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Fixes #2437 (#2438)

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* Fixes #2437

getting the canonical atom ranking no longer results in molecules have a
RingInfo structure that's been initialized but contains nothing.

* update expected results for the MMPA tests
This commit is contained in:
Greg Landrum
2019-05-10 08:25:31 +02:00
committed by GitHub
parent f47cfd36dd
commit ecf5a67acc
3 changed files with 72 additions and 14 deletions
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6
Code/GraphMol/MMPA/Wrap/testMMPA.py
View File

@@ -63,8 +63,8 @@ class TestCase(unittest.TestCase):
self.assertNotEqual(frags[1][1], '')
self.assertNotEqual(frags[2][1], '')
self.assertEqual(frags[0][1], 'CO[*:1].c1ccc(cc1)[*:1]')
self.assertEqual(frags[1][1], 'C[*:1].c1ccc(cc1)O[*:1]')
self.assertEqual(frags[0][1], 'CO[*:1].c1ccc([*:1])cc1')
self.assertEqual(frags[1][1], 'C[*:1].c1ccc(O[*:1])cc1')
self.assertEqual(frags[2][0], 'O([*:1])[*:2]')
self.assertEqual(frags[2][1], 'C[*:1].c1ccc([*:2])cc1')
@@ -78,7 +78,7 @@ class TestCase(unittest.TestCase):
self.assertEqual(frags[0][0], '')
self.assertNotEqual(frags[0][1], '')
self.assertEqual(frags[0][1], 'CO[*:1].c1ccc(cc1)[*:1]')
self.assertEqual(frags[0][1], 'CO[*:1].c1ccc([*:1])cc1')
def test4(self):
m = Chem.MolFromSmiles('Cc1ccccc1NC(=O)C(C)[NH+]1CCCC1') # ZINC00000051

66
Code/GraphMol/catch_tests.cpp
View File

@@ -3,6 +3,7 @@
#include "catch.hpp"
#include <GraphMol/RDKitBase.h>
#include <GraphMol/new_canon.h>
#include <GraphMol/RDKitQueries.h>
#include <GraphMol/Chirality.h>
#include <GraphMol/FileParsers/FileParsers.h>
@@ -11,7 +12,7 @@
#include <GraphMol/SmilesParse/SmartsWrite.h>
using namespace RDKit;
#if 1
TEST_CASE("SMILES Parsing works", "[molops]") {
std::unique_ptr<RWMol> mol(SmilesToMol("C1CC1"));
REQUIRE(mol);
@@ -255,6 +256,69 @@ TEST_CASE("github #908: AddHs() using 3D coordinates with 2D conformations",
}
}
#endif
TEST_CASE("github #2437: Canon::rankMolAtoms results in crossed double bonds in rings",
"[bug, molops]") {
SECTION("underlying problem") {
std::string molb=R"CTAB(testmol
Mrv1824 05081910082D
4 4 0 0 0 0 999 V2000
6.9312 -8.6277 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.9312 -9.4527 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.7562 -8.6277 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.7562 -9.4527 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
1 3 1 0 0 0 0
3 4 1 0 0 0 0
2 4 2 0 0 0 0
M END
)CTAB";
bool sanitize=false;
bool removeHs=false;
std::unique_ptr<RWMol> mol(MolBlockToMol(molb,sanitize,removeHs));
REQUIRE(mol);
mol->updatePropertyCache();
CHECK(mol->getBondWithIdx(3)->getBondType()==Bond::BondType::DOUBLE);
CHECK(mol->getBondWithIdx(3)->getBondDir()==Bond::BondDir::NONE);
std::vector<unsigned int> ranks;
CHECK(!mol->getRingInfo()->isInitialized());
Canon::rankMolAtoms(*mol,ranks);
CHECK(!mol->getRingInfo()->isInitialized());
}
SECTION("as discovered") {
std::string molb = R"CTAB(testmol
Mrv1824 05081910082D
4 4 0 0 0 0 999 V2000
6.9312 -8.6277 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.9312 -9.4527 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.7562 -8.6277 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.7562 -9.4527 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
1 3 1 0 0 0 0
3 4 1 0 0 0 0
2 4 2 0 0 0 0
M END
)CTAB";
bool sanitize = false;
bool removeHs = false;
std::unique_ptr<RWMol> mol(MolBlockToMol(molb, sanitize, removeHs));
REQUIRE(mol);
mol->updatePropertyCache();
CHECK(mol->getBondWithIdx(3)->getBondType() == Bond::BondType::DOUBLE);
CHECK(mol->getBondWithIdx(3)->getBondDir() == Bond::BondDir::NONE);
auto nmb = MolToMolBlock(*mol);
CHECK(nmb.find("2 4 2 3") == std::string::npos);
CHECK(nmb.find("2 4 2 0") != std::string::npos);
std::vector<unsigned int> ranks;
Canon::rankMolAtoms(*mol, ranks);
nmb = MolToMolBlock(*mol);
CHECK(nmb.find("2 4 2 3") == std::string::npos);
CHECK(nmb.find("2 4 2 0") != std::string::npos);
}
}
TEST_CASE(
"github #2423: Incorrect assignment of explicit Hs to Al+3 read from mol "
"block",

14
Code/GraphMol/new_canon.cpp
View File

@@ -64,12 +64,9 @@ void compareRingAtomsConcerningNumNeighbors(Canon::canon_atom *atoms,
unsigned int nAtoms,
const ROMol &mol) {
RingInfo *ringInfo = mol.getRingInfo();
if (!ringInfo->isInitialized()) {
ringInfo->initialize();
}
for (unsigned idx = 0; idx < nAtoms; ++idx) {
const Canon::canon_atom &a = atoms[idx];
if (ringInfo->numAtomRings(a.atom->getIdx()) < 1) {
if (!ringInfo->isInitialized() || ringInfo->numAtomRings(a.atom->getIdx()) < 1) {
continue;
}
std::deque<int> neighbors;
@@ -94,7 +91,7 @@ void compareRingAtomsConcerningNumNeighbors(Canon::canon_atom *atoms,
int nidx = neighbors.front();
neighbors.pop_front();
const Canon::canon_atom &atom = atoms[nidx];
if (ringInfo->numAtomRings(atom.atom->getIdx()) < 1) {
if (!ringInfo->isInitialized() || ringInfo->numAtomRings(atom.atom->getIdx()) < 1) {
continue;
}
lastLevelNbrs[nidx] = 1;
@@ -234,16 +231,13 @@ void rankWithFunctor(T &ftor, bool breakTies, int *order,
unsigned ringAtoms = 0;
bool branchingRingAtom = false;
RingInfo *ringInfo = mol.getRingInfo();
if (!ringInfo->isInitialized()) {
ringInfo->initialize();
}
for (unsigned i = 0; i < nAts; ++i) {
if (ringInfo->numAtomRings(order[i])) {
if (ringInfo->isInitialized() && ringInfo->numAtomRings(order[i])) {
if (count[order[i]] > 2) {
symRingAtoms += count[order[i]];
}
ringAtoms++;
if (ringInfo->numAtomRings(order[i]) > 1 && count[order[i]] > 1) {
if (ringInfo->isInitialized() && ringInfo->numAtomRings(order[i]) > 1 && count[order[i]] > 1) {
branchingRingAtom = true;
}
}