mkt.databases.properties
Amino-acid property lookups and classification of amino-acid changes.
Provides get_aa_property() for per-residue physicochemical properties and
classify_aa_change() for categorizing missense substitutions.
Module Attributes
Dictionary of amino acid properties. |
|
Dictionary of amino acid change properties. |
Functions
|
Classify the change between two amino acids. |
|
Get a specific property of an amino acid. |
- mkt.databases.properties.DICT_AA_CHANGES = {'charge change, negative to positive': {'from': ['negative'], 'property': 'charge', 'to': ['positive']}, 'charge change, positive to negative': {'from': ['positive'], 'property': 'charge', 'to': ['negative']}, 'charge gain, neutral to negative': {'from': ['nonpolar', 'polar'], 'property': 'charge', 'to': ['negative']}, 'charge gain, neutral to positive': {'from': ['nonpolar', 'polar'], 'property': 'charge', 'to': ['positive']}, 'charge loss, negative to neutral': {'from': ['negative'], 'property': 'charge', 'to': ['nonpolar', 'polar']}, 'charge loss, positive to neutral': {'from': ['positive'], 'property': 'charge', 'to': ['nonpolar', 'polar']}, 'polarity gain': {'from': ['nonpolar'], 'property': 'charge', 'to': ['polar', 'positive', 'negative']}, 'polarity loss': {'from': ['polar', 'positive', 'negative'], 'property': 'charge', 'to': ['nonpolar']}, 'volume gain, large': {'from': 75, 'property': 'volume', 'to': inf}, 'volume gain, modest': {'from': 25, 'property': 'volume', 'to': 75}, 'volume loss, large': {'from': -inf, 'property': 'volume', 'to': -75}, 'volume loss, modest': {'from': -75, 'property': 'volume', 'to': -25}}
Dictionary of amino acid change properties. Keys are descriptions of the change (e.g., “charge gain, positive”), and values are dictionaries with properties: - property: The property being changed (e.g., “charge”, “volume”). - from: The original value of the property before the change. - to: The new value of the property after the change. This dictionary can be used to look up the nature of changes in amino acid properties.
- Type:
dict[str, dict[str, str | int]]
- mkt.databases.properties.DICT_AA_PROPERTIES = {'A': {'charge': 'nonpolar', 'volume': 88.6}, 'C': {'charge': 'polar', 'volume': 108.5}, 'D': {'charge': 'negative', 'volume': 111.1}, 'E': {'charge': 'negative', 'volume': 138.4}, 'F': {'charge': 'nonpolar', 'volume': 189.9}, 'G': {'charge': 'nonpolar', 'volume': 60.1}, 'H': {'charge': 'positive', 'volume': 153.2}, 'I': {'charge': 'nonpolar', 'volume': 166.7}, 'K': {'charge': 'positive', 'volume': 168.6}, 'L': {'charge': 'nonpolar', 'volume': 166.7}, 'M': {'charge': 'nonpolar', 'volume': 162.9}, 'N': {'charge': 'polar', 'volume': 114.1}, 'P': {'charge': 'nonpolar', 'volume': 112.7}, 'Q': {'charge': 'polar', 'volume': 143.8}, 'R': {'charge': 'positive', 'volume': 173.4}, 'S': {'charge': 'polar', 'volume': 89.0}, 'T': {'charge': 'polar', 'volume': 116.1}, 'V': {'charge': 'nonpolar', 'volume': 140.0}, 'W': {'charge': 'nonpolar', 'volume': 227.8}, 'Y': {'charge': 'polar', 'volume': 193.6}}
Dictionary of amino acid properties. Keys are single-letter amino acid codes, and values are dictionaries with properties: - charge: Charge of the amino acid (e.g., “nonpolar”, “polar”, “positive”, “negative”). - volume: Volume of the amino acid in cubic angstroms (int). This dictionary can be used to look up properties of amino acids by their single-letter code.
- Type:
dict[str, dict[str, str | int]]
- mkt.databases.properties.classify_aa_change(aa_from: str, aa_to: str) str | None[source]
Classify the change between two amino acids.
- Parameters:
aa_from (str) – Single-letter code of the original amino acid.
aa_to (str) – Single-letter code of the new amino acid.
- Returns:
Description of the change (e.g., “charge gain, positive”), or None if no change is found.
- Return type:
str | None
- mkt.databases.properties.get_aa_property(aa: str, property_name: str) str | int | None[source]
Get a specific property of an amino acid.
- Parameters:
aa (str) – Single-letter code of the amino acid (e.g., “A” for Alanine).
property_name (str) – Name of the property to retrieve (e.g., “charge”, “volume”).
- Returns:
The value of the specified property, or None if the amino acid or property does not exist.
- Return type:
str | int | None