A | |
Abstract [Protein] |
Contains the lightweight, live internal representation of an
abstract protein.
|
Assocext [] |
An assocext object is used to keep associations between
non-overlapping extents of integers and values.
|
B | |
BMD [Protein.Abstract] |
Characteristics of the abstract Boolean Multiplexor Domain.
|
C | |
Cell [] |
The main cell engine.
|
Cell_options [] |
Generic command-line argument processing.
|
CheatParseRep [] |
Temporary placeholder for a built-to-order cell genome for testing
purposes.
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Compact [Genome] | |
Compartment [] |
Encapsulates the subdivisions within the Cytoplasm, along with the
transport mechanisms between them.
|
Compile [Genome] | |
Cytoplasm [] |
Implementation of the fourth layer of the Design Stack.
|
D | |
Dllist [] |
Definitions for doubly-linked lists which allow for in-place
insertion and removal.
|
G | |
Genome [] |
Contains the mapping from Monod genome to protein functional
domains.
|
GenomeParser [] |
This plate should be moved to
plates .
|
H | |
Hashnlist [] |
Extends the functionality of hash tables to map keys to lists
of values.
|
I | |
Incubator [] |
Implementation of the Incubator design pattern, which coordinates
the interactions of ligands and processing units.
|
Interact [] |
Definition of the generic interactive plate.
|
L | |
LBDE [Protein.Abstract] |
Characteristics of the abstract Ligand Binding Domain with
Extraction.
|
LBDR [Protein.Abstract] |
Characteristics of the abstract Ligand Binding Domain with
Remapping.
|
LID [Protein.Abstract] |
Characteristics of the abstract Logical Integration Domain.
|
Ligand [] |
Definitions for the ligand objects, the string-analogues living
within the Incubator layer of the design stack.
|
Log [] |
The definitions for the event logger.
|
M | |
Main [] |
Entry-point for the single-cell standalone executable.
|
Matcher [Ligand] |
Contains the definitions for the objects which are used to find
binding regions on ligands.
|
O | |
OldCompiled [Genome] | |
Optimized [Protein] |
The implementation of this module contains the meat of the protein
execution model.
|
P | |
PDMatcher [Protein.Abstract] |
Characteristics of the abstract Matcher Pseudo-Domain.
|
Procunit [Incubator] |
Contains the definitions for the processing units appearing an an
Incubator.
|
Protein [] |
The definitions for the proteins in the Cytoplasm layer.
|
S | |
SLBD [Protein.Abstract] |
Characteristics of the abstract Simple Ligand Binding
Domain.
|
SerializedSwarm [Swarm] |
A Swarm implementation - very inefficient, but simple.
|
SingleCellHarness [] |
The control harness for a single Monod Cell.
|
Skeleton [] |
Common definitions for the tectonic plates necessary at the Monod
Cell layer.
|
Swarm [] |
Implementation of the Swarm design pattern, which serves to harbor
multiple interacting residents.
|
T | |
Testinter [] |
The simplest Interactive tectonic plate - it's not interactive at
all.
|
U | |
Util [] |
Contains miscellaneous functions which have general
usefulness.
|
W | |
Wizard [Protein] |
Used to make abstract proteins with a table-driven interface.
|