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refactor: improve readability and maintainability of AAP similarity code (#9277)
* refactor: clean up AAP similarity logic and add type hints * Refactor AAP similarity implementation for clarity and maintainability * Refactor AAP similarity implementation for clarity and maintainability * ran yapf over the code
This commit is contained in:
reza bagheri alashti
committed by
greg landrum
greg landrum
parent
3c81879dc9
commit
8120d418fb
@@ -9,11 +9,10 @@ import unittest
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import numpy
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from scipy.optimize import linear_sum_assignment
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from rdkit import Chem, DataStructs
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from rdkit.Chem import AllChem, rdmolops
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from rdkit.Chem.Fingerprints import FingerprintMols
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from rdkit import Chem
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from rdkit.Chem import rdmolops
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_BK_ = {
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_bondTypeCodes = {
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Chem.rdchem.BondType.SINGLE: 1,
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Chem.rdchem.BondType.DOUBLE: 2,
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Chem.rdchem.BondType.TRIPLE: 3,
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@@ -21,9 +20,9 @@ _BK_ = {
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}
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_BONDSYMBOL_ = {1: '-', 2: '=', 3: '#', 4: ':'}
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#_nAT_ = 217 # 108*2+1
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_nAT_ = 223 # Gobbi code actually uses the first prime higher than 217, not 217 itself
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_nBT_ = 5
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#_atomHashModulus = 217 # 108*2+1
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_atomHashModulus = 223 # Gobbi code actually uses the first prime higher than 217, not 217 itself
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_bondHashModulus = 5
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#def FindAllPathsOfLengthN_Gobbi(mol, length, rootedAtAtom=-1, uniquepaths=True):
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# return FindAllPathsOfLengthMToN(mol, length, length, rootedAtAtom=rootedAtAtom, uniquepaths=uniquepaths)
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@@ -61,12 +60,12 @@ def _FindAllPathsOfLengthMToN_Gobbi(atom, path, minlength, maxlength, visited, p
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if len(path) >= minlength and len(path) <= maxlength:
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paths.append(tuple(path))
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if len(path) < maxlength:
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a1 = bond.GetBeginAtom()
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a2 = bond.GetEndAtom()
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if a1.GetIdx() == atom.GetIdx():
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nextatom = a2
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beginAtom = bond.GetBeginAtom()
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endAtom = bond.GetEndAtom()
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if beginAtom.GetIdx() == atom.GetIdx():
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nextatom = endAtom
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else:
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nextatom = a1
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nextatom = beginAtom
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nextatomidx = nextatom.GetIdx()
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if nextatomidx not in visited:
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visited.add(nextatomidx)
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@@ -79,7 +78,7 @@ def getpathintegers(m1, uptolength=7):
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'''returns a list of integers describing the paths for molecule m1. This uses numpy 16 bit unsigned integers to reproduce the data in the Gobbi paper. The returned list is sorted'''
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bondtypelookup = {}
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for b in m1.GetBonds():
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bondtypelookup[b.GetIdx()] = _BK_[b.GetBondType()], b.GetBeginAtom(), b.GetEndAtom()
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bondtypelookup[b.GetIdx()] = _bondTypeCodes[b.GetBondType()], b.GetBeginAtom(), b.GetEndAtom()
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pathintegers = {}
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for a in m1.GetAtoms():
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idx = a.GetIdx()
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@@ -88,40 +87,32 @@ def getpathintegers(m1, uptolength=7):
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# for path in rdmolops.FindAllPathsOfLengthN(m1, pathlength, rootedAtAtom=idx):
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for ipath, path in enumerate(
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FindAllPathsOfLengthMToN_Gobbi(m1, 1, uptolength, rootedAtAtom=idx, uniquepaths=False)):
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strpath = []
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currentidx = idx
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res = []
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for ip, p in enumerate(path):
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bk, a1, a2 = bondtypelookup[p]
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strpath.append(_BONDSYMBOL_[bk])
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if a1.GetIdx() == currentidx:
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a = a2
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bondTypeCode, beginAtom, endAtom = bondtypelookup[p]
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if beginAtom.GetIdx() == currentidx:
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a = endAtom
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else:
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a = a1
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ak = a.GetAtomicNum()
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a = beginAtom
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neighborAtomCode = a.GetAtomicNum()
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if a.GetIsAromatic():
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ak += 108
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neighborAtomCode += 108
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#trying to get the same behaviour as the Gobbi test code - it looks like a circular path includes the bond, but not the closure atom - this fix works
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if a.GetIdx() == idx:
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ak = None
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if ak is not None:
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astr = a.GetSymbol()
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if a.GetIsAromatic():
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strpath.append(astr.lower())
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else:
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strpath.append(astr)
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res.append((bk, ak))
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neighborAtomCode = None
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res.append((bondTypeCode, neighborAtomCode))
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currentidx = a.GetIdx()
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pathuniqueint = numpy.ushort(0) # work with 16 bit unsigned integers and ignore overflow...
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for ires, (bi, ai) in enumerate(res):
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for ires, (bondValue, atomValue) in enumerate(res):
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#use 16 bit unsigned integer arithmetic to reproduce the Gobbi ints
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# pathuniqueint = ((pathuniqueint+bi)*_nAT_+ai)*_nBT_
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val1 = pathuniqueint + numpy.ushort(bi)
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val2 = val1 * numpy.ushort(_nAT_)
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# pathuniqueint = ((pathuniqueint+bondValue)*_atomHashModulus+atomValue)*_bondHashModulus
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val1 = pathuniqueint + numpy.ushort(bondValue)
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val2 = val1 * numpy.ushort(_atomHashModulus)
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#trying to get the same behaviour as the Gobbi test code - it looks like a circular path includes the bond, but not the closure atom - this fix works
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if ai is not None:
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val3 = val2 + numpy.ushort(ai)
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val4 = val3 * numpy.ushort(_nBT_)
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if atomValue is not None:
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val3 = val2 + numpy.ushort(atomValue)
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val4 = val3 * numpy.ushort(_bondHashModulus)
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else:
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val4 = val2
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pathuniqueint = val4
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@@ -140,14 +131,14 @@ def getcommon(l1, ll1, l2, ll2):
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ix1 = 0
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ix2 = 0
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while (ix1 < ll1) and (ix2 < ll2):
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a1 = l1[ix1]
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a2 = l2[ix2]
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#a1 is < or > more often that ==
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if a1 < a2:
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beginAtom = l1[ix1]
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endAtom = l2[ix2]
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#beginAtom is < or > more often that ==
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if beginAtom < endAtom:
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ix1 += 1
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elif a1 > a2:
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elif beginAtom > endAtom:
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ix2 += 1
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else: # a1 == a2:
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else: # beginAtom == endAtom:
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ncommon += 1
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ix1 += 1
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ix2 += 1
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@@ -206,19 +197,20 @@ def getsimab(mappings, simmatrixdict):
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def getsimmatrix(m1, m1pathintegers, m2, m2pathintegers):
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'''generate a matrix of atom atom similarities. See Figure 4'''
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aidata = [((ai.GetAtomicNum(), ai.GetIsAromatic()), ai.GetIdx()) for ai in m1.GetAtoms()]
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aidata = [((atomValue.GetAtomicNum(), atomValue.GetIsAromatic()), atomValue.GetIdx())
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for atomValue in m1.GetAtoms()]
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bjdata = [((bj.GetAtomicNum(), bj.GetIsAromatic()), bj.GetIdx()) for bj in m2.GetAtoms()]
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simmatrixarray = numpy.zeros((len(aidata), len(bjdata)))
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for ai, (aitype, aiidx) in enumerate(aidata):
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for atomValue, (aitype, aiidx) in enumerate(aidata):
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aipaths = m1pathintegers[aiidx]
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naipaths = len(aipaths)
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for bj, (bjtype, bjidx) in enumerate(bjdata):
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if aitype == bjtype:
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bjpaths = m2pathintegers[bjidx]
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nbjpaths = len(bjpaths)
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simmatrixarray[ai][bj] = getsimaibj(aipaths, bjpaths, naipaths, nbjpaths)
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simmatrixarray[atomValue][bj] = getsimaibj(aipaths, bjpaths, naipaths, nbjpaths)
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return simmatrixarray
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