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Allow fragments to be grouped in cdxml (#7529)
* Allow fragments to be groups in CDXML * Add support for grouped reactants * run clang-format * Change github issue to 7528 * Add documents to the code * response to review, check grouped reactants in cdxml against rxn file * Remove unused code * Add missing file --------- Co-authored-by: Brian Kelley <bkelley@relaytx.com>
This commit is contained in:
Brian Kelley
GitHub
@@ -8,6 +8,7 @@
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// of the RDKit source tree.
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//
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#include <GraphMol/QueryOps.h>
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#include <GraphMol/ChemTransforms/ChemTransforms.h>
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#include <GraphMol/ChemReactions/Reaction.h>
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#include <GraphMol/ChemReactions/ReactionParser.h>
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#include <GraphMol/FileParsers/FileParsers.h>
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@@ -34,6 +35,17 @@ void make_query_atoms(RWMol &mol) {
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QueryOps::replaceAtomWithQueryAtom(&mol, atom);
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}
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}
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void add_template(const std::string &prop, std::map<int, ROMOL_SPTR> &templates,
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std::unique_ptr<RWMol> &mol) {
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auto reactant_idx = mol->getProp<int>(prop);
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if (templates.find(reactant_idx) != templates.end()) {
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templates[reactant_idx] =
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ROMOL_SPTR(combineMols(*templates[reactant_idx], *mol));
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} else {
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templates[reactant_idx] = ROMOL_SPTR(std::move(mol));
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}
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}
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} // namespace
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//! Parse a text stream with CDXML data into a ChemicalReaction
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@@ -46,6 +58,10 @@ CDXMLDataStreamToChemicalReactions(std::istream &inStream, bool sanitize,
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std::map<std::pair<unsigned int, unsigned int>, std::vector<unsigned int>>
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schemes;
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std::set<unsigned int> used;
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std::map<int, ROMOL_SPTR> reactant_templates;
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std::map<int, ROMOL_SPTR> product_templates;
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std::map<int, ROMOL_SPTR> agent_templates;
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for (size_t i = 0; i < mols.size(); ++i) {
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unsigned int step = 0;
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unsigned int scheme = 0;
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@@ -69,17 +85,26 @@ CDXMLDataStreamToChemicalReactions(std::istream &inStream, bool sanitize,
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if (mols[idx]->hasProp("CDX_REAGENT_ID")) {
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used.insert(idx);
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make_query_atoms(*mols[idx]);
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res->addReactantTemplate(ROMOL_SPTR(std::move(mols[idx])));
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add_template("CDX_REAGENT_ID", reactant_templates, mols[idx]);
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} else if (mols[idx]->hasProp("CDX_AGENT_ID")) {
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used.insert(idx);
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make_query_atoms(*mols[idx]);
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res->addAgentTemplate(ROMOL_SPTR(std::move(mols[idx])));
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add_template("CDX_AGENT_ID", agent_templates, mols[idx]);
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} else if (mols[idx]->hasProp("CDX_PRODUCT_ID")) {
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used.insert(idx);
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make_query_atoms(*mols[idx]);
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res->addProductTemplate(ROMOL_SPTR(std::move(mols[idx])));
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add_template("CDX_PRODUCT_ID", product_templates, mols[idx]);
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}
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}
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for (auto reactant : reactant_templates) {
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res->addReactantTemplate(reactant.second);
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}
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for (auto reactant : agent_templates) {
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res->addAgentTemplate(reactant.second);
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}
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for (auto reactant : product_templates) {
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res->addProductTemplate(reactant.second);
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}
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updateProductsStereochem(res);
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// CDXML-based reactions do not have implicit properties
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res->setImplicitPropertiesFlag(false);
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@@ -1306,6 +1306,83 @@ TEST_CASE("CDXML Parser") {
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smarts ==
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"[#6&D2:2]1:[#6&D2:3]:[#6&D2:4]:[#6&D3:1](:[#6&D2:5]:[#6&D2:6]:1)-[#17&D1].[#6&D3](-[#5&D2]-[#6&D3:7]1:[#6&D2:8]:[#6&D2:9]:[#6&D2:10]:[#6&D2:11]:[#6&D2:12]:1)(-[#8&D1])-[#8&D1]>>[#6&D2:1]1:[#6&D2:5]:[#6&D3:6](:[#6&D2:2]:[#6&D2:3]:[#6&D2:4]:1)-[#6&D3:7]1:[#6&D2:8]:[#6&D2:9]:[#6&D2:10]:[#6&D2:11]:[#6&D2:12]:1");
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}
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SECTION("Github #7528 CDXML Grouped Agents in Reactions") {
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// The failing case had fragments grouped with labels, ensure the grouped cersion and the ungrouped
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// versions have the same results
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auto fname = cdxmlbase + "github7467-grouped-fragments.cdxml";
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auto rxns = CDXMLFileToChemicalReactions(fname);
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CHECK(rxns.size() == 1);
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fname = cdxmlbase + "github7467-ungrouped-fragments.cdxml";
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auto rxns2 = CDXMLFileToChemicalReactions(fname);
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CHECK(ChemicalReactionToRxnSmarts(*rxns[0]) == ChemicalReactionToRxnSmarts(*rxns2[0]));
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// Check to see if our understanding of grouped reagents in reactions is correct
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fname = cdxmlbase + "reaction-with-grouped-templates.cdxml";
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auto rxns3 = CDXMLFileToChemicalReactions(fname);
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CHECK(rxns3.size() == 1);
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std::string rxnb = R"RXN($RXN
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Mrv2004 062120241319
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2 0
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$MOL
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Mrv2004 06212413192D
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5 5 0 0 0 0 999 V2000
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2.6221 -4.6475 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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2.6221 -5.4725 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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3.4070 -5.7274 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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3.8918 -5.0600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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3.4070 -4.3926 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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1 2 2 0 0 0 0
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2 3 1 0 0 0 0
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3 4 2 0 0 0 0
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4 5 1 0 0 0 0
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5 1 1 0 0 0 0
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M END
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$MOL
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Mrv2004 06212413192D
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11 11 0 0 0 0 999 V2000
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6.9305 -4.5100 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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6.9305 -5.3350 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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7.6450 -5.7475 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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8.3594 -5.3350 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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8.3594 -4.5100 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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7.6450 -4.0975 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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8.6171 -4.4825 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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8.6171 -5.3075 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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9.4020 -5.5624 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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9.8868 -4.8950 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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9.4020 -4.2276 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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1 2 1 0 0 0 0
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6 1 1 0 0 0 0
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2 3 1 0 0 0 0
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3 4 1 0 0 0 0
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4 5 1 0 0 0 0
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5 6 1 0 0 0 0
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7 8 2 0 0 0 0
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11 7 1 0 0 0 0
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8 9 1 0 0 0 0
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9 10 2 0 0 0 0
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10 11 1 0 0 0 0
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M END
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)RXN";
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std::unique_ptr<ChemicalReaction> rxn_mb{RxnBlockToChemicalReaction(rxnb)};
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// CDXMLToReaction is sanitized by default, this might be a mistake...
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unsigned int failed;
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RxnOps::sanitizeRxn(
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*rxn_mb, failed,
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RxnOps::SANITIZE_ADJUST_REACTANTS | RxnOps::SANITIZE_ADJUST_PRODUCTS,
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RxnOps::MatchOnlyAtRgroupsAdjustParams());
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CHECK(rxns3[0]->getNumReactantTemplates() == rxn_mb->getNumReactantTemplates());
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CHECK(ChemicalReactionToRxnSmarts(*rxns3[0]) == ChemicalReactionToRxnSmarts(*rxn_mb));
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}
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}
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TEST_CASE("Github #5785: separateAgents ignored for V3000 RXN files") {
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@@ -1800,17 +1877,26 @@ TEST_CASE("sanitizeRxnAsMols") {
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TEST_CASE("Github #7372: SMILES output option to disable dative bonds") {
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SECTION("basics") {
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auto rxn = "[C:1]-[C:2].[NH3:3]->[Fe:4]-[NH2:5]>>[C:1]=[C:2].[NH3:3]->[Fe:4]-[NH2:5]"_rxnsmarts;
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auto rxn =
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"[C:1]-[C:2].[NH3:3]->[Fe:4]-[NH2:5]>>[C:1]=[C:2].[NH3:3]->[Fe:4]-[NH2:5]"_rxnsmarts;
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REQUIRE(rxn);
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auto smi = ChemicalReactionToRxnSmiles(*rxn);
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CHECK(smi == "[CH3:1][CH3:2].[NH3:3]->[Fe:4][NH2:5]>>[CH2:1]=[CH2:2].[NH3:3]->[Fe:4][NH2:5]");
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CHECK(
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smi ==
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"[CH3:1][CH3:2].[NH3:3]->[Fe:4][NH2:5]>>[CH2:1]=[CH2:2].[NH3:3]->[Fe:4][NH2:5]");
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smi = ChemicalReactionToRxnSmarts(*rxn);
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CHECK(smi == "[C:1]-[C:2].[N&H3:3]->[#26:4]-[N&H2:5]>>[C:1]=[C:2].[N&H3:3]->[#26:4]-[N&H2:5]");
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CHECK(
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smi ==
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"[C:1]-[C:2].[N&H3:3]->[#26:4]-[N&H2:5]>>[C:1]=[C:2].[N&H3:3]->[#26:4]-[N&H2:5]");
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SmilesWriteParams ps;
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ps.includeDativeBonds = false;
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smi = ChemicalReactionToRxnSmiles(*rxn,ps);
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CHECK(smi == "[CH3:1][CH3:2].[NH3:3][Fe:4][NH2:5]>>[CH2:1]=[CH2:2].[NH3:3][Fe:4][NH2:5]");
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smi = ChemicalReactionToRxnSmarts(*rxn,ps);
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CHECK(smi == "[C:1]-[C:2].[N&H3:3]-[#26:4]-[N&H2:5]>>[C:1]=[C:2].[N&H3:3]-[#26:4]-[N&H2:5]");
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smi = ChemicalReactionToRxnSmiles(*rxn, ps);
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CHECK(
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smi ==
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"[CH3:1][CH3:2].[NH3:3][Fe:4][NH2:5]>>[CH2:1]=[CH2:2].[NH3:3][Fe:4][NH2:5]");
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smi = ChemicalReactionToRxnSmarts(*rxn, ps);
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CHECK(
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smi ==
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"[C:1]-[C:2].[N&H3:3]-[#26:4]-[N&H2:5]>>[C:1]=[C:2].[N&H3:3]-[#26:4]-[N&H2:5]");
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}
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}
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}
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@@ -29,6 +29,7 @@ namespace RDKit {
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namespace {
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const std::string NEEDS_FUSE("CDXML_NEEDS_FUSE");
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const std::string CDXML_FRAG_ID("CDXML_FRAG_ID");
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const std::string CDXML_GROUP_ID("CDXML_GROUP_ID");
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const std::string FUSE_LABEL("CDXML_NODE_ID");
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const std::string CDX_SCHEME_ID("CDX_SCHEME_ID");
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const std::string CDX_STEP_ID("CDX_STEP_ID");
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@@ -495,28 +496,200 @@ bool parse_fragment(RWMol &mol, ptree &frag,
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return !skip_fragment;
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}
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void set_reaction_data(std::string type, std::string prop, SchemeInfo &scheme,
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const std::vector<unsigned int> &frag_ids,
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const std::map<unsigned int, size_t> &fragments,
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const std::vector<std::unique_ptr<RWMol>> &mols) {
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void set_reaction_data(
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std::string type, std::string prop, SchemeInfo &scheme,
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const std::vector<unsigned int> &frag_ids,
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const std::map<unsigned int, size_t> &fragments,
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std::map<unsigned int, std::vector<int>> &grouped_fragments,
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const std::vector<std::unique_ptr<RWMol>> &mols) {
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unsigned int reagent_idx = 0;
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for (auto idx : frag_ids) {
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auto iter = fragments.find(idx);
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if (iter == fragments.end()) {
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auto iter = grouped_fragments.find(idx);
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if (iter == grouped_fragments.end()) {
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BOOST_LOG(rdWarningLog)
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<< "CDXMLParser: Schema " << scheme.scheme_id << " step "
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<< scheme.step_id << " " << type << " fragment " << idx
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<< scheme.step_id << " " << type << " reaction fragment " << idx
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<< " not found in document." << std::endl;
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continue;
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}
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if (iter->second >= mols.size()) {
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// shouldn't get here
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continue;
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for (auto reaction_fragment_id : iter->second) {
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auto fragment = fragments.find(reaction_fragment_id);
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if (fragment == fragments.end()) {
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BOOST_LOG(rdWarningLog)
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<< "CDXMLParser: Schema " << scheme.scheme_id << " step "
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<< scheme.step_id << " " << type << " fragment " << idx
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<< " not found in document." << std::endl;
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continue;
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}
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auto &mol = mols[fragment->second];
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mol->setProp(CDX_SCHEME_ID, scheme.scheme_id);
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mol->setProp(CDX_STEP_ID, scheme.step_id);
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mol->setProp(prop, reagent_idx);
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}
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reagent_idx += 1;
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}
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}
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// The parsing of fragments needed to be moved to a recursive function since they may be
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// embedded further in the documentation, i.e. a group may hold multiple fragments
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//
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// Additionally, a grouped_fragments map is included to group fragments together for the
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// purposes of reactions.
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//
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// Ungrouped fragments will end up as vectors of size 1 in the grouped_fragement list.
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// The reaction schemes in the CDXML docs appear to use the fragment id for ungrouped
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// fragments and the grouped id for grouped fragments, so the grouped_fragments
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// holds both for ease of bookkeeping.
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template <class T>
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void visit_children(T &node, std::map<unsigned int, Atom *> &ids,
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std::vector<std::unique_ptr<RWMol>> &mols, // All molecules found in the doc
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std::map<unsigned int, size_t> &fragment_lookup, // fragment.id->molecule index
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std::map<unsigned int, std::vector<int>> &grouped_fragments, //grouped.id -> [fragment.id]
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std::vector<SchemeInfo> &schemes, // reaction schemes found
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int &missing_frag_id, // if we don't have a fragment id, start at -1 and decrement
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double bondLength, // bond length of the document for assigning coordinates
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const v2::CDXMLParser::CDXMLParserParams ¶ms, // parser parameters
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int group_id = -1) { // current group id for this set of subnodes
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MolzipParams molzip_params;
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molzip_params.label = MolzipLabel::AtomProperty;
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molzip_params.atomProperty = FUSE_LABEL;
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molzip_params.enforceValenceRules = false;
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for (auto &frag : node.second) {
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if (frag.first == "fragment") { // chemical matter
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std::unique_ptr<RWMol> mol = std::make_unique<RWMol>();
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if (!parse_fragment(*mol, frag.second, ids, missing_frag_id)) {
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continue;
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}
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unsigned int frag_id = mol->getProp<int>(CDXML_FRAG_ID);
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fragment_lookup[frag_id] = mols.size();
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if (group_id != -1) {
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grouped_fragments[group_id].push_back(frag_id);
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} else {
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grouped_fragments[frag_id].push_back(frag_id);
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}
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if (mol->hasProp(NEEDS_FUSE)) {
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mol->clearProp(NEEDS_FUSE);
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std::unique_ptr<ROMol> fused;
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try {
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fused = molzip(*mol, molzip_params);
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} catch (Invar::Invariant &) {
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BOOST_LOG(rdWarningLog) << "Failed fusion of fragment skipping... "
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<< frag_id << std::endl;
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// perhaps have an option to extract all fragments?
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// mols.push_back(std::move(mol));
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continue;
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}
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fused->setProp<int>(CDXML_FRAG_ID, static_cast<int>(frag_id));
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mols.emplace_back(dynamic_cast<RWMol *>(fused.release()));
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} else {
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mols.push_back(std::move(mol));
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}
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RWMol *res = mols.back().get();
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auto conf = std::make_unique<Conformer>(res->getNumAtoms());
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conf->set3D(false);
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bool hasConf = false;
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for (auto &atm : res->atoms()) {
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RDGeom::Point3D p{0.0, 0.0, 0.0};
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if (atm->hasProp(CDX_ATOM_POS)) {
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hasConf = true;
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const std::vector<double> coord =
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atm->getProp<std::vector<double>>(CDX_ATOM_POS);
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if (coord.size() == 2) {
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p.x = coord[0];
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p.y = -1 * coord[1]; // CDXML uses an inverted coordinate
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// system, so we need to reverse that
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p.z = 0.0;
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}
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}
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conf->setAtomPos(atm->getIdx(), p);
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atm->clearProp(CDX_ATOM_POS);
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}
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if (hasConf) {
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scaleBonds(*res, *conf, RDKIT_DEPICT_BONDLENGTH, bondLength);
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auto confidx = res->addConformer(conf.release());
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DetectAtomStereoChemistry(*res, &res->getConformer(confidx));
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Atropisomers::detectAtropisomerChirality(*res,
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&res->getConformer(confidx));
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} else { // no Conformer
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Atropisomers::detectAtropisomerChirality(*res, nullptr);
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}
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// now that atom stereochem has been perceived, the wedging
|
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// information is no longer needed, so we clear
|
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// single bond dir flags:
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MolOps::clearSingleBondDirFlags(*res);
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if (params.sanitize) {
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try {
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if (params.removeHs) {
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// Bond stereo detection must happen before H removal, or
|
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// else we might be removing stereogenic H atoms in double
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// bonds (e.g. imines). But before we run stereo detection,
|
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// we need to run mol cleanup so don't have trouble with
|
||||
// e.g. nitro groups. Sadly, this a;; means we will find
|
||||
// run both cleanup and ring finding twice (a fast find
|
||||
// rings in bond stereo detection, and another in
|
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// sanitization's SSSR symmetrization).
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unsigned int failedOp = 0;
|
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MolOps::sanitizeMol(*res, failedOp, MolOps::SANITIZE_CLEANUP);
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MolOps::detectBondStereochemistry(*res);
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MolOps::removeHs(*res, false, false);
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} else {
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MolOps::sanitizeMol(*res);
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MolOps::detectBondStereochemistry(*res);
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}
|
||||
} catch (...) {
|
||||
BOOST_LOG(rdWarningLog)
|
||||
<< "CDXMLParser: failed sanitizing skipping fragment " << frag_id
|
||||
<< std::endl;
|
||||
mols.pop_back();
|
||||
continue;
|
||||
}
|
||||
MolOps::assignStereochemistry(*res, true, true, true);
|
||||
} else {
|
||||
MolOps::detectBondStereochemistry(*res);
|
||||
}
|
||||
} else if (frag.first == "scheme") { // get the reaction info
|
||||
int scheme_id = frag.second.template get<int>("<xmlattr>.id", -1);
|
||||
for (auto &node : frag.second) {
|
||||
if (node.first == "step") {
|
||||
auto step_id = node.second.template get<int>("<xmlattr>.id", -1);
|
||||
SchemeInfo scheme;
|
||||
scheme.scheme_id = scheme_id;
|
||||
scheme.step_id = step_id;
|
||||
for (auto &attrib : node.second.get_child("<xmlattr>")) {
|
||||
if (attrib.first == "ReactionStepProducts") {
|
||||
scheme.ReactionStepProducts =
|
||||
to_vec<unsigned int>(attrib.second.data());
|
||||
} else if (attrib.first == "ReactionStepReactants") {
|
||||
scheme.ReactionStepReactants =
|
||||
to_vec<unsigned int>(attrib.second.data());
|
||||
} else if (attrib.first == "ReactionStepObjectsAboveArrow") {
|
||||
scheme.ReactionStepObjectsAboveArrow =
|
||||
to_vec<unsigned int>(attrib.second.data());
|
||||
} else if (attrib.first == "ReactionStepObjectsBelowArrow") {
|
||||
scheme.ReactionStepObjectsBelowArrow =
|
||||
to_vec<unsigned int>(attrib.second.data());
|
||||
} else if (attrib.first == "ReactionStepAtomMap") {
|
||||
scheme.ReactionStepAtomMap =
|
||||
to_vec<unsigned int>(attrib.second.data());
|
||||
}
|
||||
}
|
||||
schemes.push_back(std::move(scheme));
|
||||
}
|
||||
}
|
||||
} else {
|
||||
if (frag.first == "group") {
|
||||
group_id = frag.second.template get<int>("<xmlattr>.id");
|
||||
}
|
||||
visit_children(frag, ids, mols, fragment_lookup, grouped_fragments,
|
||||
schemes, missing_frag_id, bondLength, params, group_id);
|
||||
}
|
||||
auto &mol = mols[iter->second];
|
||||
mol->setProp(CDX_SCHEME_ID, scheme.scheme_id);
|
||||
mol->setProp(CDX_STEP_ID, scheme.step_id);
|
||||
mol->setProp(prop, reagent_idx++);
|
||||
}
|
||||
}
|
||||
} // namespace
|
||||
@@ -541,151 +714,20 @@ std::vector<std::unique_ptr<RWMol>> MolsFromCDXMLDataStream(
|
||||
|
||||
throw FileParseException(e.what());
|
||||
}
|
||||
std::map<unsigned int, Atom *> ids;
|
||||
std::vector<std::unique_ptr<RWMol>> mols;
|
||||
std::map<unsigned int, size_t> fragment_lookup;
|
||||
std::vector<SchemeInfo> schemes;
|
||||
std::map<unsigned int, Atom *> ids; // atom.id to atom in fragment (used for linkages)
|
||||
std::vector<std::unique_ptr<RWMol>> mols; // All molecules found in the doc
|
||||
std::map<unsigned int, size_t> fragment_lookup; // fragment.id->molecule index
|
||||
std::map<unsigned int, std::vector<int>> grouped_fragments; //grouped.id -> [fragment.id]
|
||||
std::vector<SchemeInfo> schemes; // reaction schemes found
|
||||
|
||||
MolzipParams molzip_params;
|
||||
molzip_params.label = MolzipLabel::AtomProperty;
|
||||
molzip_params.atomProperty = FUSE_LABEL;
|
||||
molzip_params.enforceValenceRules = false;
|
||||
int missing_frag_id = -1;
|
||||
for (auto &cdxml : pt) {
|
||||
if (cdxml.first == "CDXML") {
|
||||
double bondLength = cdxml.second.get<double>("<xmlattr>.BondLength");
|
||||
for (auto &node : cdxml.second) {
|
||||
if (node.first == "page") {
|
||||
for (auto &frag : node.second) {
|
||||
if (frag.first == "fragment") { // chemical matter
|
||||
std::unique_ptr<RWMol> mol = std::make_unique<RWMol>();
|
||||
if (!parse_fragment(*mol, frag.second, ids, missing_frag_id)) {
|
||||
continue;
|
||||
}
|
||||
unsigned int frag_id = mol->getProp<int>(CDXML_FRAG_ID);
|
||||
fragment_lookup[frag_id] = mols.size();
|
||||
if (mol->hasProp(NEEDS_FUSE)) {
|
||||
mol->clearProp(NEEDS_FUSE);
|
||||
std::unique_ptr<ROMol> fused;
|
||||
try {
|
||||
fused = molzip(*mol, molzip_params);
|
||||
} catch (Invar::Invariant &) {
|
||||
BOOST_LOG(rdWarningLog)
|
||||
<< "Failed fusion of fragment skipping... " << frag_id
|
||||
<< std::endl;
|
||||
// perhaps have an option to extract all fragments?
|
||||
// mols.push_back(std::move(mol));
|
||||
continue;
|
||||
}
|
||||
fused->setProp<int>(CDXML_FRAG_ID, static_cast<int>(frag_id));
|
||||
mols.emplace_back(dynamic_cast<RWMol *>(fused.release()));
|
||||
} else {
|
||||
mols.push_back(std::move(mol));
|
||||
}
|
||||
RWMol *res = mols.back().get();
|
||||
auto conf = std::make_unique<Conformer>(res->getNumAtoms());
|
||||
conf->set3D(false);
|
||||
|
||||
bool hasConf = false;
|
||||
for (auto &atm : res->atoms()) {
|
||||
RDGeom::Point3D p{0.0, 0.0, 0.0};
|
||||
|
||||
if (atm->hasProp(CDX_ATOM_POS)) {
|
||||
hasConf = true;
|
||||
const std::vector<double> coord =
|
||||
atm->getProp<std::vector<double>>(CDX_ATOM_POS);
|
||||
|
||||
if (coord.size() == 2) {
|
||||
p.x = coord[0];
|
||||
p.y = -1 * coord[1]; // CDXML uses an inverted coordinate
|
||||
// system, so we need to reverse that
|
||||
p.z = 0.0;
|
||||
}
|
||||
}
|
||||
conf->setAtomPos(atm->getIdx(), p);
|
||||
atm->clearProp(CDX_ATOM_POS);
|
||||
}
|
||||
|
||||
if (hasConf) {
|
||||
scaleBonds(*res, *conf, RDKIT_DEPICT_BONDLENGTH, bondLength);
|
||||
auto confidx = res->addConformer(conf.release());
|
||||
DetectAtomStereoChemistry(*res, &res->getConformer(confidx));
|
||||
|
||||
Atropisomers::detectAtropisomerChirality(
|
||||
*res, &res->getConformer(confidx));
|
||||
} else { // no Conformer
|
||||
Atropisomers::detectAtropisomerChirality(*res, nullptr);
|
||||
}
|
||||
|
||||
// now that atom stereochem has been perceived, the wedging
|
||||
// information is no longer needed, so we clear
|
||||
// single bond dir flags:
|
||||
MolOps::clearSingleBondDirFlags(*res);
|
||||
|
||||
if (params.sanitize) {
|
||||
try {
|
||||
if (params.removeHs) {
|
||||
// Bond stereo detection must happen before H removal, or
|
||||
// else we might be removing stereogenic H atoms in double
|
||||
// bonds (e.g. imines). But before we run stereo detection,
|
||||
// we need to run mol cleanup so don't have trouble with
|
||||
// e.g. nitro groups. Sadly, this a;; means we will find
|
||||
// run both cleanup and ring finding twice (a fast find
|
||||
// rings in bond stereo detection, and another in
|
||||
// sanitization's SSSR symmetrization).
|
||||
unsigned int failedOp = 0;
|
||||
MolOps::sanitizeMol(*res, failedOp,
|
||||
MolOps::SANITIZE_CLEANUP);
|
||||
MolOps::detectBondStereochemistry(*res);
|
||||
MolOps::removeHs(*res, false, false);
|
||||
} else {
|
||||
MolOps::sanitizeMol(*res);
|
||||
MolOps::detectBondStereochemistry(*res);
|
||||
}
|
||||
} catch (...) {
|
||||
BOOST_LOG(rdWarningLog)
|
||||
<< "CDXMLParser: failed sanitizing skipping fragment "
|
||||
<< frag_id << std::endl;
|
||||
mols.pop_back();
|
||||
continue;
|
||||
}
|
||||
MolOps::assignStereochemistry(*res, true, true, true);
|
||||
} else {
|
||||
MolOps::detectBondStereochemistry(*res);
|
||||
}
|
||||
} else if (frag.first == "scheme") { // get the reaction info
|
||||
int scheme_id = frag.second.get<int>("<xmlattr>.id", -1);
|
||||
for (auto &node : frag.second) {
|
||||
if (node.first == "step") {
|
||||
auto step_id = node.second.get<int>("<xmlattr>.id", -1);
|
||||
SchemeInfo scheme;
|
||||
scheme.scheme_id = scheme_id;
|
||||
scheme.step_id = step_id;
|
||||
for (auto &attrib : node.second.get_child("<xmlattr>")) {
|
||||
if (attrib.first == "ReactionStepProducts") {
|
||||
scheme.ReactionStepProducts =
|
||||
to_vec<unsigned int>(attrib.second.data());
|
||||
} else if (attrib.first == "ReactionStepReactants") {
|
||||
scheme.ReactionStepReactants =
|
||||
to_vec<unsigned int>(attrib.second.data());
|
||||
} else if (attrib.first ==
|
||||
"ReactionStepObjectsAboveArrow") {
|
||||
scheme.ReactionStepObjectsAboveArrow =
|
||||
to_vec<unsigned int>(attrib.second.data());
|
||||
} else if (attrib.first ==
|
||||
"ReactionStepObjectsBelowArrow") {
|
||||
scheme.ReactionStepObjectsBelowArrow =
|
||||
to_vec<unsigned int>(attrib.second.data());
|
||||
} else if (attrib.first == "ReactionStepAtomMap") {
|
||||
scheme.ReactionStepAtomMap =
|
||||
to_vec<unsigned int>(attrib.second.data());
|
||||
}
|
||||
}
|
||||
schemes.push_back(std::move(scheme));
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
visit_children(node, ids, mols, fragment_lookup, grouped_fragments,
|
||||
schemes, missing_frag_id, bondLength, params);
|
||||
}
|
||||
}
|
||||
}
|
||||
@@ -708,15 +750,17 @@ std::vector<std::unique_ptr<RWMol>> MolsFromCDXMLDataStream(
|
||||
for (auto &scheme : schemes) {
|
||||
// Set the molecule properties
|
||||
set_reaction_data("ReactionStepReactants", CDX_REAGENT_ID, scheme,
|
||||
scheme.ReactionStepReactants, fragments, mols);
|
||||
scheme.ReactionStepReactants, fragments,
|
||||
grouped_fragments, mols);
|
||||
set_reaction_data("ReactionStepProducts", CDX_PRODUCT_ID, scheme,
|
||||
scheme.ReactionStepProducts, fragments, mols);
|
||||
scheme.ReactionStepProducts, fragments,
|
||||
grouped_fragments, mols);
|
||||
auto agents = scheme.ReactionStepObjectsAboveArrow;
|
||||
agents.insert(agents.end(),
|
||||
scheme.ReactionStepObjectsBelowArrow.begin(),
|
||||
scheme.ReactionStepObjectsBelowArrow.end());
|
||||
set_reaction_data("ReactionStepAgents", CDX_AGENT_ID, scheme, agents,
|
||||
fragments, mols);
|
||||
fragments, grouped_fragments, mols);
|
||||
// Set the Atom Maps
|
||||
int sz = scheme.ReactionStepAtomMap.size();
|
||||
if (sz % 2) {
|
||||
|
||||
@@ -40,7 +40,6 @@ void check_smiles_and_roundtrip(const RWMol &m, const std::string &expected) {
|
||||
TEST_CASE("CDXML") {
|
||||
std::string cdxmlbase =
|
||||
std::string(getenv("RDBASE")) + "/Code/GraphMol/test_data/CDXML/";
|
||||
|
||||
SECTION("SIMPLE") {
|
||||
std::string cdxml1 = R"(<?xml version="1.0" encoding="UTF-8" ?>
|
||||
<!DOCTYPE CDXML SYSTEM "http://www.cambridgesoft.com/xml/cdxml.dtd" >
|
||||
@@ -423,29 +422,30 @@ TEST_CASE("CDXML") {
|
||||
}
|
||||
}
|
||||
SECTION("Queries") {
|
||||
{
|
||||
auto fname = cdxmlbase + "query-atoms.cdxml";
|
||||
|
||||
std::vector<std::string> expected = {"*c1ccccc1", "*c1ccccc1", "*c1ccccc1"};
|
||||
std::vector<std::string> expected_smarts = {
|
||||
"[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-*",
|
||||
"[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[!#1]",
|
||||
"[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[!#6&!#1]"};
|
||||
auto mols = MolsFromCDXMLFile(fname);
|
||||
CHECK(mols.size() == expected.size());
|
||||
int i = 0;
|
||||
for (auto &mol : mols) {
|
||||
CHECK(MolToSmarts(*mol) == expected_smarts[i]);
|
||||
CHECK(MolToSmiles(*mol) == expected[i++]);
|
||||
}
|
||||
}
|
||||
{
|
||||
auto fname = cdxmlbase + "anybond.cdxml";
|
||||
auto mols = MolsFromCDXMLFile(fname);
|
||||
CHECK(mols.size() == 1);
|
||||
CHECK(MolToSmiles(*mols[0]) == "C1CCC~CC1");
|
||||
CHECK(MolToSmarts(*mols[0]) == "[#6]1~[#6]-[#6]-[#6]-[#6]-[#6]-1");
|
||||
{
|
||||
auto fname = cdxmlbase + "query-atoms.cdxml";
|
||||
|
||||
std::vector<std::string> expected = {"*c1ccccc1", "*c1ccccc1",
|
||||
"*c1ccccc1"};
|
||||
std::vector<std::string> expected_smarts = {
|
||||
"[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-*",
|
||||
"[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[!#1]",
|
||||
"[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[!#6&!#1]"};
|
||||
auto mols = MolsFromCDXMLFile(fname);
|
||||
CHECK(mols.size() == expected.size());
|
||||
int i = 0;
|
||||
for (auto &mol : mols) {
|
||||
CHECK(MolToSmarts(*mol) == expected_smarts[i]);
|
||||
CHECK(MolToSmiles(*mol) == expected[i++]);
|
||||
}
|
||||
}
|
||||
{
|
||||
auto fname = cdxmlbase + "anybond.cdxml";
|
||||
auto mols = MolsFromCDXMLFile(fname);
|
||||
CHECK(mols.size() == 1);
|
||||
CHECK(MolToSmiles(*mols[0]) == "C1CCC~CC1");
|
||||
CHECK(MolToSmarts(*mols[0]) == "[#6]1~[#6]-[#6]-[#6]-[#6]-[#6]-1");
|
||||
}
|
||||
}
|
||||
SECTION("ElementList") {
|
||||
auto fname = cdxmlbase + "element-list.cdxml";
|
||||
@@ -1175,3 +1175,15 @@ TEST_CASE("Github #6887: and1 or1 in same mol") {
|
||||
"CO[C@H](C)C[C@H](Cl)C[C@H](C)Br |o1:5,o2:8,&1:2|");
|
||||
}
|
||||
}
|
||||
|
||||
TEST_CASE("Github #7528 - read fragments in groups") {
|
||||
std::string cdxmlbase =
|
||||
std::string(getenv("RDBASE")) + "/Code/GraphMol/test_data/CDXML/";
|
||||
SECTION("case 1") {
|
||||
auto fname = cdxmlbase + "github7467-grouped-fragments.cdxml";
|
||||
CDXMLParserParams params;
|
||||
params.sanitize = false;
|
||||
auto mols = MolsFromCDXMLFile(fname, params);
|
||||
REQUIRE(mols.size() == 2);
|
||||
}
|
||||
}
|
||||
|
||||
608
Code/GraphMol/test_data/CDXML/github7467-grouped-fragments.cdxml
Normal file
608
Code/GraphMol/test_data/CDXML/github7467-grouped-fragments.cdxml
Normal file
@@ -0,0 +1,608 @@
|
||||
<?xml version="1.0" encoding="UTF-8" ?>
|
||||
<!DOCTYPE CDXML SYSTEM "http://www.cambridgesoft.com/xml/cdxml.dtd" >
|
||||
<CDXML
|
||||
CreationProgram="ChemDraw 21.0.0.28"
|
||||
Name="github7467-grouped-fragments.cdxml"
|
||||
BoundingBox="0.88 69.39 453.90 168.20"
|
||||
WindowPosition="0 0"
|
||||
WindowSize="0 0"
|
||||
FractionalWidths="yes"
|
||||
InterpretChemically="yes"
|
||||
ShowAtomQuery="yes"
|
||||
ShowAtomStereo="no"
|
||||
ShowAtomEnhancedStereo="yes"
|
||||
ShowAtomNumber="no"
|
||||
ShowResidueID="no"
|
||||
ShowBondQuery="yes"
|
||||
ShowBondRxn="yes"
|
||||
ShowBondStereo="no"
|
||||
ShowTerminalCarbonLabels="no"
|
||||
ShowNonTerminalCarbonLabels="no"
|
||||
HideImplicitHydrogens="no"
|
||||
Magnification="666"
|
||||
LabelFont="58"
|
||||
LabelSize="10"
|
||||
LabelFace="96"
|
||||
CaptionFont="58"
|
||||
CaptionSize="10"
|
||||
HashSpacing="2.50"
|
||||
MarginWidth="1.60"
|
||||
LineWidth="0.60"
|
||||
BoldWidth="2"
|
||||
BondLength="14.40"
|
||||
BondSpacing="18"
|
||||
ChainAngle="120"
|
||||
LabelJustification="Auto"
|
||||
CaptionJustification="Left"
|
||||
AminoAcidTermini="HOH"
|
||||
ShowSequenceTermini="yes"
|
||||
ShowSequenceBonds="yes"
|
||||
ShowSequenceUnlinkedBranches="no"
|
||||
ResidueWrapCount="40"
|
||||
ResidueBlockCount="10"
|
||||
ResidueZigZag="yes"
|
||||
NumberResidueBlocks="no"
|
||||
PrintMargins="36 36 36 36"
|
||||
MacPrintInfo="0003000000480048000000000300024CFFF4FFF4030C02580367052803FC0002000000480048000000000300024C000100000064000000010001010100000001270F000100010000000000000000000000000002001901900000000000400000000000000000000100000000000000000000000000000000"
|
||||
ChemPropName=""
|
||||
ChemPropFormula="Chemical Formula: "
|
||||
ChemPropExactMass="Exact Mass: "
|
||||
ChemPropMolWt="Molecular Weight: "
|
||||
ChemPropMOverZ="m/z: "
|
||||
ChemPropAnalysis="Elemental Analysis: "
|
||||
ChemPropBoilingPt="Boiling Point: "
|
||||
ChemPropMeltingPt="Melting Point: "
|
||||
ChemPropCritTemp="Critical Temp: "
|
||||
ChemPropCritPres="Critical Pres: "
|
||||
ChemPropCritVol="Critical Vol: "
|
||||
ChemPropGibbs="Gibbs Energy: "
|
||||
ChemPropLogP="Log P: "
|
||||
ChemPropMR="MR: "
|
||||
ChemPropHenry="Henry's Law: "
|
||||
ChemPropEForm="Heat of Form: "
|
||||
ChemProptPSA="tPSA: "
|
||||
ChemPropID=""
|
||||
ChemPropFragmentLabel=""
|
||||
color="0"
|
||||
bgcolor="1"
|
||||
RxnAutonumberStart="1"
|
||||
RxnAutonumberConditions="no"
|
||||
RxnAutonumberStyle="Roman"
|
||||
RxnAutonumberFormat="(#)"
|
||||
><colortable>
|
||||
<color r="1" g="1" b="1"/>
|
||||
<color r="0" g="0" b="0"/>
|
||||
<color r="1" g="0" b="0"/>
|
||||
<color r="1" g="1" b="0"/>
|
||||
<color r="0" g="1" b="0"/>
|
||||
<color r="0" g="1" b="1"/>
|
||||
<color r="0" g="0" b="1"/>
|
||||
<color r="1" g="0" b="1"/>
|
||||
</colortable><fonttable>
|
||||
<font id="21" charset="x-mac-roman" name="Helvetica"/>
|
||||
<font id="58" charset="x-mac-roman" name="Arial"/>
|
||||
</fonttable><page
|
||||
id="82"
|
||||
BoundingBox="0 0 776 240"
|
||||
Width="776"
|
||||
Height="240"
|
||||
HeaderPosition="36"
|
||||
FooterPosition="36"
|
||||
PageOverlap="0"
|
||||
PrintTrimMarks="yes"
|
||||
HeightPages="1"
|
||||
WidthPages="2"
|
||||
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Reference in New Issue
Block a user