GEN FileFormat

... raw digital DNA
C3 dDNA File
Copyright 1999+ Cyberlife Technology Ltd
Version 1.0 Release 1

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General terms and definitions

• BYTE
• Arrays

A word about this document
The overall file format
The genetic hierarchy
The structure of a gene

• The gene Header
• The Generation, SwitchOn and Flags entries
• The Mutability Weighting entry

Brain Genes (Type 00)

• Brain Lobes (Type 00 00 - Size 121)
• Brain Lobe Information
• Brain Organs (Type 00 01 - Size 5)
• Brain Tract (Type 00 02 - Size 128)
• Brain Tract Information

Biochemistry Genes (Type 01)

• Biochemical Receptors (Type 01 00 - Size 8)
• Biochemical Emitters (Type 01 01 - Size 8)
• Biochemical Reactions (Type 01 02 - Size 9)
• Biochemical Half Lives (Type 01 03 - Size 256)
• Biochemical Initial Concentrations (Type 01 04 - Size 2?)
• Biochemical Neuro Emitters (Type 01 05 - Size 15)

Creature Genes (Type 02)

• Creature Stimulus (Type 02 00 - Size 13)
• Creature Genus (Type 02 01 - Size 65)
• Creature Appearance (Type 02 02 - Size 3)
• Creature Pose (Type 02 03 - Size 17)
• Creature Gait (Type 02 04 - Size 9)
• Creature Instinct (Type 02 05 - Size 9)
• Creature Pigments (Type 02 06 - Size 2)
• Creature Pigment Bleeds (Type 02 07 - Size 2)

Organs (Type 03)

• Organs Organ (Type 03 00 - Size 5)

Appendix One: SVRules
Appendix Two: Loci

• Receptor Loci ( type = 0)
• Emitter loci (type = 1)
  

General terms and definitions

BYTE
BYTE defines a single byte of data. An 8 bit unsigned integer, a BYTE can store whole numbers ranging from zero to 255.

Arrays
Arrays of bytes are defined as BYTE[SIZE] and contain SIZE bytes of data.

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A Word about this document
This document is not meant to teach you genetics. Nor is it meant to tell you how to interpret the values within the genome. It is to explain the file format, and to give you a brief insight into how the genetics data is constructed, so that you can write utilities which operate on the genetics files.

If you find errors in this document, or have written extra information you think should be added, please contact the maintainer (currently ben. campbell@creaturelabs.com).

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The overall file format

The genetics file consists of a magic cookie of four characters at the beginning of the file, and then a series of genes, delimited by gene markers, terminated with an end token.

The cookie is:

BYTE [4] Cookie = 'd' 'n' 'a' '3'

The gene delimiter is

BYTE [4] Delimiter = 'g' 'e' 'n' 'e'

The end marker is

BYTE [4] EndMarker = 'g' 'e' 'n' 'd'

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The genetic hierarchy

Creatures in Creatures 3 have genetically specified organs, which contain certain genes. These organs and the genes which the contain are in a certain configuration within the genetics files.

Biochemical Reactions, Receptors and Emitters all belong to the organ which was last defined. If no organ has yet been defined then they are considered "orphaned" and belong to the implied "body" organ. Brain lobes belong to the "TheBrain Organ" and again, if no brain organ definition has been encountered then they are "orphaned" and belong to the next brain organ to be defined. Note that should you define multiple Brain Organs, only the very last one to be defined will be expressed. A creature can have only one brain.

There must be only one "Creature/Genus" gene, which must be gene zero in the file. If this is not so, then the genetics file is invalid.

All other types of genes belong to the body and their order does not matter.

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The structure of a gene

Genes each have a header, and a body. The header is of a fixed length, the body of the gene varies in length between gene types, but is consistent within a gene type.

The gene Header

BYTE GeneType
BYTE GeneSubType
BYTE GeneID
BYTE Generation
BYTE SwitchOnTime
BYTE Sex-Dependance/Mutability-Flags
BYTE MutabilityWeighting
BYTE Expression Variant

The Generation, SwitchOn and Flags entries

The generation byte indicates how many times this gene has been duplicated. The switch on time ranges from 0 (embryo) to 6 (senile). The flags entry is a bit field which is arranged as follows.

The Mutability Weighting entry

currently undocumented.... oooooooooh...

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Brain Genes (Type 00)

There are three types of brain genes, the first is the brain lobe (Type 00 00), the second, the brain organ (type 00 01), and the third the brain tract (type 00 02).

Brain Lobes (Type 00 00 - Size 121)

In C3 Brain lobe genes perform all their calculations by means of SV rules.

BYTE [4] Lobe ID
BYTE [2] Update Time
BYTE [2] x
BYTE [2] y
BYTE Width
BYTE Height
BYTE Red
BYTE Green
BYTE Blue
BYTE WTA
BYTE Tissue
BYTE [8] spare
BYTE [48] Initialise Neuron Rule
BYTE [48] Update Neuron Rule

Brain Lobe Information

• Lobe id is a character based token
• Width * Height define the number of neurons in the lobe.
• The Flags entry in the brain lobe indicates whether the lobe is normal (0) or a Winner-Takes-All (1) Lobe.
• Tissue numbers are used to link lobes to emitters and receptors
• An SV rule consists of 16 entries. Each entry is of the following format:

BYTE Opcode token
BYTE Operand token
BYTE Value/Chemical Token/Variable Token

Brain Organs (Type 00 01 - Size 5)

The Brain organ (of which there should be only one in any genetics file) specifies the properties of the brain organ expressed in the creature. It has the same internal format as the other organs, but a different type identifier.

BYTE ClockRate
BYTE RepairRate
BYTE LifeForce
BYTE BioTickStart
BYTE ATPDamageCoEff

Brain Tract (Type 00 02 - Size 128)

Tract define connections between lobes and detail the number of dendrites and the style in which they are attached and migrate.

BYTE [2] Update Time
BYTE [4] Source Lobe ID
BYTE [2] Source Lobe Lower Bound
BYTE [2] Source Lobe Upper Bound
BYTE [2] No Source Connections
BYTE [4] Destination Lobe ID
BYTE [2] Destination Lobe Lower Bound
BYTE [2] Destination Lobe Upper Bound
BYTE [2] No Destination Connections
BYTE Use Random and Migrating Dendrites
BYTE No Of Connections Is Random
BYTE [8] spare
BYTE [48] Initialize Dendrite Rule
BYTE [48] Update Dendrite Rule

Brain Tract Information

An SV rule consists of 16 entries. Each entry is of the following format:

BYTE Opcode token
BYTE Operand token
BYTE Value/Chemical Token/Variable Token

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Biochemistry Genes (Type 01)

The biochemistry genes govern the functions of the chemicals within the body. They govern reactions, interfaces between the brain and the chemicals, and much, much more.

Biochemical Receptors (Type 01 00 - Size 8)

The biochemical receptors latch onto a locus within the brain or the current organ, and provide feedback to the brain about chemicals within the body.

BYTE Organ
BYTE Tissue
BYTE Locus
BYTE Chemical
BYTE Threshold
BYTE Nominal
BYTE Gain
BYTE Flags

The flags indicate if the receptor output is inverted (1) or if it is digital (2).

A digital receptor has its state calculated as:

Output = Nominal ± Gain If Signal>Threshold

Biochemical Emitters (Type 01 01 - Size 8)

Emitters tie to loci² as do receptors. They read the value of the locus, and emit chemicals based on their input states.

BYTE Organ
BYTE Tissue
BYTE Locus
BYTE Chemical
BYTE Threshold
BYTE Rate
BYTE Gain
BYTE Flags

The Emitter flags can be: 1: Clear input signal after reading or 2: Invert Input Signal

Biochemical Reactions (Type 01 02 - Size 9)

These genes govern the reactions, which occur within the Biochemical Sea of the creature. The only type of reaction which is explicitly prevented is a "Nothing -> Something" reaction.

BYTE Reactant0
BYTE Quantity0
BYTE Reactant1
BYTE Quantity1
BYTE Product2
BYTE Quantity2
BYTE Product3
BYTE Quantity3
BYTE ReactionRate

The Reaction rate is such that 0=instant, 255=52 years

Biochemical Half Lives (Type 01 03 - Size 256)

These are the decay rates of all of the chemicals within the creature's Biochemical Sea. They are arranged in the same way as the reaction rate.

BYTE [256] Chemical-Half-Life

Biochemical Initial Concentrations (Type 01 04 - Size 2)

These genes allow initial amounts of certain chemicals to be present in the creature at birth, giving a certain level of energy etc to the new born.

BYTE Chemical
BYTE Amount

Biochemical Neuro Emitters (Type 01 05 - Size 15)

Neuro Emitters tie to loci² as do receptors. They emit set amounts of 3 chemicals when the three specified neurons fire.

BYTE Lobe #1
BYTE Neuron # in lobe #1
BYTE Lobe #2
BYTE Neuron # in lobe #2
BYTE Lobe #3
BYTE Neuron # in lobe #3
BYTE Sample Rate
BYTE Chemcal Emitted #1
BYTE Amount Emitted for Chemical #1
BYTE Chemcal Emitted #2
BYTE Amount Emitted for Chemical #2
BYTE Chemcal Emitted #3
BYTE Amount Emitted for Chemical #3
BYTE Chemcal Emitted #4
BYTE Amount Emitted for Chemical #4

Creature Genes (Type 02)

Creature genes govern sections of the creature such as walking gaits, poses and appearance.

Creature Stimulus (Type 02 00 - Size 13)

This is the genetically specified result of a specific stimulus being applied to the creature. For example, releasing pain into the drive 1 when hit.

BYTE StimulusNumber
BYTE Significance
BYTE Sensory-Neurone
BYTE Features
BYTE Drive0
BYTE Amount0
BYTE Drive1
BYTE Amount1
BYTE Drive2
BYTE Amount2
BYTE Drive3
BYTE Amount3

Creature Genus (Type 02 01 - Size 65)

This gene specifies the type of creature, and the monikers of its parents.

BYTE Genus

Creature Appearance (Type 02 02 - Size 3)

This specifies the appearance of the parts of the creature's body.

BYTE BodyPart
BYTE Variant
BYTE GenusOfDonor

The GenusOfDonor entry allows the creation of creatures with grendel legs, ettin head and tail, and a norn body and arms, whilst being an ettin (If you see what I mean)

Creature Pose (Type 02 03 - Size 17)

This is the arrangement of body parts for a specific pose. Note: C3 uses 1 extra byte in the pose string than C2.

BYTE PoseNumber
BYTE [16] PoseString (last byte is spare)

The Pose String can be generated from the Pose Editor.

Creature Gait (Type 02 04 - Size 9)

This is a collection of poses which show movement.

BYTE GaitNumber //A Drive
BYTE [8] PoseSequence

Creature Instinct (Type 02 05 - Size 9)

These are processed during embryology and whilst the creature is asleep. They provide a way of providing the creature wish some basic information like "Eat Food When Hungry = Good" and "Do Nothing When Bored = Bad"

BYTE Lobe0
BYTE Neuron0
BYTE Lobe1
BYTE Neuron1
BYTE Lobe2
BYTE Neuron2
BYTE Action
BYTE ReinforcementDrive
BYTE ReinforcementLevel

Creature Pigments (Type 02 06 - Size 2)

These simple genes are used to give the creature a variation of colouring from the base colour of the variant sprites.

BYTE PigmentColour
BYTE AmountOfColour

Creature Pigment Bleeds (Type 02 07 - Size 2)

These alter the colours specified by the pigments. They are used to again, provide some way of varying appearance.

BYTE Rotation
BYTE Swap

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Organs (Type 03)

Organs are the genes which specify the organ properties. Organs include the heart, skin, bones etc.

Organs Organ (Type 03 00 - Size 5)

These have the same structure as the Brain Organ. Organs contain all the receptors, emitters and reactions listed after them in the genetics file (or until another organ gene is encountered). Reactions etc, contained within the organ, will only function whilst the organ is alive.

BYTE ClockRate
BYTE RepairRate
BYTE BioTickStart
BYTE ATPDamageCoEff

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Appendix One - SVRules

SVRule (Or State-Variable Rules) are a sequence of 16 entries each of which is 3 bytes. Each entry is of the following format:

BYTE Opcode token
BYTE Operand token
BYTE Value/Chemical Token/Variable Token

These rules allow the calculation of a state (strength gain, etc), from predetermined values. The following are the valid SVRule tokens.

Opcodes

• 0 "stop"
• 1 "blank", _
• 2 "store in"
• 3 "load from", _
• 4 "if ="
• 5 "if <>"
• 6 "if >"
• 7 "if <"
• 8 "if >="
• 9 "if <="
• 10 "if zero"
• 11 "if non-zero"
• 12 "if positive"
• 13 "if negative"
• 14 "if non-negative"
• 15 "if non-positive" _
• 16 "add"
• 17 "subtract"
• 18 "subtract from"
• 19 "multiply by"
• 20 "divide by"
• 21 "divide into"
• 22 "minimum with"
• 23 "maximum with" _
• 24 "set tend rate"
• 25 "tend to"
• 26 "load negation of"
• 27 "load abs of"
• 28 "get distance to"
• 29 "flip around"
• 30 "no operation"
• 31 "register as spare"
• 32 "bound in [0,1]"
• 33 "bound in [-1,1]"
• 34 "add and store in"
• 35 "tend to, store in"

Operands

• 0 "accumulator"
• 1 "input neuron"
• 2 "dendrite"
• 3 "neuron"
• 4 "spare neuron"
• 5 "random",
• 6 "source chemical"
• 7 "chemical"
• 8 "destination chemical"
• 9 "zero"
• 10 "one"
• 11 "value"
• 12 "negative value"

Chemical Tokens

Taken in order from the chemical list

Variable Tokens

Taken in order from the variable list

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Appendix Two - Loci

The following information was taken from the Creatures2 SDK documentation by Mark Ashton.

Receptor Loci ( type = 0)

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Emitter loci (type = 1)

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