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Fixes #2647 (#2651)

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* Fixes #2647

* Updated tests

* Fixes in response to review
This commit is contained in:
Brian Kelley
2019-09-23 12:14:50 -04:00
committed by Greg Landrum
parent d458e46548
commit d55a2030cc
2 changed files with 32 additions and 11 deletions
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15
Code/GraphMol/Subgraphs/SubgraphUtils.cpp
View File

@@ -30,15 +30,17 @@ ROMol *pathToSubmol(const ROMol &mol, const PATH_TYPE &path, bool useQuery) {
ROMol *pathToSubmol(const ROMol &mol, const PATH_TYPE &path, bool useQuery,
INT_MAP_INT &atomIdxMap) {
auto *subMol = new RWMol();
PATH_TYPE::const_iterator pathIter;
// path needs to be in sorted order to preserve chirality
PATH_TYPE sorted_path(path);
std::sort(sorted_path.begin(), sorted_path.end());
atomIdxMap.clear();
if (useQuery) {
// have to do this in two different blocks because of issues with variable
// scopes.
for (pathIter = path.begin(); pathIter != path.end(); ++pathIter) {
QueryBond *bond;
bond = new QueryBond(*(mol.getBondWithIdx(*pathIter)));
for(auto bondidx : sorted_path) {
QueryBond *bond = new QueryBond(*(mol.getBondWithIdx(bondidx)));
int begIdx = bond->getBeginAtomIdx();
int endIdx = bond->getEndAtomIdx();
@@ -62,9 +64,8 @@ ROMol *pathToSubmol(const ROMol &mol, const PATH_TYPE &path, bool useQuery,
subMol->addBond(bond, true);
}
} else {
for (pathIter = path.begin(); pathIter != path.end(); ++pathIter) {
Bond *bond;
bond = mol.getBondWithIdx(*pathIter)->copy();
for(auto bondidx : sorted_path) {
Bond *bond = mol.getBondWithIdx(bondidx)->copy();
int begIdx = bond->getBeginAtomIdx();
int endIdx = bond->getEndAtomIdx();

28
Code/GraphMol/Subgraphs/test2.cpp
View File

@@ -20,6 +20,12 @@
using namespace std;
using namespace RDKit;
std::string canon(std::string smiles) {
unique_ptr<ROMol> m(SmilesToMol(smiles));
const bool useStereo = true;
return MolToSmiles(*m, useStereo);
}
void test1() {
std::cout << "-----------------------\n Test1: pathToSubmol" << std::endl;
{
@@ -123,7 +129,7 @@ void test2() {
TEST_ASSERT(pth.size() == 8);
ROMol *frag = Subgraphs::pathToSubmol(*mol, pth, false);
smiles = MolToSmiles(*frag, true, false, 0, false);
TEST_ASSERT(smiles == "C(C(C(O)C)C(C)C)C");
TEST_ASSERT(canon(smiles) == canon("C(C(C(O)C)C(C)C)C"));
delete frag;
delete mol;
}
@@ -144,7 +150,7 @@ void testGithubIssue103() {
TEST_ASSERT(pth.size() == 5);
ROMol *frag = Subgraphs::pathToSubmol(*mol, pth, false);
smiles = MolToSmiles(*frag, true);
TEST_ASSERT(smiles == "C=CC(O)C=C");
TEST_ASSERT(canon(smiles) == canon("C=CC(O)C=C"));
delete frag;
delete mol;
}
@@ -157,7 +163,7 @@ void testGithubIssue103() {
TEST_ASSERT(pth.size() == 5);
ROMol *frag = Subgraphs::pathToSubmol(*mol, pth, false);
smiles = MolToSmarts(*frag);
TEST_ASSERT(smiles == "[#6](-[#6@H](-[#8])-[#6]=[#6])=[#6]");
TEST_ASSERT(smiles == "[#6]=[#6]-[#6@H](-[#8])-[#6]=[#6]");
delete frag;
delete mol;
}
@@ -170,7 +176,7 @@ void testGithubIssue103() {
TEST_ASSERT(pth.size() == 5);
ROMol *frag = Subgraphs::pathToSubmol(*mol, pth, true);
smiles = MolToSmarts(*frag);
TEST_ASSERT(smiles == "[#6](-[#6@](-[#8])-[#6]=[#6])=[#6]");
TEST_ASSERT(smiles == "[#6]=[#6]-[#6@](-[#8])-[#6]=[#6]");
delete frag;
delete mol;
}
@@ -178,10 +184,24 @@ void testGithubIssue103() {
std::cout << "Finished" << std::endl;
}
void testGithubIssue2647() {
std::cout << "-----------------------\n Testing github Issue103: "
"more stereochemistry and pathToSubmol (path needs to be in sorted order)"
<< std::endl;
std::string smiles = "I[C@](F)(Br)O";
std::unique_ptr<ROMol> mol(SmilesToMol(smiles));
std::vector<int> path = { 0, 3, 2, 1 };
const bool useQuery=false;
std::unique_ptr<ROMol> mol2(Subgraphs::pathToSubmol(*mol, path, useQuery));
TEST_ASSERT(MolToSmiles(*mol2) == MolToSmiles(*mol));
std::cout << "Finished" << std::endl;
}
// -------------------------------------------------------------------
int main() {
test1();
test2();
testGithubIssue103();
testGithubIssue2647();
return 0;
}