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Fixes #2881 (#2882)

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* Fixes #2881

* changes in response to review
This commit is contained in:
Greg Landrum
2020-01-20 14:38:58 +01:00
committed by GitHub
parent 0b670d24e4
commit 9bc0f02b20
2 changed files with 112 additions and 0 deletions
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1
Code/GraphMol/FileParsers/MaeMolSupplier.cpp
View File

@@ -158,6 +158,7 @@ void parseChiralityLabel(RWMol &mol, const std::string &stereo_prop) {
for (++tItr; tItr != tokenizer.end(); ++tItr) {
const int nbr_idx = FileParserUtils::toInt(*tItr) - 1;
const Bond *bnd = mol.getBondBetweenAtoms(chiral_idx, nbr_idx);
CHECK_INVARIANT(bnd, "bad chiral bond");
bond_indexes.push_back(bnd->getIdx());
}
CHECK_INVARIANT(bond_indexes.size() == chiral_atom->getDegree(),

111
Code/GraphMol/FileParsers/testMolSupplier.cpp
View File

@@ -2677,6 +2677,112 @@ M END
}
}
void testGitHub2881() {
std::string data = R"DATA(f_m_ct {
s_m_title
s_m_entry_id
s_m_entry_name
s_m_Source_Path
s_m_Source_File
i_m_Source_File_Index
s_st_Chirality_1
s_st_Chirality_2
s_m_subgroup_title
s_m_subgroupid
b_m_subgroup_collapsed
i_m_ct_format
:::
"Untitled Document-4"
17
newTemplates2.1
/Users/nicola/schrodinger/coordgen_standalone
templates.mae
17
3_S_4_6_2
7_S_8_9_6_10
templates->templates->templates
templates->templates1->templates11
0
2
m_depend[2] {
# First column is dependency index #
i_m_depend_dependency
s_m_depend_property
:::
1 10 s_st_Chirality_1
2 10 s_st_Chirality_2
:::
}
m_atom[15] {
# First column is atom index #
i_m_mmod_type
r_m_x_coord
r_m_y_coord
r_m_z_coord
i_m_residue_number
i_m_color
i_m_atomic_number
s_m_color_rgb
s_m_atom_name
:::
1 5 1.186400 1.035900 0.000000 900 2 6 A0A0A0 C1
2 5 0.370300 1.157000 0.000000 900 2 6 A0A0A0 C2
3 4 -0.326500 0.715300 0.000000 900 2 6 A0A0A0 C3
4 5 0.085100 0.000400 0.000000 900 2 6 A0A0A0 C4
5 26 -0.328300 -0.713600 0.000000 900 43 7 5757FF N5
6 5 -1.151500 0.716400 0.000000 900 2 6 A0A0A0 C6
7 5 -1.564900 0.002400 0.000000 900 2 6 A0A0A0 C7
8 5 -1.153300 -0.712600 0.000000 900 2 6 A0A0A0 C9
9 2 1.724800 0.410800 0.000000 900 2 6 A0A0A0 C12
10 2 1.723800 -0.414200 0.000000 900 2 6 A0A0A0 C13
11 5 1.183800 -1.037900 0.000000 900 2 6 A0A0A0 C14
12 5 0.367400 -1.157000 0.000000 900 2 6 A0A0A0 C15
13 7 2.508100 -0.670100 0.000000 900 2 6 A0A0A0 C16
14 7 2.993800 -0.003300 0.000000 900 2 6 A0A0A0 C17
15 29 2.509700 0.664800 0.000000 900 43 7 5757FF N18
:::
}
m_bond[17] {
# First column is bond index #
i_m_from
i_m_to
i_m_order
:::
1 1 2 1
2 1 9 1
3 2 3 1
4 3 4 1
5 3 6 1
6 4 5 1
7 5 8 1
8 5 12 1
9 6 7 1
10 7 8 1
11 9 10 2
12 9 15 1
13 10 11 1
14 10 13 1
15 11 12 1
16 13 14 2
17 14 15 1
:::
}
}
)DATA";
{
std::istringstream *iss = new std::istringstream(data);
bool sanitize = false;
bool takeOwnership = true;
MaeMolSupplier suppl(iss, takeOwnership, sanitize);
ROMol *mol = nullptr;
try {
mol = suppl.next();
} catch (Invar::Invariant) {
}
TEST_ASSERT(!mol);
}
}
int main() {
RDLog::InitLogs();
@@ -2861,5 +2967,10 @@ int main() {
BOOST_LOG(rdErrorLog) << "Finished: testGitHub2479()\n";
BOOST_LOG(rdErrorLog) << "-----------------------------------------\n\n";
BOOST_LOG(rdErrorLog) << "-----------------------------------------\n";
testGitHub2881();
BOOST_LOG(rdErrorLog) << "Finished: testGitHub2881()\n";
BOOST_LOG(rdErrorLog) << "-----------------------------------------\n\n";
return 0;
}