# -*- coding: utf-8 -*-
"""Lists and annotations for compartment names and reactions.
Please send a PR if you want to add something here :)
"""
[docs]excludes = {
"demand": ["SN_", "SK_", "sink", "EX_", "exchange"],
"exchange": [
"demand",
"DM_",
"biosynthesis",
"transcription",
"replication",
"SN_",
"SK_",
"sink",
],
"sink": [
"demand",
"DM_",
"biosynthesis",
"transcription",
"replication",
"EX_",
"exchange",
],
}
"""A list of sub-strings in reaction IDs that usually indicate
that the reaction is *not* a reaction of the specified type."""
[docs]sbo_terms = {
"demand": "SBO:0000628",
"exchange": "SBO:0000627",
"sink": "SBO:0000632",
"biomass": "SBO:0000629",
"pseudoreaction": "SBO:0000631",
}
"""SBO term identifiers for various boundary types."""
[docs]compartment_shortlist = {
"ce": ["cell envelope"],
"c": [
"cytoplasm",
"cytosol",
"default",
"in",
"intra cellular",
"intracellular",
"intracellular region",
"intracellular space",
],
"er": ["endoplasmic reticulum"],
"erm": ["endoplasmic reticulum membrane"],
"e": [
"extracellular",
"extraorganism",
"out",
"extracellular space",
"extra organism",
"extra cellular",
"extra-organism",
"external",
"external medium",
],
"f": ["flagellum", "bacterial-type flagellum"],
"g": ["golgi", "golgi apparatus"],
"gm": ["golgi membrane"],
"h": ["chloroplast"],
"l": ["lysosome"],
"im": ["mitochondrial intermembrane space"],
"mm": ["mitochondrial membrane"],
"m": ["mitochondrion", "mitochondria"],
"n": ["nucleus"],
"p": ["periplasm", "periplasmic space"],
"x": ["peroxisome", "glyoxysome"],
"u": ["thylakoid"],
"vm": ["vacuolar membrane"],
"v": ["vacuole"],
"w": ["cell wall"],
"s": ["eyespot", "eyespot apparatus", "stigma"],
}
"""A list of common compartment abbreviations and alternative names."""