# PPSS - Python Protein Subunit Syntax
A simple Python package for defining protein subunit structures.
## Installation
The simplest way to install this is to do as follows:
```
pip install ppss
```
You can also install the Poetry packaging and dependency tool and then clone this repository and install with poetry, as follows:
```
pipx install poetry
git clone https://github.com/sandyjmacdonald/ppss
cd ppss
poetry install
```
## Usage
The simple example below defines a protein comprised of either an S1 *plus* S1 subunit, or just an S3 subunit. The bar (|) symbol here represents an OR condition or "alternation", while the + represents an AND condition or "concatenation". Subunit IDs can be any combination of upper and/or lowercase alphabetical and numerical characters.
```
from ppss import ProteinParser
# Instantiate the parser
parser = ProteinParser()
# Define a protein structure
protein_definition = "(S1 + S2) | S3"
# Parse the protein structure
structures = parser.parse(protein_definition)
# Display the structures
for structure in structures:
print(structure)
```
The two possible structures are printed:
```
S1 + S2
S3
```
The full grammar of the Lark parser is as follows:
```
?start: protein
protein: alternation
alternation: concatenation ("|" concatenation)*
concatenation: required_term ("+" term)*
?term: required_term
| optional_term
required_term: multiplicity
| subunit
| "(" alternation ")"
optional_term: optional
multiplicity: subunit "{" DIGIT+ "}"
| "(" alternation ")" "{" DIGIT+ "}"
optional: "[" alternation "]"
subunit: SUBUNIT
SUBUNIT: /[A-Za-z0-9]+/
DIGIT: "0" | "1" | "2" | "3" | "4" | "5" | "6" | "7" | "8" | "9"
%import common.WS
%ignore WS
```
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"description": "# PPSS - Python Protein Subunit Syntax\n\nA simple Python package for defining protein subunit structures.\n\n## Installation\n\nThe simplest way to install this is to do as follows:\n\n```\npip install ppss\n```\n\nYou can also install the Poetry packaging and dependency tool and then clone this repository and install with poetry, as follows:\n\n```\npipx install poetry\ngit clone https://github.com/sandyjmacdonald/ppss\ncd ppss\npoetry install\n```\n\n## Usage\n\nThe simple example below defines a protein comprised of either an S1 *plus* S1 subunit, or just an S3 subunit. The bar (|) symbol here represents an OR condition or \"alternation\", while the + represents an AND condition or \"concatenation\". Subunit IDs can be any combination of upper and/or lowercase alphabetical and numerical characters.\n\n```\nfrom ppss import ProteinParser\n\n# Instantiate the parser\nparser = ProteinParser()\n\n# Define a protein structure\nprotein_definition = \"(S1 + S2) | S3\"\n\n# Parse the protein structure\nstructures = parser.parse(protein_definition)\n\n# Display the structures\nfor structure in structures:\n print(structure)\n```\n\nThe two possible structures are printed:\n\n```\nS1 + S2\nS3\n```\n\nThe full grammar of the Lark parser is as follows:\n\n```\n?start: protein\n\nprotein: alternation\n\nalternation: concatenation (\"|\" concatenation)*\n\nconcatenation: required_term (\"+\" term)*\n\n?term: required_term\n | optional_term\n\nrequired_term: multiplicity\n | subunit\n | \"(\" alternation \")\"\n\noptional_term: optional\n\nmultiplicity: subunit \"{\" DIGIT+ \"}\"\n | \"(\" alternation \")\" \"{\" DIGIT+ \"}\"\n\noptional: \"[\" alternation \"]\"\n\nsubunit: SUBUNIT\n\nSUBUNIT: /[A-Za-z0-9]+/\n\nDIGIT: \"0\" | \"1\" | \"2\" | \"3\" | \"4\" | \"5\" | \"6\" | \"7\" | \"8\" | \"9\"\n\n%import common.WS\n%ignore WS\n```",
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