From 4c901d8d6cd5eaf0799eaf9102d4d0c0f4eb4bc2 Mon Sep 17 00:00:00 2001 From: Aliaksandr Dziarkach <18146690+AliaksandrDziarkach@users.noreply.github.com> Date: Fri, 22 Mar 2024 12:43:23 +0300 Subject: [PATCH] #1777 Some bonds don't display correctly in ChemDraw when opening a saved Ketcher CDX file. Fix bond saving. Add UT. --- .../integration/ref/formats/cdx_export.py.out | 4 + .../ref/formats/mol_to_cdxml.py.out | 16 +- .../integration/tests/formats/cdx_export.py | 1 + .../tests/formats/molecules/issue_1777.ket | 1938 +++++++++++++++++ .../tests/formats/ref/issue_1777.b64cdx | 1 + .../formats/ref/stereo_either-0020.b64cdx | 2 +- core/indigo-core/molecule/CDXCommons.h | 28 + .../molecule/src/molecule_cdxml_loader.cpp | 27 +- .../molecule/src/molecule_cdxml_saver.cpp | 52 +- .../molecule/src/molecule_json_loader.cpp | 8 +- 10 files changed, 2039 insertions(+), 38 deletions(-) create mode 100644 api/tests/integration/tests/formats/molecules/issue_1777.ket create mode 100644 api/tests/integration/tests/formats/ref/issue_1777.b64cdx diff --git a/api/tests/integration/ref/formats/cdx_export.py.out b/api/tests/integration/ref/formats/cdx_export.py.out index 1d69b29c7d..2ea2e11060 100644 --- a/api/tests/integration/ref/formats/cdx_export.py.out +++ b/api/tests/integration/ref/formats/cdx_export.py.out @@ -8,6 +8,10 @@ two_bn:success *** KET to CDX *** issue_1774:success issue_1775:success +molecule json loader: 'any' bonds are allowed only for queries +*** Try as Query *** +CDXML loader: Queries not supported +issue_1777:success agents:success *** CDXML to CDX *** AlcoholOxidation_Rxn1:success diff --git a/api/tests/integration/ref/formats/mol_to_cdxml.py.out b/api/tests/integration/ref/formats/mol_to_cdxml.py.out index 1846da5287..579260cbe5 100644 --- a/api/tests/integration/ref/formats/mol_to_cdxml.py.out +++ b/api/tests/integration/ref/formats/mol_to_cdxml.py.out @@ -374,10 +374,10 @@ stereo_either-0020.mol - - - - + + + + @@ -386,14 +386,14 @@ stereo_either-0020.mol - + - - - + + + diff --git a/api/tests/integration/tests/formats/cdx_export.py b/api/tests/integration/tests/formats/cdx_export.py index a17c4ce851..9b67ccb072 100644 --- a/api/tests/integration/tests/formats/cdx_export.py +++ b/api/tests/integration/tests/formats/cdx_export.py @@ -72,6 +72,7 @@ def test_file(filename, suffix=".mol"): print("*** KET to CDX ***") test_file("issue_1774", ".ket") test_file("issue_1775", ".ket") +test_file("issue_1777", ".ket") root = joinPathPy("reactions/", __file__) files = ["agents"] diff --git a/api/tests/integration/tests/formats/molecules/issue_1777.ket b/api/tests/integration/tests/formats/molecules/issue_1777.ket new file mode 100644 index 0000000000..79c014963f --- /dev/null +++ b/api/tests/integration/tests/formats/molecules/issue_1777.ket @@ -0,0 +1,1938 @@ +{ + "root": { + "nodes": [ + { + "$ref": "mol0" + }, + { + "$ref": "mol1" + }, + { + "$ref": "mol2" + }, + { + "$ref": "mol3" + }, + { + "$ref": "mol4" + }, + { + "$ref": "mol5" + }, + { + "$ref": "mol6" + }, + { + "$ref": "mol7" + }, + { + "$ref": "mol8" + }, + { + "$ref": "mol9" + }, + { + "$ref": "mol10" + }, + { + "$ref": "mol11" + }, + { + "$ref": "mol12" + }, + { + "$ref": "mol13" + }, + { + "$ref": "mol14" + }, + { + "$ref": "mol15" + }, + { + "$ref": "mol16" + }, + { + "$ref": 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\ No newline at end of file diff --git a/core/indigo-core/molecule/CDXCommons.h b/core/indigo-core/molecule/CDXCommons.h index 9ccad8b4f0..ab54065664 100644 --- a/core/indigo-core/molecule/CDXCommons.h +++ b/core/indigo-core/molecule/CDXCommons.h @@ -2,6 +2,7 @@ #define _H_CDXCommons #include "CDXConstants.h" +#include "reaction/reaction.h" #include #include #include @@ -1278,6 +1279,33 @@ namespace indigo {kCDXBondTopology_Ring, "Ring"}, {kCDXBondTopology_Chain, "Chain"}, {kCDXBondTopology_RingOrChain, "RingOrChain"}}; + + static const std::unordered_map bond_rxn_participation_to_reaction_center = { + {kCDXBondReactionParticipation_Unspecified, RC_UNMARKED}, + {kCDXBondReactionParticipation_ReactionCenter, RC_CENTER}, + {kCDXBondReactionParticipation_MakeOrBreak, RC_MADE_OR_BROKEN}, + {kCDXBondReactionParticipation_ChangeType, RC_ORDER_CHANGED}, + {kCDXBondReactionParticipation_MakeAndChange, RC_MADE_OR_BROKEN | RC_ORDER_CHANGED}, + {kCDXBondReactionParticipation_NotReactionCenter, RC_NOT_CENTER}, + {kCDXBondReactionParticipation_NoChange, RC_UNCHANGED}, + {kCDXBondReactionParticipation_Unmapped, RC_UNMARKED}}; + static const std::unordered_map reaction_center_to_bond_rxn_participation = { + {RC_UNMARKED, kCDXBondReactionParticipation_Unspecified}, + {RC_CENTER, kCDXBondReactionParticipation_ReactionCenter}, + {RC_MADE_OR_BROKEN, kCDXBondReactionParticipation_MakeOrBreak}, + {RC_ORDER_CHANGED, kCDXBondReactionParticipation_ChangeType}, + {RC_MADE_OR_BROKEN | RC_ORDER_CHANGED, kCDXBondReactionParticipation_MakeAndChange}, + {RC_NOT_CENTER, kCDXBondReactionParticipation_NotReactionCenter}, + {RC_UNCHANGED, kCDXBondReactionParticipation_NoChange}, + {RC_UNMARKED, kCDXBondReactionParticipation_Unmapped}}; + + static const std::unordered_map cdx_topology_to_topology = {{kCDXBondTopology_Unspecified, TOPOLOGY_ANY}, + {kCDXBondTopology_Ring, TOPOLOGY_RING}, + {kCDXBondTopology_Chain, TOPOLOGY_CHAIN}, + {kCDXBondTopology_RingOrChain, TOPOLOGY_ANY}}; + static const std::unordered_map topology_to_cdx_topology = { + {TOPOLOGY_ANY, kCDXBondTopology_Unspecified}, {TOPOLOGY_RING, kCDXBondTopology_Ring}, {TOPOLOGY_CHAIN, kCDXBondTopology_Chain}}; + } #ifdef _WIN32 diff --git a/core/indigo-core/molecule/src/molecule_cdxml_loader.cpp b/core/indigo-core/molecule/src/molecule_cdxml_loader.cpp index 7690721cd8..df5fdd12f6 100644 --- a/core/indigo-core/molecule/src/molecule_cdxml_loader.cpp +++ b/core/indigo-core/molecule/src/molecule_cdxml_loader.cpp @@ -756,14 +756,18 @@ void MoleculeCdxmlLoader::_updateConnection(const CdxmlNode& node, int atom_idx) int MoleculeCdxmlLoader::_addBond(Molecule& mol, const CdxmlBond& bond, int begin, int end) { - int bond_idx = mol.addBond_Silent(begin, end, bond.order); + // 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) mol.cis_trans.ignore(bond_idx); else if (bond.dir > 0) mol.setBondDirection(bond_idx, bond.dir); if (bond.reaction_center > 0) mol.reaction_bond_reacting_center[bond_idx] = bond.reaction_center; - // bond topology is allowed only for queries but queries not supported for now + return bond_idx; } @@ -1285,27 +1289,14 @@ void MoleculeCdxmlLoader::_parseBond(CdxmlBond& bond, BaseCDXProperty& prop) auto reaction_center_lambda = [&bond](const std::string& data) { uint8_t rxn_participation = kBondReactionParticipationNameToInt.at(data); - static const std::unordered_map bond_rxn_participation_map = { - {kCDXBondReactionParticipation_Unspecified, RC_UNMARKED}, - {kCDXBondReactionParticipation_ReactionCenter, RC_CENTER}, - {kCDXBondReactionParticipation_MakeOrBreak, RC_MADE_OR_BROKEN}, - {kCDXBondReactionParticipation_ChangeType, RC_ORDER_CHANGED}, - {kCDXBondReactionParticipation_MakeAndChange, RC_MADE_OR_BROKEN | RC_ORDER_CHANGED}, - {kCDXBondReactionParticipation_NotReactionCenter, RC_NOT_CENTER}, - {kCDXBondReactionParticipation_NoChange, RC_UNCHANGED}, - {kCDXBondReactionParticipation_Unmapped, RC_UNMARKED}}; - auto it = bond_rxn_participation_map.find(rxn_participation); - if (it != bond_rxn_participation_map.end()) + auto it = bond_rxn_participation_to_reaction_center.find(rxn_participation); + if (it != bond_rxn_participation_to_reaction_center.end()) bond.reaction_center = it->second; }; auto topology_lambda = [&bond](const std::string& data) { uint8_t topology = kBondTopologyNameToInt.at(data); - static const std::unordered_map topology_map = {{kCDXBondTopology_Unspecified, TOPOLOGY_ANY}, - {kCDXBondTopology_Ring, TOPOLOGY_RING}, - {kCDXBondTopology_Chain, TOPOLOGY_CHAIN}, - {kCDXBondTopology_RingOrChain, TOPOLOGY_ANY}}; - bond.topology = topology_map.at(topology); + bond.topology = cdx_topology_to_topology.at(topology); }; std::unordered_map> bond_dispatcher = {{"id", id_lambda}, diff --git a/core/indigo-core/molecule/src/molecule_cdxml_saver.cpp b/core/indigo-core/molecule/src/molecule_cdxml_saver.cpp index 227dcd8924..ac64b6df2a 100644 --- a/core/indigo-core/molecule/src/molecule_cdxml_saver.cpp +++ b/core/indigo-core/molecule/src/molecule_cdxml_saver.cpp @@ -957,44 +957,57 @@ void MoleculeCdxmlSaver::addBondToFragment(BaseMolecule& mol, tinyxml2::XMLEleme bond->SetAttribute("E", _atoms_ids[edge.end]); int order = mol.getBondOrder(bond_idx); + if (order < 0 && mol.isQueryMolecule()) + order = QueryMolecule::getQueryBondType(mol.asQueryMolecule().getBond(bond_idx)); + + int dir = mol.getBondDirection(bond_idx); + + if (mol.cis_trans.isIgnored(bond_idx)) + { + order = BOND_DOUBLE; + dir = BOND_EITHER; + } if (order == BOND_DOUBLE || order == BOND_TRIPLE) bond->SetAttribute("Order", order); else if (order == BOND_AROMATIC) { - bond->SetAttribute("Order", "1.5"); - bond->SetAttribute("Display", "Dash"); - bond->SetAttribute("Display2", "Dash"); + bond->SetAttribute("Order", kBondOrderIntToStr.at(kCDXBondOrder_OneHalf).c_str()); + bond->SetAttribute("Display", kCDXProp_Bond_DisplayIdToStr.at(kCDXBondDisplay_Dash).c_str()); + bond->SetAttribute("Display2", kCDXProp_Bond_DisplayIdToStr.at(kCDXBondDisplay_Dash).c_str()); } else if (order == _BOND_SINGLE_OR_DOUBLE) { - bond->SetAttribute("Order", "1 2"); + bond->SetAttribute("Order", (kBondOrderIntToStr.at(kCDXBondOrder_Single) + " " + kBondOrderIntToStr.at(kCDXBondOrder_Double)).c_str()); } else if (order == _BOND_SINGLE_OR_AROMATIC) { - bond->SetAttribute("Order", "1 1.5"); + bond->SetAttribute("Order", (kBondOrderIntToStr.at(kCDXBondOrder_Single) + " " + kBondOrderIntToStr.at(kCDXBondOrder_OneHalf)).c_str()); } else if (order == _BOND_DOUBLE_OR_AROMATIC) { - bond->SetAttribute("Order", "1.5 2"); + bond->SetAttribute("Order", (kBondOrderIntToStr.at(kCDXBondOrder_Double) + " " + kBondOrderIntToStr.at(kCDXBondOrder_OneHalf)).c_str()); + } + else if (order == _BOND_ANY) + { + bond->SetAttribute("Order", kBondOrderIntToStr.at(kCDXBondOrder_Any).c_str()); } else if (order == _BOND_COORDINATION) { - bond->SetAttribute("Order", "dative"); + bond->SetAttribute("Order", kBondOrderIntToStr.at(kCDXBondOrder_Dative).c_str()); } else if (order == _BOND_HYDROGEN) { - bond->SetAttribute("Order", "hydrogen"); + bond->SetAttribute("Order", kBondOrderIntToStr.at(kCDXBondOrder_Hydrogen).c_str()); } else ; // Do not write single bond order - int dir = mol.getBondDirection(bond_idx); int parity = mol.cis_trans.getParity(bond_idx); if (mol.have_xyz && (dir == BOND_UP || dir == BOND_DOWN)) { - bond->SetAttribute("Display", (dir == BOND_UP) ? "WedgeBegin" : "WedgedHashBegin"); + bond->SetAttribute("Display", kCDXProp_Bond_DisplayIdToStr.at((dir == BOND_UP) ? kCDXBondDisplay_WedgeBegin : kCDXBondDisplay_WedgedHashBegin).c_str()); } else if (!mol.have_xyz && parity != 0) { @@ -1013,6 +1026,25 @@ void MoleculeCdxmlSaver::addBondToFragment(BaseMolecule& mol, tinyxml2::XMLEleme buf.push(0); bond->SetAttribute("BondCircularOrdering", buf.ptr()); } + else if (dir == BOND_EITHER) + { + bond->SetAttribute("Display", kCDXProp_Bond_DisplayIdToStr.at(kCDXBondDisplay_Wavy).c_str()); + } + + if (mol.reaction_bond_reacting_center[bond_idx] != RC_UNMARKED) + { + auto it = reaction_center_to_bond_rxn_participation.find(mol.reaction_bond_reacting_center[bond_idx]); + if (it != reaction_center_to_bond_rxn_participation.end()) + bond->SetAttribute("RxnParticipation", it->second); + } + + if (mol.isQueryMolecule()) + { + int topology = VALUE_UNKNOWN; + mol.asQueryMolecule().getBond(bond_idx).sureValue(QueryMolecule::BOND_TOPOLOGY, topology); + if (topology > 0) + bond->SetAttribute("Topology", topology_to_cdx_topology.at(topology)); + } } void MoleculeCdxmlSaver::addBondsToFragment(BaseMolecule& mol, tinyxml2::XMLElement* fragment) diff --git a/core/indigo-core/molecule/src/molecule_json_loader.cpp b/core/indigo-core/molecule/src/molecule_json_loader.cpp index 24fe6cbd12..56b01f0f38 100644 --- a/core/indigo-core/molecule/src/molecule_json_loader.cpp +++ b/core/indigo-core/molecule/src/molecule_json_loader.cpp @@ -708,6 +708,7 @@ void MoleculeJsonLoader::parseBonds(const rapidjson::Value& bonds, BaseMolecule& break; case BIOVIA_STEREO_DOUBLE_CISTRANS: mol.cis_trans.ignore(bond_idx); + mol.setBondDirection(bond_idx, BOND_EITHER); break; case BIOVIA_STEREO_ETHER: mol.setBondDirection(bond_idx, BOND_EITHER); @@ -1458,7 +1459,12 @@ void MoleculeJsonLoader::loadMolecule(BaseMolecule& mol, bool load_arrows) for (int i = 0; i < mol.edgeCount(); i++) if (mol.getBondDirection(i) == BOND_EITHER) { - if (MoleculeCisTrans::isGeomStereoBond(mol, i, 0, true)) + if (mol.cis_trans.isIgnored(i)) + { + ignore_cistrans[i] = 1; + sensible_bond_directions[i] = 1; + } + else if (MoleculeCisTrans::isGeomStereoBond(mol, i, 0, true)) { ignore_cistrans[i] = 1; sensible_bond_directions[i] = 1;