mirror of
https://github.com/rdkit/rdkit.git
synced 2026-06-03 21:44:30 +08:00
- allowRGroups now also includes terminal query atoms matching hydrogen in additional to terminal dummy atoms (#6280)
- added relevant unit tests Co-authored-by: Tosco, Paolo <paolo.tosco@novartis.com>
This commit is contained in:
Paolo Tosco
GitHub
@@ -22,6 +22,7 @@
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#include <cmath>
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#include <GraphMol/MolOps.h>
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#include <GraphMol/Rings.h>
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#include <GraphMol/QueryAtom.h>
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#include <Geometry/point.h>
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#include <Geometry/Transform2D.h>
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#include <Geometry/Transform3D.h>
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@@ -751,7 +752,7 @@ RDKit::MatchVectType generateDepictionMatching2DStructure(
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// terminal dummy atoms
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allowOptionalAttachments = false;
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for (const auto queryAtom : query.atoms()) {
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if (queryAtom->getAtomicNum() == 0 && queryAtom->getDegree() == 1) {
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if (RDKit::isAtomTerminalRGroupOrQueryHydrogen(queryAtom)) {
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allowOptionalAttachments = true;
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break;
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}
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@@ -1288,6 +1288,79 @@ M END)RES"_ctab;
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msd /= static_cast<double>(matchVect.size());
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TEST_ASSERT(msd < 1.0e-4);
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}
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// test that using a reference with query atoms including H works
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auto scaffold = R"CTAB(
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MJ201100
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12 13 0 0 0 0 0 0 0 0999 V2000
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-0.5398 0.0400 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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||||
-1.3648 0.0400 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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-1.7773 -0.6745 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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-1.3649 -1.3889 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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-0.5399 -1.3889 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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-0.1273 -0.6744 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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||||
0.6976 -0.6744 0.0000 L 0 0 0 0 0 0 0 0 0 0 0 0
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-1.9167 0.6531 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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-2.6704 0.3176 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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-2.5842 -0.5028 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
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-3.3849 0.7302 0.0000 L 0 0 0 0 0 0 0 0 0 0 0 0
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-1.7451 1.4600 0.0000 L 0 0 0 0 0 0 0 0 0 0 0 0
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1 2 2 0 0 0 0
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2 3 1 0 0 0 0
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3 4 2 0 0 0 0
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4 5 1 0 0 0 0
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5 6 2 0 0 0 0
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6 1 1 0 0 0 0
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6 7 1 0 0 0 0
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8 9 2 0 0 0 0
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2 8 1 0 0 0 0
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9 10 1 0 0 0 0
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3 10 1 0 0 0 0
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9 11 1 0 0 0 0
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8 12 1 0 0 0 0
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M ALS 7 10 F H C N O F P S Cl Br I
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M ALS 11 10 F H C N O F P S Cl Br I
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M ALS 12 10 F H C N O F P S Cl Br I
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M END
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)CTAB"_ctab;
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auto mol = R"CTAB(
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MJ201100
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13 14 0 0 0 0 0 0 0 0999 V2000
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-0.6112 0.3665 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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-1.3648 0.0310 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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-1.4510 -0.7895 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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-0.7836 -1.2744 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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-0.0299 -0.9389 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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0.0562 -0.1183 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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0.8099 0.2172 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
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-2.1184 0.3666 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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-2.6705 -0.2464 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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-2.2580 -0.9608 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
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0.6374 -1.4238 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
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0.8961 1.0377 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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0.5512 -2.2443 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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1 2 2 0 0 0 0
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2 3 1 0 0 0 0
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3 4 2 0 0 0 0
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4 5 1 0 0 0 0
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5 6 2 0 0 0 0
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6 1 1 0 0 0 0
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8 9 2 0 0 0 0
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2 8 1 0 0 0 0
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9 10 1 0 0 0 0
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3 10 1 0 0 0 0
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6 7 1 0 0 0 0
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5 11 1 0 0 0 0
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7 12 1 0 0 0 0
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11 13 1 0 0 0 0
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M END
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)CTAB"_ctab;
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auto matchVect = RDDepict::generateDepictionMatching2DStructure(
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*mol, *scaffold, -1, nullptr, false, false, true);
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TEST_ASSERT(mol->getNumConformers() == 1);
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TEST_ASSERT(matchVect.size() == 10);
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BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
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}
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@@ -79,8 +79,8 @@ class ScoreMatchesByDegreeOfCoreSubstitution {
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bool doesRGroupMatchHydrogen(const std::pair<int, int> &pair) const {
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const auto queryAtom = d_query.getAtomWithIdx(pair.first);
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const auto molAtom = d_mol.getAtomWithIdx(pair.second);
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return (queryAtom->getAtomicNum() == 0 && queryAtom->getDegree() == 1 &&
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molAtom->getAtomicNum() == 1);
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return (molAtom->getAtomicNum() == 1 &&
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isAtomTerminalRGroupOrQueryHydrogen(queryAtom));
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}
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double computeScore(const RDKit::MatchVectType &match) const {
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double penalty = 0.0;
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@@ -217,6 +217,14 @@ std::vector<MatchVectType> sortMatchesByDegreeOfCoreSubstitution(
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return matchScorer.sortMatchesByDegreeOfCoreSubstitution();
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}
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bool isAtomTerminalRGroupOrQueryHydrogen(const Atom *atom) {
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return atom->getDegree() == 1 &&
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(atom->getAtomicNum() == 0 ||
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(atom->hasQuery() &&
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describeQuery(atom).find("AtomAtomicNum 1 = val") !=
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std::string::npos));
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}
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#define PT_OPT_GET(opt) params.opt = pt.get(#opt, params.opt)
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#define PT_OPT_PUT(opt) pt.put(#opt, params.opt);
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@@ -39,6 +39,9 @@ RDKIT_SUBSTRUCTMATCH_EXPORT std::vector<MatchVectType>
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sortMatchesByDegreeOfCoreSubstitution(
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const ROMol& mol, const ROMol& core,
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const std::vector<MatchVectType>& matches);
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RDKIT_SUBSTRUCTMATCH_EXPORT bool isAtomTerminalRGroupOrQueryHydrogen(
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const Atom* atom);
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} // namespace RDKit
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#endif
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@@ -1947,6 +1947,110 @@ void testLongRing() {
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delete mol;
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}
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void testIsAtomTerminalRGroupOrQueryHydrogen() {
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BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
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BOOST_LOG(rdErrorLog) << "Test isAtomTerminalRGroupOrQueryHydrogen"
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<< std::endl;
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{
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auto mol = R"CTAB(
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MJ201100
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7 7 0 0 0 0 0 0 0 0999 V2000
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-0.3795 1.5839 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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-1.0939 1.1714 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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-1.0939 0.3463 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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-0.3795 -0.0661 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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0.3349 0.3463 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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0.3349 1.1714 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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1.0494 1.5839 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0
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1 2 4 0 0 0 0
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2 3 4 0 0 0 0
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3 4 4 0 0 0 0
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4 5 4 0 0 0 0
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5 6 4 0 0 0 0
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6 1 4 0 0 0 0
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6 7 1 0 0 0 0
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M RGP 1 7 1
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M END
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)CTAB"_ctab;
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const auto rAtom = mol->getAtomWithIdx(mol->getNumAtoms() - 1);
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TEST_ASSERT(isAtomTerminalRGroupOrQueryHydrogen(rAtom));
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}
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{
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auto mol = R"CTAB(
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MJ201100
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6 6 0 0 0 0 0 0 0 0999 V2000
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-0.7589 1.4277 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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-1.4733 1.0152 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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-1.4733 0.1901 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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-0.7589 -0.2223 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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-0.0444 0.1901 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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-0.0444 1.0152 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0
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1 2 2 0 0 0 0
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2 3 1 0 0 0 0
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3 4 2 0 0 0 0
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4 5 1 0 0 0 0
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5 6 2 0 0 0 0
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6 1 1 0 0 0 0
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M RGP 1 6 1
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M END
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)CTAB"_ctab;
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const auto rAtom = mol->getAtomWithIdx(mol->getNumAtoms() - 1);
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TEST_ASSERT(!isAtomTerminalRGroupOrQueryHydrogen(rAtom));
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}
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{
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auto mol = R"CTAB(
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MJ201100
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7 7 0 0 0 0 0 0 0 0999 V2000
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-0.9152 0.2893 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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-1.6296 -0.1231 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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-1.6296 -0.9482 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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-0.9152 -1.3607 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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-0.2007 -0.9482 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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-0.2007 -0.1231 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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0.5137 0.2893 0.0000 L 0 0 0 0 0 0 0 0 0 0 0 0
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1 2 4 0 0 0 0
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2 3 4 0 0 0 0
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3 4 4 0 0 0 0
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4 5 4 0 0 0 0
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5 6 4 0 0 0 0
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6 1 4 0 0 0 0
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6 7 1 0 0 0 0
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M ALS 7 10 F H C N O F P S Cl Br I
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M END
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)CTAB"_ctab;
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const auto rAtom = mol->getAtomWithIdx(mol->getNumAtoms() - 1);
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TEST_ASSERT(isAtomTerminalRGroupOrQueryHydrogen(rAtom));
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}
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{
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auto mol = R"CTAB(
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MJ201100
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7 7 0 0 0 0 0 0 0 0999 V2000
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-0.9152 0.2893 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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-1.6296 -0.1231 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-1.6296 -0.9482 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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||||
-0.9152 -1.3607 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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||||
-0.2007 -0.9482 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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||||
-0.2007 -0.1231 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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0.5137 0.2893 0.0000 L 0 0 0 0 0 0 0 0 0 0 0 0
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1 2 4 0 0 0 0
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2 3 4 0 0 0 0
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3 4 4 0 0 0 0
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4 5 4 0 0 0 0
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5 6 4 0 0 0 0
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6 1 4 0 0 0 0
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6 7 1 0 0 0 0
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M ALS 7 9 F C N O F P S Cl Br I
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M END
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)CTAB"_ctab;
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const auto rAtom = mol->getAtomWithIdx(mol->getNumAtoms() - 1);
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TEST_ASSERT(!isAtomTerminalRGroupOrQueryHydrogen(rAtom));
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}
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}
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int main(int argc, char *argv[]) {
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RDLog::InitLogs();
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test1();
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@@ -1974,6 +2078,7 @@ int main(int argc, char *argv[]) {
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testEZVsCisTransMatch();
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testMostSubstitutedCoreMatch();
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testLongRing();
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testIsAtomTerminalRGroupOrQueryHydrogen();
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return 0;
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}
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@@ -844,6 +844,10 @@ void test_coords() {
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printf(" test_coords\n");
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char *mpkl;
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size_t mpkl_size;
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char *mpkl2;
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size_t mpkl2_size;
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char *mpkl3;
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size_t mpkl3_size;
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mpkl = get_mol("C1CNC1CC", &mpkl_size, "");
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char *cxsmi = get_cxsmiles(mpkl, mpkl_size, NULL);
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@@ -870,6 +874,10 @@ void test_coords() {
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// aligned
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char *tpkl;
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size_t tpkl_size;
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char *tpkl2;
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size_t tpkl2_size;
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char *tpkl3;
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size_t tpkl3_size;
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tpkl = get_mol(
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"\n\
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Mrv2102 04062106432D\n\
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@@ -1004,6 +1012,75 @@ M END\n",
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8 7 1 0\n\
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M END\n",
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&mpkl_size, "");
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tpkl3 = get_mol(
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"\n\
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||||
MJ201100 \n\
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\n\
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12 13 0 0 0 0 0 0 0 0999 V2000\n\
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-0.5398 0.0400 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n\
|
||||
-1.3648 0.0400 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n\
|
||||
-1.7773 -0.6745 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n\
|
||||
-1.3649 -1.3889 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n\
|
||||
-0.5399 -1.3889 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n\
|
||||
-0.1273 -0.6744 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n\
|
||||
0.6976 -0.6744 0.0000 L 0 0 0 0 0 0 0 0 0 0 0 0\n\
|
||||
-1.9167 0.6531 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n\
|
||||
-2.6704 0.3176 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n\
|
||||
-2.5842 -0.5028 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n\
|
||||
-3.3849 0.7302 0.0000 L 0 0 0 0 0 0 0 0 0 0 0 0\n\
|
||||
-1.7451 1.4600 0.0000 L 0 0 0 0 0 0 0 0 0 0 0 0\n\
|
||||
1 2 2 0 0 0 0\n\
|
||||
2 3 1 0 0 0 0\n\
|
||||
3 4 2 0 0 0 0\n\
|
||||
4 5 1 0 0 0 0\n\
|
||||
5 6 2 0 0 0 0\n\
|
||||
6 1 1 0 0 0 0\n\
|
||||
6 7 1 0 0 0 0\n\
|
||||
8 9 2 0 0 0 0\n\
|
||||
2 8 1 0 0 0 0\n\
|
||||
9 10 1 0 0 0 0\n\
|
||||
3 10 1 0 0 0 0\n\
|
||||
9 11 1 0 0 0 0\n\
|
||||
8 12 1 0 0 0 0\n\
|
||||
M ALS 7 10 F H C N O F P S Cl Br I \n\
|
||||
M ALS 11 10 F H C N O F P S Cl Br I \n\
|
||||
M ALS 12 10 F H C N O F P S Cl Br I \n\
|
||||
M END\n",
|
||||
&tpkl3_size, "");
|
||||
mpkl3 = get_mol(
|
||||
"\n\
|
||||
MJ201100 \n\
|
||||
\n\
|
||||
13 14 0 0 0 0 0 0 0 0999 V2000\n\
|
||||
-0.6112 0.3665 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n\
|
||||
-1.3648 0.0310 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n\
|
||||
-1.4510 -0.7895 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n\
|
||||
-0.7836 -1.2744 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n\
|
||||
-0.0299 -0.9389 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n\
|
||||
0.0562 -0.1183 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n\
|
||||
0.8099 0.2172 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n\
|
||||
-2.1184 0.3666 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n\
|
||||
-2.6705 -0.2464 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n\
|
||||
-2.2580 -0.9608 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n\
|
||||
0.6374 -1.4238 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n\
|
||||
0.8961 1.0377 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n\
|
||||
0.5512 -2.2443 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n\
|
||||
1 2 2 0 0 0 0\n\
|
||||
2 3 1 0 0 0 0\n\
|
||||
3 4 2 0 0 0 0\n\
|
||||
4 5 1 0 0 0 0\n\
|
||||
5 6 2 0 0 0 0\n\
|
||||
6 1 1 0 0 0 0\n\
|
||||
8 9 2 0 0 0 0\n\
|
||||
2 8 1 0 0 0 0\n\
|
||||
9 10 1 0 0 0 0\n\
|
||||
3 10 1 0 0 0 0\n\
|
||||
6 7 1 0 0 0 0\n\
|
||||
5 11 1 0 0 0 0\n\
|
||||
7 12 1 0 0 0 0\n\
|
||||
11 13 1 0 0 0 0\n\
|
||||
M END\n",
|
||||
&mpkl3_size, "");
|
||||
float **mol_coords = _get_coord_array(mpkl, mpkl_size);
|
||||
assert(mol_coords);
|
||||
float bond_length11_12 = sqrt(_sq_dist(mol_coords[11], mol_coords[12]));
|
||||
@@ -1025,8 +1102,6 @@ M END\n",
|
||||
char *mpkl2_molblock_after = NULL;
|
||||
char *mpkl_smi = NULL;
|
||||
size_t mpkl_smi_size;
|
||||
char *mpkl2 = NULL;
|
||||
size_t mpkl2_size;
|
||||
|
||||
for (i = 0; i < 2; ++i) {
|
||||
// this has no initial coordinates and matches the template
|
||||
@@ -1124,12 +1199,25 @@ M END\n",
|
||||
// coordinates should be present since coordinate generation has taken place anyway using CoordGen
|
||||
assert(has_coords(mpkl_smi, mpkl_smi_size));
|
||||
free(mpkl_smi);
|
||||
|
||||
memset(details, 0, 200);
|
||||
sprintf(details,
|
||||
"{\"acceptFailure\":false,\"allowRGroups\":true,\"alignOnly\":%s}",
|
||||
align_only_choices[i]);
|
||||
assert(set_2d_coords_aligned(&mpkl3, &mpkl3_size, tpkl3, tpkl3_size,
|
||||
details, &match_json));
|
||||
assert(!strcmp(
|
||||
match_json,
|
||||
"{\"atoms\":[0,1,2,3,4,5,6,7,8,9],\"bonds\":[0,1,2,3,4,5,10,6,7,8,9]}"));
|
||||
free(match_json);
|
||||
}
|
||||
|
||||
_free_coord_array(mol_coords);
|
||||
_free_coord_array(tpl_coords);
|
||||
free(mpkl);
|
||||
free(tpkl);
|
||||
free(mpkl3);
|
||||
free(tpkl3);
|
||||
|
||||
printf(" done\n");
|
||||
printf("--------------------------\n");
|
||||
|
||||
@@ -881,13 +881,9 @@ std::string generate_aligned_coords(ROMol &mol, const ROMol &templateMol,
|
||||
std::unique_ptr<ROMol> molHs;
|
||||
ROMol *prbMol = &mol;
|
||||
if (allowRGroups) {
|
||||
allowRGroups = false;
|
||||
for (const auto templateAtom : templateMol.atoms()) {
|
||||
if (templateAtom->getAtomicNum() == 0 && templateAtom->getDegree() == 1) {
|
||||
allowRGroups = true;
|
||||
break;
|
||||
}
|
||||
}
|
||||
auto atoms = templateMol.atoms();
|
||||
allowRGroups = std::any_of(atoms.begin(), atoms.end(),
|
||||
isAtomTerminalRGroupOrQueryHydrogen);
|
||||
}
|
||||
if (allowRGroups) {
|
||||
molHs.reset(MolOps::addHs(mol));
|
||||
@@ -906,8 +902,7 @@ std::string generate_aligned_coords(ROMol &mol, const ROMol &templateMol,
|
||||
for (const auto &pair : match) {
|
||||
const auto templateAtom = templateMol.getAtomWithIdx(pair.first);
|
||||
const auto prbAtom = prbMol->getAtomWithIdx(pair.second);
|
||||
bool isRGroup = templateAtom->getAtomicNum() == 0 && templateAtom->getDegree() == 1;
|
||||
if (isRGroup) {
|
||||
if (isAtomTerminalRGroupOrQueryHydrogen(templateAtom)) {
|
||||
if (prbAtom->getAtomicNum() == 1) {
|
||||
continue;
|
||||
}
|
||||
|
||||
Reference in New Issue
Block a user