https://github.com/vatj/polyomino_core
Polyomino Assembly Algorithms Core Repository
https://github.com/vatj/polyomino_core
Last synced: 4 months ago
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Polyomino Assembly Algorithms Core Repository
- Host: GitHub
- URL: https://github.com/vatj/polyomino_core
- Owner: vatj
- License: mit
- Created: 2019-01-22T16:36:19.000Z (over 6 years ago)
- Default Branch: master
- Last Pushed: 2019-08-27T09:58:50.000Z (almost 6 years ago)
- Last Synced: 2025-01-10T01:02:18.584Z (5 months ago)
- Language: C++
- Homepage:
- Size: 48.8 KB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE.md
- Codeowners: CODEOWNERS
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README
## Forked from ASleonard repository
## Polyomino self-assembly core
[](https://www.codacy.com/app/ASLeonard/polyomino_core?utm_source=github.com&utm_medium=referral&utm_content=ASLeonard/polyomino_core&utm_campaign=Badge_Grade)
Base repository for the polyomino model development. This is mainly useful for extending the functionality provided here in a new repository, using this one as a submodule. For an example, see an example [here](https://github.com/ASLeonard/polyomino_interfaces).
### Extending the polyomino core model
Including this repository as a submodule allows for rapid prototyping of the polyomino model.
Generic assembly can be quickly implemented using existing functions. Extending the model **requires**
- extend base assembly (using the curiously recursive template pattern)
```cpp
class NewAssemblyModel : public PolyominoAssembly
```
- determine the interface type (e.g. integer, string, something more complex, etc.)
```cpp
using subunit_type = ...
using Genotype = std::vector
```
- implement the interaction matrix that returns the interaction strength between two interfaces
```cpp
double NewAssemblyModel::InteractionMatrix(subunit A, subunit B)
```
- optional features to implement may include more specific methods
- mutations
- random initilising
- reversing alignment
### Using the core model
The main calls to the core model are to the assembly and classification functions
- get interaction edges
```cpp
const auto edges = NewAssemblyModel::GetActiveInterfaces(genotype)
```
- assemble polyomino (and track edges used in assembly)
```cpp
auto [assembly_information,interacting_indices] = NewAssemblyModel::AssemblePolyomino(edges)
```
- get phenotype from the raw assembly information
```cpp
Phenotype phen=GetPhenotypeFromGrid(assembly_information)
```
- potentially classify phenotype using a runtime filled table
```cpp
Phenotype_ID pid = phenotypeTable->GetPhenotypeID(phen)
```
More robust examples available in the implementation of _polyomino\_interfaces_ model
### Building
The core library is header only, so need to add an include path to whatever building process used
```make
-Ipath/to/library/polyomino_core
```
Some of the code makes use of the relatively modern c++17, and so a relatively up to date compiler may be needed. Again a more full example of a makefile used in compiling may be found in the _polyomino\_iterfaces_ repository.
### Visuals
There are some skeleton methods in python3 to plot polyominoes and more elaborate interactive plots to show evolutionary transitions between polyominoes, but these are still under design and development.