/usr/lib/python2.7/dist-packages/chemfp/openbabel_patterns.py is in python-chemfp 1.1p1-2.1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 | from __future__ import absolute_import
from openbabel import OBSmartsPattern, OBBitVec
from . import openbabel
from . import pattern_fingerprinter
from . import types
from . import __version__ as chemfp_version
SOFTWARE = openbabel.SOFTWARE + (" chemfp/%s" % (chemfp_version,))
# HasMatch was added to OpenBabel 2.3 .
_HAS_HASMATCH = hasattr(OBSmartsPattern(), "HasMatch")
class Matcher(object):
def __init__(self, ob_matcher):
self.ob_matcher = ob_matcher
if _HAS_HASMATCH:
def HasMatch(self, mol):
return self.ob_matcher.HasMatch(mol)
else:
def HasMatch(self, mol):
return self.ob_matcher.Match(mol, True)
def NumUniqueMatches(self, mol):
self.ob_matcher.Match(mol)
return sum(1 for x in self.ob_matcher.GetUMapList())
class HydrogenMatcher(object):
def __init__(self, max_count):
self.max_count = max_count
def HasMatch(self, mol):
for i in range(1, mol.NumAtoms()+1):
atom = mol.GetAtom(i)
if atom.GetAtomicNum() == 1:
return True
if atom.ImplicitHydrogenCount():
return True
return False
def NumUniqueMatches(self, mol):
count = 0
for i in range(1, mol.NumAtoms()+1):
atom = mol.GetAtom(i)
if atom.GetAtomicNum() == 1:
count += 1
count += atom.ImplicitHydrogenCount()
if count >= self.max_count:
return count
return count
class AromaticRings(object):
def __init__(self, max_count):
self.max_count = max_count
# The single ring case is easy; if there's an aromatic atom in a ring
# then there's an aromatic ring.
self._single_matcher = OBSmartsPattern()
assert self._single_matcher.Init("[aR]")
if _HAS_HASMATCH:
def HasMatch(self, mol):
return self._single_matcher.HasMatch(mol)
else:
def HasMatch(self, mol):
return self._single_matcher.Match(mol, True)
def NumUniqueMatches(self, mol):
num_rings = 0
for ring in mol.GetSSSR():
if ring.IsAromatic():
num_rings += 1
if num_rings == self.max_count:
break
return num_rings
###
class HeteroAromaticRings(object):
def __init__(self, max_count):
self.max_count = max_count
# The single ring case is easy; if there's an non-carbon aromatic atom
# in a ring then there's a hetero-aromatic ring
self._single_matcher = OBSmartsPattern()
assert self._single_matcher.Init("[aR;!#6]")
if _HAS_HASMATCH:
def HasMatch(self, mol):
return self._single_matcher.HasMatch(mol)
else:
def HasMatch(self, mol):
return self._single_matcher.Match(mol, True)
def NumUniqueMatches(self, mol):
num_rings = 0
for ring in mol.GetSSSR():
if (ring.IsAromatic() and
any(mol.GetAtom(atom_id).GetAtomicNum() != 6 for atom_id in ring._path)):
num_rings += 1
if num_rings == self.max_count:
break
return num_rings
class NumFragments(object):
def __init__(self, max_count):
if max_count >= 3:
raise NotImplemented("<fragment> >= 3 not implemented")
def HasMatch(self, mol):
# Has at least one fragment, which is the same as having atoms
return (mol.NumAtoms() > 0)
def NumUniqueMatches(self, mol):
# If the largest fragment is not the same size as the entire molecule
# then there are at least two fragments
n = mol.NumAtoms()
if n == 0:
# No atoms means no fragments
return 0
v = OBBitVec()
mol.FindLargestFragment(v)
if v.CountBits() == n:
return 1
return 2
_pattern_classes = {
"<H>": HydrogenMatcher,
"<aromatic-rings>": AromaticRings,
"<hetero-aromatic-rings>": HeteroAromaticRings,
"<fragments>": NumFragments,
}
def ob_compile_pattern(pattern, max_count):
if pattern in _pattern_classes:
return _pattern_classes[pattern](max_count)
if pattern.startswith("<"):
raise NotImplementedError(pattern)
matcher = OBSmartsPattern()
if not matcher.Init(pattern):
raise pattern_fingerprinter.UnsupportedPatternError(
pattern, "Uninterpretable SMARTS pattern")
return Matcher(matcher)
class OBPatternFingerprinter(pattern_fingerprinter.PatternFingerprinter):
def __init__(self, patterns):
assert patterns is not None
super(OBPatternFingerprinter, self).__init__(patterns, ob_compile_pattern)
def fingerprint(self, mol):
bytes = [0] * self.num_bytes
for matcher, largest_count, count_info_tuple in self.matcher_definitions:
#print matcher, largest_count, count_info_tuple
if largest_count == 1:
if matcher.HasMatch(mol):
count_info = count_info_tuple[0]
bytes[count_info.byteno] |= count_info.bitmask
else:
# There's no good way to get the number of unique
# matches without iterating over all of them.
actual_count = matcher.NumUniqueMatches(mol)
for count_info in count_info_tuple:
if actual_count >= count_info.count:
bytes[count_info.byteno] |= count_info.bitmask
else:
break
return "".join(map(chr, bytes))
class _CachedFingerprinters(dict):
def __missing__(self, name):
patterns = pattern_fingerprinter._load_named_patterns(name)
fingerprinter = OBPatternFingerprinter(patterns)
self[name] = fingerprinter
return fingerprinter
_cached_fingerprinters = _CachedFingerprinters()
# XXX Why are there two "Fingerprinter" classes?
# XX Shouldn't they be merged?
_base = openbabel._base.clone(
software = SOFTWARE)
SubstructOpenBabelFingerprinter_v1 = _base.clone(
name = "ChemFP-Substruct-OpenBabel/1",
num_bits = 881,
make_fingerprinter = lambda: _cached_fingerprinters["substruct"].fingerprint)
RDMACCSOpenBabelFingerprinter_v1 = _base.clone(
name = "RDMACCS-OpenBabel/1",
num_bits = 166,
make_fingerprinter = lambda: _cached_fingerprinters["rdmaccs"].fingerprint)
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