void

Abstract setSequence

setSequence(seq: MonomerType[]): void

- Defined in backend/src/catana/data_model/cg-polymer.ts:129
Changes sequence of the whole polymer. If the newly provided sequence is shorter, it will be applied in a "circular fashion".

Parameters
- seq: MonomerType[]
  
  new sequence to be applied to the current polymer
Returns void

Protected truncate

truncate(newLength: number): void

- Defined in backend/src/catana/data_model/cg-polymer.ts:322
Shortens this polymer to a new length, discarding the original data beyond this new size.

Parameters
- newLength: number
  
  new lenght of this polymer
Returns void

Hierarchy

Index

Constructors

Properties

Accessors

Methods

Constructors

constructor

Parameters

globalId: number

name: string

parentStructure: CgStructure | undefined

monStore: CgMonomerStore

Returns CgPolymer

Properties

Private _customColor

Private _globalId

Protected _monomerStore

Private _name

Private _parentStructure

Accessors

customColor

Returns Color | undefined

Parameters

val: Color | undefined

Returns void

globalId

Returns number

Parameters

val: number

Returns void

length

Returns number

monomerStore

Returns CgMonomerStore

name

Returns string

Parameters

val: string

Returns void

parentStructure

Returns CgStructure | undefined

Parameters

newPar: CgStructure | undefined

Returns void

sequence

Returns MonomerType[]

Methods

Abstract applyMatrixTransformation

Parameters

matrix: Matrix4

Returns void

Protected commonFindIndex

Parameters

pred: (a: CgMonomerProxy, i: number) => boolean

Parameters

a: CgMonomerProxy

i: number

Returns boolean

Returns number

Protected commonForEach

Parameters

callback: (a: CgMonomerProxy, i: number) => void

Parameters

a: CgMonomerProxy

i: number

Returns void

Returns void

Protected commonForEachReverse

Parameters

callback: (a: CgMonomerProxy, i: number) => void

Parameters

a: CgMonomerProxy

i: number

Returns void

Returns void

copyFrom

Parameters

other: CgPolymer

startIdx: number