Class Replisome

The replisome - coordinated DNA replication machinery.

Constructors

constructor

new Replisome(fork, organism, config?): Replisome
Creates a new replisome complex.
Parameters
- fork: ReplicationFork
  Replication fork this replisome is advancing
- organism: OrganismProfile
  Organism profile for biological parameters
- config: ReplisomeConfig = {}
  Configuration options
Returns Replisome
- Defined in src/model/replication/Replisome.ts:69

Properties

`Private` `Readonly` activeFragments

activeFragments: Map<string, OkazakiFragment> = ...

`Private` `Readonly` completedFragments

completedFragments: OkazakiFragment[] = []

`Private` `Readonly` config

config: ReplisomeConfig = {}

Configuration options

`Private` `Readonly` eventLog

eventLog: ReplicationEvent[] = []

`Private` exonuclease

exonuclease: Exonuclease

`Private` `Readonly` fork

fork: ReplicationFork

Replication fork this replisome is advancing

`Private` fragmentCounter

fragmentCounter: number = 0

`Private` helicase

helicase: Helicase

`Private` laggingPolymerase

laggingPolymerase: DNAPolymerase

`Private` leadingPolymerase

leadingPolymerase: DNAPolymerase

`Private` ligase

ligase: DNALigase

`Readonly` organism

organism: OrganismProfile

Organism profile for biological parameters

`Private` primase

primase: Primase

Methods

advanceFork

advanceFork(basePairs): ReplicationEvent[]
Advances the replication fork by the specified number of base pairs. Coordinates all enzyme activities.
Parameters
- basePairs: number
  Number of base pairs to advance
Returns ReplicationEvent[]
Array of replication events that occurred
- Defined in src/model/replication/Replisome.ts:106

`Private` calculateFragmentStatistics

calculateFragmentStatistics(): {
averageSize: number;
total: number;
}
Private: Calculate fragment statistics.

Returns {
averageSize: number;
total: number;
}
- averageSize: number
- total: number
- Defined in src/model/replication/Replisome.ts:506

`Private` canContinueFragment

canContinueFragment(fragment): boolean
Private: Check if fragment synthesis can continue.
Parameters
- fragment: OkazakiFragment
Returns boolean
- Defined in src/model/replication/Replisome.ts:368

`Private` continueFragmentSynthesis

continueFragmentSynthesis(fragment, maxBasePairs): ReplicationEvent[]
Private: Continue synthesis on existing fragment.
Parameters
- fragment: OkazakiFragment
- maxBasePairs: number
Returns ReplicationEvent[]
- Defined in src/model/replication/Replisome.ts:375

getCompletedFragments

getCompletedFragments(): OkazakiFragment[]
Gets all completed Okazaki fragments.

Returns OkazakiFragment[]
- Defined in src/model/replication/Replisome.ts:159

getCurrentState

getCurrentState(): ReplicationRuntimeState
Gets the current state of replication.

Returns ReplicationRuntimeState
- Defined in src/model/replication/Replisome.ts:138

`Private` getEnzymePositions

getEnzymePositions(): EnzymePosition[]
Private: Get positions of all enzymes.

Returns EnzymePosition[]
- Defined in src/model/replication/Replisome.ts:462

getEventLog

getEventLog(): ReplicationEvent[]
Gets all replication events (if logging enabled).

Returns ReplicationEvent[]
- Defined in src/model/replication/Replisome.ts:166

getStatistics

getStatistics(): {
    activeFragments: number;
    averageFragmentSize: number;
    completedFragments: number;
    completionPercentage: number;
    estimatedTimeRemaining: number;
    eventsGenerated: number;
    expectedFragmentsRemaining: number;
    laggingStrandProgress: number;
    organismType: string;
    position: number;
    remainingDistance: number;
    speed: number;
    totalFragmentsSynthesized: number;
    totalLength: number;
}
Gets statistics about the replication process.

Returns {
    activeFragments: number;
    averageFragmentSize: number;
    completedFragments: number;
    completionPercentage: number;
    estimatedTimeRemaining: number;
    eventsGenerated: number;
    expectedFragmentsRemaining: number;
    laggingStrandProgress: number;
    organismType: string;
    position: number;
    remainingDistance: number;
    speed: number;
    totalFragmentsSynthesized: number;
    totalLength: number;
}
- activeFragments: number
- averageFragmentSize: number
- completedFragments: number
- completionPercentage: number
- estimatedTimeRemaining: number
- eventsGenerated: number
- expectedFragmentsRemaining: number
- laggingStrandProgress: number
- organismType: string
- position: number
- remainingDistance: number
- speed: number
- totalFragmentsSynthesized: number
- totalLength: number
- Defined in src/model/replication/Replisome.ts:173

`Private` getlaggingStrandProgress

getlaggingStrandProgress(): number
Private: Get lagging strand progress.

Returns number
- Defined in src/model/replication/Replisome.ts:450

`Private` helicaseUnwind

helicaseUnwind(basePairs): ReplicationEvent
Private: Helicase unwinds DNA.
Parameters
- basePairs: number
Returns ReplicationEvent
- Defined in src/model/replication/Replisome.ts:255

`Private` initializeEnzymes

initializeEnzymes(): void
Private: Initialize all enzymes in the replisome.

Returns void
- Defined in src/model/replication/Replisome.ts:207

`Private` initiateNewFragment

initiateNewFragment(): ReplicationEvent[]
Private: Initiate a new Okazaki fragment.

Returns ReplicationEvent[]
- Defined in src/model/replication/Replisome.ts:330

isComplete

isComplete(): boolean
Checks if replication is complete.

Returns boolean
- Defined in src/model/replication/Replisome.ts:152

`Private` processCompletedFragments

processCompletedFragments(): ReplicationEvent[]
Private: Process completed Okazaki fragments.

Returns ReplicationEvent[]
- Defined in src/model/replication/Replisome.ts:401

`Private` shouldStartNewFragment

shouldStartNewFragment(): boolean
Private: Check if a new Okazaki fragment should be started.

Returns boolean
- Defined in src/model/replication/Replisome.ts:309

`Private` synthesizeLaggingStrand

synthesizeLaggingStrand(basePairs): ReplicationEvent[]
Private: Synthesize lagging strand (discontinuous).
Parameters
- basePairs: number
Returns ReplicationEvent[]
- Defined in src/model/replication/Replisome.ts:288

`Private` synthesizeLeadingStrand

synthesizeLeadingStrand(basePairs): ReplicationEvent[]
Private: Synthesize leading strand (continuous).
Parameters
- basePairs: number
Returns ReplicationEvent[]
- Defined in src/model/replication/Replisome.ts:271

`Static` create

create(fork, organism, config?): ValidationResult<Replisome>
Creates a replisome with validation.
Parameters
- fork: ReplicationFork
  Replication fork
- organism: OrganismProfile
  Organism profile
- config: ReplisomeConfig = {}
  Configuration options
Returns ValidationResult<Replisome>
ValidationResult containing Replisome or error
- Defined in src/model/replication/Replisome.ts:85

Class Replisome

Index

Constructors

Properties

Methods

Constructors

constructor

Parameters

Returns Replisome

Properties

Private Readonly activeFragments

Private Readonly completedFragments

Private Readonly config

Private Readonly eventLog

Private exonuclease

Private Readonly fork

Private fragmentCounter

Private helicase

Private laggingPolymerase

Private leadingPolymerase

Private ligase

Readonly organism

Private primase

Methods

advanceFork

Parameters

Returns ReplicationEvent[]

Private calculateFragmentStatistics

Returns { averageSize: number; total: number; }

averageSize: number

total: number

Private canContinueFragment

Parameters

Returns boolean

Private continueFragmentSynthesis

Parameters

Returns ReplicationEvent[]

getCompletedFragments

Returns OkazakiFragment[]

getCurrentState

Returns ReplicationRuntimeState

Private getEnzymePositions

Returns EnzymePosition[]

getEventLog

Returns ReplicationEvent[]

getStatistics

activeFragments: number

averageFragmentSize: number

completedFragments: number

completionPercentage: number

estimatedTimeRemaining: number

eventsGenerated: number

expectedFragmentsRemaining: number

laggingStrandProgress: number

organismType: string

position: number

remainingDistance: number

speed: number

totalFragmentsSynthesized: number

totalLength: number

Private getlaggingStrandProgress

Returns number

Private helicaseUnwind

Parameters

Returns ReplicationEvent

Private initializeEnzymes

Returns void

Private initiateNewFragment

Returns ReplicationEvent[]

isComplete

Returns boolean

Private processCompletedFragments

Returns ReplicationEvent[]

Private shouldStartNewFragment

Returns boolean

Private synthesizeLaggingStrand

Parameters

Returns ReplicationEvent[]

Private synthesizeLeadingStrand

Parameters

`Private` `Readonly` activeFragments

`Private` `Readonly` completedFragments

`Private` `Readonly` config

`Private` `Readonly` eventLog

`Private` exonuclease

`Private` `Readonly` fork

`Private` fragmentCounter

`Private` helicase

`Private` laggingPolymerase

`Private` leadingPolymerase

`Private` ligase

`Readonly` organism

`Private` primase

`Private` calculateFragmentStatistics

Returns {
averageSize: number;
total: number;
}

`Private` canContinueFragment

`Private` continueFragmentSynthesis

`Private` getEnzymePositions

`Private` getlaggingStrandProgress

`Private` helicaseUnwind

`Private` initializeEnzymes

`Private` initiateNewFragment

`Private` processCompletedFragments

`Private` shouldStartNewFragment

`Private` synthesizeLaggingStrand

`Private` synthesizeLeadingStrand

`Static` create