propy.AAIndex

This module is used for obtaining the properties of amino acids or their pairs from the aaindex database.

Authors: Dongsheng Cao and Yizeng Liang. Date: 2012.09.10 Email: oriental-cds@163.com

propy.AAIndex.GetAAIndex1(name: str, path: str = '.') → Dict[str, float][source]

Get the amino acid property values from aaindex1.

Parameters:name (str) – name of amino acid property (e.g., KRIW790103)
Returns:result – contains the properties of 20 amino acids
Return type:Dict[str, float]

Examples

>>> result = GetAAIndex1("KRIW790103")
propy.AAIndex.GetAAIndex23(name: str, path: str = '.') → Dict[str, float][source]

Get the amino acid property values from aaindex2 and aaindex3.

Parameters:name (str) – name of amino acid property (e.g. TANS760101, GRAR740104)
Returns:result – contains the properties of 400 amino acid pairs
Return type:Dict[str, float]

Examples

>>> result = GetAAIndex23("TANS760101")
class propy.AAIndex.MatrixRecord[source]

Bases: propy.AAIndex.Record

Matrix record for mutation matrices or pair-wise contact potentials.

extend(row)[source]

Extend self.index by the elements of the list.

get(aai, aaj, d=None)[source]
median()[source]
class propy.AAIndex.Record[source]

Bases: object

Amino acid index (AAindex) Record.

aakeys = 'ARNDCQEGHILKMFPSTWYV'
extend(row: List[Optional[float]]) → None[source]

Extend self.index by the elements of the list.

get(aai, aaj=None, d=None)[source]
median()[source]
propy.AAIndex.get(key: str)[source]

Get record for key.

propy.AAIndex.grep(pattern)[source]

Search for pattern in title and description of all records (case insensitive) and print results on standard output.

propy.AAIndex.init(path=None, index='123')[source]

Read in the aaindex files. You need to run this (once) before you can access any records. If the files are not within the current directory, you need to specify the correct directory path. By default all three aaindex files are read in.

propy.AAIndex.init_from_file(filename, type=<class 'propy.AAIndex.Record'>)[source]
propy.AAIndex.search(pattern, searchtitle=True, casesensitive=False)[source]

Search for pattern in description and title (optional) of all records and return matched records as list. By default search case insensitive.