AAindex
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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 you have to download:
- ftp://ftp.genome.jp/pub/db/community/aaindex/aaindex1
- ftp://ftp.genome.jp/pub/db/community/aaindex/aaindex2
- ftp://ftp.genome.jp/pub/db/community/aaindex/aaindex3
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.grep('blosum')
x = aaindex.get('HENS920102')
print x.get('A', 'K')
PyMOL Example
import aaindex
aaindex.init(path='.')
aaindex2b KYTJ820101
spectrum b, yellow_white_blue
show surface
The Script
'''
(c) 2010 Thomas Holder
Python parser for AAindex: Amino Acid Index Database
http://www.genome.jp/aaindex/
PyMOL commands:
aaindex2b
pmf
'''
_aaindex = dict()
_pymol_auto_arg_update = lambda: None
def search(pattern, searchtitle=True, casesensitive=False):
'''
Search for pattern in description and title (optional) of all records and
return matched records as list. By default search case insensitive.
'''
whatcase = lambda i: i
if not casesensitive:
pattern = pattern.lower()
whatcase = lambda i: i.lower()
matches = []
for record in _aaindex.itervalues():
if pattern in whatcase(record.desc) or searchtitle and pattern in whatcase(record.title):
matches.append(record)
return matches
def grep(pattern):
'''
Search for pattern in title and description of all records (case
insensitive) and print results on standard output.
'''
for record in search(pattern):
print record
class Record:
'''
Amino acid index (AAindex) Record
'''
aakeys = 'ARNDCQEGHILKMFPSTWYV'
def __init__(self):
self.key = None
self.desc = ''
self.ref = ''
self.authors = ''
self.title = ''
self.journal = ''
self.correlated = dict()
self.index = dict()
self.comment = ''
def extend(self, row):
i = len(self.index)
for x in row:
self.index[self.aakeys[i]] = x
i += 1
def get(self, aai, aaj=None, d=None):
assert aaj is None
return self.index.get(aai, d)
def median(self):
x = sorted(filter(None, self.index.values()))
half = len(x)/2
if len(x) % 2 == 1:
return x[half]
return (x[half-1] + x[half])/2.0
def __str__(self):
desc = self.desc.replace('\n', ' ').strip()
return '%s(%s: %s)' % (self.__class__.__name__, self.key, desc)
class MatrixRecord(Record):
'''
Matrix record for mutation matrices or pair-wise contact potentials
'''
def __init__(self):
Record.__init__(self)
self.index = []
self.rows = dict()
self.cols = dict()
def extend(self, row):
self.index.append(row)
def _get(self, aai, aaj):
i = self.rows[aai]
j = self.cols[aaj]
return self.index[i][j]
def get(self, aai, aaj, d=None):
try:
return self._get(aai, aaj)
except:
pass
try:
return self._get(aaj, aai)
except:
return d
def median(self):
x = []
for y in self.index:
x.extend(filter(None, y))
x.sort()
if len(x) % 2 == 1:
return x[len(x)/2]
return sum(x[len(x)/2-1:len(x)/2+1])/2.0
def get(key):
'''
Get record for key
'''
if len(_aaindex) == 0:
init()
return _aaindex.get(key)
def _float_or_None(x):
if x == 'NA' or x == '-':
return None
return float(x)
def init(path=None, index='123'):
'''
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.
'''
if path is None:
import sys
from os.path import sep
path = __file__.rsplit(sep, 1)[0]
print >> sys.stderr, 'path =', path
index = str(index)
if '1' in index:
_parse(path + '/aaindex1', Record)
if '2' in index:
_parse(path + '/aaindex2', MatrixRecord)
if '3' in index:
_parse(path + '/aaindex3', MatrixRecord)
_pymol_auto_arg_update()
def init_from_file(filename, type=Record):
_parse(filename, type)
def _parse(filename, rec, quiet=True):
'''
Parse aaindex input file. `rec` must be `Record` for aaindex1 and
`MarixRecord` for aaindex2 and aaindex3.
'''
try:
f = file(filename, 'rU')
except:
print ('Cannot open "%s", please download it from ' + \
'ftp://ftp.genome.jp/pub/db/community/aaindex/') % filename
return
current = rec()
lastkey = None
for line in f:
key = line[0:2]
if key[0] == ' ':
key = lastkey
if key == '//':
_aaindex[current.key] = current
current = rec()
elif key == 'H ':
current.key = line[2:].strip()
elif key == 'R ':
current.ref += line[2:]
elif key == 'D ':
current.desc += line[2:]
elif key == 'A ':
current.authors += line[2:]
elif key == 'T ':
current.title += line[2:]
elif key == 'J ':
current.journal += line[2:]
elif key == '* ':
current.comment += line[2:]
elif key == 'C ':
a = line[2:].split()
for i in range(0, len(a), 2):
current.correlated[a[i]] = float(a[i+1])
elif key == 'I ':
a = line[1:].split()
if a[0] != 'A/L':
current.extend(map(_float_or_None, a))
elif list(Record.aakeys) != [i[0] for i in a] + [i[-1] for i in a]:
print 'Warning: wrong amino acid sequence for', current.key
else:
try:
assert list(Record.aakeys[:10]) == [i[0] for i in a]
assert list(Record.aakeys[10:]) == [i[2] for i in a]
except:
print 'Warning: wrong amino acid sequence for', current.key
elif key =='M ':
a = line[2:].split()
if a[0] == 'rows':
if a[4] == 'rows':
a.pop(4)
assert a[3] == 'cols' and len(a) == 6
i = 0
for aa in a[2]:
current.rows[aa] = i
i += 1
i = 0
for aa in a[5]:
current.cols[aa] = i
i += 1
else:
current.extend(map(_float_or_None, a))
elif not quiet:
print 'Warning: line starts with "%s"' % (key)
lastkey = key
########## PYMOL ###########
# from Bio.SCOP.Raf import to_one_letter_code
# See also http://www.pymolwiki.org/index.php/Aa_codes
to_one_letter_code = {'PAQ': 'Y', 'AGM': 'R', 'ILE': 'I', 'PR3': 'C',
'GLN': 'Q', 'DVA': 'V', 'CCS': 'C', 'ACL': 'R', 'GLX': 'Z', 'GLY': 'G',
'GLZ': 'G', 'DTH': 'T', 'OAS': 'S', 'C6C': 'C', 'NEM': 'H', 'DLY': 'K',
'MIS': 'S', 'SMC': 'C', 'GLU': 'E', 'NEP': 'H', 'BCS': 'C', 'ASQ': 'D',
'ASP': 'D', 'SCY': 'C', 'SER': 'S', 'LYS': 'K', 'SAC': 'S', 'PRO': 'P',
'ASX': 'B', 'DGN': 'Q', 'DGL': 'E', 'MHS': 'H', 'ASB': 'D', 'ASA': 'D',
'NLE': 'L', 'DCY': 'C', 'ASK': 'D', 'GGL': 'E', 'STY': 'Y', 'SEL': 'S',
'CGU': 'E', 'ASN': 'N', 'ASL': 'D', 'LTR': 'W', 'DAR': 'R', 'VAL': 'V',
'CHG': 'A', 'TPO': 'T', 'CLE': 'L', 'GMA': 'E', 'HAC': 'A', 'AYA': 'A',
'THR': 'T', 'TIH': 'A', 'SVA': 'S', 'MVA': 'V', 'SAR': 'G', 'LYZ': 'K',
'BNN': 'A', '5HP': 'E', 'IIL': 'I', 'SHR': 'K', 'HAR': 'R', 'FME': 'M',
'PYX': 'C', 'ALO': 'T', 'PHI': 'F', 'ALM': 'A', 'PHL': 'F', 'MEN': 'N',
'TPQ': 'A', 'GSC': 'G', 'PHE': 'F', 'ALA': 'A', 'MAA': 'A', 'MET': 'M',
'UNK': 'X', 'LEU': 'L', 'ALY': 'K', 'SET': 'S', 'GL3': 'G', 'TRG': 'K',
'CXM': 'M', 'TYR': 'Y', 'SCS': 'C', 'DIL': 'I', 'TYQ': 'Y', '3AH': 'H',
'DPR': 'P', 'PRR': 'A', 'CME': 'C', 'IYR': 'Y', 'CY1': 'C', 'TYY': 'Y',
'HYP': 'P', 'DTY': 'Y', '2AS': 'D', 'DTR': 'W', 'FLA': 'A', 'DPN': 'F',
'DIV': 'V', 'PCA': 'E', 'MSE': 'M', 'MSA': 'G', 'AIB': 'A', 'CYS': 'C',
'NLP': 'L', 'CYQ': 'C', 'HIS': 'H', 'DLE': 'L', 'CEA': 'C', 'DAL': 'A',
'LLP': 'K', 'DAH': 'F', 'HMR': 'R', 'TRO': 'W', 'HIC': 'H', 'CYG': 'C',
'BMT': 'T', 'DAS': 'D', 'TYB': 'Y', 'BUC': 'C', 'PEC': 'C', 'BUG': 'L',
'CYM': 'C', 'NLN': 'L', 'CY3': 'C', 'HIP': 'H', 'CSO': 'C', 'TPL': 'W',
'LYM': 'K', 'DHI': 'H', 'MLE': 'L', 'CSD': 'A', 'HPQ': 'F', 'MPQ': 'G',
'LLY': 'K', 'DHA': 'A', 'DSN': 'S', 'SOC': 'C', 'CSX': 'C', 'OMT': 'M',
'DSP': 'D', 'PTR': 'Y', 'TRP': 'W', 'CSW': 'C', 'EFC': 'C', 'CSP': 'C',
'CSS': 'C', 'SCH': 'C', 'OCS': 'C', 'NMC': 'G', 'SEP': 'S', 'BHD': 'D',
'KCX': 'K', 'SHC': 'C', 'C5C': 'C', 'HTR': 'W', 'ARG': 'R', 'TYS': 'Y',
'ARM': 'R', 'DNP': 'A'}
def aaindex2b(key='KYTJ820101', selection='(all)', quiet=0, var='b'):
'''
DESCRIPTION
"aaindex" 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
spectrum b, yellow_white_blue
show surface
'''
from pymol import cmd, stored
entry = get(key)
median = entry.median()
if int(quiet) != 0:
print entry.desc.strip()
def lookup(resn):
one_letter = to_one_letter_code.get(resn, 'X')
value = entry.get(one_letter)
if value is None:
return median
return value
stored.aaindex = lookup
cmd.alter(selection, var + '=stored.aaindex(resn)')
def pmf(key, cutoff=7.0, selection1='(name CB)', selection2='', state=1, quiet=1):
'''
DESCRIPTION
Potential of Mean Force
ARGUMENTS
key = string: aaindex key
cutoff = float: distance cutoff {default: 7.0}
cutoff = (float, float): distance shell
selection1 = string: atom selection {default: (name CB)}
selection2 = string: atom selection {default: selection1}
NOTES
Does also support a list of keys and a list of cutoffs to deal with
multiple distance shells.
EXAMPLES
# load databases
aaindex.init('/path/to/aaindex/directory')
# distance dependent c-beta contact potentials
pmf SIMK990101, 5, /2x19//A//CB
pmf SIMK990102, [5, 7.5], /2x19//A//CB
pmf [SIMK990101, SIMK990102, SIMK990103], [0, 5, 7.5, 10], /2x19//A//CB
# interface potential
pseudo_sidechaincenters 2x19_scc, 2x19
pmf KESO980102, 7.0, /2x19_scc//A, /2x19_scc//B
distance /2x19_scc//A, /2x19_scc//B, cutoff=7.0
'''
from pymol import cmd, stored
from chempy import cpv
if cmd.is_string(key):
if key.lstrip().startswith('['):
key = cmd.safe_alpha_list_eval(key)
else:
key = [key]
if cmd.is_string(cutoff):
cutoff = eval(cutoff)
if not cmd.is_sequence(cutoff):
cutoff = [cutoff]
if len(cutoff) == len(key):
cutoff = [0.0] + list(cutoff)
if len(cutoff) != len(key) + 1:
print 'Error: Number of keys and number of cutoffs inconsistent'
return
state = int(state)
quiet = int(quiet)
if len(selection2) == 0:
selection2 = selection1
if not quiet and len(key) > 1:
print 'Distance shells:'
for i in range(len(key)):
print '%s %.1f-%.1f' % (key[i], cutoff[i], cutoff[i+1])
stored.idmap = dict()
cmd.iterate_state(state, '(%s) or (%s)' % (selection1, selection2),
'stored.idmap[model,index] = [(resn,name),(x,y,z)]')
twoN = cmd.count_atoms(selection1) + cmd.count_atoms(selection2)
pairs = cmd.find_pairs(selection1, selection2, cutoff=max(cutoff),
state1=state, state2=state)
if len(pairs) == 0:
print 'Empty pair list'
return 0.0
matrix = map(get, key)
for i in matrix:
assert isinstance(i, MatrixRecord)
i_list = range(len(key))
u_sum = 0
count = 0
for id1, id2 in pairs:
a1 = stored.idmap[id1]
a2 = stored.idmap[id2]
r = cpv.distance(a1[1], a2[1])
for i in i_list:
if cutoff[i] <= r and r < cutoff[i+1]:
try:
aa1 = to_one_letter_code[a1[0][0]]
aa2 = to_one_letter_code[a2[0][0]]
u_sum += matrix[i].get(aa1, aa2)
count += 1
except:
print 'Failed for', a1[0], a2[0]
value = float(u_sum) / twoN
if not quiet:
print 'PMF: %.4f (%d contacts, %d residues)' % (value, count, twoN)
return value
try:
from pymol import cmd
cmd.extend('aaindex2b', aaindex2b)
cmd.extend('pmf', pmf)
def pymol_auto_arg_update():
aaindexkey_sc = cmd.Shortcut(_aaindex.keys())
cmd.auto_arg[0].update({
'aaindex2b' : [ aaindexkey_sc , 'aaindexkey' , ', ' ],
'pmf' : [ aaindexkey_sc , 'aaindexkey' , ', ' ],
})
cmd.auto_arg[1].update({
'aaindex2b' : [ cmd.selection_sc , 'selection' , '' ],
})
cmd.auto_arg[2].update({
'pmf' : [ cmd.selection_sc , 'selection' , '' ],
})
cmd.auto_arg[3].update({
'pmf' : [ cmd.selection_sc , 'selection' , '' ],
})
_pymol_auto_arg_update = pymol_auto_arg_update
except:
pass
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