psico.aaindex

Python parser for AAindex: Amino Acid Index Database

License: BSD-2-Clause

Functions

`aaindex2b`(key[, selection, var, quiet, _self])	Looks up the Amino Acid Index from http://www.genome.jp/aaindex/ for the given key and assignes b-factors to the given selection.
`hydropathy2b`([selection, var, quiet, _self])	Load Kyte-Doolittle hydropathy index values into b-factor column.
`hydropathy2b_exposed`([selection, state, ...])	Multiply residue hydrophathy (b) with residue exposure (q) and color with a gradient.

Classes

`AAindex`([index, path, quiet])	Represents an aaindex database file as key => record mapping.
`MatrixRecord`()	Matrix record for mutation matrices or pair-wise contact potentials
`Record`()	Amino acid index (AAindex) Record

class psico.aaindex.AAindex(index='', path=None, quiet=1)[source]

Bases: dict

Represents an aaindex database file as key => record mapping.

grep(pattern)[source]: Search for pattern in title and description of all records (case insensitive) and print results on standard output.

parse(filename, rec, quiet=True)[source]: Parse aaindex input file. “rec” must be “Record” for aaindex1 and “MarixRecord” for aaindex2 and aaindex3.

search(pattern, searchtitle=False, 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.

class psico.aaindex.MatrixRecord[source]

Bases: Record

Matrix record for mutation matrices or pair-wise contact potentials

class psico.aaindex.Record[source]

Bases: object

Amino acid index (AAindex) Record

psico.aaindex.aaindex2b(key, selection='all', var='b', quiet=1, *, _self=...)[source]: Looks up the Amino Acid Index from http://www.genome.jp/aaindex/ for the given key and assignes b-factors to the given selection. Unknown residues get the average index value assigned.

Usage

aaindex2b key [, selection ]

Arguments

key = string: Key of AAindex entry

selection = string: atoms to assign b-factors {default: (all)}

Example

# Hydropathy index by Kyte-Doolittle aaindex2b KYTJ820101 spectrumany b, white yellow forest show surface

See Also

hydropathy2b

psico.aaindex.hydropathy2b(selection='all', var='b', quiet=1, *, _self=...)[source]: Load Kyte-Doolittle hydropathy index values into b-factor column.

See Also

aaindex2b, hydropathy2b_exposed

psico.aaindex.hydropathy2b_exposed(selection='polymer', state: int = -1, *, key='KYTJ820101', palette='white forest', quiet=1, _self=...)[source]: Multiply residue hydrophathy (b) with residue exposure (q) and color with a gradient.

See Also

get_sasa_relative, hydropathy2b

Usage