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Backmerge: #1796 Some bonds from ChemDraw don't display correctly in …
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…the Ketcher. (#1895)
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@AliaksandrDziarkach
AliaksandrDziarkach authored Apr 1, 2024
1 parent 6c2a46e commit d0224f9
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Showing 4 changed files with 49 additions and 23 deletions.
4 changes: 2 additions & 2 deletions api/tests/integration/ref/formats/cdx.py.out
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Expand Up @@ -692,15 +692,15 @@ Properties:
*****
5
Smiles:
c:c
CC
Molfile:

-INDIGO-01000000002D

2 1 0 0 0 0 0 0 0 0999 V2000
9.3843 -4.2500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
10.2507 -3.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 4 0 0 0 0
1 2 5 0 0 0 0
M END

Properties:
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11 changes: 11 additions & 0 deletions core/indigo-core/molecule/CDXCommons.h
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Expand Up @@ -456,6 +456,17 @@ namespace indigo
{kCDXBondDisplay_Dot, "Dot"},
{kCDXBondDisplay_DashDot, "DashDot"}};

static const std::unordered_map<int, std::pair<int, bool>> display_to_direction = {{kCDXBondDisplay_WedgedHashBegin, {BOND_DOWN, false}},
{kCDXBondDisplay_WedgedHashEnd, {BOND_DOWN, true}},
{kCDXBondDisplay_Hash, {BOND_DOWN, false}},
{kCDXBondDisplay_Dash, {BOND_DOWN, false}},
{kCDXBondDisplay_WedgeBegin, {BOND_UP, false}},
{kCDXBondDisplay_WedgeEnd, {BOND_UP, true}},
{kCDXBondDisplay_HollowWedgeBegin, {BOND_UP, false}},
{kCDXBondDisplay_HollowWedgeEnd, {BOND_UP, true}},
{kCDXBondDisplay_Bold, {BOND_UP, false}},
{kCDXBondDisplay_Wavy, {BOND_EITHER, false}}};

const std::unordered_map<std::string, EnhancedStereoType> kCDXEnhancedStereoStrToID = {{"Unspecified", EnhancedStereoType::UNSPECIFIED},
{"None", EnhancedStereoType::NONE},
{"Absolute", EnhancedStereoType::ABSOLUTE},
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4 changes: 3 additions & 1 deletion core/indigo-core/molecule/molecule_cdxml_loader.h
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Expand Up @@ -159,14 +159,16 @@ namespace indigo

struct CdxmlBond
{
CdxmlBond() : order(1), stereo(0), dir(0), topology(0), reaction_center(0), swap_bond(false)
CdxmlBond() : order(1), stereo(0), dir(0), display(0), display2(0), topology(0), reaction_center(0), swap_bond(false)
{
}
AutoInt id;
std::pair<AutoInt, AutoInt> be;
AutoInt order;
AutoInt stereo;
AutoInt dir;
AutoInt display;
AutoInt display2;
AutoInt topology;
AutoInt reaction_center;
bool swap_bond;
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53 changes: 33 additions & 20 deletions core/indigo-core/molecule/src/molecule_cdxml_loader.cpp
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Expand Up @@ -253,7 +253,8 @@ std::string CDXProperty::parseCDXINT16(int16_t val) const
return KNodeTypeIntToName.at(val);
}
break;
case kCDXProp_Bond_Display: {
case kCDXProp_Bond_Display:
case kCDXProp_Bond_Display2: {
return kCDXProp_Bond_DisplayIdToStr.at((CDXBondDisplay)val);
}
break;
Expand Down Expand Up @@ -759,12 +760,20 @@ int MoleculeCdxmlLoader::_addBond(Molecule& mol, const CdxmlBond& bond, int begi
// bond topology is allowed only for queries but queries not supported for now
// if (bond.topology > 0 && _pqmol == nullptr)
// throw Error("bond topology is allowed only for queries");
int bond_idx = _pmol != nullptr ? _pmol->addBond_Silent(begin, end, bond.order)
: _pqmol->addBond(begin, end, QueryMolecule::createQueryMoleculeBond(bond.order, bond.topology, bond.dir));
if (bond.order == BOND_DOUBLE && bond.dir == BOND_EITHER)
int order = bond.order;
int direction = bond.dir;

if (order == BOND_AROMATIC && bond.display == kCDXBondDisplay_Solid && bond.display2 == kCDXBondDisplay_Dash) // tautomeric bond
{
order = _BOND_SINGLE_OR_DOUBLE;
}

int bond_idx = _pmol != nullptr ? _pmol->addBond_Silent(begin, end, order)
: _pqmol->addBond(begin, end, QueryMolecule::createQueryMoleculeBond(order, bond.topology, direction));
if (order == BOND_DOUBLE && direction == BOND_EITHER)
mol.cis_trans.ignore(bond_idx);
else if (bond.dir > 0 && bond.order == BOND_SINGLE)
mol.setBondDirection(bond_idx, bond.dir);
else if (direction > 0 && order == BOND_SINGLE)
mol.setBondDirection(bond_idx, direction);
if (bond.reaction_center > 0)
mol.reaction_bond_reacting_center[bond_idx] = bond.reaction_center;

Expand Down Expand Up @@ -1267,26 +1276,29 @@ void MoleculeCdxmlLoader::_parseBond(CdxmlBond& bond, BaseCDXProperty& prop)

auto stereo_lambda = [&bond](const std::string& data) { bond.stereo = kCIPBondStereochemistryCharToIndex.at(data.front()); };

auto bond_dir_lambda = [&bond](const std::string& data) {
static const std::unordered_map<std::string, std::pair<int, bool>> dir_map = {{"WedgedHashBegin", {BOND_DOWN, false}},
{"WedgedHashEnd", {BOND_DOWN, true}},
{"Hash", {BOND_DOWN, false}},
{"Dash", {BOND_DOWN, false}},
{"WedgeBegin", {BOND_UP, false}},
{"WedgeEnd", {BOND_UP, true}},
{"HollowWedgeBegin", {BOND_UP, false}},
{"HollowWedgeEnd", {BOND_UP, true}},
{"Bold", {BOND_UP, false}},
{"Wavy", {BOND_EITHER, false}}};
auto disp_it = dir_map.find(data);
if (disp_it != dir_map.end())
auto bond_display_lambda = [&bond](const std::string& data) {
auto dislay_it = kCDXProp_Bond_DisplayStrToID.find(data);
if (dislay_it != kCDXProp_Bond_DisplayStrToID.end())
{
bond.display = dislay_it->second;
}
auto disp_it = display_to_direction.find(bond.display);
if (disp_it != display_to_direction.end())
{
auto& dir = disp_it->second;
bond.dir = dir.first;
bond.swap_bond = dir.second;
}
};

auto bond_display2_lambda = [&bond](const std::string& data) {
auto disp_it = kCDXProp_Bond_DisplayStrToID.find(data);
if (disp_it != kCDXProp_Bond_DisplayStrToID.end())
{
bond.display2 = disp_it->second;
}
};

auto reaction_center_lambda = [&bond](const std::string& data) {
uint8_t rxn_participation = kBondReactionParticipationNameToInt.at(data);
auto it = bond_rxn_participation_to_reaction_center.find(rxn_participation);
Expand All @@ -1303,7 +1315,8 @@ void MoleculeCdxmlLoader::_parseBond(CdxmlBond& bond, BaseCDXProperty& prop)
{"B", bond_begin_lambda},
{"E", bond_end_lambda},
{"Order", bond_order_lambda},
{"Display", bond_dir_lambda},
{"Display", bond_display_lambda},
{"Display2", bond_display2_lambda},
{"BS", stereo_lambda},
{"RxnParticipation", reaction_center_lambda},
{"Topology", topology_lambda}};
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