This is a read-only mirror of pymolwiki.org
Difference between revisions of "AAindex"
Jump to navigation
Jump to search
m (1 revision) |
|||
| (7 intermediate revisions by 3 users not shown) | |||
| Line 1: | Line 1: | ||
| + | {{Infobox script-repo | ||
| + | |type = script | ||
| + | |filename = aaindex.py | ||
| + | |author = [[User:Speleo3|Thomas Holder]] | ||
| + | |license = BSD | ||
| + | }} | ||
| + | |||
| + | == Introduction == | ||
[[File:AAindexExample.png|200px|thumb|right|Hydrophobicity coloring with KYTJ820101]] | [[File:AAindexExample.png|200px|thumb|right|Hydrophobicity coloring with KYTJ820101]] | ||
| Line 20: | Line 28: | ||
aaindex.grep('volume') | aaindex.grep('volume') | ||
x = aaindex.get('KRIW790103') | x = aaindex.get('KRIW790103') | ||
| − | print x | + | print(x) |
| − | print x.get('A') | + | print(x.get('A')) |
| + | aaindex.init(index='2') | ||
aaindex.grep('blosum') | aaindex.grep('blosum') | ||
x = aaindex.get('HENS920102') | x = aaindex.get('HENS920102') | ||
| − | print x.get('A', 'K') | + | print(x.get('A', 'K')) |
</source> | </source> | ||
| Line 36: | Line 45: | ||
show surface | show surface | ||
</source> | </source> | ||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
== See Also == | == See Also == | ||
| Line 49: | Line 50: | ||
* Protscale from [http://www.rubor.de/pymol_extensions_de.html rTools] does a similar job in coloring by amino acid properties | * Protscale from [http://www.rubor.de/pymol_extensions_de.html rTools] does a similar job in coloring by amino acid properties | ||
| − | |||
[[Category:Script_Library]] | [[Category:Script_Library]] | ||
[[Category:Biochemical_Scripts]] | [[Category:Biochemical_Scripts]] | ||
[[Category:Structural_Biology_Scripts]] | [[Category:Structural_Biology_Scripts]] | ||
| + | [[Category:Pymol-script-repo]] | ||
Latest revision as of 03:58, 4 March 2019
| Type | Python Script |
|---|---|
| Download | aaindex.py |
| Author(s) | Thomas Holder |
| License | BSD |
| This code has been put under version control in the project Pymol-script-repo | |
Introduction
AAindex is a database of numerical indices representing various physicochemical and biochemical properties of amino acids and pairs of amino acids. See http://www.genome.jp/aaindex/
This script is a python parser for the AAindex flat files which will be downloaded from ftp://ftp.genome.jp/pub/db/community/aaindex/
The script provides two PyMOL commands (but can also be used without PyMOL).
- aaindex2b: Loads numerical indices from aaindex1 as b-factors into your structure
- pmf: Potential of Mean Force (aaindex3)
Python Example
Consider the script is called aaindex.py, it is placed somewhere in your PYTHONPATH and the aaindex flatfiles are found in the current directory.
import aaindex
aaindex.init(path='.')
aaindex.grep('volume')
x = aaindex.get('KRIW790103')
print(x)
print(x.get('A'))
aaindex.init(index='2')
aaindex.grep('blosum')
x = aaindex.get('HENS920102')
print(x.get('A', 'K'))
PyMOL Example
import aaindex
aaindex2b KYTJ820101
spectrum b, yellow_white_blue
show surface
See Also
- Protscale from rTools does a similar job in coloring by amino acid properties