AAindex

Hydrophobicity coloring with KYTJ820101

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.grep('blosum')
x = aaindex.get('HENS920102')
print x.get('A', 'K')

PyMOL Example

import aaindex
aaindex2b KYTJ820101
spectrum b, yellow_white_blue
show surface

The Script

'''
(c) 2010-2011 Thomas Holder, MPI for Developmental Biology

Python parser for AAindex: Amino Acid Index Database
http://www.genome.jp/aaindex/

PyMOL commands:

    aaindex2b
    pmf
'''

import sys, os

_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 __getitem__(self, aai):
        return self.get(aai)
    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 __getitem__(self, aaij):
        return self.get(aaij[0], aaij[1])
    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[key]

def _float_or_None(x):
    if x == 'NA' or x == '-':
        return None
    return float(x)

def init(path=None, index='13'):
    '''
    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.
    '''
    index = str(index)
    if path is None:
        for path in [os.path.split(__file__)[0], '.', cmd.get('fetch_path')]:
            if os.path.exists(os.path.join(path, 'aaindex' + index[0])):
                break
        print >> sys.stderr, 'path =', path
    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.
    '''
    if not os.path.exists(filename):
        import urllib
        url = 'ftp://ftp.genome.jp/pub/db/community/aaindex/' + os.path.split(filename)[1]
        print 'Downloading "%s"' % (url)
        filename = urllib.urlretrieve(url, filename)[0]
        print 'Saved to "%s"' % (filename)
    f = open(filename)

    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
    spectrumany b, white yellow forest
    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

    # 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
    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])

    idmap = dict()
    cmd.iterate_state(state, '(%s) or (%s)' % (selection1, selection2),
            'idmap[model,index] = [(resn,name),(x,y,z)]', space={'idmap': idmap})
    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 = idmap[id1]
        a2 = 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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