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Add support for Marvin files (#6575)
* Add support for Marvin files * And MRV lib to the Java wrapper * And MRV lib to the Java wrapper * Removed use of void * in MarvinParser.cpp and MarvinParser.h * Changes as per code review from Greg * Changes for PR review - many virtual methods * changes as per Jonathan's comments * some suggested changes * PR review changes and fixed unit tests * after merge, changes to make it run * More PR review changes * removed unneeded std::move()s · rdkit/rdkit@b4b8b9a · GitHub * More PR review changes * fix a compile error * more defensive programming * reorder * final? PR review updates * Erata --------- Co-authored-by: Tad Hurst <tad.hurst@collaborativedrug.com> Co-authored-by: greg landrum <greg.landrum@gmail.com> Co-authored-by: tadhurst-cdd <112502803+tadhurst-cdd@users.noreply.github.com>
This commit is contained in:
Jonathan Bisson
GitHub
@@ -58,6 +58,7 @@ rdkit_headers(Atom.h
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add_subdirectory(SmilesParse)
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add_subdirectory(Depictor)
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add_subdirectory(MarvinParse)
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add_subdirectory(FileParsers)
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add_subdirectory(Substruct)
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add_subdirectory(GenericGroups)
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@@ -3,8 +3,9 @@ rdkit_python_extension(rdChemReactions
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Enumerate.cpp
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rdChemReactions.cpp
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DEST Chem
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LINK_LIBRARIES
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ChemReactions )
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LINK_LIBRARIES
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MarvinParser
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ChemReactions )
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add_pytest(pyChemReactions
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${CMAKE_CURRENT_SOURCE_DIR}/testReactionWrapper.py)
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@@ -40,6 +40,7 @@
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#include <GraphMol/ChemReactions/ReactionRunner.h>
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#include <GraphMol/ChemReactions/PreprocessRxn.h>
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#include <GraphMol/ChemReactions/SanitizeRxn.h>
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#include <GraphMol/MarvinParse/MarvinParser.h>
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#include <GraphMol/Depictor/DepictUtils.h>
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#include <GraphMol/FilterCatalog/FunctionalGroupHierarchy.h>
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@@ -67,6 +68,15 @@ void rdChemicalReactionExceptionTranslator(
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}
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namespace RDKit {
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std::string pyObjectToString(python::object input) {
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python::extract<std::string> ex(input);
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if (ex.check()) {
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return ex();
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}
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std::wstring ws = python::extract<std::wstring>(input);
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return std::string(ws.begin(), ws.end());
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}
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python::object ReactionToBinaryWithProps(const ChemicalReaction &self,
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unsigned int props) {
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std::string res;
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@@ -302,6 +312,34 @@ ChemicalReaction *ReactionFromSmarts(const char *smarts, python::dict replDict,
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return res;
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}
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ChemicalReaction *ReactionFromMrvFile(const char *rxnFilename, bool sanitize,
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bool removeHs) {
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ChemicalReaction *newR = nullptr;
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try {
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newR = MrvFileToChemicalReaction(rxnFilename, sanitize, removeHs);
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} catch (RDKit::BadFileException &e) {
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PyErr_SetString(PyExc_IOError, e.what());
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throw python::error_already_set();
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} catch (RDKit::FileParseException &e) {
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BOOST_LOG(rdWarningLog) << e.what() << std::endl;
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} catch (...) {
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}
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return newR;
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}
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ChemicalReaction *ReactionFromMrvBlock(python::object imolBlock, bool sanitize,
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bool removeHs) {
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std::istringstream inStream(pyObjectToString(imolBlock));
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ChemicalReaction *newR = nullptr;
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try {
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newR = MrvDataStreamToChemicalReaction(inStream, sanitize, removeHs);
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} catch (RDKit::FileParseException &e) {
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BOOST_LOG(rdWarningLog) << e.what() << std::endl;
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} catch (...) {
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}
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return newR;
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}
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python::object GetReactingAtoms(const ChemicalReaction &self,
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bool mappedAtomsOnly) {
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python::list res;
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@@ -806,10 +844,29 @@ of the replacements argument.",
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python::arg("removeHs") = false, python::arg("strictParsing") = true),
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"construct a ChemicalReaction from a string in MDL rxn format",
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python::return_value_policy<python::manage_new_object>());
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python::def("ReactionFromMrvFile", RDKit::ReactionFromMrvFile,
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(python::arg("filename"), python::arg("sanitize") = false,
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python::arg("removeHs") = false),
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"construct a ChemicalReaction from an Marvin (mrv) rxn file",
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python::return_value_policy<python::manage_new_object>());
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python::def(
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"ReactionFromMrvBlock", RDKit::ReactionFromMrvBlock,
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(python::arg("rxnblock"), python::arg("sanitize") = false,
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python::arg("removeHs") = false),
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"construct a ChemicalReaction from a string in Marvin (mrv) format",
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python::return_value_policy<python::manage_new_object>());
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python::def("ReactionToRxnBlock", RDKit::ChemicalReactionToRxnBlock,
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(python::arg("reaction"), python::arg("separateAgents") = false,
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python::arg("forceV3000") = false),
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"construct a string in MDL rxn format for a ChemicalReaction");
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python::def(
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"ReactionToMrvBlock", RDKit::ChemicalReactionToMrvBlock,
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(python::arg("reaction")),
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"construct a string in Marvin (MRV) rxn format for a ChemicalReaction");
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python::def(
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"ReactionToV3KRxnBlock", RDKit::ChemicalReactionToV3KRxnBlock,
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(python::arg("reaction"), python::arg("separateAgents") = false),
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@@ -0,0 +1,23 @@
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RDKit 2D
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0 0 0 0 0 0 0 0 0 0999 V3000
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M V30 BEGIN CTAB
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M V30 COUNTS 6 5 0 0 0
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M V30 BEGIN ATOM
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M V30 1 C -5.167400 0.803500 0.000000 0
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M V30 2 C -4.413700 1.139100 0.000000 0
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M V30 3 N -4.413700 1.964100 0.000000 0
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M V30 4 C -3.699200 0.726600 0.000000 0
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M V30 5 C -2.874200 0.726600 0.000000 0
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M V30 6 C -1.987400 -0.087300 0.000000 0
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M V30 END ATOM
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M V30 BEGIN BOND
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M V30 1 1 1 2
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M V30 2 1 2 4
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M V30 3 2 4 5 CFG=2
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M V30 4 1 5 6 CFG=2
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M V30 5 1 2 3
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M V30 END BOND
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M V30 END CTAB
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M END
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16
Code/GraphMol/MarvinParse/CMakeLists.txt
Normal file
16
Code/GraphMol/MarvinParse/CMakeLists.txt
Normal file
@@ -0,0 +1,16 @@
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rdkit_library(MarvinParser
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MarvinParser.cpp
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MarvinWriter.cpp
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MarvinDefs.cpp
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${maesupplier}
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LINK_LIBRARIES GenericGroups Depictor GraphMol ChemReactions ${RDK_MAEPARSER_LIBS} ${regex_lib} ${link_iostreams} ${zlib_lib})
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target_compile_definitions(MarvinParser PRIVATE RDKIT_MARVINPARSER_BUILD)
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rdkit_headers(MarvinParser.h
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DEST GraphMol/MarvinParser)
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rdkit_test(testMrvToMol testMrvToMol.cpp
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LINK_LIBRARIES MarvinParser FileParsers SubstructMatch )
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4309
Code/GraphMol/MarvinParse/MarvinDefs.cpp
Normal file
4309
Code/GraphMol/MarvinParse/MarvinDefs.cpp
Normal file
File diff suppressed because it is too large
Load Diff
639
Code/GraphMol/MarvinParse/MarvinDefs.h
Normal file
639
Code/GraphMol/MarvinParse/MarvinDefs.h
Normal file
@@ -0,0 +1,639 @@
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//
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// Copyright (C) 2022-2023 Tad Hurst, Greg Landrum and other RDKit contributors
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//
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// @@ All Rights Reserved @@
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// This file is part of the RDKit.
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// The contents are covered by the terms of the BSD license
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// which is included in the file license.txt, found at the root
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// of the RDKit source tree.
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//
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// This software is based on the Chemaxon documentation for the MRV format:P
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// https://docs.chemaxon.com/display/docs/marvin-documents-mrv.md
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// and this implmentation is tested against the parsing and generation in the
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// Marvin JS sketcher: https://marvinjs-demo.chemaxon.com/latest/demo.html
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#ifndef RD_MARVINDEFS_H
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#define RD_MARVINDEFS_H
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#include <GraphMol/RDKitBase.h>
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#include <GraphMol/FileParsers/FileParsers.h>
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#include <GraphMol/FileParsers/MolSGroupParsing.h>
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#include <RDGeneral/FileParseException.h>
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#include <RDGeneral/BadFileException.h>
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#include <RDGeneral/LocaleSwitcher.h>
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#include <RDGeneral/BoostStartInclude.h>
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#include <boost/property_tree/ptree.hpp>
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#include <boost/property_tree/xml_parser.hpp>
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#include <boost/foreach.hpp>
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#include <boost/algorithm/string.hpp>
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#include <RDGeneral/BoostEndInclude.h>
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#include <float.h> // Needed for DBL_MAX on Clang
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using boost::property_tree::ptree;
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namespace RDKit {
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const std::vector<std::string> sruSgroupConnectChoices{"hh", "ht", "eu"};
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const std::vector<std::string> marvinBondOrders{"1", "2", "3", "A"};
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const std::vector<std::string> marvinQueryBondsTypes{"SD", "SA", "DA", "Any"};
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const std::vector<std::string> marvinConventionTypes{"cxn:coord"};
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const std::vector<std::string> marvinStereoDictRefTypes{"cml:W", "cml:H"};
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const std::vector<std::string> marvinStereoConventionTypes{"1", "3", "4", "6"};
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const std::vector<std::string> marvinRadicalVals{
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"monovalent", "divalent", "divalent1", "divalent3",
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"trivalent", "trivalent2", "trivalent4", "4"};
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const std::map<std::string, int> marvinRadicalToRadicalElectrons{
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{"monovalent", 1}, {"divalent", 2}, {"divalent1", 2}, {"divalent3", 2},
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{"trivalent", 3}, {"trivalent2", 3}, {"trivalent4", 3}, {"4", 4}};
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const std::map<int, std::string> radicalElectronsToMarvinRadical{
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{1, "monovalent"}, {2, "divalent"}, {3, "trivalent4"}, {4, "4"}};
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enum IsSgroupInAtomSetResult {
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SgroupInAtomSet,
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SgroupNotInAtomSet,
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SgroupBothInAndNotInAtomSet,
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};
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class MarvinWriterException : public std::runtime_error {
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public:
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explicit MarvinWriterException(std::string message)
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: std::runtime_error(message){};
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};
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class MarvinArrow {
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public:
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std::string type;
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double x1;
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double y1;
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double x2;
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double y2;
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std::string toString() const;
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ptree toPtree() const;
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};
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class MarvinPlus {
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public:
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std::string id;
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double x1;
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double y1;
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double x2;
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double y2;
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std::string toString() const;
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ptree toPtree() const;
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};
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class MarvinCondition {
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public:
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std::string id;
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std::string text;
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double x;
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double y;
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double fontScale = 0.0;
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std::string halign;
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std::string valign;
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std::string toString() const;
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ptree toPtree() const;
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};
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class MarvinAttachmentPoint {
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public:
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// <attachmentPoint atom="a7" order="1" bond="b6"/>
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std::string atom;
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std::string bond;
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std::string order;
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std::string toString() const;
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ptree toPtree() const;
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};
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class MarvinAtom {
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public:
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std::string id;
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std::string elementType;
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double x2;
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double y2;
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double x3;
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double y3;
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double z3;
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int formalCharge;
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std::string radical;
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int isotope;
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int mrvValence;
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int hydrogenCount;
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std::string mrvAlias;
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std::string mrvStereoGroup;
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int mrvMap;
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std::string sgroupRef;
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bool sGroupRefIsSuperatom; // if set, we will not change the sgroupRef - the
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// superatom really needs it
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std::string sgroupAttachmentPoint;
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int rgroupRef;
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MarvinAtom();
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MarvinAtom(const MarvinAtom &atomToCopy, std::string newId);
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~MarvinAtom() {}
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bool operator==(const MarvinAtom &rhs) const;
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bool operator==(const MarvinAtom *rhs) const;
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bool isElement() const;
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std::string toString() const;
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ptree toPtree() const;
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};
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class MarvinBondStereo {
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public:
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std::string value;
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std::string convention;
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std::string conventionValue;
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std::string dictRef;
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std::string toString() const;
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ptree toPtree() const;
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};
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class MarvinBond {
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public:
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std::string id;
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std::string atomRefs2[2];
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std::string order;
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MarvinBondStereo bondStereo;
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std::string queryType;
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std::string convention;
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MarvinBond() {}
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||||
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MarvinBond(const MarvinBond &bondToCopy, std::string newId,
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std::string atomRef1, std::string atomRef2);
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bool isEqual(const MarvinAtom &other) const;
|
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bool operator==(const MarvinAtom &rhs) const;
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const std::string getBondType() const;
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std::string toString() const;
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ptree toPtree() const;
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};
|
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|
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class MarvinRectangle {
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protected:
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RDGeom::Point3D center;
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||||
bool centerIsStale = true;
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|
||||
public:
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||||
RDGeom::Point3D upperLeft;
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RDGeom::Point3D lowerRight;
|
||||
|
||||
MarvinRectangle(double left, double right, double top, double bottom);
|
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MarvinRectangle(const RDGeom::Point3D &upperLeftInit,
|
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const RDGeom::Point3D &lowerRightInit);
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MarvinRectangle(const std::vector<MarvinAtom *> &atoms);
|
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MarvinRectangle(const std::vector<MarvinRectangle> &rects);
|
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|
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void extend(const MarvinRectangle &otherRectangle);
|
||||
|
||||
RDGeom::Point3D &getCenter();
|
||||
|
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bool overlapsVertically(const MarvinRectangle &otherRectangle) const;
|
||||
|
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bool overlapsVHorizontally(const MarvinRectangle &otherRectangle) const;
|
||||
|
||||
static bool compareRectanglesByX(MarvinRectangle &r1, MarvinRectangle &r2);
|
||||
|
||||
static bool compareRectanglesByYReverse(MarvinRectangle &r1,
|
||||
MarvinRectangle &r2);
|
||||
};
|
||||
|
||||
template <typename T>
|
||||
typename std::vector<std::unique_ptr<T>>::iterator findUniquePtr(
|
||||
std::vector<std ::unique_ptr<T>> &vector, T *itemToFind) {
|
||||
auto foundUniqIter = find_if(vector.begin(), vector.end(),
|
||||
[itemToFind](std::unique_ptr<T> &uniquePtr) {
|
||||
return uniquePtr.get() == itemToFind;
|
||||
});
|
||||
|
||||
if (foundUniqIter == vector.end()) {
|
||||
throw FileParseException("Unexpected error - item to find not found");
|
||||
}
|
||||
|
||||
return foundUniqIter;
|
||||
}
|
||||
|
||||
template <typename T>
|
||||
void eraseUniquePtr(std::vector<std ::unique_ptr<T>> &vector, T *itemToErase) {
|
||||
auto removeUniqIter = findUniquePtr<T>(vector, itemToErase);
|
||||
|
||||
if (removeUniqIter == vector.end()) {
|
||||
throw FileParseException("Unexpected error - item to remove not found");
|
||||
}
|
||||
|
||||
vector.erase(removeUniqIter);
|
||||
}
|
||||
|
||||
class MarvinMolBase {
|
||||
public:
|
||||
std::string molID;
|
||||
std::string id; // used in all sGroups
|
||||
|
||||
// these atoms and bonds are only owned by this mol if it is a MarvinMol or
|
||||
// MarvinSuperatomSgroup all other derived classes have atoms that are owned
|
||||
// by the actual parent, and are references
|
||||
std::vector<MarvinAtom *> atoms;
|
||||
std::vector<MarvinBond *> bonds;
|
||||
|
||||
std::vector<std::unique_ptr<MarvinMolBase>> sgroups;
|
||||
MarvinMolBase *parent;
|
||||
|
||||
virtual std::string role() const = 0;
|
||||
virtual bool hasAtomBondBlocks() const = 0;
|
||||
virtual std::string toString() const = 0;
|
||||
virtual ptree toPtree() const;
|
||||
void addSgroupsToPtree(ptree &pt) const;
|
||||
|
||||
virtual MarvinMolBase *copyMol(std::string idAppend) const = 0;
|
||||
virtual void pushOwnedAtom(MarvinAtom *atom);
|
||||
virtual void pushOwnedBond(MarvinBond *bond);
|
||||
|
||||
virtual void pushOwnedAtomUniqPtr(std::unique_ptr<MarvinAtom> atom);
|
||||
virtual void pushOwnedBondUniqPtr(std::unique_ptr<MarvinBond> bond);
|
||||
|
||||
virtual void removeOwnedAtom(MarvinAtom *atom);
|
||||
virtual void removeOwnedBond(MarvinBond *bond);
|
||||
|
||||
int getExplicitValence(const MarvinAtom &marvinAtom) const;
|
||||
|
||||
MarvinMolBase() {}
|
||||
|
||||
virtual ~MarvinMolBase();
|
||||
|
||||
int getAtomIndex(std::string id) const;
|
||||
int getBondIndex(std::string id) const;
|
||||
|
||||
const std::vector<std::string> getBondList() const;
|
||||
const std::vector<std::string> getAtomList() const;
|
||||
bool AnyOverLappingAtoms(const MarvinMolBase *otherMol) const;
|
||||
|
||||
void cleanUpNumbering(
|
||||
int &molCount // this is the starting mol count, and receives the ending
|
||||
// mol count - THis is used when
|
||||
// MarvinMol->convertToSuperAtaoms is called multiple times
|
||||
// from a RXN
|
||||
,
|
||||
int &atomCount // starting and ending atom count
|
||||
,
|
||||
int &bondCount // starting and ending bond count
|
||||
,
|
||||
int &sgCount // starting and ending sq count
|
||||
,
|
||||
std::map<std::string, std::string>
|
||||
&sgMap // map from old sg number to new sg number
|
||||
,
|
||||
std::map<std::string, std::string>
|
||||
&atomMap // map from old atom number to new atom number
|
||||
,
|
||||
std::map<std::string, std::string>
|
||||
&bondMap // map from old bond number to new bond number
|
||||
);
|
||||
|
||||
// the following is vitual because some dirived classes need to do more than
|
||||
// just call the base class. Currently, only MarvinSuperatomSgroup does this
|
||||
public:
|
||||
virtual void cleanUpNumberingMolsAtomsBonds(
|
||||
int &molCount, // this is the starting mol count, and receives the ending
|
||||
// mol count - THis is used when
|
||||
// MarvinMol->convertToSuperAtaoms is called multiple
|
||||
// times from a RXN
|
||||
int &atomCount, // starting and ending atom count
|
||||
int &bondCount, // starting and ending bond count
|
||||
std::map<std::string, std::string> &sgMap,
|
||||
std::map<std::string, std::string> &atomMap,
|
||||
std::map<std::string, std::string> &bondMap);
|
||||
|
||||
void cleanUpSgNumbering(int &sgCount,
|
||||
std::map<std::string, std::string> &sgMap);
|
||||
|
||||
// the following is vitual because some dirived classes need to do more than
|
||||
// just call the base class. Currently, only MarvinSuperatomSgroup does this
|
||||
|
||||
virtual IsSgroupInAtomSetResult isSgroupInSetOfAtoms(
|
||||
const std::vector<MarvinAtom *> &setOfAtoms) const;
|
||||
|
||||
public:
|
||||
static bool atomRefInAtoms(MarvinAtom *a, std::string b);
|
||||
static bool bondRefInBonds(MarvinBond *a, std::string b);
|
||||
static bool molIDInSgroups(std::string a, std::string b);
|
||||
MarvinAtom *findAtomByRef(std::string atomId);
|
||||
MarvinBond *findBondByRef(std::string atomId);
|
||||
|
||||
void clearMaps();
|
||||
|
||||
void prepSgroupsForRDKit();
|
||||
void processSgroupsFromRDKit();
|
||||
|
||||
virtual bool isPassiveRoleForExpansion() const;
|
||||
virtual bool isPassiveRoleForContraction() const;
|
||||
virtual void processSpecialSgroups();
|
||||
virtual void parseMoleculeSpecific(RDKit::RWMol *mol,
|
||||
std::unique_ptr<SubstanceGroup> &sgroup,
|
||||
int sequenceId);
|
||||
|
||||
bool has2dCoords() const;
|
||||
bool has3dCoords() const;
|
||||
bool hasAny3dCoords() const;
|
||||
bool hasAny2dCoords() const;
|
||||
bool hasCoords() const;
|
||||
void removeCoords();
|
||||
|
||||
void parseAtomsAndBonds(ptree &molTree);
|
||||
};
|
||||
|
||||
class MarvinSruCoModSgroup : public MarvinMolBase {
|
||||
private:
|
||||
std::string roleName; // could be MarvinSruSgroup, MarvinCopolymerSgroup or
|
||||
// MarvinModificationSgroup
|
||||
public:
|
||||
MarvinSruCoModSgroup(std::string type, MarvinMolBase *parent);
|
||||
MarvinSruCoModSgroup(MarvinMolBase *parent, std::string role, ptree &molTree);
|
||||
|
||||
MarvinMolBase *copyMol(std::string idAppendage) const override;
|
||||
|
||||
std::string title;
|
||||
std::string connect;
|
||||
std::string correspondence;
|
||||
|
||||
std::string toString() const override;
|
||||
ptree toPtree() const override;
|
||||
|
||||
std::string role() const override;
|
||||
bool hasAtomBondBlocks() const override;
|
||||
void parseMoleculeSpecific(RDKit::RWMol *mol,
|
||||
std::unique_ptr<SubstanceGroup> &sgroup,
|
||||
int sequenceId) override;
|
||||
};
|
||||
|
||||
class MarvinDataSgroup : public MarvinMolBase {
|
||||
public:
|
||||
MarvinDataSgroup(MarvinMolBase *parent);
|
||||
MarvinDataSgroup(MarvinMolBase *parent, ptree &molTree);
|
||||
|
||||
MarvinMolBase *copyMol(std::string idAppendage) const override;
|
||||
|
||||
std::string context;
|
||||
std::string fieldName;
|
||||
std::string placement;
|
||||
std::string unitsDisplayed;
|
||||
std::string queryType;
|
||||
std::string queryOp;
|
||||
std::string fieldData;
|
||||
std::string units;
|
||||
double x;
|
||||
double y;
|
||||
|
||||
std::string toString() const override;
|
||||
ptree toPtree() const override;
|
||||
|
||||
std::string role() const override;
|
||||
bool hasAtomBondBlocks() const override;
|
||||
void parseMoleculeSpecific(RDKit::RWMol *mol,
|
||||
std::unique_ptr<SubstanceGroup> &sgroup,
|
||||
int sequenceId) override;
|
||||
};
|
||||
|
||||
class MarvinSuperatomSgroupExpanded : public MarvinMolBase {
|
||||
public:
|
||||
std::string title;
|
||||
|
||||
MarvinSuperatomSgroupExpanded(MarvinMolBase *parent);
|
||||
MarvinSuperatomSgroupExpanded(MarvinMolBase *parent, ptree &molTree);
|
||||
|
||||
MarvinMolBase *copyMol(std::string idAppendage) const override;
|
||||
|
||||
~MarvinSuperatomSgroupExpanded() override;
|
||||
|
||||
MarvinMolBase *convertToOneSuperAtom();
|
||||
|
||||
std::string toString() const override;
|
||||
ptree toPtree() const override;
|
||||
|
||||
std::string role() const override;
|
||||
bool hasAtomBondBlocks() const override;
|
||||
bool isPassiveRoleForContraction() const override;
|
||||
|
||||
void parseMoleculeSpecific(RDKit::RWMol *mol,
|
||||
std::unique_ptr<SubstanceGroup> &sgroup,
|
||||
int sequenceId) override;
|
||||
};
|
||||
|
||||
class MarvinMultipleSgroup : public MarvinMolBase {
|
||||
public:
|
||||
MarvinMultipleSgroup(MarvinMolBase *parent);
|
||||
MarvinMultipleSgroup(MarvinMolBase *parent, ptree &molTree);
|
||||
|
||||
MarvinMolBase *copyMol(std::string idAppendage) const override;
|
||||
|
||||
std::string title;
|
||||
bool isExpanded = false;
|
||||
std::vector<MarvinAtom *> parentAtoms;
|
||||
std::vector<MarvinBond *>
|
||||
bondsToAtomsNotInExpandedGroup; // only when expanded
|
||||
|
||||
void expandOneMultipleSgroup();
|
||||
void contractOneMultipleSgroup();
|
||||
int getMatchedOrphanBondIndex(std::string atomIdToCheck,
|
||||
std::vector<MarvinBond *> &bondsToTry,
|
||||
std::vector<MarvinBond *> &orphanedBonds) const;
|
||||
|
||||
std::string toString() const override;
|
||||
ptree toPtree() const override;
|
||||
|
||||
std::string role() const override;
|
||||
bool hasAtomBondBlocks() const override;
|
||||
bool isPassiveRoleForExpansion() const override;
|
||||
bool isPassiveRoleForContraction() const override;
|
||||
void processSpecialSgroups() override;
|
||||
|
||||
void parseMoleculeSpecific(RDKit::RWMol *mol,
|
||||
std::unique_ptr<SubstanceGroup> &sgroup,
|
||||
int sequenceId) override;
|
||||
};
|
||||
|
||||
class MarvinMulticenterSgroup : public MarvinMolBase {
|
||||
// <molecule molID="m2" id="sg1" role="MulticenterSgroup" atomRefs="a2 a6 a5
|
||||
// a4 a3" center="a18"/>sgroup->
|
||||
public:
|
||||
MarvinMulticenterSgroup(MarvinMolBase *parent);
|
||||
MarvinMulticenterSgroup(MarvinMolBase *parent, ptree &molTree);
|
||||
|
||||
MarvinMolBase *copyMol(std::string idAppendage) const override;
|
||||
|
||||
void processOneMulticenterSgroup();
|
||||
|
||||
std::string toString() const override;
|
||||
ptree toPtree() const override;
|
||||
|
||||
MarvinAtom *center;
|
||||
std::string role() const override;
|
||||
bool hasAtomBondBlocks() const override;
|
||||
void processSpecialSgroups() override;
|
||||
void parseMoleculeSpecific(RDKit::RWMol *mol,
|
||||
std::unique_ptr<SubstanceGroup> &sgroup,
|
||||
int sequenceId) override;
|
||||
};
|
||||
|
||||
class MarvinGenericSgroup : public MarvinMolBase {
|
||||
// <molecule molID="m2" id="sg1" role="GenericSgroup" atomRefs="a1 a2 a3 a4 a5
|
||||
// a6 a7 a8 a9 a13 a10 a11 a12" charge="onAtoms"/></molecule>
|
||||
public:
|
||||
MarvinGenericSgroup(MarvinMolBase *parent);
|
||||
MarvinGenericSgroup(MarvinMolBase *parent, ptree &molTree);
|
||||
|
||||
MarvinMolBase *copyMol(std::string idAppendage) const override;
|
||||
|
||||
std::string charge; // onAtoms or onBrackets
|
||||
std::string toString() const override;
|
||||
ptree toPtree() const override;
|
||||
|
||||
std::string role() const override;
|
||||
bool hasAtomBondBlocks() const override;
|
||||
void parseMoleculeSpecific(RDKit::RWMol *mol,
|
||||
std::unique_ptr<SubstanceGroup> &sgroup,
|
||||
int sequenceId) override;
|
||||
};
|
||||
|
||||
class MarvinMonomerSgroup : public MarvinMolBase {
|
||||
// <molecule id="sg1" role="MonomerSgroup" title="mon" charge="onAtoms"
|
||||
// molID="m2" atomRefs="a2 a1 a3 a4">
|
||||
// </molecule>
|
||||
public:
|
||||
MarvinMonomerSgroup(MarvinMolBase *parent);
|
||||
MarvinMonomerSgroup(MarvinMolBase *parent, ptree &molTree);
|
||||
|
||||
MarvinMolBase *copyMol(std::string idAppendage) const override;
|
||||
|
||||
std::string title;
|
||||
std::string charge; // onAtoms or onBrackets
|
||||
std::string toString() const override;
|
||||
ptree toPtree() const override;
|
||||
|
||||
std::string role() const override;
|
||||
bool hasAtomBondBlocks() const override;
|
||||
void parseMoleculeSpecific(RDKit::RWMol *mol,
|
||||
std::unique_ptr<SubstanceGroup> &sgroup,
|
||||
int sequenceId) override;
|
||||
};
|
||||
|
||||
class MarvinSuperatomSgroup : public MarvinMolBase {
|
||||
public:
|
||||
std::string title;
|
||||
std::vector<std::unique_ptr<MarvinAttachmentPoint>> attachmentPoints;
|
||||
|
||||
MarvinSuperatomSgroup(MarvinMolBase *parent);
|
||||
MarvinSuperatomSgroup(MarvinMolBase *parent, ptree &molTree);
|
||||
|
||||
MarvinMolBase *copyMol(std::string idAppendage) const override;
|
||||
|
||||
~MarvinSuperatomSgroup() override;
|
||||
|
||||
void convertFromOneSuperAtom();
|
||||
|
||||
std::string role() const override;
|
||||
bool hasAtomBondBlocks() const override;
|
||||
bool isPassiveRoleForExpansion() const override;
|
||||
|
||||
std::string toString() const override;
|
||||
ptree toPtree() const override;
|
||||
|
||||
void cleanUpNumberingMolsAtomsBonds(
|
||||
int &molCount, // this is the starting mol count, and receives the ending
|
||||
// mol count - THis is used when
|
||||
// MarvinMol->convertToSuperAtaoms is called multiple
|
||||
// times from a RXN
|
||||
int &atomCount, // starting and ending atom count
|
||||
int &bondCount, // starting and ending bond count
|
||||
std::map<std::string, std::string> &sgMap,
|
||||
std::map<std::string, std::string> &atomMap,
|
||||
std::map<std::string, std::string> &bondMap) override;
|
||||
|
||||
IsSgroupInAtomSetResult isSgroupInSetOfAtoms(
|
||||
const std::vector<MarvinAtom *> &setOfAtoms) const override;
|
||||
|
||||
void processSpecialSgroups() override;
|
||||
};
|
||||
|
||||
class MarvinMol : public MarvinMolBase {
|
||||
public:
|
||||
MarvinMol();
|
||||
MarvinMol(ptree &molTree);
|
||||
|
||||
MarvinMolBase *copyMol(std::string idAppendage) const override;
|
||||
|
||||
~MarvinMol() override;
|
||||
|
||||
std::vector<std::unique_ptr<MarvinAtom>> ownedAtoms;
|
||||
std::vector<std::unique_ptr<MarvinBond>> ownedBonds;
|
||||
|
||||
void pushOwnedAtom(MarvinAtom *atom) override;
|
||||
void pushOwnedBond(MarvinBond *bond) override;
|
||||
|
||||
void pushOwnedAtomUniqPtr(std::unique_ptr<MarvinAtom> atom) override;
|
||||
void pushOwnedBondUniqPtr(std::unique_ptr<MarvinBond> bond) override;
|
||||
|
||||
void removeOwnedAtom(MarvinAtom *atom) override;
|
||||
void removeOwnedBond(MarvinBond *bond) override;
|
||||
|
||||
std::string role() const override;
|
||||
bool hasAtomBondBlocks() const override;
|
||||
bool isPassiveRoleForContraction() const override;
|
||||
|
||||
std::string toString() const override;
|
||||
ptree toPtree() const override;
|
||||
|
||||
std::string generateMolString();
|
||||
ptree toMolPtree() const;
|
||||
};
|
||||
|
||||
class MarvinReaction {
|
||||
public:
|
||||
std::vector<std::unique_ptr<MarvinMol>> reactants;
|
||||
std::vector<std::unique_ptr<MarvinMol>> agents;
|
||||
std::vector<std::unique_ptr<MarvinMol>> products;
|
||||
|
||||
MarvinArrow arrow;
|
||||
std::vector<std::unique_ptr<MarvinPlus>> pluses;
|
||||
std::vector<std::unique_ptr<MarvinCondition>> conditions;
|
||||
|
||||
~MarvinReaction();
|
||||
|
||||
void prepSgroupsForRDKit();
|
||||
|
||||
std::string toString();
|
||||
ptree toPtree() const;
|
||||
};
|
||||
|
||||
class MarvinStereoGroup {
|
||||
public:
|
||||
StereoGroupType groupType; // one of ABS AND OR
|
||||
int groupNumber;
|
||||
std::vector<unsigned int> atoms;
|
||||
|
||||
MarvinStereoGroup(StereoGroupType grouptypeInit, int groupNumberInit);
|
||||
};
|
||||
|
||||
template <typename T>
|
||||
bool getCleanNumber(std::string strToParse, T &outInt);
|
||||
} // namespace RDKit
|
||||
|
||||
#endif // RD_MARVINDEFS_H
|
||||
1092
Code/GraphMol/MarvinParse/MarvinParser.cpp
Normal file
1092
Code/GraphMol/MarvinParse/MarvinParser.cpp
Normal file
File diff suppressed because it is too large
Load Diff
72
Code/GraphMol/MarvinParse/MarvinParser.h
Normal file
72
Code/GraphMol/MarvinParse/MarvinParser.h
Normal file
@@ -0,0 +1,72 @@
|
||||
//
|
||||
// Copyright (C) 2022-2023 Tad Hurst, Greg Landrum and other RDKit contributors
|
||||
//
|
||||
// @@ All Rights Reserved @@
|
||||
// This file is part of the RDKit.
|
||||
// The contents are covered by the terms of the BSD license
|
||||
// which is included in the file license.txt, found at the root
|
||||
// of the RDKit source tree.
|
||||
//
|
||||
|
||||
#include <RDGeneral/export.h>
|
||||
|
||||
#ifndef RD_MARVINPARSER_H
|
||||
#define RD_MARVINPARSER_H
|
||||
|
||||
#include <GraphMol/RDKitBase.h>
|
||||
#include <GraphMol/ChemReactions/Reaction.h>
|
||||
|
||||
#include <string>
|
||||
#include <iostream>
|
||||
|
||||
namespace RDKit {
|
||||
|
||||
RDKIT_MARVINPARSER_EXPORT bool MrvFileIsReaction(const std::string &fname);
|
||||
RDKIT_MARVINPARSER_EXPORT bool MrvDataStreamIsReaction(std::istream *inStream);
|
||||
|
||||
RDKIT_MARVINPARSER_EXPORT bool MrvDataStreamIsReaction(std::istream &inStream);
|
||||
RDKIT_MARVINPARSER_EXPORT bool MrvBlockIsReaction(
|
||||
const std::string &molmrvText);
|
||||
|
||||
RDKIT_MARVINPARSER_EXPORT RWMol *MrvDataStreamToMol(std::istream *inStream,
|
||||
bool sanitize = false,
|
||||
bool removeHs = false);
|
||||
RDKIT_MARVINPARSER_EXPORT RWMol *MrvDataStreamToMol(std::istream &inStream,
|
||||
bool sanitize = false,
|
||||
bool removeHs = false);
|
||||
RDKIT_MARVINPARSER_EXPORT RWMol *MrvBlockToMol(const std::string &molmrvText,
|
||||
bool sanitize = false,
|
||||
bool removeHs = false);
|
||||
RDKIT_MARVINPARSER_EXPORT RWMol *MrvFileToMol(const std::string &fName,
|
||||
bool sanitize = false,
|
||||
bool removeHs = false);
|
||||
|
||||
RDKIT_MARVINPARSER_EXPORT ChemicalReaction *MrvDataStreamToChemicalReaction(
|
||||
std::istream *inStream, bool sanitize = false, bool removeHs = false);
|
||||
RDKIT_MARVINPARSER_EXPORT ChemicalReaction *MrvDataStreamToChemicalReaction(
|
||||
std::istream &inStream, bool sanitize = false, bool removeHs = false);
|
||||
RDKIT_MARVINPARSER_EXPORT ChemicalReaction *MrvBlockToChemicalReaction(
|
||||
const std::string &molmrvText, bool sanitize = false,
|
||||
bool removeHs = false);
|
||||
RDKIT_MARVINPARSER_EXPORT ChemicalReaction *MrvFileToChemicalReaction(
|
||||
const std::string &fName, bool sanitize = false, bool removeHs = false);
|
||||
|
||||
RDKIT_MARVINPARSER_EXPORT void MolToMrvFile(const ROMol &mol,
|
||||
const std::string &fName,
|
||||
bool includeStereo, int confId,
|
||||
bool kekulize,
|
||||
bool prettyPrint = false);
|
||||
RDKIT_MARVINPARSER_EXPORT std::string MolToMrvBlock(const ROMol &mol,
|
||||
bool includeStereo,
|
||||
int confId, bool kekulize,
|
||||
bool prettyPrint = false);
|
||||
|
||||
RDKIT_MARVINPARSER_EXPORT std::string ChemicalReactionToMrvBlock(
|
||||
const ChemicalReaction &rxn, bool prettyPrint = false);
|
||||
|
||||
RDKIT_MARVINPARSER_EXPORT void ChemicalReactionToMrvFile(
|
||||
const ChemicalReaction &rxn, const std::string &fName,
|
||||
bool prettyPrint = false);
|
||||
} // namespace RDKit
|
||||
|
||||
#endif
|
||||
1336
Code/GraphMol/MarvinParse/MarvinWriter.cpp
Normal file
1336
Code/GraphMol/MarvinParse/MarvinWriter.cpp
Normal file
File diff suppressed because it is too large
Load Diff
706
Code/GraphMol/MarvinParse/testMrvToMol.cpp
Normal file
706
Code/GraphMol/MarvinParse/testMrvToMol.cpp
Normal file
@@ -0,0 +1,706 @@
|
||||
//
|
||||
// Copyright (C) 2022-2023 Tad Hurst, Greg Landrum and other RDKit contributors
|
||||
// @@ All Rights Reserved @@
|
||||
// This file is part of the RDKit.
|
||||
// The contents are covered by the terms of the BSD license
|
||||
// which is included in the file license.txt, found at the root
|
||||
// of the RDKit source tree.
|
||||
//
|
||||
|
||||
#include <RDGeneral/RDLog.h>
|
||||
#include <GraphMol/RDKitBase.h>
|
||||
#include <GraphMol/FileParsers/FileParsers.h>
|
||||
#include <GraphMol/FileParsers/SequenceParsers.h>
|
||||
#include <GraphMol/FileParsers/SequenceWriters.h>
|
||||
#include <GraphMol/FileParsers/MolFileStereochem.h>
|
||||
#include <GraphMol/Depictor/RDDepictor.h>
|
||||
#include "MarvinParser.h"
|
||||
|
||||
#include <GraphMol/ChemReactions/Reaction.h>
|
||||
#include <GraphMol/ChemReactions/ReactionParser.h>
|
||||
#include <GraphMol/SmilesParse/SmilesParse.h>
|
||||
#include <GraphMol/SmilesParse/SmilesWrite.h>
|
||||
#include <GraphMol/SmilesParse/SmilesWrite.h>
|
||||
|
||||
#include <string>
|
||||
#include <fstream>
|
||||
#include <filesystem>
|
||||
|
||||
using namespace RDKit;
|
||||
|
||||
enum LoadAs { LoadAsMolOrRxn, LoadAsMol, LoadAsRxn };
|
||||
|
||||
class MrvTests {
|
||||
public:
|
||||
std::string testToRun;
|
||||
bool generateExpectedFiles;
|
||||
|
||||
MrvTests() {
|
||||
testToRun = "";
|
||||
generateExpectedFiles = false;
|
||||
}
|
||||
|
||||
class MolTest {
|
||||
public:
|
||||
unsigned int atomCount;
|
||||
unsigned int bondCount;
|
||||
std::string fileName;
|
||||
bool expectedResult;
|
||||
|
||||
MolTest(std::string fileNameInit, bool expectedResultInit,
|
||||
int atomCountInit, int bondCountInit)
|
||||
: atomCount(atomCountInit),
|
||||
bondCount(bondCountInit),
|
||||
fileName(fileNameInit),
|
||||
expectedResult(expectedResultInit){};
|
||||
};
|
||||
|
||||
class RxnTest {
|
||||
public:
|
||||
std::string fileName;
|
||||
bool expectedResult;
|
||||
unsigned int reactantCount;
|
||||
unsigned int agentCount;
|
||||
unsigned int productCount;
|
||||
unsigned int warnings;
|
||||
unsigned int errors;
|
||||
|
||||
RxnTest(std::string fileNameInit, bool expectedResultInit,
|
||||
int reactantCountInit, int agentCountInit, int productCountInit,
|
||||
int warnInit, int errorInit)
|
||||
: fileName(fileNameInit),
|
||||
expectedResult(expectedResultInit),
|
||||
reactantCount(reactantCountInit),
|
||||
agentCount(agentCountInit),
|
||||
productCount(productCountInit),
|
||||
warnings(warnInit),
|
||||
errors(errorInit){};
|
||||
};
|
||||
|
||||
class SmilesTest {
|
||||
public:
|
||||
std::string name;
|
||||
std::string smiles;
|
||||
bool expectedResult;
|
||||
unsigned int atomCount;
|
||||
unsigned int bondCount;
|
||||
|
||||
SmilesTest(std::string nameInit, std::string smilesInit,
|
||||
bool expectedResultInit, int atomCountInit, int bondCountInit)
|
||||
: name(nameInit),
|
||||
smiles(smilesInit),
|
||||
expectedResult(expectedResultInit),
|
||||
atomCount(atomCountInit),
|
||||
bondCount(bondCountInit){};
|
||||
|
||||
bool isRxnTest() const { return false; }
|
||||
};
|
||||
|
||||
std::string GetExpectedValue(std::string expectedFileName) {
|
||||
std::stringstream expectedMolStr;
|
||||
std::ifstream in;
|
||||
in.open(expectedFileName);
|
||||
expectedMolStr << in.rdbuf();
|
||||
return expectedMolStr.str();
|
||||
}
|
||||
|
||||
void generateNewExpectedFilesIfSoSpecified(std::string filename,
|
||||
std::string dataToWrite) {
|
||||
if (generateExpectedFiles) {
|
||||
std::ofstream out;
|
||||
out.open(filename);
|
||||
out << dataToWrite;
|
||||
}
|
||||
}
|
||||
|
||||
void testSmilesToMarvin(const SmilesTest *smilesTest) {
|
||||
BOOST_LOG(rdInfoLog) << "testing smiles to marin " << std::endl;
|
||||
std::string rdbase = getenv("RDBASE");
|
||||
std::string fName =
|
||||
rdbase + "/Code/GraphMol/MarvinParse/test_data/" + smilesTest->name;
|
||||
|
||||
class LocalVars // protect against mem leak on error
|
||||
{
|
||||
public:
|
||||
RWMol *smilesMol = nullptr;
|
||||
|
||||
LocalVars(){};
|
||||
|
||||
~LocalVars() { delete smilesMol; }
|
||||
} localVars;
|
||||
|
||||
try {
|
||||
SmilesParserParams smilesParserParams;
|
||||
smilesParserParams.sanitize = true;
|
||||
|
||||
localVars.smilesMol = SmilesToMol(smilesTest->smiles, smilesParserParams);
|
||||
reapplyMolBlockWedging(*localVars.smilesMol);
|
||||
|
||||
TEST_ASSERT(localVars.smilesMol->getNumAtoms() == smilesTest->atomCount);
|
||||
TEST_ASSERT(localVars.smilesMol->getNumBonds() == smilesTest->bondCount);
|
||||
|
||||
// test round trip back to smiles
|
||||
{
|
||||
std::string expectedMrvName = fName + ".expected.smi";
|
||||
|
||||
SmilesWriteParams ps;
|
||||
ps.canonical = false;
|
||||
|
||||
std::string smilesOut = MolToSmiles(*localVars.smilesMol, ps);
|
||||
|
||||
generateNewExpectedFilesIfSoSpecified(fName + ".NEW.smi", smilesOut);
|
||||
|
||||
TEST_ASSERT(GetExpectedValue(expectedMrvName) == smilesOut);
|
||||
}
|
||||
|
||||
{
|
||||
std::string expectedMrvName = fName + ".expected.sdf";
|
||||
std::string outMolStr = "";
|
||||
try {
|
||||
outMolStr = MolToMolBlock(*localVars.smilesMol, true, 0, true, true);
|
||||
} catch (const RDKit::KekulizeException &e) {
|
||||
outMolStr = "";
|
||||
}
|
||||
if (outMolStr == "") {
|
||||
outMolStr = MolToMolBlock(*localVars.smilesMol, true, 0, false,
|
||||
true); // try without kekule'ing
|
||||
}
|
||||
|
||||
generateNewExpectedFilesIfSoSpecified(fName + ".NEW.sdf", outMolStr);
|
||||
|
||||
TEST_ASSERT(GetExpectedValue(expectedMrvName) == outMolStr);
|
||||
}
|
||||
{
|
||||
std::string mrvBlock;
|
||||
std::string expectedMrvName = fName + ".expected.mrv";
|
||||
std::string outMolStr = "";
|
||||
try {
|
||||
outMolStr =
|
||||
MolToMrvBlock(*localVars.smilesMol, true, -1, true, false);
|
||||
} catch (const RDKit::KekulizeException &e) {
|
||||
outMolStr = "";
|
||||
} catch (...) {
|
||||
throw; // re-throw the error if not a kekule error
|
||||
}
|
||||
if (outMolStr == "") {
|
||||
outMolStr = MolToMrvBlock(*localVars.smilesMol, true, -1, false,
|
||||
false); // try without kekule'ing
|
||||
}
|
||||
|
||||
generateNewExpectedFilesIfSoSpecified(fName + ".NEW.mrv", outMolStr);
|
||||
|
||||
TEST_ASSERT(GetExpectedValue(expectedMrvName) == outMolStr);
|
||||
}
|
||||
BOOST_LOG(rdInfoLog) << "done" << std::endl;
|
||||
} catch (const std::exception &e) {
|
||||
if (smilesTest->expectedResult != false) {
|
||||
throw;
|
||||
}
|
||||
return;
|
||||
}
|
||||
|
||||
TEST_ASSERT(smilesTest->expectedResult == true);
|
||||
}
|
||||
|
||||
RWMol *GetMol(const MolTest *molTest) {
|
||||
std::string rdbase = getenv("RDBASE");
|
||||
std::string fName =
|
||||
rdbase + "/Code/GraphMol/MarvinParse/test_data/" + molTest->fileName;
|
||||
|
||||
for (bool sanitize : {true, false}) {
|
||||
try {
|
||||
return MrvFileToMol(fName, sanitize, false);
|
||||
} catch (const std::exception &e) {
|
||||
std::cerr << e.what() << '\n';
|
||||
}
|
||||
}
|
||||
throw BadFileException("Could not parse the MRV block");
|
||||
}
|
||||
|
||||
ChemicalReaction *GetReaction(const RxnTest *rxnTest) {
|
||||
std::string rdbase = getenv("RDBASE");
|
||||
std::string fName =
|
||||
rdbase + "/Code/GraphMol/MarvinParse/test_data/" + rxnTest->fileName;
|
||||
|
||||
for (bool sanitize : {true, false}) {
|
||||
try {
|
||||
return MrvFileToChemicalReaction(fName, sanitize, false);
|
||||
} catch (const std::exception &e) {
|
||||
std::cerr << e.what() << '\n';
|
||||
}
|
||||
}
|
||||
throw BadFileException("Could not parse the MRV block");
|
||||
}
|
||||
|
||||
void testMarvinMol(const MolTest *molTest) {
|
||||
BOOST_LOG(rdInfoLog) << "testing marvin parsing" << std::endl;
|
||||
|
||||
std::string rdbase = getenv("RDBASE");
|
||||
std::string fName =
|
||||
rdbase + "/Code/GraphMol/MarvinParse/test_data/" + molTest->fileName;
|
||||
|
||||
class LocalVars // protect against mem leak on error
|
||||
{
|
||||
public:
|
||||
RWMol *mol = nullptr;
|
||||
|
||||
LocalVars(){};
|
||||
|
||||
~LocalVars() { delete (RWMol *)mol; }
|
||||
} localVars;
|
||||
|
||||
try {
|
||||
if (MrvFileIsReaction(fName)) {
|
||||
TEST_ASSERT(molTest->expectedResult == false);
|
||||
return;
|
||||
}
|
||||
|
||||
localVars.mol = GetMol(molTest);
|
||||
reapplyMolBlockWedging(*localVars.mol);
|
||||
|
||||
TEST_ASSERT(localVars.mol != nullptr);
|
||||
|
||||
TEST_ASSERT(localVars.mol->getNumAtoms() == molTest->atomCount)
|
||||
TEST_ASSERT(localVars.mol->getNumBonds() == molTest->bondCount)
|
||||
|
||||
{
|
||||
std::string expectedMrvName = fName + ".expected.sdf";
|
||||
std::string outMolStr = "";
|
||||
try {
|
||||
outMolStr = MolToMolBlock(*localVars.mol, true, 0, true, true);
|
||||
} catch (const RDKit::KekulizeException &e) {
|
||||
outMolStr = "";
|
||||
}
|
||||
if (outMolStr == "") {
|
||||
outMolStr = MolToMolBlock(*localVars.mol, true, 0, false,
|
||||
true); // try without kekule'ing
|
||||
}
|
||||
|
||||
generateNewExpectedFilesIfSoSpecified(fName + ".NEW.sdf", outMolStr);
|
||||
|
||||
TEST_ASSERT(GetExpectedValue(expectedMrvName) == outMolStr);
|
||||
}
|
||||
|
||||
{
|
||||
std::string expectedMrvName = fName + ".expected.mrv";
|
||||
|
||||
std::string outMolStr = "";
|
||||
try {
|
||||
outMolStr = MolToMrvBlock(*localVars.mol, true, -1, true, false);
|
||||
} catch (const RDKit::KekulizeException &e) {
|
||||
outMolStr = "";
|
||||
}
|
||||
if (outMolStr == "") {
|
||||
outMolStr = MolToMrvBlock(*localVars.mol, true, -1, false,
|
||||
false); // try without kekule'ing
|
||||
}
|
||||
|
||||
generateNewExpectedFilesIfSoSpecified(fName + ".NEW.mrv", outMolStr);
|
||||
|
||||
TEST_ASSERT(GetExpectedValue(expectedMrvName) == outMolStr);
|
||||
|
||||
BOOST_LOG(rdInfoLog) << "done" << std::endl;
|
||||
}
|
||||
} catch (const std::exception &e) {
|
||||
if (molTest->expectedResult != false) {
|
||||
throw;
|
||||
}
|
||||
return;
|
||||
}
|
||||
TEST_ASSERT(molTest->expectedResult == true);
|
||||
|
||||
return;
|
||||
}
|
||||
|
||||
void testMarvinRxn(const RxnTest *rxnTest) {
|
||||
BOOST_LOG(rdInfoLog) << "testing marvin parsing" << std::endl;
|
||||
|
||||
std::string rdbase = getenv("RDBASE");
|
||||
std::string fName =
|
||||
rdbase + "/Code/GraphMol/MarvinParse/test_data/" + rxnTest->fileName;
|
||||
|
||||
class LocalVars // protect against mem leak on error
|
||||
{
|
||||
public:
|
||||
ChemicalReaction *rxn = nullptr;
|
||||
|
||||
LocalVars(){};
|
||||
|
||||
~LocalVars() { delete (ChemicalReaction *)rxn; }
|
||||
} localVars;
|
||||
|
||||
try {
|
||||
if (!MrvFileIsReaction(fName)) {
|
||||
TEST_ASSERT(rxnTest->expectedResult == false);
|
||||
return;
|
||||
}
|
||||
|
||||
localVars.rxn = GetReaction(rxnTest);
|
||||
|
||||
// check for errors
|
||||
|
||||
unsigned int nWarn = 0, nError = 0;
|
||||
|
||||
TEST_ASSERT(localVars.rxn != nullptr);
|
||||
|
||||
TEST_ASSERT(localVars.rxn->getNumReactantTemplates() ==
|
||||
rxnTest->reactantCount);
|
||||
TEST_ASSERT(localVars.rxn->getNumProductTemplates() ==
|
||||
rxnTest->productCount);
|
||||
TEST_ASSERT(localVars.rxn->getNumAgentTemplates() == rxnTest->agentCount);
|
||||
localVars.rxn->initReactantMatchers(true);
|
||||
|
||||
if (localVars.rxn->getNumReactantTemplates() > 0 &&
|
||||
localVars.rxn->getNumProductTemplates() > 0) {
|
||||
TEST_ASSERT(localVars.rxn->validate(nWarn, nError, true));
|
||||
} else {
|
||||
nWarn = 0;
|
||||
nError = 0;
|
||||
}
|
||||
|
||||
TEST_ASSERT(nWarn == rxnTest->warnings);
|
||||
TEST_ASSERT(nError == rxnTest->errors);
|
||||
|
||||
// make sure the Rxn is kekule'ed
|
||||
|
||||
for (auto mol : localVars.rxn->getReactants()) {
|
||||
auto rwMol = (RWMol *)mol.get();
|
||||
if (rwMol->needsUpdatePropertyCache()) {
|
||||
rwMol->updatePropertyCache(false);
|
||||
}
|
||||
MolOps::Kekulize(*rwMol);
|
||||
}
|
||||
for (auto mol : localVars.rxn->getAgents()) {
|
||||
auto rwMol = (RWMol *)mol.get();
|
||||
if (rwMol->needsUpdatePropertyCache()) {
|
||||
rwMol->updatePropertyCache(false);
|
||||
}
|
||||
MolOps::Kekulize(*rwMol);
|
||||
}
|
||||
for (auto mol : localVars.rxn->getProducts()) {
|
||||
auto rwMol = (RWMol *)mol.get();
|
||||
if (rwMol->needsUpdatePropertyCache()) {
|
||||
rwMol->updatePropertyCache(false);
|
||||
}
|
||||
MolOps::Kekulize(*rwMol);
|
||||
}
|
||||
|
||||
{
|
||||
std::string outMolStr =
|
||||
ChemicalReactionToRxnBlock(*localVars.rxn, false, true);
|
||||
|
||||
std::string expectedRxnName = fName + ".expected.rxn";
|
||||
|
||||
generateNewExpectedFilesIfSoSpecified(fName + ".NEW.rxn", outMolStr);
|
||||
|
||||
TEST_ASSERT(GetExpectedValue(expectedRxnName) == outMolStr);
|
||||
}
|
||||
|
||||
{
|
||||
std::string outMolStr =
|
||||
ChemicalReactionToMrvBlock(*localVars.rxn, false);
|
||||
|
||||
std::string expectedRxnName = fName + ".expected.mrv";
|
||||
|
||||
generateNewExpectedFilesIfSoSpecified(fName + ".NEW.mrv", outMolStr);
|
||||
|
||||
TEST_ASSERT(GetExpectedValue(expectedRxnName) == outMolStr);
|
||||
}
|
||||
BOOST_LOG(rdInfoLog) << "done" << std::endl;
|
||||
BOOST_LOG(rdInfoLog) << "done" << std::endl;
|
||||
} catch (const std::exception &e) {
|
||||
if (rxnTest->expectedResult != false) {
|
||||
throw;
|
||||
}
|
||||
return;
|
||||
}
|
||||
|
||||
TEST_ASSERT(rxnTest->expectedResult == true);
|
||||
|
||||
return;
|
||||
}
|
||||
|
||||
void testMolFiles(const MolTest *molFileTest) {
|
||||
BOOST_LOG(rdInfoLog) << "testing marvin writing" << std::endl;
|
||||
|
||||
std::string rdbase = getenv("RDBASE");
|
||||
std::string fName = rdbase + "/Code/GraphMol/MarvinParse/test_data/" +
|
||||
molFileTest->fileName;
|
||||
|
||||
class LocalVars // protext against mem leak on error
|
||||
{
|
||||
public:
|
||||
RWMol *mol = nullptr;
|
||||
|
||||
LocalVars(){};
|
||||
|
||||
~LocalVars() { delete mol; }
|
||||
} localVars;
|
||||
|
||||
try {
|
||||
localVars.mol = MolFileToMol(fName, true, false, false);
|
||||
reapplyMolBlockWedging(*localVars.mol);
|
||||
|
||||
TEST_ASSERT(localVars.mol != nullptr);
|
||||
TEST_ASSERT(localVars.mol->getNumAtoms() == molFileTest->atomCount)
|
||||
TEST_ASSERT(localVars.mol->getNumBonds() == molFileTest->bondCount)
|
||||
|
||||
{
|
||||
std::string expectedMrvName = fName + ".expected.sdf";
|
||||
std::string outMolStr = "";
|
||||
try {
|
||||
outMolStr = MolToMolBlock(*localVars.mol, true, 0, true, true);
|
||||
} catch (const RDKit::KekulizeException &e) {
|
||||
outMolStr = "";
|
||||
}
|
||||
if (outMolStr == "") {
|
||||
outMolStr = MolToMolBlock(*localVars.mol, true, 0, false,
|
||||
true); // try without kekule'ing
|
||||
}
|
||||
|
||||
generateNewExpectedFilesIfSoSpecified(fName + ".NEW.sdf", outMolStr);
|
||||
|
||||
TEST_ASSERT(GetExpectedValue(expectedMrvName) == outMolStr);
|
||||
}
|
||||
|
||||
{
|
||||
std::string expectedMrvName = fName + ".expected.mrv";
|
||||
|
||||
std::string outMolStr = "";
|
||||
try {
|
||||
outMolStr = MolToMrvBlock(*localVars.mol, true, -1, true, false);
|
||||
} catch (const RDKit::KekulizeException &e) {
|
||||
outMolStr = "";
|
||||
}
|
||||
if (outMolStr == "") {
|
||||
// try without kekule'ing
|
||||
outMolStr = MolToMrvBlock(*localVars.mol, true, -1, false, false);
|
||||
}
|
||||
|
||||
generateNewExpectedFilesIfSoSpecified(fName + ".NEW.mrv", outMolStr);
|
||||
|
||||
TEST_ASSERT(GetExpectedValue(expectedMrvName) == outMolStr);
|
||||
}
|
||||
|
||||
BOOST_LOG(rdInfoLog) << "done" << std::endl;
|
||||
} catch (const std::exception &e) {
|
||||
if (molFileTest->expectedResult != false) {
|
||||
throw;
|
||||
}
|
||||
return;
|
||||
}
|
||||
|
||||
TEST_ASSERT(molFileTest->expectedResult == true);
|
||||
|
||||
return;
|
||||
}
|
||||
|
||||
void RunTests() {
|
||||
// the molecule tests - starting with molfiles/sdf
|
||||
if (testToRun == "" || testToRun == "sdfTests") {
|
||||
std::list<MolTest> sdfTests{
|
||||
MolTest("ProblemShort.mol", true, 993, 992),
|
||||
MolTest("lostStereoAnd.sdf", true, 6, 5),
|
||||
MolTest("DoubleBondChain.sdf", true, 22, 22),
|
||||
MolTest("UnitsError.sdf", true, 17, 18),
|
||||
MolTest("StarAtom.sdf", true, 17, 16),
|
||||
MolTest("nonProprietary.mol", true, 17, 16),
|
||||
MolTest("ChiralTest.sdf", true, 8, 7),
|
||||
MolTest("TestBond1.mol", true, 10, 10),
|
||||
MolTest("Sgroup_MUL_ParentInMiddle.sdf", true, 17, 16)};
|
||||
|
||||
for (auto sdfTest : sdfTests) {
|
||||
BOOST_LOG(rdInfoLog) << "Test: " << sdfTest.fileName << std::endl;
|
||||
|
||||
printf("Test\n\n %s\n\n", sdfTest.fileName.c_str());
|
||||
testMolFiles(&sdfTest);
|
||||
}
|
||||
}
|
||||
|
||||
if (testToRun == "" || testToRun == "molFileTests") {
|
||||
std::list<MolTest> molFileTests{
|
||||
MolTest("Cubane.mrv", true, 16, 20),
|
||||
MolTest("lostStereoAnd.mrv", true, 6, 5),
|
||||
MolTest("DoubleBondChain.mrv", true, 22, 22),
|
||||
MolTest("WigglyAndCrossed.mrv", true, 8, 7),
|
||||
MolTest("BondTypes.mrv", true, 26, 25),
|
||||
MolTest("EmbeddedSGroupSUP_MUL.mrv", true, 17, 17),
|
||||
MolTest("EmbeddedSgroupCOP_SUP.mrv", true, 10, 10),
|
||||
MolTest("EmbeddedSgroupDAT_SUP.mrv", true, 10, 10),
|
||||
MolTest("EmbeddedSgroupMULTICENTER_SUP.mrv", true, 11, 10),
|
||||
MolTest("EmbeddedSgroupMUL_MUL.mrv", true, 141, 140),
|
||||
MolTest("EmbeddedSgroupMUL_MUL2.mrv", true, 23, 22),
|
||||
MolTest("EmbeddedSgroupMUL_SUP.mrv", true, 129, 128),
|
||||
MolTest("EmbeddedSgroupSRU_SUP.mrv", true, 10, 10),
|
||||
MolTest("EmbeddedSgroupSUPEXP_SUP.mrv", true, 10, 10),
|
||||
MolTest("EmbeddedSgroupSUPEXP_SUP2.mrv", true, 10, 10),
|
||||
MolTest("EmbeddedSgroupSUP_MULTICENTER.mrv", true, 10, 8),
|
||||
MolTest("EmbeddedSgroupSUP_SUP.mrv", true, 12, 11),
|
||||
MolTest("EmbeddedSgroupSUP_SUP2.mrv", true, 12, 12),
|
||||
MolTest("RgroupBad.mrv", true, 9, 9),
|
||||
MolTest("valenceLessThanDrawn.mrv", true, 14, 14),
|
||||
MolTest("data_sgroup_no_fieldname.mrv", true, 4, 3),
|
||||
MolTest("data_sgroup_empty_field_data.mrv", true, 2, 1),
|
||||
MolTest("radical_value.mrv", true, 3, 2),
|
||||
MolTest("emptyOneLineAtomList.mrv", true, 0, 0),
|
||||
MolTest("mrvValence_value.mrv", true, 3, 2),
|
||||
MolTest("ChiralTest2.mrv", true, 46, 47),
|
||||
MolTest("ChiralTest.mrv", true, 8, 7),
|
||||
MolTest("SnCl2.mrv", true, 3, 2),
|
||||
MolTest("SnH2Cl2.mrv", true, 3, 2),
|
||||
MolTest("marvin01.mrv", true, 11, 11),
|
||||
MolTest("marvin02.mrv", true, 9, 9),
|
||||
MolTest("marvin07.mrv", true, 12, 11),
|
||||
MolTest("marvin10.mrv", true, 10, 10),
|
||||
MolTest("marvin06.mrv", true, 11, 11),
|
||||
MolTest("marvin12.mrv", true, 31, 33),
|
||||
MolTest("EmptyMol.mrv", true, 0, 0),
|
||||
MolTest("Sparse.mrv", true, 0, 0),
|
||||
MolTest("Sparse2.mrv", true, 0, 0),
|
||||
MolTest("Sparse3.mrv", true, 0, 0),
|
||||
MolTest("MarvinNoCoords.mrv", true, 6, 6),
|
||||
MolTest("aspirin.mrv", true, 13, 13),
|
||||
MolTest("MarvinStereoGroupsZeros.mrv", true, 8, 8),
|
||||
MolTest("MarvinStereoGroupsAbs.mrv", true, 8, 8),
|
||||
MolTest("triphenylphosphine.mrv", true, 19, 21),
|
||||
MolTest("MarvinOldSuperGroupTest.mrv", true, 89, 93),
|
||||
MolTest("RadicalTests.mrv", true, 8, 7),
|
||||
MolTest("AnyBond.mrv", true, 4, 3),
|
||||
MolTest("cisBenzene.mrv", true, 6, 6),
|
||||
MolTest("DativeBond.mrv", true, 6, 5),
|
||||
MolTest("MultipleSgroup.mrv", true, 123, 122),
|
||||
MolTest("SgroupExpanded.mrv", true, 5, 4),
|
||||
MolTest("SgroupMultAttach.mrv", true, 44, 45),
|
||||
MolTest("MarvinMissingX2.mrv", true, 12, 11),
|
||||
MolTest("MarvinMissingY2.mrv", true, 12, 11),
|
||||
MolTest("DataSgroup.mrv", true, 7, 6),
|
||||
MolTest("MulticenterSgroup.mrv", true, 17, 16),
|
||||
MolTest("GenericSgroup.mrv", true, 13, 13),
|
||||
MolTest("MonomerSgroup.mrv", true, 4, 3),
|
||||
MolTest("modification_sgroup.mrv", true, 54, 40),
|
||||
MolTest("copolymer_sgroup.mrv", true, 19, 18),
|
||||
MolTest("MultipleSgroupParentInMiddleOfAtomBlock.mrv", true, 23, 22),
|
||||
MolTest("EmbeddedSgroups.mrv", false, 14, 14),
|
||||
MolTest("marvin03.mrv", false, 31, 33),
|
||||
MolTest("MarvinBadMissingMolID.mrv", false, 12, 11),
|
||||
MolTest("MarvinBadMissingAtomID.mrv", false, 12, 11),
|
||||
MolTest("MarvinBadX2.mrv", false, 12, 11),
|
||||
MolTest("MarvinBadY2.mrv", false, 12, 11),
|
||||
MolTest("MarvinBadStereoGroupsAbs.mrv", false, 8, 8),
|
||||
MolTest("MarvinBadElementType.mrv", false, 12, 11),
|
||||
MolTest("MarvinBadMissingBondID.mrv", false, 12, 11),
|
||||
MolTest("MarvinBadMissingBondAtomRefs", false, 12, 11),
|
||||
MolTest("MarvinBadMissingBondOrder.mrv", false, 12, 11),
|
||||
MolTest("MarvinBadMissingSruMolID.mrv", false, 12, 11),
|
||||
MolTest("MarvinBadMissingSruID.mrv", false, 12, 11),
|
||||
MolTest("MarvinBadMissingSruRole.mrv", false, 12, 11),
|
||||
MolTest("MarvinBadMissingSruAtomRef.mrv", false, 12, 11),
|
||||
MolTest("MarvinBadMissingSruTitle.mrv", false, 12, 11),
|
||||
MolTest("MarvinBadSruAtomRef.mrv", false, 12, 11),
|
||||
MolTest("MarvinBadSruID.mrv", false, 12, 11),
|
||||
MolTest("MarvinBadSruRole.mrv", false, 12, 11),
|
||||
MolTest("MarvinBadSruAtomRef.mrv", false, 12, 11),
|
||||
MolTest("MarvinBadSruAtomRef.mrv", false, 12, 11),
|
||||
MolTest("MarvinBadSruConnect.mrv", false, 12, 11),
|
||||
MolTest("MarvinBadSupAttachAtom.mrv", false, 9, 9),
|
||||
MolTest("MarvinBadSupAttachBond.mrv", false, 9, 9),
|
||||
MolTest("MarvinBadSupAttachOrder.mrv", false, 9, 9),
|
||||
MolTest("MarvinBadSupAttachAtom.mrv", false, 9, 9),
|
||||
MolTest("MarvinBadSupAttachAtom.mrv", false, 9, 9),
|
||||
MolTest("MarvinBadSupAttachAtom.mrv", false, 9, 9),
|
||||
MolTest("MarvinBadSupMissingAttachBond.mrv", false, 9, 9),
|
||||
MolTest("MarvinBadSupMissingAttachOrder.mrv", false, 9, 9),
|
||||
MolTest("marvin03.mrv", false, 1, 1)}; // should fail
|
||||
|
||||
for (auto molFileTest : molFileTests) {
|
||||
BOOST_LOG(rdInfoLog) << "Test: " << molFileTest.fileName << std::endl;
|
||||
|
||||
printf("Test\n\n %s\n\n", molFileTest.fileName.c_str());
|
||||
testMarvinMol(&molFileTest);
|
||||
}
|
||||
}
|
||||
// now the reactions
|
||||
|
||||
if (testToRun == "" || testToRun == "rxnFileTests") {
|
||||
std::list<RxnTest> rxnFileTests{
|
||||
|
||||
RxnTest("AlexRxn.mrv", true, 1, 0, 1, 2, 0),
|
||||
RxnTest("BadReactionSign.mrv", true, 2, 0, 1, 3, 0),
|
||||
RxnTest("bondArray_node.mrv", true, 2, 4, 1, 3, 0),
|
||||
RxnTest("marvin03.mrv", true, 1, 1, 1, 2, 0),
|
||||
RxnTest("marvin04.mrv", true, 2, 1, 2, 4, 0),
|
||||
RxnTest("marvin08.mrv", true, 2, 3, 2, 4, 0),
|
||||
RxnTest("marvin09.mrv", true, 2, 3, 2, 4, 0),
|
||||
RxnTest("marvin11.mrv", true, 2, 0, 1, 0, 0),
|
||||
RxnTest("marvin05.mrv", true, 2, 1, 1, 3, 0),
|
||||
RxnTest("EmptyRxn.mrv", true, 0, 0, 0, 0, 0),
|
||||
RxnTest("RxnNoCoords.mrv", true, 2, 0, 1, 3, 0),
|
||||
RxnTest("mrvValenceZero.mrv", true, 3, 0, 1, 4, 0),
|
||||
RxnTest("condition_coordinates_mpoint.mrv", true, 1, 0, 1, 0, 0),
|
||||
RxnTest("marvin01.mrv", false, 2, 1, 1, 3, 0),
|
||||
RxnTest("aspirineSynthesisWithAttributes.mrv", true, 2, 0, 1, 3, 0),
|
||||
RxnTest("marvin01.mrv", false, 2, 1, 1, 3, 0)}; // should fail
|
||||
|
||||
for (auto rxnFileTest : rxnFileTests) {
|
||||
printf("Test\n\n %s\n\n", rxnFileTest.fileName.c_str());
|
||||
testMarvinRxn(&rxnFileTest);
|
||||
}
|
||||
}
|
||||
|
||||
// now smiles tests
|
||||
|
||||
if (testToRun == "" || testToRun == "smiTests") {
|
||||
std::list<SmilesTest> smiTests{
|
||||
|
||||
SmilesTest("DoubleBondChain",
|
||||
R"(CC1=C(\C=C\C(C)=C\C=C\C(C)=C/C(O)=O)C(C)(C)CCC1)", true,
|
||||
22, 22),
|
||||
// SmilesTest(
|
||||
// "Macrocycle2",
|
||||
// R"(CC1OC(=O)CC(O)CC(O)CC(O)CCC(O)C(O)CC2(O)CC(O)C(C(CC(O[C@@H]3O[C@H](C)[C@@H](O)[C@H](N)[C@@H]3O)\C=C\C=C\C=C\C=C\CC\C=C\C=C\C(C)C(O)C1C)O2)C(O)=O
|
||||
// |t:42,44,46,48,52,54|)",
|
||||
// true, 65, 67),
|
||||
SmilesTest(
|
||||
"Na_Mg_Al_OH",
|
||||
"[OH-].[OH-].[OH-].[O--].[Na+].[Mg++].[Al+3].[Si].OC([O-])=O",
|
||||
true, 12, 3),
|
||||
SmilesTest("Pb", "[Pb]", true, 1, 0),
|
||||
SmilesTest("O_Mg_Si", "[O].[Mg].[Si]", true, 3, 0),
|
||||
SmilesTest("SquiggleBond", "CN1N=C(SC1=NC(C)=O)S(N)(=O)=O |c:2|",
|
||||
true, 14, 14),
|
||||
SmilesTest(
|
||||
"BigMacrocycle",
|
||||
"C[C@@H]1CCCCCCCCC(=O)OCCN[C@H](C)CCCCCCCCC(=O)OCCN[C@H](C)CCCCCCCCC(=O)OCCN1",
|
||||
true, 48, 48),
|
||||
SmilesTest("Smiles1", "N[C@@H]([O-])c1cc[13c]cc1", true, 9, 9)};
|
||||
|
||||
for (auto smiTest : smiTests) {
|
||||
printf("Test\n\n %s\n\n", smiTest.name.c_str());
|
||||
// RDDepict::preferCoordGen = true;
|
||||
testSmilesToMarvin(&smiTest);
|
||||
}
|
||||
}
|
||||
}
|
||||
};
|
||||
|
||||
int main(int argc, char *argv[]) {
|
||||
(void)argc;
|
||||
(void)argv;
|
||||
|
||||
MrvTests mrvTests;
|
||||
|
||||
if (argc > 1) {
|
||||
mrvTests.testToRun = argv[1];
|
||||
}
|
||||
|
||||
if (argc > 2 && std::string(argv[2]) == "generate") {
|
||||
mrvTests.generateExpectedFiles = true;
|
||||
}
|
||||
|
||||
RDLog::InitLogs();
|
||||
BOOST_LOG(rdInfoLog) << " ---- Running with POSIX locale ----- " << std::endl;
|
||||
|
||||
mrvTests.RunTests(); // run with C locale
|
||||
|
||||
return 0;
|
||||
}
|
||||
54
Code/GraphMol/MarvinParse/test_data/AlexRxn.mrv
Normal file
54
Code/GraphMol/MarvinParse/test_data/AlexRxn.mrv
Normal file
@@ -0,0 +1,54 @@
|
||||
<cml xmlns="http://www.chemaxon.com" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" version="ChemAxon file format v20.20.0, generated by vunknown" xsi:schemaLocation="http://www.chemaxon.com http://www.chemaxon.com/marvin/schema/mrvSchema_20_20_0.xsd">
|
||||
<MDocument>
|
||||
<MChemicalStruct>
|
||||
<reaction>
|
||||
<reactantList>
|
||||
<molecule molID="m1">
|
||||
<atomArray>
|
||||
<atom id="a1" elementType="C" x2="14.0398" y2="-18.000099999999996"/>
|
||||
<atom id="a2" elementType="C" x2="16.6352" y2="-17.9994"/>
|
||||
<atom id="a3" elementType="C" x2="15.34" y2="-17.25"/>
|
||||
<atom id="a4" elementType="C" x2="16.6352" y2="-19.500799999999998"/>
|
||||
<atom id="a5" elementType="C" x2="14.0398" y2="-19.5075"/>
|
||||
<atom id="a6" elementType="C" x2="15.3432" y2="-20.25"/>
|
||||
<atom id="a7" elementType="C" x2="15.34094841147386" y2="-15.750000299828137"/>
|
||||
</atomArray>
|
||||
<bondArray>
|
||||
<bond id="b1" atomRefs2="a3 a1" order="2"/>
|
||||
<bond id="b2" atomRefs2="a4 a2" order="2"/>
|
||||
<bond id="b3" atomRefs2="a1 a5" order="1"/>
|
||||
<bond id="b4" atomRefs2="a2 a3" order="1"/>
|
||||
<bond id="b5" atomRefs2="a5 a6" order="2"/>
|
||||
<bond id="b6" atomRefs2="a6 a4" order="1"/>
|
||||
<bond id="b7" atomRefs2="a3 a7" order="1"/>
|
||||
</bondArray>
|
||||
<molecule molID="m2" id="sg1" role="DataSgroup" atomRefs="a3 a7" fieldName="foo" fieldData="bar" units=""/></molecule>
|
||||
</reactantList>
|
||||
<agentList/>
|
||||
<productList>
|
||||
<molecule molID="m3">
|
||||
<atomArray>
|
||||
<atom id="a8" elementType="C" x2="21.614800000000002" y2="-18.000099999999996"/>
|
||||
<atom id="a9" elementType="C" x2="24.210199999999997" y2="-17.9994"/>
|
||||
<atom id="a10" elementType="C" x2="22.915" y2="-17.25"/>
|
||||
<atom id="a11" elementType="C" x2="24.210199999999997" y2="-19.500799999999998"/>
|
||||
<atom id="a12" elementType="C" x2="21.614800000000002" y2="-19.5075"/>
|
||||
<atom id="a13" elementType="C" x2="22.9182" y2="-20.25"/>
|
||||
<atom id="a14" elementType="C" x2="22.91594841147386" y2="-15.750000299828137"/>
|
||||
</atomArray>
|
||||
<bondArray>
|
||||
<bond id="b8" atomRefs2="a10 a8" order="2"/>
|
||||
<bond id="b9" atomRefs2="a11 a9" order="2"/>
|
||||
<bond id="b10" atomRefs2="a8 a12" order="1"/>
|
||||
<bond id="b11" atomRefs2="a9 a10" order="1"/>
|
||||
<bond id="b12" atomRefs2="a12 a13" order="2"/>
|
||||
<bond id="b13" atomRefs2="a13 a11" order="1"/>
|
||||
<bond id="b14" atomRefs2="a10 a14" order="1"/>
|
||||
</bondArray>
|
||||
</molecule>
|
||||
</productList>
|
||||
<arrow type="DEFAULT" x1="17.924999999999997" y1="-18.674999999999997" x2="20.924999999999997" y2="-18.674999999999997"/>
|
||||
</reaction>
|
||||
</MChemicalStruct>
|
||||
</MDocument>
|
||||
</cml>
|
||||
@@ -0,0 +1,2 @@
|
||||
<?xml version="1.0" encoding="utf-8"?>
|
||||
<cml xmlns="http://www.chemaxon.com" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.chemaxon.com http://www.chemaxon.com/marvin/schema/mrvSchema_20_20_0.xsd"><MDocument><MChemicalStruct><reaction><reactantList><molecule molID="m1"><atomArray><atom id="a1" elementType="C" x2="14.0398" y2="-18.0001"/><atom id="a2" elementType="C" x2="16.6352" y2="-17.9994"/><atom id="a3" elementType="C" x2="15.34" y2="-17.25" sgroupRef="sg1"/><atom id="a4" elementType="C" x2="16.6352" y2="-19.5008"/><atom id="a5" elementType="C" x2="14.0398" y2="-19.5075"/><atom id="a6" elementType="C" x2="15.3432" y2="-20.25"/><atom id="a7" elementType="C" x2="15.3409" y2="-15.75" sgroupRef="sg1"/></atomArray><bondArray><bond id="b1" atomRefs2="a3 a1" order="2"/><bond id="b2" atomRefs2="a4 a2" order="2"/><bond id="b3" atomRefs2="a1 a5" order="1"/><bond id="b4" atomRefs2="a2 a3" order="1"/><bond id="b5" atomRefs2="a5 a6" order="2"/><bond id="b6" atomRefs2="a6 a4" order="1"/><bond id="b7" atomRefs2="a3 a7" order="1"/></bondArray><molecule molID="m2" id="sg1" role="DataSgroup" atomRefs="a3 a7" context="" fieldName="foo" placement="" unitsDisplayed="Unit not displayed" fieldData="bar" x="0" y="0"/></molecule></reactantList><productList><molecule molID="m3"><atomArray><atom id="a8" elementType="C" x2="21.6148" y2="-18.0001"/><atom id="a9" elementType="C" x2="24.2102" y2="-17.9994"/><atom id="a10" elementType="C" x2="22.915" y2="-17.25"/><atom id="a11" elementType="C" x2="24.2102" y2="-19.5008"/><atom id="a12" elementType="C" x2="21.6148" y2="-19.5075"/><atom id="a13" elementType="C" x2="22.9182" y2="-20.25"/><atom id="a14" elementType="C" x2="22.9159" y2="-15.75"/></atomArray><bondArray><bond id="b8" atomRefs2="a10 a8" order="2"/><bond id="b9" atomRefs2="a11 a9" order="2"/><bond id="b10" atomRefs2="a8 a12" order="1"/><bond id="b11" atomRefs2="a9 a10" order="1"/><bond id="b12" atomRefs2="a12 a13" order="2"/><bond id="b13" atomRefs2="a13 a11" order="1"/><bond id="b14" atomRefs2="a10 a14" order="1"/></bondArray></molecule></productList><arrow type="DEFAULT" x1="17.1352" y1="-18" x2="21.1148" y2="-18"/></reaction></MChemicalStruct></MDocument></cml>
|
||||
57
Code/GraphMol/MarvinParse/test_data/AlexRxn.mrv.expected.rxn
Normal file
57
Code/GraphMol/MarvinParse/test_data/AlexRxn.mrv.expected.rxn
Normal file
@@ -0,0 +1,57 @@
|
||||
$RXN V3000
|
||||
|
||||
RDKit
|
||||
|
||||
M V30 COUNTS 1 1
|
||||
M V30 BEGIN REACTANT
|
||||
M V30 BEGIN CTAB
|
||||
M V30 COUNTS 7 7 1 0 0
|
||||
M V30 BEGIN ATOM
|
||||
M V30 1 C 14.039800 -18.000100 0.000000 0
|
||||
M V30 2 C 16.635200 -17.999400 0.000000 0
|
||||
M V30 3 C 15.340000 -17.250000 0.000000 0
|
||||
M V30 4 C 16.635200 -19.500800 0.000000 0
|
||||
M V30 5 C 14.039800 -19.507500 0.000000 0
|
||||
M V30 6 C 15.343200 -20.250000 0.000000 0
|
||||
M V30 7 C 15.340948 -15.750000 0.000000 0
|
||||
M V30 END ATOM
|
||||
M V30 BEGIN BOND
|
||||
M V30 1 2 3 1
|
||||
M V30 2 2 4 2
|
||||
M V30 3 1 1 5
|
||||
M V30 4 1 2 3
|
||||
M V30 5 2 5 6
|
||||
M V30 6 1 6 4
|
||||
M V30 7 1 3 7
|
||||
M V30 END BOND
|
||||
M V30 BEGIN SGROUP
|
||||
M V30 1 DAT 0 ATOMS=(2 3 7) FIELDNAME=foo -
|
||||
M V30 FIELDDISP=" 0.0000 0.0000 DRU ALL 0 0" -
|
||||
M V30 FIELDDATA="bar"
|
||||
M V30 END SGROUP
|
||||
M V30 END CTAB
|
||||
M V30 END REACTANT
|
||||
M V30 BEGIN PRODUCT
|
||||
M V30 BEGIN CTAB
|
||||
M V30 COUNTS 7 7 0 0 0
|
||||
M V30 BEGIN ATOM
|
||||
M V30 1 C 21.614800 -18.000100 0.000000 0
|
||||
M V30 2 C 24.210200 -17.999400 0.000000 0
|
||||
M V30 3 C 22.915000 -17.250000 0.000000 0
|
||||
M V30 4 C 24.210200 -19.500800 0.000000 0
|
||||
M V30 5 C 21.614800 -19.507500 0.000000 0
|
||||
M V30 6 C 22.918200 -20.250000 0.000000 0
|
||||
M V30 7 C 22.915948 -15.750000 0.000000 0
|
||||
M V30 END ATOM
|
||||
M V30 BEGIN BOND
|
||||
M V30 1 2 3 1
|
||||
M V30 2 2 4 2
|
||||
M V30 3 1 1 5
|
||||
M V30 4 1 2 3
|
||||
M V30 5 2 5 6
|
||||
M V30 6 1 6 4
|
||||
M V30 7 1 3 7
|
||||
M V30 END BOND
|
||||
M V30 END CTAB
|
||||
M V30 END PRODUCT
|
||||
M END
|
||||
31
Code/GraphMol/MarvinParse/test_data/AnyBond.mrv
Normal file
31
Code/GraphMol/MarvinParse/test_data/AnyBond.mrv
Normal file
@@ -0,0 +1,31 @@
|
||||
<cml xmlns="http://www.chemaxon.com" version="ChemAxon file format v20.20.0, generated by vunknown" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.chemaxon.com http://www.chemaxon.com/marvin/schema/mrvSchema_20_20_0.xsd">
|
||||
<MDocument>
|
||||
<MChemicalStruct>
|
||||
<molecule molID="m1">
|
||||
<atomArray>
|
||||
<atom id="a1" elementType="C" x2="-3.7496542115052973" y2="1.8741666666666665"/>
|
||||
<atom id="a2" elementType="C" x2="-5.083333333333333" y2="1.1041666666666667"/>
|
||||
<atom id="a3" elementType="C" x2="-3.7496542115052978" y2="3.4141666666666666" lonePair="1"/>
|
||||
<atom id="a4" elementType="C" x2="-5.083333333333334" y2="4.184166666666666" lonePair="2"/>
|
||||
</atomArray>
|
||||
<bondArray>
|
||||
<bond id="b1" atomRefs2="a2 a1" order="1"/>
|
||||
<bond id="b2" atomRefs2="a1 a3" order="1"/>
|
||||
<bond id="b3" atomRefs2="a3 a4" order="1" queryType="Any"/>
|
||||
</bondArray>
|
||||
</molecule>
|
||||
</MChemicalStruct>
|
||||
<MElectronContainer occupation="0 0" radical="0" id="o1">
|
||||
<MElectron atomRefs="m1.a3" difLoc="0.0 0.0 0.0"/>
|
||||
<MElectron atomRefs="m1.a3" difLoc="0.0 0.0 0.0"/>
|
||||
</MElectronContainer>
|
||||
<MElectronContainer occupation="0 0" radical="0" id="o2">
|
||||
<MElectron atomRefs="m1.a4" difLoc="0.0 0.0 0.0"/>
|
||||
<MElectron atomRefs="m1.a4" difLoc="0.0 0.0 0.0"/>
|
||||
</MElectronContainer>
|
||||
<MElectronContainer occupation="0 0" radical="0" id="o3">
|
||||
<MElectron atomRefs="m1.a4" difLoc="0.0 0.0 0.0"/>
|
||||
<MElectron atomRefs="m1.a4" difLoc="0.0 0.0 0.0"/>
|
||||
</MElectronContainer>
|
||||
</MDocument>
|
||||
</cml>
|
||||
@@ -0,0 +1,2 @@
|
||||
<?xml version="1.0" encoding="utf-8"?>
|
||||
<cml xmlns="http://www.chemaxon.com" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.chemaxon.com http://www.chemaxon.com/marvin/schema/mrvSchema_20_20_0.xsd"><MDocument><MChemicalStruct><molecule molID="m1"><atomArray><atom id="a1" elementType="C" x2="-3.74965" y2="1.87417"/><atom id="a2" elementType="C" x2="-5.08333" y2="1.10417"/><atom id="a3" elementType="C" x2="-3.74965" y2="3.41417"/><atom id="a4" elementType="C" x2="-5.08333" y2="4.18417"/></atomArray><bondArray><bond id="b1" atomRefs2="a2 a1" order="1"/><bond id="b2" atomRefs2="a1 a3" order="1"/><bond id="b3" atomRefs2="a3 a4" order="1" queryType="Any"/></bondArray></molecule></MChemicalStruct></MDocument></cml>
|
||||
19
Code/GraphMol/MarvinParse/test_data/AnyBond.mrv.expected.sdf
Normal file
19
Code/GraphMol/MarvinParse/test_data/AnyBond.mrv.expected.sdf
Normal file
@@ -0,0 +1,19 @@
|
||||
|
||||
RDKit 2D
|
||||
|
||||
0 0 0 0 0 0 0 0 0 0999 V3000
|
||||
M V30 BEGIN CTAB
|
||||
M V30 COUNTS 4 3 0 0 0
|
||||
M V30 BEGIN ATOM
|
||||
M V30 1 C -3.749654 1.874167 0.000000 0
|
||||
M V30 2 C -5.083333 1.104167 0.000000 0
|
||||
M V30 3 C -3.749654 3.414167 0.000000 0
|
||||
M V30 4 C -5.083333 4.184167 0.000000 0
|
||||
M V30 END ATOM
|
||||
M V30 BEGIN BOND
|
||||
M V30 1 1 2 1
|
||||
M V30 2 1 1 3
|
||||
M V30 3 8 3 4
|
||||
M V30 END BOND
|
||||
M V30 END CTAB
|
||||
M END
|
||||
235
Code/GraphMol/MarvinParse/test_data/BMS-986142_3d.mrv
Normal file
235
Code/GraphMol/MarvinParse/test_data/BMS-986142_3d.mrv
Normal file
@@ -0,0 +1,235 @@
|
||||
<cml xmlns="http://www.chemaxon.com" version="ChemAxon file format v20.20.0, generated by vunknown" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.chemaxon.com http://www.chemaxon.com/marvin/schema/mrvSchema_20_20_0.xsd">
|
||||
<MDocument>
|
||||
<MChemicalStruct>
|
||||
<molecule molID="m1" absStereo="true">
|
||||
<atomArray>
|
||||
<atom id="a1" elementType="F" x3="-2.6596266453896535" y3="-3.6622133040356264" z3="-4.145493300169387" lonePair="3"/>
|
||||
<atom id="a2" elementType="F" x3="7.858106603801813" y3="-2.6043733124983466" z3="-0.57231999542144" lonePair="3"/>
|
||||
<atom id="a3" elementType="O" x3="-3.9423999684608" y3="2.93943997648448" z3="4.551306630256214" lonePair="2"/>
|
||||
<atom id="a4" elementType="O" x3="-7.939306603152213" y3="-3.6097599711219197" z3="0.18890666515541332" lonePair="2"/>
|
||||
<atom id="a5" elementType="O" x3="2.2403733154103467" y3="1.2234133235460267" z3="-0.12413333234026667" lonePair="2"/>
|
||||
<atom id="a6" elementType="O" x3="3.0180266425224533" y3="-2.68127997854976" z3="-3.738186636761174" lonePair="2"/>
|
||||
<atom id="a7" elementType="N" x3="-5.935813285846827" y3="-1.1164533244017065" z3="0.5607466621806934" lonePair="1"/>
|
||||
<atom id="a8" elementType="N" x3="2.5364266463752534" y3="-0.7339733274615466" z3="-1.95663998434688" lonePair="1"/>
|
||||
<atom id="a9" elementType="N" x3="-7.474693273535786" y3="-5.452906623043413" z3="-1.6310933202845868" lonePair="1"/>
|
||||
<atom id="a10" elementType="N" x3="4.932666627205333" y3="-2.086746649972693" z3="-2.01487998388096" lonePair="1"/>
|
||||
<atom id="a11" elementType="C" x3="-4.4813066308162135" y3="2.7693866445115733" z3="1.8543466518318932"/>
|
||||
<atom id="a12" elementType="C" x3="-2.7985066442786133" y3="2.3887733142231466" z3="1.4225866552859734"/>
|
||||
<atom id="a13" elementType="C" x3="-5.438719956490241" y3="1.2926666563253333" z3="2.103173316507947"/>
|
||||
<atom id="a14" elementType="C" x3="-4.542533296993066" y3="3.7850399697196795" z3="3.2812266404168535"/>
|
||||
<atom id="a15" elementType="C" x3="-2.6872533118353066" y3="1.4518933217181866" z3="-0.07373333274346666"/>
|
||||
<atom id="a16" elementType="C" x3="-5.084613292656426" y3="0.15997333205354666" z3="0.8765866596539733"/>
|
||||
<atom id="a17" elementType="C" x3="-3.84215996926272" y3="0.19170666513301332" z3="-0.10303999917567999"/>
|
||||
<atom id="a18" elementType="C" x3="-3.946506635094613" y3="-1.12335999101312" z3="-1.0660533248049067"/>
|
||||
<atom id="a19" elementType="C" x3="-5.26735995786112" y3="-1.9234133179460267" z3="-0.6243999950048"/>
|
||||
<atom id="a20" elementType="C" x3="-3.5705599714355203" y3="5.22927995816576" z3="3.0646933088157864"/>
|
||||
<atom id="a21" elementType="C" x3="-6.199013283741227" y3="4.210453299649706" z3="3.6666933039997867"/>
|
||||
<atom id="a22" elementType="C" x3="-3.0486399756108797" y3="-1.71471998628224" z3="-2.2747199818022397"/>
|
||||
<atom id="a23" elementType="C" x3="-5.7287999541696" y3="-3.2888799736889602" z3="-1.33335998933312"/>
|
||||
<atom id="a24" elementType="C" x3="-3.4983199720134404" y3="-3.07887997536896" z3="-2.9930133093892266"/>
|
||||
<atom id="a25" elementType="C" x3="-1.6857866531803734" y3="-0.9133599926931201" z3="-2.77087997783296"/>
|
||||
<atom id="a26" elementType="C" x3="-4.817866628123733" y3="-3.8526133025124265" z3="-2.52727997978176"/>
|
||||
<atom id="a27" elementType="C" x3="-0.2575999979392" y3="-1.2232266568808534" z3="-2.117173316395947"/>
|
||||
<atom id="a28" elementType="C" x3="-7.103413276506027" y3="-4.103306633840213" z3="-0.85903999312768"/>
|
||||
<atom id="a29" elementType="C" x3="-1.8157066521410132" y3="0.18722666516885333" z3="-3.925786635260373"/>
|
||||
<atom id="a30" elementType="C" x3="1.0402933250109867" y3="-0.43231999654144" z3="-2.61855997905152"/>
|
||||
<atom id="a31" elementType="C" x3="-0.10863999913088" y3="-2.4055733140887465" z3="-0.8771466596494933"/>
|
||||
<atom id="a32" elementType="C" x3="-0.5176266625256533" y3="0.9785066588386133" z3="-4.426986631250773"/>
|
||||
<atom id="a33" elementType="C" x3="0.91055999271552" y3="0.6690133279812267" z3="-3.7732799698137596"/>
|
||||
<atom id="a34" elementType="C" x3="2.9689333095818666" y3="0.14429333217898666" z3="-0.6691999946464"/>
|
||||
<atom id="a35" elementType="C" x3="3.4673333055946665" y3="-1.8754399849964798" z3="-2.659253312059307"/>
|
||||
<atom id="a36" elementType="C" x3="4.4674932975933865" y3="-0.22287999821696" z3="0.017733333191466666"/>
|
||||
<atom id="a37" elementType="C" x3="5.426026623258453" y3="-1.3005066562626133" z3="-0.67087999463296"/>
|
||||
<atom id="a38" elementType="C" x3="4.925386627263573" y3="0.5517866622523733" z3="1.3555733224887465"/>
|
||||
<atom id="a39" elementType="C" x3="5.969973285573547" y3="-3.20487997436096" z3="-2.719733311575467"/>
|
||||
<atom id="a40" elementType="C" x3="6.86335994509312" y3="-1.5846133206564266" z3="0.007653333272106667"/>
|
||||
<atom id="a41" elementType="C" x3="6.34983994920128" y3="0.2527466646446933" z3="2.01375998388992"/>
|
||||
<atom id="a42" elementType="C" x3="7.3205066081026136" y3="-0.8144266601512534" z3="1.33783998929728"/>
|
||||
<atom id="a43" elementType="H" x3="-4.981946626811093" y3="3.3991999728063997" z3="0.8808799929529599"/>
|
||||
<atom id="a44" elementType="H" x3="-2.25847998193216" y3="1.7343199861254401" z3="2.3546133144964267"/>
|
||||
<atom id="a45" elementType="H" x3="-2.1097066497890133" y3="3.4243999726048" z3="1.2506666566613334"/>
|
||||
<atom id="a46" elementType="H" x3="-5.184853291854507" y3="0.7587999939296" z3="3.2136533076241065"/>
|
||||
<atom id="a47" elementType="H" x3="-6.668106613321814" y3="1.5567999875456" z3="2.0747999834015998"/>
|
||||
<atom id="a48" elementType="H" x3="-1.5189066545154133" y3="1.0042666586325333" z3="-0.16221333203562668"/>
|
||||
<atom id="a49" elementType="H" x3="-2.8869866435707734" y3="2.2129333156298667" z3="-1.0559733248855465"/>
|
||||
<atom id="a50" elementType="H" x3="-6.9075999447392" y3="-1.42687998858496" z3="1.11327999109376"/>
|
||||
<atom id="a51" elementType="H" x3="-3.843093302588587" y3="5.8211999534304" z3="1.99023998407808"/>
|
||||
<atom id="a52" elementType="H" x3="-2.3383733146263466" y3="4.98735996010112" z3="3.109866641787733"/>
|
||||
<atom id="a53" elementType="H" x3="-3.7727199698182403" y3="6.039413285018027" z3="4.006986634610773"/>
|
||||
<atom id="a54" elementType="H" x3="-6.781226612416853" y3="4.746746628692693" z3="2.6907999784736"/>
|
||||
<atom id="a55" elementType="H" x3="-6.235226616784853" y3="5.020586626501974" z3="4.629333296298666"/>
|
||||
<atom id="a56" elementType="H" x3="-6.8683999450528" y3="3.2171999742624" z3="4.048053300948907"/>
|
||||
<atom id="a57" elementType="H" x3="-3.9722666348885336" y3="3.60023997119808" z3="5.45047995639616"/>
|
||||
<atom id="a58" elementType="H" x3="-5.077706626045013" y3="-4.89887996080896" z3="-3.148133308148267"/>
|
||||
<atom id="a59" elementType="H" x3="-2.91983997664128" y3="0.44482666310805336" z3="-4.448453297745707"/>
|
||||
<atom id="a60" elementType="H" x3="-0.53423999572608" y3="-3.518853305182507" z3="-1.27735998978112"/>
|
||||
<atom id="a61" elementType="H" x3="1.0682933247869868" y3="-2.605866645819733" z3="-0.49335999605312"/>
|
||||
<atom id="a62" elementType="H" x3="-0.75935999392512" y3="-2.0559466502190933" z3="0.13943999888448"/>
|
||||
<atom id="a63" elementType="H" x3="-0.6187999950496" y3="1.83623998531008" z3="-5.325786624060373"/>
|
||||
<atom id="a64" elementType="H" x3="1.9140799846873602" y3="1.29303998965568" z3="-4.172746633284693"/>
|
||||
<atom id="a65" elementType="H" x3="-6.865039945079681" y3="-5.930959952552319" z3="-2.4962933133629863"/>
|
||||
<atom id="a66" elementType="H" x3="-8.434346599191892" y3="-6.039413285018027" z3="-1.32607998939136"/>
|
||||
<atom id="a67" elementType="H" x3="4.18655996650752" y3="1.3953333221706667" z3="1.9025066514466136"/>
|
||||
<atom id="a68" elementType="H" x3="6.179786617228373" y3="-4.14903996680768" z3="-1.91855998465152"/>
|
||||
<atom id="a69" elementType="H" x3="7.03807994369536" y3="-2.6374133122340266" z3="-3.0585333088650666"/>
|
||||
<atom id="a70" elementType="H" x3="5.472693289551787" y3="-3.7014133037220267" z3="-3.760213303251627"/>
|
||||
<atom id="a71" elementType="H" x3="6.700586613061973" y3="0.8530666598421334" z3="3.0478933089501865"/>
|
||||
<atom id="a72" elementType="H" x3="8.434346599191892" y3="-1.0537333249034666" z3="1.8437066519170133"/>
|
||||
</atomArray>
|
||||
<bondArray>
|
||||
<bond id="b1" atomRefs2="a1 a24" order="1"/>
|
||||
<bond id="b2" atomRefs2="a2 a40" order="1"/>
|
||||
<bond id="b3" atomRefs2="a3 a14" order="1"/>
|
||||
<bond id="b4" atomRefs2="a3 a57" order="1"/>
|
||||
<bond id="b5" atomRefs2="a4 a28" order="2"/>
|
||||
<bond id="b6" atomRefs2="a5 a34" order="2"/>
|
||||
<bond id="b7" atomRefs2="a6 a35" order="2"/>
|
||||
<bond id="b8" atomRefs2="a7 a16" order="1"/>
|
||||
<bond id="b9" atomRefs2="a7 a19" order="1"/>
|
||||
<bond id="b10" atomRefs2="a7 a50" order="1"/>
|
||||
<bond id="b11" atomRefs2="a8 a30" order="1"/>
|
||||
<bond id="b12" atomRefs2="a8 a34" order="1"/>
|
||||
<bond id="b13" atomRefs2="a8 a35" order="1">
|
||||
<bondStereo>H</bondStereo>
|
||||
</bond>
|
||||
<bond id="b14" atomRefs2="a9 a28" order="1"/>
|
||||
<bond id="b15" atomRefs2="a9 a65" order="1"/>
|
||||
<bond id="b16" atomRefs2="a9 a66" order="1"/>
|
||||
<bond id="b17" atomRefs2="a10 a35" order="1"/>
|
||||
<bond id="b18" atomRefs2="a10 a37" order="1"/>
|
||||
<bond id="b19" atomRefs2="a10 a39" order="1"/>
|
||||
<bond id="b20" atomRefs2="a11 a12" order="1"/>
|
||||
<bond id="b21" atomRefs2="a11 a13" order="1"/>
|
||||
<bond id="b22" atomRefs2="a11 a14" order="1"/>
|
||||
<bond id="b23" atomRefs2="a11 a43" order="1"/>
|
||||
<bond id="b24" atomRefs2="a12 a15" order="1"/>
|
||||
<bond id="b25" atomRefs2="a12 a44" order="1"/>
|
||||
<bond id="b26" atomRefs2="a12 a45" order="1"/>
|
||||
<bond id="b27" atomRefs2="a13 a16" order="1"/>
|
||||
<bond id="b28" atomRefs2="a13 a46" order="1"/>
|
||||
<bond id="b29" atomRefs2="a13 a47" order="1"/>
|
||||
<bond id="b30" atomRefs2="a14 a20" order="1"/>
|
||||
<bond id="b31" atomRefs2="a14 a21" order="1"/>
|
||||
<bond id="b32" atomRefs2="a15 a17" order="1"/>
|
||||
<bond id="b33" atomRefs2="a15 a48" order="1"/>
|
||||
<bond id="b34" atomRefs2="a15 a49" order="1"/>
|
||||
<bond id="b35" atomRefs2="a16 a17" order="2"/>
|
||||
<bond id="b36" atomRefs2="a17 a18" order="1"/>
|
||||
<bond id="b37" atomRefs2="a18 a19" order="2"/>
|
||||
<bond id="b38" atomRefs2="a18 a22" order="1"/>
|
||||
<bond id="b39" atomRefs2="a19 a23" order="1"/>
|
||||
<bond id="b40" atomRefs2="a20 a51" order="1"/>
|
||||
<bond id="b41" atomRefs2="a20 a52" order="1"/>
|
||||
<bond id="b42" atomRefs2="a20 a53" order="1"/>
|
||||
<bond id="b43" atomRefs2="a21 a54" order="1"/>
|
||||
<bond id="b44" atomRefs2="a21 a55" order="1"/>
|
||||
<bond id="b45" atomRefs2="a21 a56" order="1"/>
|
||||
<bond id="b46" atomRefs2="a22 a24" order="2"/>
|
||||
<bond id="b47" atomRefs2="a22 a25" order="1"/>
|
||||
<bond id="b48" atomRefs2="a23 a26" order="2"/>
|
||||
<bond id="b49" atomRefs2="a23 a28" order="1"/>
|
||||
<bond id="b50" atomRefs2="a24 a26" order="1"/>
|
||||
<bond id="b51" atomRefs2="a25 a27" order="2"/>
|
||||
<bond id="b52" atomRefs2="a25 a29" order="1"/>
|
||||
<bond id="b53" atomRefs2="a26 a58" order="1"/>
|
||||
<bond id="b54" atomRefs2="a27 a30" order="1"/>
|
||||
<bond id="b55" atomRefs2="a27 a31" order="1"/>
|
||||
<bond id="b56" atomRefs2="a29 a32" order="2"/>
|
||||
<bond id="b57" atomRefs2="a29 a59" order="1"/>
|
||||
<bond id="b58" atomRefs2="a30 a33" order="2"/>
|
||||
<bond id="b59" atomRefs2="a31 a60" order="1"/>
|
||||
<bond id="b60" atomRefs2="a31 a61" order="1"/>
|
||||
<bond id="b61" atomRefs2="a31 a62" order="1"/>
|
||||
<bond id="b62" atomRefs2="a32 a33" order="1"/>
|
||||
<bond id="b63" atomRefs2="a32 a63" order="1"/>
|
||||
<bond id="b64" atomRefs2="a33 a64" order="1"/>
|
||||
<bond id="b65" atomRefs2="a34 a36" order="1"/>
|
||||
<bond id="b66" atomRefs2="a36 a37" order="2"/>
|
||||
<bond id="b67" atomRefs2="a36 a38" order="1"/>
|
||||
<bond id="b68" atomRefs2="a37 a40" order="1"/>
|
||||
<bond id="b69" atomRefs2="a38 a41" order="2"/>
|
||||
<bond id="b70" atomRefs2="a38 a67" order="1"/>
|
||||
<bond id="b71" atomRefs2="a39 a68" order="1"/>
|
||||
<bond id="b72" atomRefs2="a39 a69" order="1"/>
|
||||
<bond id="b73" atomRefs2="a39 a70" order="1"/>
|
||||
<bond id="b74" atomRefs2="a40 a42" order="2"/>
|
||||
<bond id="b75" atomRefs2="a41 a42" order="1"/>
|
||||
<bond id="b76" atomRefs2="a41 a71" order="1"/>
|
||||
<bond id="b77" atomRefs2="a42 a72" order="1"/>
|
||||
</bondArray>
|
||||
</molecule>
|
||||
</MChemicalStruct>
|
||||
<MElectronContainer occupation="0 0" radical="0" id="o1">
|
||||
<MElectron atomRefs="m1.a1" difLoc="0.0 0.0 0.0"/>
|
||||
<MElectron atomRefs="m1.a1" difLoc="0.0 0.0 0.0"/>
|
||||
</MElectronContainer>
|
||||
<MElectronContainer occupation="0 0" radical="0" id="o2">
|
||||
<MElectron atomRefs="m1.a1" difLoc="0.0 0.0 0.0"/>
|
||||
<MElectron atomRefs="m1.a1" difLoc="0.0 0.0 0.0"/>
|
||||
</MElectronContainer>
|
||||
<MElectronContainer occupation="0 0" radical="0" id="o3">
|
||||
<MElectron atomRefs="m1.a1" difLoc="0.0 0.0 0.0"/>
|
||||
<MElectron atomRefs="m1.a1" difLoc="0.0 0.0 0.0"/>
|
||||
</MElectronContainer>
|
||||
<MElectronContainer occupation="0 0" radical="0" id="o4">
|
||||
<MElectron atomRefs="m1.a2" difLoc="0.0 0.0 0.0"/>
|
||||
<MElectron atomRefs="m1.a2" difLoc="0.0 0.0 0.0"/>
|
||||
</MElectronContainer>
|
||||
<MElectronContainer occupation="0 0" radical="0" id="o5">
|
||||
<MElectron atomRefs="m1.a2" difLoc="0.0 0.0 0.0"/>
|
||||
<MElectron atomRefs="m1.a2" difLoc="0.0 0.0 0.0"/>
|
||||
</MElectronContainer>
|
||||
<MElectronContainer occupation="0 0" radical="0" id="o6">
|
||||
<MElectron atomRefs="m1.a2" difLoc="0.0 0.0 0.0"/>
|
||||
<MElectron atomRefs="m1.a2" difLoc="0.0 0.0 0.0"/>
|
||||
</MElectronContainer>
|
||||
<MElectronContainer occupation="0 0" radical="0" id="o7">
|
||||
<MElectron atomRefs="m1.a3" difLoc="0.0 0.0 0.0"/>
|
||||
<MElectron atomRefs="m1.a3" difLoc="0.0 0.0 0.0"/>
|
||||
</MElectronContainer>
|
||||
<MElectronContainer occupation="0 0" radical="0" id="o8">
|
||||
<MElectron atomRefs="m1.a3" difLoc="0.0 0.0 0.0"/>
|
||||
<MElectron atomRefs="m1.a3" difLoc="0.0 0.0 0.0"/>
|
||||
</MElectronContainer>
|
||||
<MElectronContainer occupation="0 0" radical="0" id="o9">
|
||||
<MElectron atomRefs="m1.a4" difLoc="0.0 0.0 0.0"/>
|
||||
<MElectron atomRefs="m1.a4" difLoc="0.0 0.0 0.0"/>
|
||||
</MElectronContainer>
|
||||
<MElectronContainer occupation="0 0" radical="0" id="o10">
|
||||
<MElectron atomRefs="m1.a4" difLoc="0.0 0.0 0.0"/>
|
||||
<MElectron atomRefs="m1.a4" difLoc="0.0 0.0 0.0"/>
|
||||
</MElectronContainer>
|
||||
<MElectronContainer occupation="0 0" radical="0" id="o11">
|
||||
<MElectron atomRefs="m1.a5" difLoc="0.0 0.0 0.0"/>
|
||||
<MElectron atomRefs="m1.a5" difLoc="0.0 0.0 0.0"/>
|
||||
</MElectronContainer>
|
||||
<MElectronContainer occupation="0 0" radical="0" id="o12">
|
||||
<MElectron atomRefs="m1.a5" difLoc="0.0 0.0 0.0"/>
|
||||
<MElectron atomRefs="m1.a5" difLoc="0.0 0.0 0.0"/>
|
||||
</MElectronContainer>
|
||||
<MElectronContainer occupation="0 0" radical="0" id="o13">
|
||||
<MElectron atomRefs="m1.a6" difLoc="0.0 0.0 0.0"/>
|
||||
<MElectron atomRefs="m1.a6" difLoc="0.0 0.0 0.0"/>
|
||||
</MElectronContainer>
|
||||
<MElectronContainer occupation="0 0" radical="0" id="o14">
|
||||
<MElectron atomRefs="m1.a6" difLoc="0.0 0.0 0.0"/>
|
||||
<MElectron atomRefs="m1.a6" difLoc="0.0 0.0 0.0"/>
|
||||
</MElectronContainer>
|
||||
<MElectronContainer occupation="0 0" radical="0" id="o15">
|
||||
<MElectron atomRefs="m1.a7" difLoc="0.0 0.0 0.0"/>
|
||||
<MElectron atomRefs="m1.a7" difLoc="0.0 0.0 0.0"/>
|
||||
</MElectronContainer>
|
||||
<MElectronContainer occupation="0 0" radical="0" id="o16">
|
||||
<MElectron atomRefs="m1.a8" difLoc="0.0 0.0 0.0"/>
|
||||
<MElectron atomRefs="m1.a8" difLoc="0.0 0.0 0.0"/>
|
||||
</MElectronContainer>
|
||||
<MElectronContainer occupation="0 0" radical="0" id="o17">
|
||||
<MElectron atomRefs="m1.a9" difLoc="0.0 0.0 0.0"/>
|
||||
<MElectron atomRefs="m1.a9" difLoc="0.0 0.0 0.0"/>
|
||||
</MElectronContainer>
|
||||
<MElectronContainer occupation="0 0" radical="0" id="o18">
|
||||
<MElectron atomRefs="m1.a10" difLoc="0.0 0.0 0.0"/>
|
||||
<MElectron atomRefs="m1.a10" difLoc="0.0 0.0 0.0"/>
|
||||
</MElectronContainer>
|
||||
</MDocument>
|
||||
</cml>
|
||||
59
Code/GraphMol/MarvinParse/test_data/BadReactionSign.mrv
Normal file
59
Code/GraphMol/MarvinParse/test_data/BadReactionSign.mrv
Normal file
@@ -0,0 +1,59 @@
|
||||
<?xml version="1.0"?>
|
||||
<cml xmlns="http://www.chemaxon.com" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" version="ChemAxon file format v18.11.0, generated by vunknown" xsi:schemaLocation="http://www.chemaxon.com http://www.chemaxon.com/marvin/schema/mrvSchema_18_11_0.xsd">
|
||||
<MDocument>
|
||||
<MChemicalStruct>
|
||||
<reaction>
|
||||
<arrow type="DEFAULT" x1="-2.25" y1="-0.22916666666666666" x2="3.208333333333334" y2="-0.22916666666666666"/>
|
||||
<reactantList>
|
||||
<molecule molID="m1">
|
||||
<atomArray>
|
||||
<atom id="a1" elementType="C" x2="-12.958333333333334" y2="3.3958333333333335"/>
|
||||
</atomArray>
|
||||
<bondArray/>
|
||||
</molecule>
|
||||
<molecule molID="m2">
|
||||
<atomArray>
|
||||
<atom id="a1" elementType="C" x2="-6.208426666665918" y2="-2.105740012320748"/>
|
||||
<atom id="a2" elementType="C" x2="-7.541973322664212" y2="-2.875740006160747"/>
|
||||
<atom id="a3" elementType="C" x2="-7.541973322664212" y2="-4.415926660505921"/>
|
||||
<atom id="a4" elementType="C" x2="-6.208426666665918" y2="-5.185926654345921"/>
|
||||
<atom id="a5" elementType="C" x2="-4.874693344002454" y2="-4.415926660505921"/>
|
||||
<atom id="a6" elementType="C" x2="-4.874693344002454" y2="-2.875740006160747"/>
|
||||
</atomArray>
|
||||
<bondArray>
|
||||
<bond id="b1" atomRefs2="a1 a2" order="2"/>
|
||||
<bond id="b2" atomRefs2="a2 a3" order="1"/>
|
||||
<bond id="b3" atomRefs2="a3 a4" order="2"/>
|
||||
<bond id="b4" atomRefs2="a4 a5" order="1"/>
|
||||
<bond id="b5" atomRefs2="a5 a6" order="2"/>
|
||||
<bond id="b6" atomRefs2="a6 a1" order="1"/>
|
||||
</bondArray>
|
||||
</molecule>
|
||||
</reactantList>
|
||||
<agentList/>
|
||||
<productList>
|
||||
<molecule molID="m3">
|
||||
<atomArray>
|
||||
<atom id="a1" elementType="C" x2="8.416573333334082" y2="-1.18907334565408"/>
|
||||
<atom id="a2" elementType="C" x2="7.083026677335788" y2="-1.9590733394940791"/>
|
||||
<atom id="a3" elementType="C" x2="7.083026677335788" y2="-3.499259993839253"/>
|
||||
<atom id="a4" elementType="C" x2="8.416573333334082" y2="-4.269259987679253"/>
|
||||
<atom id="a5" elementType="C" x2="9.750306655997546" y2="-3.499259993839253"/>
|
||||
<atom id="a6" elementType="C" x2="9.750306655997546" y2="-1.9590733394940791"/>
|
||||
<atom id="a7" elementType="C" x2="8.577547166766267" y2="0.34249037321306086"/>
|
||||
</atomArray>
|
||||
<bondArray>
|
||||
<bond id="b1" atomRefs2="a1 a2" order="2"/>
|
||||
<bond id="b2" atomRefs2="a2 a3" order="1"/>
|
||||
<bond id="b3" atomRefs2="a3 a4" order="2"/>
|
||||
<bond id="b4" atomRefs2="a4 a5" order="1"/>
|
||||
<bond id="b5" atomRefs2="a5 a6" order="2"/>
|
||||
<bond id="b6" atomRefs2="a6 a1" order="1"/>
|
||||
<bond id="b7" atomRefs2="a1 a7" order="1"/>
|
||||
</bondArray>
|
||||
</molecule>
|
||||
</productList>
|
||||
</reaction>
|
||||
</MChemicalStruct>
|
||||
</MDocument>
|
||||
</cml>
|
||||
@@ -0,0 +1,2 @@
|
||||
<?xml version="1.0" encoding="utf-8"?>
|
||||
<cml xmlns="http://www.chemaxon.com" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.chemaxon.com http://www.chemaxon.com/marvin/schema/mrvSchema_20_20_0.xsd"><MDocument><MChemicalStruct><reaction><reactantList><molecule molID="m1"><atomArray><atom id="a1" elementType="C" x2="-12.9583" y2="3.39583"/></atomArray></molecule><molecule molID="m2"><atomArray><atom id="a2" elementType="C" x2="-6.20843" y2="-2.10574"/><atom id="a3" elementType="C" x2="-7.54197" y2="-2.87574"/><atom id="a4" elementType="C" x2="-7.54197" y2="-4.41593"/><atom id="a5" elementType="C" x2="-6.20843" y2="-5.18593"/><atom id="a6" elementType="C" x2="-4.87469" y2="-4.41593"/><atom id="a7" elementType="C" x2="-4.87469" y2="-2.87574"/></atomArray><bondArray><bond id="b1" atomRefs2="a2 a3" order="2"/><bond id="b2" atomRefs2="a3 a4" order="1"/><bond id="b3" atomRefs2="a4 a5" order="2"/><bond id="b4" atomRefs2="a5 a6" order="1"/><bond id="b5" atomRefs2="a6 a7" order="2"/><bond id="b6" atomRefs2="a7 a2" order="1"/></bondArray></molecule></reactantList><productList><molecule molID="m3"><atomArray><atom id="a8" elementType="C" x2="8.41657" y2="-1.18907"/><atom id="a9" elementType="C" x2="7.08303" y2="-1.95907"/><atom id="a10" elementType="C" x2="7.08303" y2="-3.49926"/><atom id="a11" elementType="C" x2="8.41657" y2="-4.26926"/><atom id="a12" elementType="C" x2="9.75031" y2="-3.49926"/><atom id="a13" elementType="C" x2="9.75031" y2="-1.95907"/><atom id="a14" elementType="C" x2="8.57755" y2="0.34249"/></atomArray><bondArray><bond id="b7" atomRefs2="a8 a9" order="2"/><bond id="b8" atomRefs2="a9 a10" order="1"/><bond id="b9" atomRefs2="a10 a11" order="2"/><bond id="b10" atomRefs2="a11 a12" order="1"/><bond id="b11" atomRefs2="a12 a13" order="2"/><bond id="b12" atomRefs2="a13 a8" order="1"/><bond id="b13" atomRefs2="a8 a14" order="1"/></bondArray></molecule></productList><arrow type="DEFAULT" x1="-4.37469" y1="-1.42922" x2="6.58303" y2="-1.42922"/></reaction></MChemicalStruct><MReactionSign id="o1" toptions="NOROT" fontScale="14.0" halign="CENTER" valign="CENTER" autoSize="true"><Field name="text">{D font=SansSerif,size=18,bold}+</Field><MPoint x="-9.58333" y="0.645047"/><MPoint x="-8.58333" y="0.645047"/><MPoint x="-8.58333" y="1.64505"/><MPoint x="-9.58333" y="1.64505"/></MReactionSign></MDocument></cml>
|
||||
@@ -0,0 +1,56 @@
|
||||
$RXN V3000
|
||||
|
||||
RDKit
|
||||
|
||||
M V30 COUNTS 2 1
|
||||
M V30 BEGIN REACTANT
|
||||
M V30 BEGIN CTAB
|
||||
M V30 COUNTS 1 0 0 0 0
|
||||
M V30 BEGIN ATOM
|
||||
M V30 1 C -12.958333 3.395833 0.000000 0
|
||||
M V30 END ATOM
|
||||
M V30 END CTAB
|
||||
M V30 BEGIN CTAB
|
||||
M V30 COUNTS 6 6 0 0 0
|
||||
M V30 BEGIN ATOM
|
||||
M V30 1 C -6.208427 -2.105740 0.000000 0
|
||||
M V30 2 C -7.541973 -2.875740 0.000000 0
|
||||
M V30 3 C -7.541973 -4.415927 0.000000 0
|
||||
M V30 4 C -6.208427 -5.185927 0.000000 0
|
||||
M V30 5 C -4.874693 -4.415927 0.000000 0
|
||||
M V30 6 C -4.874693 -2.875740 0.000000 0
|
||||
M V30 END ATOM
|
||||
M V30 BEGIN BOND
|
||||
M V30 1 2 1 2
|
||||
M V30 2 1 2 3
|
||||
M V30 3 2 3 4
|
||||
M V30 4 1 4 5
|
||||
M V30 5 2 5 6
|
||||
M V30 6 1 6 1
|
||||
M V30 END BOND
|
||||
M V30 END CTAB
|
||||
M V30 END REACTANT
|
||||
M V30 BEGIN PRODUCT
|
||||
M V30 BEGIN CTAB
|
||||
M V30 COUNTS 7 7 0 0 0
|
||||
M V30 BEGIN ATOM
|
||||
M V30 1 C 8.416573 -1.189073 0.000000 0
|
||||
M V30 2 C 7.083027 -1.959073 0.000000 0
|
||||
M V30 3 C 7.083027 -3.499260 0.000000 0
|
||||
M V30 4 C 8.416573 -4.269260 0.000000 0
|
||||
M V30 5 C 9.750307 -3.499260 0.000000 0
|
||||
M V30 6 C 9.750307 -1.959073 0.000000 0
|
||||
M V30 7 C 8.577547 0.342490 0.000000 0
|
||||
M V30 END ATOM
|
||||
M V30 BEGIN BOND
|
||||
M V30 1 2 1 2
|
||||
M V30 2 1 2 3
|
||||
M V30 3 2 3 4
|
||||
M V30 4 1 4 5
|
||||
M V30 5 2 5 6
|
||||
M V30 6 1 6 1
|
||||
M V30 7 1 1 7
|
||||
M V30 END BOND
|
||||
M V30 END CTAB
|
||||
M V30 END PRODUCT
|
||||
M END
|
||||
92
Code/GraphMol/MarvinParse/test_data/BadRxn.rxn
Normal file
92
Code/GraphMol/MarvinParse/test_data/BadRxn.rxn
Normal file
@@ -0,0 +1,92 @@
|
||||
$RXN
|
||||
|
||||
RDKit
|
||||
|
||||
2 1 0
|
||||
$MOL
|
||||
|
||||
RDKit 2D
|
||||
|
||||
5 4 0 0 0 0 0 0 0 0999 V2000
|
||||
0.6757 -0.8003 0.0000 C 0 0 0 0 0 0 0 1 0 0 0 0
|
||||
1.0897 -1.0393 0.0000 C 0 0 0 0 0 0 0 1 0 0 0 0
|
||||
1.5040 -0.8003 0.0000 C 0 0 0 0 0 0 0 1 0 0 0 0
|
||||
1.9183 -1.0393 0.0000 C 0 0 0 0 0 0 0 1 0 0 0 0
|
||||
0.2613 -1.0393 0.0000 Cl 0 0 0 0 0 0 0 1 0 0 0 0
|
||||
1 2 2 0
|
||||
2 3 1 0
|
||||
3 4 2 0
|
||||
1 5 1 0
|
||||
M END
|
||||
$MOL
|
||||
|
||||
RDKit 2D
|
||||
|
||||
10 9 0 1 0 0 0 0 0 0999 V2000
|
||||
3.6693 -0.2480 0.0000 C 0 0 0 0 0 0 0 1 0 0 0 0
|
||||
3.6693 -0.7263 0.0000 C 0 0 0 0 0 0 0 1 0 0 0 0
|
||||
3.2550 -0.0087 0.0000 C 0 0 0 0 0 0 0 1 0 0 0 0
|
||||
3.2550 -0.9653 0.0000 O 0 0 0 0 0 0 0 1 0 0 0 0
|
||||
4.0833 -0.9653 0.0000 O 0 0 0 0 0 0 0 1 0 0 0 0
|
||||
4.0833 -1.4437 0.0000 C 0 0 0 0 0 0 0 1 0 0 0 0
|
||||
4.4977 -1.6830 0.0000 C 0 0 0 0 0 0 0 1 0 0 0 0
|
||||
4.1593 -2.0213 0.0000 F 0 0 0 0 0 0 0 1 0 0 0 0
|
||||
4.8357 -2.0213 0.0000 F 0 0 0 0 0 0 0 1 0 0 0 0
|
||||
4.8357 -1.3450 0.0000 F 0 0 0 0 0 0 0 1 0 0 0 0
|
||||
7 8 1 0
|
||||
7 9 1 0
|
||||
7 10 1 0
|
||||
1 2 1 0
|
||||
1 3 2 0
|
||||
2 4 2 0
|
||||
2 5 1 0
|
||||
5 6 1 0
|
||||
6 7 1 0
|
||||
M STY 1 1 SUP
|
||||
M SLB 1 1 1
|
||||
M SAL 1 4 7 8 9 10
|
||||
M SDI 1 4 0.0000 0.0000 0.0000 0.0000
|
||||
M SDI 1 4 0.0000 0.0000 0.0000 0.0000
|
||||
M SMT 1 CF3
|
||||
M END
|
||||
$MOL
|
||||
|
||||
RDKit 2D
|
||||
|
||||
14 14 0 1 1 0 0 0 0 0999 V2000
|
||||
6.9843 -1.0150 0.0000 C 0 0 0 0 0 0 0 2 0 0 0 0
|
||||
6.9843 -1.4933 0.0000 C 0 0 0 0 0 0 0 2 0 0 0 0
|
||||
7.3987 -1.7327 0.0000 C 0 0 0 0 0 0 0 2 0 0 0 0
|
||||
7.8130 -1.4933 0.0000 C 0 0 0 0 0 0 0 2 0 0 0 0
|
||||
7.8130 -1.0150 0.0000 C 0 0 0 0 0 0 0 2 0 0 0 0
|
||||
7.3987 -0.7760 0.0000 C 0 0 0 0 0 0 0 2 0 0 0 0
|
||||
8.2270 -0.7760 0.0000 C 0 0 0 0 0 0 0 2 0 0 0 0
|
||||
8.2270 -0.2977 0.0000 O 0 0 0 0 0 0 0 2 0 0 0 0
|
||||
8.6413 -1.0150 0.0000 O 0 0 0 0 0 0 0 2 0 0 0 0
|
||||
9.0557 -0.7760 0.0000 C 0 0 0 0 0 0 0 2 0 0 0 0
|
||||
9.4700 -1.0150 0.0000 C 0 0 0 0 0 0 0 2 0 0 0 0
|
||||
9.7090 -0.6007 0.0000 F 0 0 0 0 0 0 0 2 0 0 0 0
|
||||
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108
Code/GraphMol/MarvinParse/test_data/BigMacrocycle.expected.sdf
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Normal file
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||||
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108
Code/GraphMol/MarvinParse/test_data/BigMacrocycle.sdf
Normal file
108
Code/GraphMol/MarvinParse/test_data/BigMacrocycle.sdf
Normal file
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|
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|
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RDKit 2D
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
103
Code/GraphMol/MarvinParse/test_data/BondTypes.mrv
Normal file
103
Code/GraphMol/MarvinParse/test_data/BondTypes.mrv
Normal file
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||||
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||||
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|
||||
<atom id="a16" elementType="C" x2="-0.34367984228391935" y2="3.800110497522623"/>
|
||||
<atom id="a17" elementType="C" x2="-3.5366733309241507" y2="3.6664716775288415"/>
|
||||
<atom id="a18" elementType="C" x2="0.31894503662735685" y2="-0.2724307253030429"/>
|
||||
<atom id="a19" elementType="C" x2="3.4313411526534545" y2="1.3990975782127824"/>
|
||||
<atom id="a20" elementType="C" x2="4.937688457783516" y2="1.7192815820721317"/>
|
||||
<atom id="a21" elementType="C" x2="6.444035762913576" y2="1.3990975782127824"/>
|
||||
<atom id="a22" elementType="C" x2="7.850895767683181" y2="2.0254720085495146"/>
|
||||
<atom id="a23" elementType="C" x2="1.8861167449447838" y2="3.4128732330722453"/>
|
||||
<atom id="a24" elementType="C" x2="3.3507437800393203" y2="-0.13879190530926144"/>
|
||||
<atom id="a25" elementType="C" x2="4.937688457783516" y2="3.2592815820721315"/>
|
||||
<atom id="a26" elementType="C" x2="6.605009596345763" y2="-0.13246614065435858"/>
|
||||
</atomArray>
|
||||
<bondArray>
|
||||
<bond id="b1" atomRefs2="a2 a1" order="1"/>
|
||||
<bond id="b2" atomRefs2="a1 a3" order="1"/>
|
||||
<bond id="b3" atomRefs2="a3 a4" order="1"/>
|
||||
<bond id="b4" atomRefs2="a4 a5" order="1"/>
|
||||
<bond id="b5" atomRefs2="a5 a6" order="1"/>
|
||||
<bond id="b6" atomRefs2="a6 a7" order="1"/>
|
||||
<bond id="b7" atomRefs2="a7 a8" order="1"/>
|
||||
<bond id="b8" atomRefs2="a8 a9" order="1"/>
|
||||
<bond id="b9" atomRefs2="a9 a10" order="1"/>
|
||||
<bond id="b10" atomRefs2="a1 a11" order="1">
|
||||
<bondStereo>W</bondStereo>
|
||||
</bond>
|
||||
<bond id="b11" atomRefs2="a3 a12" order="1">
|
||||
<bondStereo convention="MDL" conventionValue="4"/>
|
||||
</bond>
|
||||
<bond id="b12" atomRefs2="a4 a13" convention="cxn:coord"/>
|
||||
<bond id="b13" atomRefs2="a5 a14" order="1" queryType="Any"/>
|
||||
<bond id="b14" atomRefs2="a7 a15" order="1" queryType="SA"/>
|
||||
<bond id="b15" atomRefs2="a8 a16" order="2">
|
||||
<bondStereo convention="MDL" conventionValue="1"/>
|
||||
</bond>
|
||||
<bond id="b16" atomRefs2="a6 a17" order="2">
|
||||
<bondStereo convention="MDL" conventionValue="3"/>
|
||||
</bond>
|
||||
<bond id="b17" atomRefs2="a9 a18" order="2">
|
||||
<bondStereo convention="MDL" conventionValue="4"/>
|
||||
</bond>
|
||||
<bond id="b18" atomRefs2="a10 a19" order="1"/>
|
||||
<bond id="b19" atomRefs2="a19 a20" order="1"/>
|
||||
<bond id="b20" atomRefs2="a20 a21" order="1"/>
|
||||
<bond id="b21" atomRefs2="a21 a22" order="1"/>
|
||||
<bond id="b22" atomRefs2="a10 a23" order="1">
|
||||
<bondStereo dictRef="cml:W"/>
|
||||
</bond>
|
||||
<bond id="b23" atomRefs2="a19 a24" order="1">
|
||||
<bondStereo convention="MDL" conventionValue="6"/>
|
||||
</bond>
|
||||
<bond id="b24" atomRefs2="a20 a25" order="1">
|
||||
<bondStereo dictRef="cml:H"/>
|
||||
</bond>
|
||||
<bond id="b25" atomRefs2="a21 a26" order="1"/>
|
||||
</bondArray>
|
||||
</molecule>
|
||||
</MChemicalStruct>
|
||||
<MElectronContainer occupation="0 0" radical="0" id="o1">
|
||||
<MElectron atomRefs="m1.a5" difLoc="0.0 0.0 0.0"/>
|
||||
<MElectron atomRefs="m1.a5" difLoc="0.0 0.0 0.0"/>
|
||||
</MElectronContainer>
|
||||
<MElectronContainer occupation="0 0" radical="0" id="o2">
|
||||
<MElectron atomRefs="m1.a7" difLoc="0.0 0.0 0.0"/>
|
||||
<MElectron atomRefs="m1.a7" difLoc="0.0 0.0 0.0"/>
|
||||
</MElectronContainer>
|
||||
<MElectronContainer occupation="0 0" radical="0" id="o3">a
|
||||
<MElectron atomRefs="m1.a14" difLoc="0.0 0.0 0.0"/>
|
||||
<MElectron atomRefs="m1.a14" difLoc="0.0 0.0 0.0"/>
|
||||
</MElectronContainer>
|
||||
<MElectronContainer occupation="0 0" radical="0" id="o4">
|
||||
<MElectron atomRefs="m1.a14" difLoc="0.0 0.0 0.0"/>
|
||||
<MElectron atomRefs="m1.a14" difLoc="0.0 0.0 0.0"/>
|
||||
</MElectronContainer>
|
||||
<MElectronContainer occupation="0 0" radical="0" id="o5">
|
||||
<MElectron atomRefs="m1.a15" difLoc="0.0 0.0 0.0"/>
|
||||
<MElectron atomRefs="m1.a15" difLoc="0.0 0.0 0.0"/>
|
||||
</MElectronContainer>
|
||||
<MElectronContainer occupation="0 0" radical="0" id="o6">
|
||||
<MElectron atomRefs="m1.a15" difLoc="0.0 0.0 0.0"/>
|
||||
<MElectron atomRefs="m1.a15" difLoc="0.0 0.0 0.0"/>
|
||||
</MElectronContainer>
|
||||
</MDocument>
|
||||
</cml>
|
||||
@@ -0,0 +1,2 @@
|
||||
<?xml version="1.0" encoding="utf-8"?>
|
||||
<cml xmlns="http://www.chemaxon.com" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.chemaxon.com http://www.chemaxon.com/marvin/schema/mrvSchema_20_20_0.xsd"><MDocument><MChemicalStruct><molecule molID="m1"><atomArray><atom id="a1" elementType="C" x2="-8.93715" y2="2.41583"/><atom id="a2" elementType="C" x2="-10.2708" y2="1.64583"/><atom id="a3" elementType="C" x2="-7.60348" y2="1.64583"/><atom id="a4" elementType="C" x2="-6.19662" y2="2.27221"/><atom id="a5" elementType="C" x2="-4.86294" y2="1.50221"/><atom id="a6" elementType="C" x2="-3.45608" y2="2.12858"/><atom id="a7" elementType="C" x2="-1.99145" y2="1.6527"/><atom id="a8" elementType="C" x2="-0.584589" y2="2.27907"/><atom id="a9" elementType="C" x2="0.559854" y2="1.24861"/><atom id="a10" elementType="C" x2="1.96671" y2="1.87498"/><atom id="a11" elementType="C" x2="-8.93715" y2="3.95583"/><atom id="a12" elementType="C" x2="-7.68407" y2="0.107944"/><atom id="a13" elementType="C" x2="-6.11602" y2="3.8101"/><atom id="a14" elementType="C" x2="-4.94353" y2="-0.0356817"/><atom id="a15" elementType="C" x2="-1.91085" y2="0.114807"/><atom id="a16" elementType="C" x2="-0.34368" y2="3.80011"/><atom id="a17" elementType="C" x2="-3.53667" y2="3.66647"/><atom id="a18" elementType="C" x2="0.318945" y2="-0.272431"/><atom id="a19" elementType="C" x2="3.43134" y2="1.3991"/><atom id="a20" elementType="C" x2="4.93769" y2="1.71928"/><atom id="a21" elementType="C" x2="6.44404" y2="1.3991"/><atom id="a22" elementType="C" x2="7.8509" y2="2.02547"/><atom id="a23" elementType="C" x2="1.88612" y2="3.41287"/><atom id="a24" elementType="C" x2="3.35074" y2="-0.138792"/><atom id="a25" elementType="C" x2="4.93769" y2="3.25928"/><atom id="a26" elementType="C" x2="6.60501" y2="-0.132466"/></atomArray><bondArray><bond id="b1" atomRefs2="a2 a1" order="1"/><bond id="b2" atomRefs2="a1 a3" order="1"/><bond id="b3" atomRefs2="a3 a4" order="1"/><bond id="b4" atomRefs2="a4 a5" order="1"/><bond id="b5" atomRefs2="a5 a6" order="1"/><bond id="b6" atomRefs2="a6 a7" order="1"/><bond id="b7" atomRefs2="a7 a8" order="1"/><bond id="b8" atomRefs2="a8 a9" order="1"/><bond id="b9" atomRefs2="a9 a10" order="1"/><bond id="b10" atomRefs2="a1 a11" order="1"><bondStereo>W</bondStereo></bond><bond id="b11" atomRefs2="a3 a12" order="1"><bondStereo convention="MDL" conventionValue="4"/></bond><bond id="b12" atomRefs2="a4 a13" convention="cxn:coord"/><bond id="b13" atomRefs2="a5 a14" order="1" queryType="Any"/><bond id="b14" atomRefs2="a7 a15" order="1" queryType="SA"/><bond id="b15" atomRefs2="a8 a16" order="1"><bondStereo>W</bondStereo></bond><bond id="b16" atomRefs2="a6 a17" order="2"><bondStereo convention="MDL" conventionValue="3"/></bond><bond id="b17" atomRefs2="a9 a18" order="1"><bondStereo convention="MDL" conventionValue="4"/></bond><bond id="b18" atomRefs2="a10 a19" order="1"/><bond id="b19" atomRefs2="a19 a20" order="1"/><bond id="b20" atomRefs2="a20 a21" order="1"/><bond id="b21" atomRefs2="a21 a22" order="1"/><bond id="b22" atomRefs2="a10 a23" order="1"><bondStereo>W</bondStereo></bond><bond id="b23" atomRefs2="a19 a24" order="1"><bondStereo>H</bondStereo></bond><bond id="b24" atomRefs2="a20 a25" order="1"><bondStereo>H</bondStereo></bond><bond id="b25" atomRefs2="a21 a26" order="1"/></bondArray></molecule></MChemicalStruct></MDocument></cml>
|
||||
@@ -0,0 +1,63 @@
|
||||
|
||||
RDKit 2D
|
||||
|
||||
0 0 0 0 0 0 0 0 0 0999 V3000
|
||||
M V30 BEGIN CTAB
|
||||
M V30 COUNTS 26 25 0 0 0
|
||||
M V30 BEGIN ATOM
|
||||
M V30 1 C -8.937154 2.415833 0.000000 0
|
||||
M V30 2 C -10.270833 1.645833 0.000000 0
|
||||
M V30 3 C -7.603475 1.645833 0.000000 0
|
||||
M V30 4 C -6.196615 2.272208 0.000000 0
|
||||
M V30 5 C -4.862936 1.502208 0.000000 0
|
||||
M V30 6 C -3.456076 2.128582 0.000000 0
|
||||
M V30 7 C -1.991449 1.652696 0.000000 0
|
||||
M V30 8 C -0.584589 2.279070 0.000000 0
|
||||
M V30 9 C 0.559854 1.248609 0.000000 0
|
||||
M V30 10 C 1.966714 1.874984 0.000000 0
|
||||
M V30 11 C -8.937154 3.955833 0.000000 0
|
||||
M V30 12 C -7.684072 0.107944 0.000000 0
|
||||
M V30 13 C -6.116018 3.810097 0.000000 0
|
||||
M V30 14 C -4.943533 -0.035682 0.000000 0
|
||||
M V30 15 C -1.910852 0.114807 0.000000 0
|
||||
M V30 16 C -0.343680 3.800110 0.000000 0
|
||||
M V30 17 C -3.536673 3.666472 0.000000 0
|
||||
M V30 18 C 0.318945 -0.272431 0.000000 0
|
||||
M V30 19 C 3.431341 1.399098 0.000000 0
|
||||
M V30 20 C 4.937688 1.719282 0.000000 0
|
||||
M V30 21 C 6.444036 1.399098 0.000000 0
|
||||
M V30 22 C 7.850896 2.025472 0.000000 0
|
||||
M V30 23 C 1.886117 3.412873 0.000000 0
|
||||
M V30 24 C 3.350744 -0.138792 0.000000 0
|
||||
M V30 25 C 4.937688 3.259282 0.000000 0
|
||||
M V30 26 C 6.605010 -0.132466 0.000000 0
|
||||
M V30 END ATOM
|
||||
M V30 BEGIN BOND
|
||||
M V30 1 1 2 1
|
||||
M V30 2 1 1 3
|
||||
M V30 3 1 3 4
|
||||
M V30 4 1 4 5
|
||||
M V30 5 1 5 6
|
||||
M V30 6 1 6 7
|
||||
M V30 7 1 7 8
|
||||
M V30 8 1 8 9
|
||||
M V30 9 1 9 10
|
||||
M V30 10 1 1 11 CFG=1
|
||||
M V30 11 1 3 12 CFG=2
|
||||
M V30 12 9 4 13
|
||||
M V30 13 8 5 14
|
||||
M V30 14 6 7 15
|
||||
M V30 15 1 8 16 CFG=1
|
||||
M V30 16 2 6 17 CFG=2
|
||||
M V30 17 1 9 18 CFG=2
|
||||
M V30 18 1 10 19
|
||||
M V30 19 1 19 20
|
||||
M V30 20 1 20 21
|
||||
M V30 21 1 21 22
|
||||
M V30 22 1 10 23 CFG=1
|
||||
M V30 23 1 19 24 CFG=3
|
||||
M V30 24 1 20 25 CFG=3
|
||||
M V30 25 1 21 26
|
||||
M V30 END BOND
|
||||
M V30 END CTAB
|
||||
M END
|
||||
67
Code/GraphMol/MarvinParse/test_data/ChiralTest.mrv
Normal file
67
Code/GraphMol/MarvinParse/test_data/ChiralTest.mrv
Normal file
@@ -0,0 +1,67 @@
|
||||
<cml xmlns="http://www.chemaxon.com" version="ChemAxon file format v20.20.0, generated by vunknown" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.chemaxon.com http://www.chemaxon.com/marvin/schema/mrvSchema_20_20_0.xsd">
|
||||
<MDocument>
|
||||
<MChemicalStruct>
|
||||
<molecule molID="m1">
|
||||
<atomArray>
|
||||
<atom id="a1" elementType="Cl" x2="0.8753360077149247" y2="0.09332404408597261" lonePair="3" mrvAlias="1"/>
|
||||
<atom id="a2" elementType="C" x2="-0.45833333333333337" y2="-0.6766928964730679" mrvAlias="2"/>
|
||||
<atom id="a3" elementType="Br" x2="-1.7920026743815916" y2="0.09332404408597261" lonePair="3" mrvAlias="3"/>
|
||||
<atom id="a4" elementType="I" x2="-0.45833333333333337" y2="-2.216726777591149" lonePair="3" mrvAlias="4"/>
|
||||
<atom id="a5" elementType="C" x2="0.7875528380040858" y2="1.7684963920573407" mrvAlias="5"/>
|
||||
<atom id="a6" elementType="C" x2="0.6265790045718983" y2="3.300060110924482" mrvAlias="6"/>
|
||||
<atom id="a7" elementType="C" x2="-0.7802810001977075" y2="3.9264345412612127" mrvAlias="7"/>
|
||||
<atom id="a8" elementType="C" x2="-0.45833333333333326" y2="0.8633071035269322" mrvAlias="8"/>
|
||||
</atomArray>
|
||||
<bondArray>
|
||||
<bond id="b1" atomRefs2="a1 a2" order="1"/>
|
||||
<bond id="b2" atomRefs2="a2 a3" order="1"/>
|
||||
<bond id="b3" atomRefs2="a2 a4" order="1">
|
||||
<bondStereo>H</bondStereo>
|
||||
</bond>
|
||||
<bond id="b4" atomRefs2="a5 a6" order="2"/>
|
||||
<bond id="b5" atomRefs2="a6 a7" order="1">
|
||||
</bond>
|
||||
<bond id="b6" atomRefs2="a5 a8" order="1">
|
||||
</bond>
|
||||
<bond id="b7" atomRefs2="a2 a8" order="1"/>
|
||||
</bondArray>
|
||||
</molecule>
|
||||
</MChemicalStruct>
|
||||
<MElectronContainer occupation="0 0" radical="0" id="o1">
|
||||
<MElectron atomRefs="m1.a1" difLoc="0.0 0.0 0.0"/>
|
||||
<MElectron atomRefs="m1.a1" difLoc="0.0 0.0 0.0"/>
|
||||
</MElectronContainer>
|
||||
<MElectronContainer occupation="0 0" radical="0" id="o2">
|
||||
<MElectron atomRefs="m1.a1" difLoc="0.0 0.0 0.0"/>
|
||||
<MElectron atomRefs="m1.a1" difLoc="0.0 0.0 0.0"/>
|
||||
</MElectronContainer>
|
||||
<MElectronContainer occupation="0 0" radical="0" id="o3">
|
||||
<MElectron atomRefs="m1.a1" difLoc="0.0 0.0 0.0"/>
|
||||
<MElectron atomRefs="m1.a1" difLoc="0.0 0.0 0.0"/>
|
||||
</MElectronContainer>
|
||||
<MElectronContainer occupation="0 0" radical="0" id="o4">
|
||||
<MElectron atomRefs="m1.a3" difLoc="0.0 0.0 0.0"/>
|
||||
<MElectron atomRefs="m1.a3" difLoc="0.0 0.0 0.0"/>
|
||||
</MElectronContainer>
|
||||
<MElectronContainer occupation="0 0" radical="0" id="o5">
|
||||
<MElectron atomRefs="m1.a3" difLoc="0.0 0.0 0.0"/>
|
||||
<MElectron atomRefs="m1.a3" difLoc="0.0 0.0 0.0"/>
|
||||
</MElectronContainer>
|
||||
<MElectronContainer occupation="0 0" radical="0" id="o6">
|
||||
<MElectron atomRefs="m1.a3" difLoc="0.0 0.0 0.0"/>
|
||||
<MElectron atomRefs="m1.a3" difLoc="0.0 0.0 0.0"/>
|
||||
</MElectronContainer>
|
||||
<MElectronContainer occupation="0 0" radical="0" id="o7">
|
||||
<MElectron atomRefs="m1.a4" difLoc="0.0 0.0 0.0"/>
|
||||
<MElectron atomRefs="m1.a4" difLoc="0.0 0.0 0.0"/>
|
||||
</MElectronContainer>
|
||||
<MElectronContainer occupation="0 0" radical="0" id="o8">
|
||||
<MElectron atomRefs="m1.a4" difLoc="0.0 0.0 0.0"/>
|
||||
<MElectron atomRefs="m1.a4" difLoc="0.0 0.0 0.0"/>
|
||||
</MElectronContainer>
|
||||
<MElectronContainer occupation="0 0" radical="0" id="o9">
|
||||
<MElectron atomRefs="m1.a4" difLoc="0.0 0.0 0.0"/>
|
||||
<MElectron atomRefs="m1.a4" difLoc="0.0 0.0 0.0"/>
|
||||
</MElectronContainer>
|
||||
</MDocument>
|
||||
</cml>
|
||||
@@ -0,0 +1,2 @@
|
||||
<?xml version="1.0" encoding="utf-8"?>
|
||||
<cml xmlns="http://www.chemaxon.com" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.chemaxon.com http://www.chemaxon.com/marvin/schema/mrvSchema_20_20_0.xsd"><MDocument><MChemicalStruct><molecule molID="m1"><atomArray><atom id="a1" elementType="Cl" x2="0.875336" y2="0.093324"/><atom id="a2" elementType="C" x2="-0.458333" y2="-0.676693"/><atom id="a3" elementType="Br" x2="-1.792" y2="0.093324"/><atom id="a4" elementType="I" x2="-0.458333" y2="-2.21673"/><atom id="a5" elementType="C" x2="0.787553" y2="1.7685"/><atom id="a6" elementType="C" x2="0.626579" y2="3.30006"/><atom id="a7" elementType="C" x2="-0.780281" y2="3.92643"/><atom id="a8" elementType="C" x2="-0.458333" y2="0.863307"/></atomArray><bondArray><bond id="b1" atomRefs2="a1 a2" order="1"/><bond id="b2" atomRefs2="a2 a3" order="1"/><bond id="b3" atomRefs2="a2 a4" order="1"><bondStereo>H</bondStereo></bond><bond id="b4" atomRefs2="a5 a6" order="2"/><bond id="b5" atomRefs2="a6 a7" order="1"/><bond id="b6" atomRefs2="a5 a8" order="1"/><bond id="b7" atomRefs2="a2 a8" order="1"/></bondArray></molecule></MChemicalStruct></MDocument></cml>
|
||||
@@ -0,0 +1,27 @@
|
||||
|
||||
RDKit 2D
|
||||
|
||||
0 0 0 0 0 0 0 0 0 0999 V3000
|
||||
M V30 BEGIN CTAB
|
||||
M V30 COUNTS 8 7 0 0 0
|
||||
M V30 BEGIN ATOM
|
||||
M V30 1 Cl 0.875336 0.093324 0.000000 0
|
||||
M V30 2 C -0.458333 -0.676693 0.000000 0
|
||||
M V30 3 Br -1.792003 0.093324 0.000000 0
|
||||
M V30 4 I -0.458333 -2.216727 0.000000 0
|
||||
M V30 5 C 0.787553 1.768496 0.000000 0
|
||||
M V30 6 C 0.626579 3.300060 0.000000 0
|
||||
M V30 7 C -0.780281 3.926435 0.000000 0
|
||||
M V30 8 C -0.458333 0.863307 0.000000 0
|
||||
M V30 END ATOM
|
||||
M V30 BEGIN BOND
|
||||
M V30 1 1 1 2
|
||||
M V30 2 1 2 3
|
||||
M V30 3 1 2 4 CFG=3
|
||||
M V30 4 2 5 6
|
||||
M V30 5 1 6 7
|
||||
M V30 6 1 5 8
|
||||
M V30 7 1 2 8
|
||||
M V30 END BOND
|
||||
M V30 END CTAB
|
||||
M END
|
||||
27
Code/GraphMol/MarvinParse/test_data/ChiralTest.sdf
Normal file
27
Code/GraphMol/MarvinParse/test_data/ChiralTest.sdf
Normal file
@@ -0,0 +1,27 @@
|
||||
|
||||
RDKit 2D
|
||||
|
||||
0 0 0 0 0 0 0 0 0 0999 V3000
|
||||
M V30 BEGIN CTAB
|
||||
M V30 COUNTS 8 7 0 0 0
|
||||
M V30 BEGIN ATOM
|
||||
M V30 1 Cl 0.875336 0.093324 0.000000 0
|
||||
M V30 2 C -0.458333 -0.676693 0.000000 0
|
||||
M V30 3 Br -1.792003 0.093324 0.000000 0
|
||||
M V30 4 I -0.458333 -2.216727 0.000000 0
|
||||
M V30 5 C 0.787553 1.768496 0.000000 0
|
||||
M V30 6 C 0.626579 3.300060 0.000000 0
|
||||
M V30 7 C -0.780281 3.926435 0.000000 0
|
||||
M V30 8 C -0.458333 0.863307 0.000000 0
|
||||
M V30 END ATOM
|
||||
M V30 BEGIN BOND
|
||||
M V30 1 1 1 2
|
||||
M V30 2 1 2 3
|
||||
M V30 3 1 2 4 CFG=3
|
||||
M V30 4 2 5 6
|
||||
M V30 5 1 6 7
|
||||
M V30 6 1 5 8
|
||||
M V30 7 1 2 8
|
||||
M V30 END BOND
|
||||
M V30 END CTAB
|
||||
M END
|
||||
@@ -0,0 +1 @@
|
||||
C/C=C\C[C@@](Cl)(Br)I |(-0.780281,3.92644,;0.626579,3.30006,;0.787553,1.7685,;-0.458333,0.863307,;-0.458333,-0.676693,;0.875336,0.093324,;-1.792,0.093324,;-0.458333,-2.21673,),wD:4.6|
|
||||
@@ -0,0 +1,2 @@
|
||||
<?xml version="1.0" encoding="utf-8"?>
|
||||
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|
||||
@@ -0,0 +1,27 @@
|
||||
|
||||
RDKit 2D
|
||||
|
||||
0 0 0 0 0 0 0 0 0 0999 V3000
|
||||
M V30 BEGIN CTAB
|
||||
M V30 COUNTS 8 7 0 0 0
|
||||
M V30 BEGIN ATOM
|
||||
M V30 1 Cl 0.875336 0.093324 0.000000 0
|
||||
M V30 2 C -0.458333 -0.676693 0.000000 0
|
||||
M V30 3 Br -1.792003 0.093324 0.000000 0
|
||||
M V30 4 I -0.458333 -2.216727 0.000000 0
|
||||
M V30 5 C 0.787553 1.768496 0.000000 0
|
||||
M V30 6 C 0.626579 3.300060 0.000000 0
|
||||
M V30 7 C -0.780281 3.926435 0.000000 0
|
||||
M V30 8 C -0.458333 0.863307 0.000000 0
|
||||
M V30 END ATOM
|
||||
M V30 BEGIN BOND
|
||||
M V30 1 1 1 2
|
||||
M V30 2 1 2 3
|
||||
M V30 3 1 2 4 CFG=3
|
||||
M V30 4 2 5 6
|
||||
M V30 5 1 6 7
|
||||
M V30 6 1 5 8
|
||||
M V30 7 1 2 8
|
||||
M V30 END BOND
|
||||
M V30 END CTAB
|
||||
M END
|
||||
173
Code/GraphMol/MarvinParse/test_data/ChiralTest2.mrv
Normal file
173
Code/GraphMol/MarvinParse/test_data/ChiralTest2.mrv
Normal file
@@ -0,0 +1,173 @@
|
||||
<cml xmlns="http://www.chemaxon.com" version="ChemAxon file format v20.20.0, generated by vunknown" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.chemaxon.com http://www.chemaxon.com/marvin/schema/mrvSchema_20_20_0.xsd">
|
||||
<MDocument>
|
||||
<MChemicalStruct>
|
||||
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|
||||
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|
||||
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|
||||
<atom id="a2" elementType="R" x2="-2.31" y2="0" sgroupRef="sg1"/>
|
||||
<atom id="a3" elementType="R" x2="-0.77" y2="0" sgroupRef="sg2"/>
|
||||
<atom id="a4" elementType="R" x2="0.77" y2="0" sgroupRef="sg3"/>
|
||||
<atom id="a5" elementType="R" x2="2.31" y2="0" sgroupRef="sg4"/>
|
||||
<atom id="a6" elementType="O" x2="3.3083333333333336" y2="0.04166666666666667" lonePair="2"/>
|
||||
<atom id="a7" elementType="C" x2="4.022049253769431" y2="1.4062946690600127"/>
|
||||
<atom id="a8" elementType="C" x2="3.19710469719923" y2="2.706704788439739" mrvAlias="L"/>
|
||||
</atomArray>
|
||||
<bondArray>
|
||||
<bond id="b1" atomRefs2="a1 a2" order="1"/>
|
||||
<bond id="b2" atomRefs2="a2 a3" order="1"/>
|
||||
<bond id="b3" atomRefs2="a3 a4" order="1"/>
|
||||
<bond id="b4" atomRefs2="a4 a5" order="1"/>
|
||||
<bond id="b5" atomRefs2="a5 a6" order="1"/>
|
||||
<bond id="b6" atomRefs2="a6 a7" order="1"/>
|
||||
<bond id="b7" atomRefs2="a7 a8" order="1"/>
|
||||
</bondArray>
|
||||
<molecule molID="m2" id="sg1" role="SuperatomSgroup" title="His">
|
||||
<atomArray>
|
||||
<atom id="a9" elementType="N" x2="-2.31" y2="0" sgroupAttachmentPoint="1"/>
|
||||
<atom id="a10" elementType="C" x2="-3.6436" y2="-2.3099999999999996" sgroupAttachmentPoint="2"/>
|
||||
<atom id="a11" elementType="C" x2="-0.9762999999999997" y2="-2.3099999999999996"/>
|
||||
<atom id="a12" elementType="C" x2="-0.9762999999999997" y2="-3.8499999999999996"/>
|
||||
<atom id="a13" elementType="C" x2="0.26960000000000006" y2="-4.755199999999999"/>
|
||||
<atom id="a14" elementType="N" x2="-0.20630000000000015" y2="-6.219799999999999" sgroupAttachmentPoint="3"/>
|
||||
<atom id="a15" elementType="C" x2="-1.7463000000000002" y2="-6.219799999999999"/>
|
||||
<atom id="a16" elementType="N" x2="-2.2222" y2="-4.755199999999999"/>
|
||||
<atom id="a17" elementType="C" x2="-2.31" y2="-1.54"/>
|
||||
<atom id="a18" elementType="O" x2="-4.9773" y2="-1.54"/>
|
||||
</atomArray>
|
||||
<bondArray>
|
||||
<bond id="b8" atomRefs2="a17 a9" order="1">
|
||||
<bondStereo>W</bondStereo>
|
||||
</bond>
|
||||
<bond id="b9" atomRefs2="a17 a11" order="1"/>
|
||||
<bond id="b10" atomRefs2="a11 a12" order="1"/>
|
||||
<bond id="b11" atomRefs2="a12 a13" order="2"/>
|
||||
<bond id="b12" atomRefs2="a13 a14" order="1"/>
|
||||
<bond id="b13" atomRefs2="a14 a15" order="1"/>
|
||||
<bond id="b14" atomRefs2="a15 a16" order="2"/>
|
||||
<bond id="b15" atomRefs2="a12 a16" order="1"/>
|
||||
<bond id="b16" atomRefs2="a17 a10" order="1"/>
|
||||
<bond id="b17" atomRefs2="a10 a18" order="2"/>
|
||||
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|
||||
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||||
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|
||||
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|
||||
<attachmentPoint atom="a14" order="3"/>
|
||||
</AttachmentPointArray>
|
||||
</molecule>
|
||||
<molecule molID="m3" id="sg2" role="SuperatomSgroup" title="Pyl">
|
||||
<atomArray>
|
||||
<atom id="a19" elementType="N" x2="-0.77" y2="0" sgroupAttachmentPoint="1"/>
|
||||
<atom id="a20" elementType="C" x2="0.5637000000000003" y2="2.31" sgroupAttachmentPoint="2"/>
|
||||
<atom id="a21" elementType="C" x2="-8.0021" y2="-2.3698"/>
|
||||
<atom id="a22" elementType="C" x2="-9.5421" y2="-2.3698"/>
|
||||
<atom id="a23" elementType="N" x2="-10.017900000000001" y2="-0.9052000000000002"/>
|
||||
<atom id="a24" elementType="C" x2="-8.7721" y2="0"/>
|
||||
<atom id="a25" elementType="C" x2="-8.7721" y2="1.5399999999999998"/>
|
||||
<atom id="a26" elementType="O" x2="-10.1057" y2="2.31"/>
|
||||
<atom id="a27" elementType="N" x2="-7.4384" y2="2.31"/>
|
||||
<atom id="a28" elementType="C" x2="-6.104700000000001" y2="1.5399999999999998"/>
|
||||
<atom id="a29" elementType="C" x2="-4.771000000000001" y2="2.31"/>
|
||||
<atom id="a30" elementType="C" x2="-3.437300000000001" y2="1.5399999999999998"/>
|
||||
<atom id="a31" elementType="C" x2="-2.1037000000000003" y2="2.31"/>
|
||||
<atom id="a32" elementType="C" x2="-0.77" y2="1.5399999999999998"/>
|
||||
<atom id="a33" elementType="C" x2="-6.0615000000000006" y2="-0.4293"/>
|
||||
<atom id="a34" elementType="C" x2="-7.526200000000001" y2="-0.9052000000000002"/>
|
||||
<atom id="a35" elementType="O" x2="1.8973999999999989" y2="1.5399999999999998"/>
|
||||
</atomArray>
|
||||
<bondArray>
|
||||
<bond id="b18" atomRefs2="a34 a33" order="1">
|
||||
<bondStereo>H</bondStereo>
|
||||
</bond>
|
||||
<bond id="b19" atomRefs2="a34 a21" order="1"/>
|
||||
<bond id="b20" atomRefs2="a21 a22" order="1"/>
|
||||
<bond id="b21" atomRefs2="a22 a23" order="2"/>
|
||||
<bond id="b22" atomRefs2="a23 a24" order="1"/>
|
||||
<bond id="b23" atomRefs2="a34 a24" order="1"/>
|
||||
<bond id="b24" atomRefs2="a24 a25" order="1">
|
||||
<bondStereo>W</bondStereo>
|
||||
</bond>
|
||||
<bond id="b25" atomRefs2="a25 a26" order="2"/>
|
||||
<bond id="b26" atomRefs2="a25 a27" order="1"/>
|
||||
<bond id="b27" atomRefs2="a27 a28" order="1"/>
|
||||
<bond id="b28" atomRefs2="a28 a29" order="1"/>
|
||||
<bond id="b29" atomRefs2="a29 a30" order="1"/>
|
||||
<bond id="b30" atomRefs2="a30 a31" order="1"/>
|
||||
<bond id="b31" atomRefs2="a31 a32" order="1"/>
|
||||
<bond id="b32" atomRefs2="a32 a19" order="1">
|
||||
<bondStereo>W</bondStereo>
|
||||
</bond>
|
||||
<bond id="b33" atomRefs2="a32 a20" order="1"/>
|
||||
<bond id="b34" atomRefs2="a20 a35" order="2"/>
|
||||
</bondArray>
|
||||
<AttachmentPointArray>
|
||||
<attachmentPoint atom="a19" order="1" bond="b2"/>
|
||||
<attachmentPoint atom="a20" order="2" bond="b3"/>
|
||||
</AttachmentPointArray>
|
||||
</molecule>
|
||||
<molecule molID="m4" id="sg3" role="SuperatomSgroup" title="Asx">
|
||||
<atomArray>
|
||||
<atom id="a36" elementType="N" x2="0.77" y2="0" sgroupAttachmentPoint="1"/>
|
||||
<atom id="a37" elementType="C" x2="2.1037000000000003" y2="2.3099999999999996" sgroupAttachmentPoint="2"/>
|
||||
<atom id="a38" elementType="C" x2="-0.5636999999999999" y2="2.3099999999999996"/>
|
||||
<atom id="a39" elementType="C" x2="-1.8974" y2="1.54"/>
|
||||
<atom id="a40" elementType="N" x2="-1.8974" y2="0" mrvQueryProps="L,N,O:"/>
|
||||
<atom id="a41" elementType="O" x2="-3.2310999999999996" y2="2.3099999999999996"/>
|
||||
<atom id="a42" elementType="C" x2="0.77" y2="1.54"/>
|
||||
<atom id="a43" elementType="O" x2="3.4373" y2="1.54"/>
|
||||
</atomArray>
|
||||
<bondArray>
|
||||
<bond id="b35" atomRefs2="a42 a36" order="1">
|
||||
<bondStereo>W</bondStereo>
|
||||
</bond>
|
||||
<bond id="b36" atomRefs2="a42 a38" order="1"/>
|
||||
<bond id="b37" atomRefs2="a38 a39" order="1"/>
|
||||
<bond id="b38" atomRefs2="a39 a40" order="1"/>
|
||||
<bond id="b39" atomRefs2="a39 a41" order="2"/>
|
||||
<bond id="b40" atomRefs2="a42 a37" order="1"/>
|
||||
<bond id="b41" atomRefs2="a37 a43" order="2"/>
|
||||
</bondArray>
|
||||
<AttachmentPointArray>
|
||||
<attachmentPoint atom="a36" order="1" bond="b3"/>
|
||||
<attachmentPoint atom="a37" order="2" bond="b4"/>
|
||||
</AttachmentPointArray>
|
||||
</molecule>
|
||||
<molecule molID="m5" id="sg4" role="SuperatomSgroup" title="Thr">
|
||||
<atomArray>
|
||||
<atom id="a44" elementType="N" x2="2.31" y2="0" sgroupAttachmentPoint="1"/>
|
||||
<atom id="a45" elementType="C" x2="0.9762999999999997" y2="2.31" sgroupAttachmentPoint="2"/>
|
||||
<atom id="a46" elementType="O" x2="-1.6910999999999996" y2="0.77" sgroupAttachmentPoint="3"/>
|
||||
<atom id="a47" elementType="C" x2="0.9762999999999997" y2="0.77"/>
|
||||
<atom id="a48" elementType="C" x2="-0.3573999999999997" y2="-1.54"/>
|
||||
<atom id="a49" elementType="C" x2="-0.3573999999999997" y2="0"/>
|
||||
<atom id="a50" elementType="O" x2="2.31" y2="3.08"/>
|
||||
</atomArray>
|
||||
<bondArray>
|
||||
<bond id="b42" atomRefs2="a48 a49" order="1"/>
|
||||
<bond id="b43" atomRefs2="a49 a46" order="1">
|
||||
<bondStereo>W</bondStereo>
|
||||
</bond>
|
||||
<bond id="b44" atomRefs2="a49 a47" order="1"/>
|
||||
<bond id="b45" atomRefs2="a47 a44" order="1">
|
||||
<bondStereo>W</bondStereo>
|
||||
</bond>
|
||||
<bond id="b46" atomRefs2="a47 a45" order="1"/>
|
||||
<bond id="b47" atomRefs2="a45 a50" order="2"/>
|
||||
</bondArray>
|
||||
<AttachmentPointArray>
|
||||
<attachmentPoint atom="a44" order="1" bond="b4"/>
|
||||
<attachmentPoint atom="a45" order="2" bond="b5"/>
|
||||
<attachmentPoint atom="a46" order="3"/>
|
||||
</AttachmentPointArray>
|
||||
</molecule>
|
||||
</molecule>
|
||||
</MChemicalStruct>
|
||||
<MElectronContainer occupation="0 0" radical="0" id="o1">
|
||||
<MElectron atomRefs="m1.a6" difLoc="0.0 0.0 0.0"/>
|
||||
<MElectron atomRefs="m1.a6" difLoc="0.0 0.0 0.0"/>
|
||||
</MElectronContainer>
|
||||
<MElectronContainer occupation="0 0" radical="0" id="o2">
|
||||
<MElectron atomRefs="m1.a6" difLoc="0.0 0.0 0.0"/>
|
||||
<MElectron atomRefs="m1.a6" difLoc="0.0 0.0 0.0"/>
|
||||
</MElectronContainer>
|
||||
</MDocument>
|
||||
</cml>
|
||||
File diff suppressed because one or more lines are too long
112
Code/GraphMol/MarvinParse/test_data/ChiralTest2.mrv.expected.sdf
Normal file
112
Code/GraphMol/MarvinParse/test_data/ChiralTest2.mrv.expected.sdf
Normal file
@@ -0,0 +1,112 @@
|
||||
|
||||
RDKit 2D
|
||||
|
||||
0 0 0 0 0 0 0 0 0 0999 V3000
|
||||
M V30 BEGIN CTAB
|
||||
M V30 COUNTS 46 47 4 0 0
|
||||
M V30 BEGIN ATOM
|
||||
M V30 1 H -3.850000 0.000000 0.000000 0
|
||||
M V30 2 O 3.308333 0.041667 0.000000 0
|
||||
M V30 3 C 4.022049 1.406295 0.000000 0
|
||||
M V30 4 C 3.197105 2.706705 0.000000 0
|
||||
M V30 5 N -1.643200 1.155000 0.000000 0
|
||||
M V30 6 C -2.976800 -1.155000 0.000000 0
|
||||
M V30 7 C -0.309500 -1.155000 0.000000 0
|
||||
M V30 8 C -0.309500 -2.695000 0.000000 0
|
||||
M V30 9 C 0.936400 -3.600200 0.000000 0
|
||||
M V30 10 N 0.460500 -5.064800 0.000000 0
|
||||
M V30 11 C -1.079500 -5.064800 0.000000 0
|
||||
M V30 12 N -1.555400 -3.600200 0.000000 0
|
||||
M V30 13 C -1.643200 -0.385000 0.000000 0
|
||||
M V30 14 O -4.310500 -0.385000 0.000000 0
|
||||
M V30 15 N -1.436850 -1.155000 0.000000 0
|
||||
M V30 16 C -0.103150 1.155000 0.000000 0
|
||||
M V30 17 C -8.668950 -3.524800 0.000000 0
|
||||
M V30 18 C -10.208950 -3.524800 0.000000 0
|
||||
M V30 19 N -10.684750 -2.060200 0.000000 0
|
||||
M V30 20 C -9.438950 -1.155000 0.000000 0
|
||||
M V30 21 C -9.438950 0.385000 0.000000 0
|
||||
M V30 22 O -10.772550 1.155000 0.000000 0
|
||||
M V30 23 N -8.105250 1.155000 0.000000 0
|
||||
M V30 24 C -6.771550 0.385000 0.000000 0
|
||||
M V30 25 C -5.437850 1.155000 0.000000 0
|
||||
M V30 26 C -4.104150 0.385000 0.000000 0
|
||||
M V30 27 C -2.770550 1.155000 0.000000 0
|
||||
M V30 28 C -1.436850 0.385000 0.000000 0
|
||||
M V30 29 C -6.728350 -1.584300 0.000000 0
|
||||
M V30 30 C -8.193050 -2.060200 0.000000 0
|
||||
M V30 31 O 1.230550 0.385000 0.000000 0
|
||||
M V30 32 N 0.103150 -1.155000 0.000000 0
|
||||
M V30 33 C 1.436850 1.155000 0.000000 0
|
||||
M V30 34 C -1.230550 1.155000 0.000000 0
|
||||
M V30 35 C -2.564250 0.385000 0.000000 0
|
||||
M V30 36 N -2.564250 -1.155000 0.000000 0
|
||||
M V30 37 O -3.897950 1.155000 0.000000 0
|
||||
M V30 38 C 0.103150 0.385000 0.000000 0
|
||||
M V30 39 O 2.770450 0.385000 0.000000 0
|
||||
M V30 40 N 2.976850 -1.155000 0.000000 0
|
||||
M V30 41 C 1.643150 1.155000 0.000000 0
|
||||
M V30 42 O -1.024250 -0.385000 0.000000 0
|
||||
M V30 43 C 1.643150 -0.385000 0.000000 0
|
||||
M V30 44 C 0.309450 -2.695000 0.000000 0
|
||||
M V30 45 C 0.309450 -1.155000 0.000000 0
|
||||
M V30 46 O 2.976850 1.925000 0.000000 0
|
||||
M V30 END ATOM
|
||||
M V30 BEGIN BOND
|
||||
M V30 1 1 1 5
|
||||
M V30 2 1 6 15
|
||||
M V30 3 1 16 32
|
||||
M V30 4 1 33 40
|
||||
M V30 5 1 41 2
|
||||
M V30 6 1 2 3
|
||||
M V30 7 1 3 4
|
||||
M V30 8 1 13 5 CFG=1
|
||||
M V30 9 1 13 7
|
||||
M V30 10 1 7 8
|
||||
M V30 11 2 8 9
|
||||
M V30 12 1 9 10
|
||||
M V30 13 1 10 11
|
||||
M V30 14 2 11 12
|
||||
M V30 15 1 8 12
|
||||
M V30 16 1 13 6
|
||||
M V30 17 2 6 14
|
||||
M V30 18 1 30 29 CFG=3
|
||||
M V30 19 1 30 17
|
||||
M V30 20 1 17 18
|
||||
M V30 21 2 18 19
|
||||
M V30 22 1 19 20
|
||||
M V30 23 1 30 20
|
||||
M V30 24 1 20 21 CFG=1
|
||||
M V30 25 2 21 22
|
||||
M V30 26 1 21 23
|
||||
M V30 27 1 23 24
|
||||
M V30 28 1 24 25
|
||||
M V30 29 1 25 26
|
||||
M V30 30 1 26 27
|
||||
M V30 31 1 27 28
|
||||
M V30 32 1 28 15 CFG=1
|
||||
M V30 33 1 28 16
|
||||
M V30 34 2 16 31
|
||||
M V30 35 1 38 32 CFG=1
|
||||
M V30 36 1 38 34
|
||||
M V30 37 1 34 35
|
||||
M V30 38 1 35 36
|
||||
M V30 39 2 35 37
|
||||
M V30 40 1 38 33
|
||||
M V30 41 2 33 39
|
||||
M V30 42 1 44 45
|
||||
M V30 43 1 45 42 CFG=1
|
||||
M V30 44 1 45 43
|
||||
M V30 45 1 43 40 CFG=1
|
||||
M V30 46 1 43 41
|
||||
M V30 47 2 41 46
|
||||
M V30 END BOND
|
||||
M V30 BEGIN SGROUP
|
||||
M V30 1 SUP 0 ATOMS=(10 5 6 7 8 9 10 11 12 13 14) XBONDS=(2 1 2) LABEL=His
|
||||
M V30 2 SUP 0 ATOMS=(17 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31) -
|
||||
M V30 XBONDS=(2 2 3) LABEL=Pyl
|
||||
M V30 3 SUP 0 ATOMS=(8 32 33 34 35 36 37 38 39) XBONDS=(2 3 4) LABEL=Asx
|
||||
M V30 4 SUP 0 ATOMS=(7 40 41 42 43 44 45 46) XBONDS=(2 4 5) LABEL=Thr
|
||||
M V30 END SGROUP
|
||||
M V30 END CTAB
|
||||
M END
|
||||
1
Code/GraphMol/MarvinParse/test_data/Cubane.mrv
Normal file
1
Code/GraphMol/MarvinParse/test_data/Cubane.mrv
Normal file
@@ -0,0 +1 @@
|
||||
<cml xmlns="http://www.chemaxon.com" version="ChemAxon file format v20.20.0, generated by vunknown" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.chemaxon.com http://www.chemaxon.com/marvin/schema/mrvSchema_20_20_0.xsd"><MDocument><MChemicalStruct><molecule molID="m1"><atomArray><atom id="a1" elementType="C" x3="-0.76705" y3="0.7494999999999999" z3="0.0104"/><atom id="a2" elementType="C" x3="-0.74625" y3="-0.7804000000000001" z3="0.002"/><atom id="a3" elementType="C" x3="0.7627500000000002" y3="0.7702999999999999" z3="-0.0041"/><atom id="a4" elementType="C" x3="-0.78165" y3="0.7576999999999999" z3="-1.5195"/><atom id="a5" elementType="C" x3="0.7835500000000001" y3="-0.7595000000000001" z3="-0.0125"/><atom id="a6" elementType="C" x3="-0.7608499999999999" y3="-0.7722000000000001" z3="-1.5279"/><atom id="a7" elementType="C" x3="0.7689500000000001" y3="-0.7513000000000001" z3="-1.5424"/><atom id="a8" elementType="C" x3="0.74815" y3="0.7784999999999999" z3="-1.534"/><atom id="a9" elementType="H" x3="-1.39815" y3="1.3660999999999999" z3="0.6504"/><atom id="a10" elementType="H" x3="-1.36035" y3="-1.4209" z3="0.635"/><atom id="a11" elementType="H" x3="1.3888500000000001" y3="1.4041000000000001" z3="0.624"/><atom id="a12" elementType="H" x3="-1.42665" y3="1.3811" z3="-2.1387"/><atom id="a13" elementType="H" x3="1.42665" y3="-1.383" z3="0.6086"/><atom id="a14" elementType="H" x3="-1.38885" y3="-1.4060000000000001" z3="-2.154"/><atom id="a15" elementType="H" x3="1.4000500000000002" y3="-1.3699000000000001" z3="-2.1805"/><atom id="a16" elementType="H" x3="1.36225" y3="1.4209" z3="-2.1651"/></atomArray><bondArray><bond id="b1" atomRefs2="a1 a2" order="1"/><bond id="b2" atomRefs2="a1 a3" order="1"/><bond id="b3" atomRefs2="a1 a4" order="1"/><bond id="b4" atomRefs2="a1 a9" order="1"/><bond id="b5" atomRefs2="a2 a5" order="1"/><bond id="b6" atomRefs2="a2 a6" order="1"/><bond id="b7" atomRefs2="a2 a10" order="1"/><bond id="b8" atomRefs2="a3 a5" order="1"/><bond id="b9" atomRefs2="a3 a8" order="1"/><bond id="b10" atomRefs2="a3 a11" order="1"/><bond id="b11" atomRefs2="a4 a6" order="1"/><bond id="b12" atomRefs2="a4 a8" order="1"/><bond id="b13" atomRefs2="a4 a12" order="1"/><bond id="b14" atomRefs2="a5 a7" order="1"/><bond id="b15" atomRefs2="a5 a13" order="1"/><bond id="b16" atomRefs2="a6 a7" order="1"/><bond id="b17" atomRefs2="a6 a14" order="1"/><bond id="b18" atomRefs2="a7 a8" order="1"/><bond id="b19" atomRefs2="a7 a15" order="1"/><bond id="b20" atomRefs2="a8 a16" order="1"/></bondArray></molecule></MChemicalStruct></MDocument></cml>
|
||||
@@ -0,0 +1,2 @@
|
||||
<?xml version="1.0" encoding="utf-8"?>
|
||||
<cml xmlns="http://www.chemaxon.com" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.chemaxon.com http://www.chemaxon.com/marvin/schema/mrvSchema_20_20_0.xsd"><MDocument><MChemicalStruct><molecule molID="m1"><atomArray><atom id="a1" elementType="C" x3="-0.76705" y3="0.7495" z3="0.0104"/><atom id="a2" elementType="C" x3="-0.74625" y3="-0.7804" z3="0.002"/><atom id="a3" elementType="C" x3="0.76275" y3="0.7703" z3="-0.0041"/><atom id="a4" elementType="C" x3="-0.78165" y3="0.7577" z3="-1.5195"/><atom id="a5" elementType="C" x3="0.78355" y3="-0.7595" z3="-0.0125"/><atom id="a6" elementType="C" x3="-0.76085" y3="-0.7722" z3="-1.5279"/><atom id="a7" elementType="C" x3="0.76895" y3="-0.7513" z3="-1.5424"/><atom id="a8" elementType="C" x3="0.74815" y3="0.7785" z3="-1.534"/><atom id="a9" elementType="H" x3="-1.39815" y3="1.3661" z3="0.6504"/><atom id="a10" elementType="H" x3="-1.36035" y3="-1.4209" z3="0.635"/><atom id="a11" elementType="H" x3="1.38885" y3="1.4041" z3="0.624"/><atom id="a12" elementType="H" x3="-1.42665" y3="1.3811" z3="-2.1387"/><atom id="a13" elementType="H" x3="1.42665" y3="-1.383" z3="0.6086"/><atom id="a14" elementType="H" x3="-1.38885" y3="-1.406" z3="-2.154"/><atom id="a15" elementType="H" x3="1.40005" y3="-1.3699" z3="-2.1805"/><atom id="a16" elementType="H" x3="1.36225" y3="1.4209" z3="-2.1651"/></atomArray><bondArray><bond id="b1" atomRefs2="a1 a2" order="1"/><bond id="b2" atomRefs2="a1 a3" order="1"/><bond id="b3" atomRefs2="a1 a4" order="1"/><bond id="b4" atomRefs2="a1 a9" order="1"/><bond id="b5" atomRefs2="a2 a5" order="1"/><bond id="b6" atomRefs2="a2 a6" order="1"/><bond id="b7" atomRefs2="a2 a10" order="1"/><bond id="b8" atomRefs2="a3 a5" order="1"/><bond id="b9" atomRefs2="a3 a8" order="1"/><bond id="b10" atomRefs2="a3 a11" order="1"/><bond id="b11" atomRefs2="a4 a6" order="1"/><bond id="b12" atomRefs2="a4 a8" order="1"/><bond id="b13" atomRefs2="a4 a12" order="1"/><bond id="b14" atomRefs2="a5 a7" order="1"/><bond id="b15" atomRefs2="a5 a13" order="1"/><bond id="b16" atomRefs2="a6 a7" order="1"/><bond id="b17" atomRefs2="a6 a14" order="1"/><bond id="b18" atomRefs2="a7 a8" order="1"/><bond id="b19" atomRefs2="a7 a15" order="1"/><bond id="b20" atomRefs2="a8 a16" order="1"/></bondArray></molecule></MChemicalStruct></MDocument></cml>
|
||||
48
Code/GraphMol/MarvinParse/test_data/Cubane.mrv.expected.sdf
Normal file
48
Code/GraphMol/MarvinParse/test_data/Cubane.mrv.expected.sdf
Normal file
@@ -0,0 +1,48 @@
|
||||
|
||||
RDKit 3D
|
||||
|
||||
0 0 0 0 0 0 0 0 0 0999 V3000
|
||||
M V30 BEGIN CTAB
|
||||
M V30 COUNTS 16 20 0 0 0
|
||||
M V30 BEGIN ATOM
|
||||
M V30 1 C -0.767050 0.749500 0.010400 0
|
||||
M V30 2 C -0.746250 -0.780400 0.002000 0
|
||||
M V30 3 C 0.762750 0.770300 -0.004100 0
|
||||
M V30 4 C -0.781650 0.757700 -1.519500 0
|
||||
M V30 5 C 0.783550 -0.759500 -0.012500 0
|
||||
M V30 6 C -0.760850 -0.772200 -1.527900 0
|
||||
M V30 7 C 0.768950 -0.751300 -1.542400 0
|
||||
M V30 8 C 0.748150 0.778500 -1.534000 0
|
||||
M V30 9 H -1.398150 1.366100 0.650400 0
|
||||
M V30 10 H -1.360350 -1.420900 0.635000 0
|
||||
M V30 11 H 1.388850 1.404100 0.624000 0
|
||||
M V30 12 H -1.426650 1.381100 -2.138700 0
|
||||
M V30 13 H 1.426650 -1.383000 0.608600 0
|
||||
M V30 14 H -1.388850 -1.406000 -2.154000 0
|
||||
M V30 15 H 1.400050 -1.369900 -2.180500 0
|
||||
M V30 16 H 1.362250 1.420900 -2.165100 0
|
||||
M V30 END ATOM
|
||||
M V30 BEGIN BOND
|
||||
M V30 1 1 1 2
|
||||
M V30 2 1 1 3
|
||||
M V30 3 1 1 4
|
||||
M V30 4 1 1 9
|
||||
M V30 5 1 2 5
|
||||
M V30 6 1 2 6
|
||||
M V30 7 1 2 10
|
||||
M V30 8 1 3 5
|
||||
M V30 9 1 3 8
|
||||
M V30 10 1 3 11
|
||||
M V30 11 1 4 6
|
||||
M V30 12 1 4 8
|
||||
M V30 13 1 4 12
|
||||
M V30 14 1 5 7
|
||||
M V30 15 1 5 13
|
||||
M V30 16 1 6 7
|
||||
M V30 17 1 6 14
|
||||
M V30 18 1 7 8
|
||||
M V30 19 1 7 15
|
||||
M V30 20 1 8 16
|
||||
M V30 END BOND
|
||||
M V30 END CTAB
|
||||
M END
|
||||
45
Code/GraphMol/MarvinParse/test_data/DataSgroup.mrv
Normal file
45
Code/GraphMol/MarvinParse/test_data/DataSgroup.mrv
Normal file
@@ -0,0 +1,45 @@
|
||||
<cml xmlns="http://www.chemaxon.com" version="ChemAxon file format v20.20.0, generated by vunknown" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.chemaxon.com http://www.chemaxon.com/marvin/schema/mrvSchema_20_20_0.xsd">
|
||||
<MDocument>
|
||||
<MChemicalStruct>
|
||||
<molecule molID="m1">
|
||||
<atomArray>
|
||||
<atom id="a1" elementType="C" x2="-0.6668413869397369" y2="1.540000000000001" sgroupRef="sg3"/>
|
||||
<atom id="a2" elementType="C" x2="-2.000481732890549" y2="2.3100000000000005" sgroupRef="sg3"/>
|
||||
<atom id="a3" elementType="O" x2="0.6667973271676573" y2="-2.3100000000000005" lonePair="2" sgroupRef="sg1"/>
|
||||
<atom id="a4" elementType="N" x2="-2.000481732890549" y2="-0.7700000000000014" lonePair="1" sgroupRef="sg1"/>
|
||||
<atom id="a5" elementType="C" x2="0.6667973271676573" y2="-0.7700000000000014" sgroupRef="sg1"/>
|
||||
<atom id="a6" elementType="C" x2="-0.6668413869397369" y2="-1.7763568394002505e-15" sgroupRef="sg1"/>
|
||||
<atom id="a7" elementType="N" x2="2.000481732890549" y2="-0.000008159217054881651" lonePair="1" sgroupRef="sg2"/>
|
||||
</atomArray>
|
||||
<bondArray>
|
||||
<bond id="b1" atomRefs2="a6 a1" order="1">
|
||||
<bondStereo>W</bondStereo>
|
||||
</bond>
|
||||
<bond id="b2" atomRefs2="a1 a2" order="1"/>
|
||||
<bond id="b3" atomRefs2="a5 a3" order="2"/>
|
||||
<bond id="b4" atomRefs2="a6 a4" order="1"/>
|
||||
<bond id="b5" atomRefs2="a6 a5" order="1"/>
|
||||
<bond id="b6" atomRefs2="a5 a7" order="1"/>
|
||||
</bondArray>
|
||||
<molecule molID="m2" id="sg1" role="DataSgroup" atomRefs="a1 a2 a3 a4 a5 a6 a7" context="Fragment" fieldName="TestFrag" x="-0.6668413869397369" y="1.540000000000001" placement="Relative" unitsDisplayed="Unit displayed" queryType="mQ" queryOp="<>" fieldData="qqwwq" units="mg"/>
|
||||
<molecule molID="m3" id="sg2" role="DataSgroup" atomRefs="a7" context="Atom" fieldName="TestAtom" x="0" y="0" placement="Relative" unitsDisplayed="Unit not displayed" fieldData="OH"/>
|
||||
<molecule molID="m4" id="sg3" role="DataSgroup" atomRefs="a1 a2" context="Single Bond" fieldName="testBond" x="0" y="0" placement="Relative" fieldData="wqreqwer"/></molecule>
|
||||
</MChemicalStruct>
|
||||
<MElectronContainer occupation="0 0" radical="0" id="o1">
|
||||
<MElectron atomRefs="m1.a3" difLoc="0.0 0.0 0.0"/>
|
||||
<MElectron atomRefs="m1.a3" difLoc="0.0 0.0 0.0"/>
|
||||
</MElectronContainer>
|
||||
<MElectronContainer occupation="0 0" radical="0" id="o2">
|
||||
<MElectron atomRefs="m1.a3" difLoc="0.0 0.0 0.0"/>
|
||||
<MElectron atomRefs="m1.a3" difLoc="0.0 0.0 0.0"/>
|
||||
</MElectronContainer>
|
||||
<MElectronContainer occupation="0 0" radical="0" id="o3">
|
||||
<MElectron atomRefs="m1.a4" difLoc="0.0 0.0 0.0"/>
|
||||
<MElectron atomRefs="m1.a4" difLoc="0.0 0.0 0.0"/>
|
||||
</MElectronContainer>
|
||||
<MElectronContainer occupation="0 0" radical="0" id="o4">
|
||||
<MElectron atomRefs="m1.a7" difLoc="0.0 0.0 0.0"/>
|
||||
<MElectron atomRefs="m1.a7" difLoc="0.0 0.0 0.0"/>
|
||||
</MElectronContainer>
|
||||
</MDocument>
|
||||
</cml>
|
||||
@@ -0,0 +1,2 @@
|
||||
<?xml version="1.0" encoding="utf-8"?>
|
||||
<cml xmlns="http://www.chemaxon.com" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.chemaxon.com http://www.chemaxon.com/marvin/schema/mrvSchema_20_20_0.xsd"><MDocument><MChemicalStruct><molecule molID="m1"><atomArray><atom id="a1" elementType="C" x2="-0.666841" y2="1.54" sgroupRef="sg3"/><atom id="a2" elementType="C" x2="-2.00048" y2="2.31" sgroupRef="sg3"/><atom id="a3" elementType="O" x2="0.666797" y2="-2.31" sgroupRef="sg1"/><atom id="a4" elementType="N" x2="-2.00048" y2="-0.77" sgroupRef="sg1"/><atom id="a5" elementType="C" x2="0.666797" y2="-0.77" sgroupRef="sg1"/><atom id="a6" elementType="C" x2="-0.666841" y2="0.00000" sgroupRef="sg1"/><atom id="a7" elementType="N" x2="2.00048" y2="0.00000" sgroupRef="sg2"/></atomArray><bondArray><bond id="b1" atomRefs2="a6 a1" order="1"><bondStereo>W</bondStereo></bond><bond id="b2" atomRefs2="a1 a2" order="1"/><bond id="b3" atomRefs2="a5 a3" order="2"/><bond id="b4" atomRefs2="a6 a4" order="1"/><bond id="b5" atomRefs2="a6 a5" order="1"/><bond id="b6" atomRefs2="a5 a7" order="1"/></bondArray><molecule molID="m2" id="sg1" role="DataSgroup" atomRefs="a1 a2 a3 a4 a5 a6 a7" context="Fragment" fieldName="TestFrag" placement="Relative" unitsDisplayed="Unit displayed" fieldData="qqwwq" units="mg" queryType="mQ" queryOp="<>" x="-0.666841" y="1.54"/><molecule molID="m3" id="sg2" role="DataSgroup" atomRefs="a7" context="Atom" fieldName="TestAtom" placement="Relative" unitsDisplayed="Unit not displayed" fieldData="OH" x="0" y="0"/><molecule molID="m4" id="sg3" role="DataSgroup" atomRefs="a1 a2" context="Single Bond" fieldName="testBond" placement="Relative" unitsDisplayed="Unit not displayed" fieldData="wqreqwer" x="0" y="0"/></molecule></MChemicalStruct></MDocument></cml>
|
||||
@@ -0,0 +1,36 @@
|
||||
|
||||
RDKit 2D
|
||||
|
||||
0 0 0 0 0 0 0 0 0 0999 V3000
|
||||
M V30 BEGIN CTAB
|
||||
M V30 COUNTS 7 6 3 0 0
|
||||
M V30 BEGIN ATOM
|
||||
M V30 1 C -0.666841 1.540000 0.000000 0
|
||||
M V30 2 C -2.000482 2.310000 0.000000 0
|
||||
M V30 3 O 0.666797 -2.310000 0.000000 0
|
||||
M V30 4 N -2.000482 -0.770000 0.000000 0
|
||||
M V30 5 C 0.666797 -0.770000 0.000000 0
|
||||
M V30 6 C -0.666841 -0.000000 0.000000 0
|
||||
M V30 7 N 2.000482 -0.000008 0.000000 0
|
||||
M V30 END ATOM
|
||||
M V30 BEGIN BOND
|
||||
M V30 1 1 6 1 CFG=1
|
||||
M V30 2 1 1 2
|
||||
M V30 3 2 5 3
|
||||
M V30 4 1 6 4
|
||||
M V30 5 1 6 5
|
||||
M V30 6 1 5 7
|
||||
M V30 END BOND
|
||||
M V30 BEGIN SGROUP
|
||||
M V30 1 DAT 0 ATOMS=(7 1 2 3 4 5 6 7) FIELDNAME=TestFrag -
|
||||
M V30 FIELDDISP=" -0.6668 1.5400 DRU ALL 0 0" QUERYTYPE=mQ -
|
||||
M V30 QUERYOP=<> FIELDDATA="qqwwq"
|
||||
M V30 2 DAT 0 ATOMS=(1 7) FIELDNAME=TestAtom -
|
||||
M V30 FIELDDISP=" 0.0000 0.0000 DRU ALL 0 0" -
|
||||
M V30 FIELDDATA="OH"
|
||||
M V30 3 DAT 0 ATOMS=(2 1 2) FIELDNAME=testBond -
|
||||
M V30 FIELDDISP=" 0.0000 0.0000 DRU ALL 0 0" -
|
||||
M V30 FIELDDATA="wqreqwer"
|
||||
M V30 END SGROUP
|
||||
M V30 END CTAB
|
||||
M END
|
||||
@@ -0,0 +1,46 @@
|
||||
<?xml version="1.0" encoding="utf-8"?>
|
||||
<cml xmlns="http://www.chemaxon.com" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.chemaxon.com http://www.chemaxon.com/marvin/schema/mrvSchema_20_20_0.xsd">
|
||||
<MDocument>
|
||||
<MChemicalStruct>
|
||||
<molecule molID="m1">
|
||||
<atomArray>
|
||||
<atom id="a1" elementType="C" x2="6.3148" y2="-10.5751"/>
|
||||
<atom id="a2" elementType="C" x2="8.9102" y2="-10.5744"/>
|
||||
<atom id="a3" elementType="C" x2="7.615" y2="-9.825"/>
|
||||
<atom id="a4" elementType="C" x2="8.9102" y2="-12.0758"/>
|
||||
<atom id="a5" elementType="C" x2="6.3148" y2="-12.0825"/>
|
||||
<atom id="a6" elementType="C" x2="7.6182" y2="-12.825"/>
|
||||
<atom id="a7" elementType="C" x2="10.2093" y2="-9.8244" sgroupRef="sg1"/>
|
||||
<atom id="a8" elementType="C" x2="11.5049" y2="-7.5754"/>
|
||||
<atom id="a9" elementType="C" x2="10.2087" y2="-8.3233"/>
|
||||
<atom id="a10" elementType="C" x2="12.8056" y2="-8.3253"/>
|
||||
<atom id="a11" elementType="C" x2="11.5152" y2="-10.5772" sgroupRef="sg1"/>
|
||||
<atom id="a12" elementType="C" x2="12.8095" y2="-9.8188"/>
|
||||
<atom id="a13" elementType="S" x2="7.6159" y2="-8.325"/>
|
||||
<atom id="a14" elementType="P" x2="10.21" y2="-12.8245"/>
|
||||
<atom id="a15" elementType="I" x2="11.5206" y2="-12.0772"/>
|
||||
</atomArray>
|
||||
<bondArray>
|
||||
<bond id="b1" atomRefs2="a3 a1" order="2"/>
|
||||
<bond id="b2" atomRefs2="a4 a2" order="2"/>
|
||||
<bond id="b3" atomRefs2="a1 a5" order="1"/>
|
||||
<bond id="b4" atomRefs2="a2 a3" order="1">
|
||||
<bondStereo>H</bondStereo>
|
||||
</bond>
|
||||
<bond id="b5" atomRefs2="a5 a6" order="2"/>
|
||||
<bond id="b6" atomRefs2="a6 a4" order="1"/>
|
||||
<bond id="b7" atomRefs2="a2 a7" order="1"/>
|
||||
<bond id="b8" atomRefs2="a9 a7" order="2"/>
|
||||
<bond id="b9" atomRefs2="a10 a8" order="2"/>
|
||||
<bond id="b10" atomRefs2="a7 a11" order="1"/>
|
||||
<bond id="b11" atomRefs2="a8 a9" order="1"/>
|
||||
<bond id="b12" atomRefs2="a11 a12" order="2"/>
|
||||
<bond id="b13" atomRefs2="a12 a10" order="1"/>
|
||||
<bond id="b14" atomRefs2="a3 a13" order="1"/>
|
||||
<bond id="b15" atomRefs2="a4 a14" order="1"/>
|
||||
<bond id="b16" atomRefs2="a11 a15" order="1"/>
|
||||
</bondArray>
|
||||
<molecule molID="m2" id="sg1" role="DataSgroup" atomRefs="a7 a11" context="" fieldName="atropisomer" placement="" unitsDisplayed="" fieldData="test" x="0" y="0"/></molecule>
|
||||
</MChemicalStruct>
|
||||
</MDocument>
|
||||
</cml>
|
||||
@@ -0,0 +1,2 @@
|
||||
<?xml version="1.0" encoding="utf-8"?>
|
||||
<cml xmlns="http://www.chemaxon.com" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.chemaxon.com http://www.chemaxon.com/marvin/schema/mrvSchema_20_20_0.xsd"><MDocument><MChemicalStruct><molecule molID="m1"><atomArray><atom id="a1" elementType="C" x2="6.3148" y2="-10.5751"/><atom id="a2" elementType="C" x2="8.9102" y2="-10.5744"/><atom id="a3" elementType="C" x2="7.615" y2="-9.825"/><atom id="a4" elementType="C" x2="8.9102" y2="-12.0758"/><atom id="a5" elementType="C" x2="6.3148" y2="-12.0825"/><atom id="a6" elementType="C" x2="7.6182" y2="-12.825"/><atom id="a7" elementType="C" x2="10.2093" y2="-9.8244" sgroupRef="sg1"/><atom id="a8" elementType="C" x2="11.5049" y2="-7.5754"/><atom id="a9" elementType="C" x2="10.2087" y2="-8.3233"/><atom id="a10" elementType="C" x2="12.8056" y2="-8.3253"/><atom id="a11" elementType="C" x2="11.5152" y2="-10.5772" sgroupRef="sg1"/><atom id="a12" elementType="C" x2="12.8095" y2="-9.8188"/><atom id="a13" elementType="S" x2="7.6159" y2="-8.325"/><atom id="a14" elementType="P" x2="10.21" y2="-12.8245"/><atom id="a15" elementType="I" x2="11.5206" y2="-12.0772"/></atomArray><bondArray><bond id="b1" atomRefs2="a3 a1" order="2"/><bond id="b2" atomRefs2="a4 a2" order="2"/><bond id="b3" atomRefs2="a1 a5" order="1"/><bond id="b4" atomRefs2="a2 a3" order="1"><bondStereo>H</bondStereo></bond><bond id="b5" atomRefs2="a5 a6" order="2"/><bond id="b6" atomRefs2="a6 a4" order="1"/><bond id="b7" atomRefs2="a2 a7" order="1"/><bond id="b8" atomRefs2="a9 a7" order="2"/><bond id="b9" atomRefs2="a10 a8" order="2"/><bond id="b10" atomRefs2="a7 a11" order="1"/><bond id="b11" atomRefs2="a8 a9" order="1"/><bond id="b12" atomRefs2="a11 a12" order="2"/><bond id="b13" atomRefs2="a12 a10" order="1"/><bond id="b14" atomRefs2="a3 a13" order="1"/><bond id="b15" atomRefs2="a4 a14" order="1"/><bond id="b16" atomRefs2="a11 a15" order="1"/></bondArray><molecule molID="m2" id="sg1" role="DataSgroup" atomRefs="a7 a11" context="" fieldName="atropisomer" placement="" unitsDisplayed="Unit not displayed" fieldData="test" x="0" y="0"/></molecule></MChemicalStruct></MDocument></cml>
|
||||
@@ -0,0 +1,48 @@
|
||||
|
||||
RDKit 2D
|
||||
|
||||
0 0 0 0 0 0 0 0 0 0999 V3000
|
||||
M V30 BEGIN CTAB
|
||||
M V30 COUNTS 15 16 1 0 0
|
||||
M V30 BEGIN ATOM
|
||||
M V30 1 C 6.314800 -10.575100 0.000000 0
|
||||
M V30 2 C 8.910200 -10.574400 0.000000 0
|
||||
M V30 3 C 7.615000 -9.825000 0.000000 0
|
||||
M V30 4 C 8.910200 -12.075800 0.000000 0
|
||||
M V30 5 C 6.314800 -12.082500 0.000000 0
|
||||
M V30 6 C 7.618200 -12.825000 0.000000 0
|
||||
M V30 7 C 10.209300 -9.824400 0.000000 0
|
||||
M V30 8 C 11.504900 -7.575400 0.000000 0
|
||||
M V30 9 C 10.208700 -8.323300 0.000000 0
|
||||
M V30 10 C 12.805600 -8.325300 0.000000 0
|
||||
M V30 11 C 11.515200 -10.577200 0.000000 0
|
||||
M V30 12 C 12.809500 -9.818800 0.000000 0
|
||||
M V30 13 S 7.615900 -8.325000 0.000000 0
|
||||
M V30 14 P 10.210000 -12.824500 0.000000 0
|
||||
M V30 15 I 11.520600 -12.077200 0.000000 0
|
||||
M V30 END ATOM
|
||||
M V30 BEGIN BOND
|
||||
M V30 1 2 3 1
|
||||
M V30 2 2 4 2
|
||||
M V30 3 1 1 5
|
||||
M V30 4 1 2 3 CFG=3
|
||||
M V30 5 2 5 6
|
||||
M V30 6 1 6 4
|
||||
M V30 7 1 2 7
|
||||
M V30 8 2 9 7
|
||||
M V30 9 2 10 8
|
||||
M V30 10 1 7 11
|
||||
M V30 11 1 8 9
|
||||
M V30 12 2 11 12
|
||||
M V30 13 1 12 10
|
||||
M V30 14 1 3 13
|
||||
M V30 15 1 4 14
|
||||
M V30 16 1 11 15
|
||||
M V30 END BOND
|
||||
M V30 BEGIN SGROUP
|
||||
M V30 1 DAT 0 ATOMS=(2 7 11) FIELDNAME=atropisomer -
|
||||
M V30 FIELDDISP=" 0.0000 0.0000 DRU ALL 0 0" -
|
||||
M V30 FIELDDATA="test"
|
||||
M V30 END SGROUP
|
||||
M V30 END CTAB
|
||||
M END
|
||||
17
Code/GraphMol/MarvinParse/test_data/DativeBond.mrv
Normal file
17
Code/GraphMol/MarvinParse/test_data/DativeBond.mrv
Normal file
@@ -0,0 +1,17 @@
|
||||
<?xml version="1.0" encoding="UTF-8"?>
|
||||
<cml xmlns="http://www.chemaxon.com" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.chemaxon.com/marvin/schema/mrvSchema_18_11_0.xsd" version="ChemAxon file format v18.11.0, generated by v20.3.0">
|
||||
<MDocument>
|
||||
<MChemicalStruct>
|
||||
<molecule molID="m1">
|
||||
<atomArray atomID="a1 a2 a3 a4 a5 a6" elementType="Mg Cl Cl C C C" lonePair="0 3 3 0 0 0" x2="-11.2867 -12.0567 -9.7467 -11.5434 -12.3134 -13.8534" y2="0.8474 2.1811 0.8474 -2.2645 -0.9308 -0.9308"></atomArray>
|
||||
<bondArray>
|
||||
<bond id="b1" atomRefs2="a1 a2" order="1"></bond>
|
||||
<bond id="b2" atomRefs2="a1 a3" order="1"></bond>
|
||||
<bond id="b3" atomRefs2="a4 a5" order="1"></bond>
|
||||
<bond id="b4" atomRefs2="a5 a6" order="1"></bond>
|
||||
<bond id="b5" atomRefs2="a5 a1" convention="cxn:coord"></bond>
|
||||
</bondArray>
|
||||
</molecule>
|
||||
</MChemicalStruct>
|
||||
</MDocument>
|
||||
</cml>
|
||||
@@ -0,0 +1,2 @@
|
||||
<?xml version="1.0" encoding="utf-8"?>
|
||||
<cml xmlns="http://www.chemaxon.com" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.chemaxon.com http://www.chemaxon.com/marvin/schema/mrvSchema_20_20_0.xsd"><MDocument><MChemicalStruct><molecule molID="m1"><atomArray><atom id="a1" elementType="Mg" x2="-11.2867" y2="0.8474" mrvValence="3"/><atom id="a2" elementType="Cl" x2="-12.0567" y2="2.1811"/><atom id="a3" elementType="Cl" x2="-9.7467" y2="0.8474"/><atom id="a4" elementType="C" x2="-11.5434" y2="-2.2645"/><atom id="a5" elementType="C" x2="-12.3134" y2="-0.9308"/><atom id="a6" elementType="C" x2="-13.8534" y2="-0.9308"/></atomArray><bondArray><bond id="b1" atomRefs2="a1 a2" order="1"/><bond id="b2" atomRefs2="a1 a3" order="1"/><bond id="b3" atomRefs2="a4 a5" order="1"/><bond id="b4" atomRefs2="a5 a6" order="1"/><bond id="b5" atomRefs2="a5 a1" convention="cxn:coord"/></bondArray></molecule></MChemicalStruct></MDocument></cml>
|
||||
@@ -0,0 +1,23 @@
|
||||
|
||||
RDKit 2D
|
||||
|
||||
0 0 0 0 0 0 0 0 0 0999 V3000
|
||||
M V30 BEGIN CTAB
|
||||
M V30 COUNTS 6 5 0 0 0
|
||||
M V30 BEGIN ATOM
|
||||
M V30 1 Mg -11.286700 0.847400 0.000000 0 VAL=3
|
||||
M V30 2 Cl -12.056700 2.181100 0.000000 0
|
||||
M V30 3 Cl -9.746700 0.847400 0.000000 0
|
||||
M V30 4 C -11.543400 -2.264500 0.000000 0
|
||||
M V30 5 C -12.313400 -0.930800 0.000000 0
|
||||
M V30 6 C -13.853400 -0.930800 0.000000 0
|
||||
M V30 END ATOM
|
||||
M V30 BEGIN BOND
|
||||
M V30 1 1 1 2
|
||||
M V30 2 1 1 3
|
||||
M V30 3 1 4 5
|
||||
M V30 4 1 5 6
|
||||
M V30 5 9 5 1
|
||||
M V30 END BOND
|
||||
M V30 END CTAB
|
||||
M END
|
||||
@@ -0,0 +1,2 @@
|
||||
<?xml version="1.0" encoding="utf-8"?>
|
||||
<cml xmlns="http://www.chemaxon.com" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.chemaxon.com http://www.chemaxon.com/marvin/schema/mrvSchema_20_20_0.xsd"><MDocument><MChemicalStruct><molecule molID="m1"><atomArray><atom id="a1" elementType="C" x2="3" y2="0.00000"/><atom id="a2" elementType="C" x2="1.5" y2="0.00000"/><atom id="a3" elementType="C" x2="0.75" y2="-1.29904"/><atom id="a4" elementType="C" x2="1.5" y2="-2.59808"/><atom id="a5" elementType="C" x2="3" y2="-2.59808"/><atom id="a6" elementType="C" x2="3.75" y2="-3.89711"/><atom id="a7" elementType="C" x2="3" y2="-5.19615"/><atom id="a8" elementType="C" x2="5.25" y2="-3.89711"/><atom id="a9" elementType="C" x2="6" y2="-5.19615"/><atom id="a10" elementType="C" x2="7.5" y2="-5.19615"/><atom id="a11" elementType="C" x2="8.25" y2="-6.49519"/><atom id="a12" elementType="C" x2="7.5" y2="-7.79423"/><atom id="a13" elementType="C" x2="9.75" y2="-6.49519"/><atom id="a14" elementType="C" x2="10.5" y2="-5.19615"/><atom id="a15" elementType="O" x2="12" y2="-5.19615"/><atom id="a16" elementType="O" x2="9.75" y2="-3.89711"/><atom id="a17" elementType="C" x2="-0.75" y2="-1.29904"/><atom id="a18" elementType="C" x2="-0.489528" y2="-2.77625"/><atom id="a19" elementType="C" x2="-2.15954" y2="-1.81207"/><atom id="a20" elementType="C" x2="-1.5" y2="0.00000"/><atom id="a21" elementType="C" x2="-0.75" y2="1.29904"/><atom id="a22" elementType="C" x2="0.75" y2="1.29904"/></atomArray><bondArray><bond id="b1" atomRefs2="a1 a2" order="1"/><bond id="b2" atomRefs2="a2 a3" order="2"/><bond id="b3" atomRefs2="a3 a4" order="1"/><bond id="b4" atomRefs2="a4 a5" order="2"/><bond id="b5" atomRefs2="a5 a6" order="1"/><bond id="b6" atomRefs2="a6 a7" order="1"/><bond id="b7" atomRefs2="a6 a8" order="2"/><bond id="b8" atomRefs2="a8 a9" order="1"/><bond id="b9" atomRefs2="a9 a10" order="2"/><bond id="b10" atomRefs2="a10 a11" order="1"/><bond id="b11" atomRefs2="a11 a12" order="1"/><bond id="b12" atomRefs2="a11 a13" order="2"/><bond id="b13" atomRefs2="a13 a14" order="1"/><bond id="b14" atomRefs2="a14 a15" order="1"/><bond id="b15" atomRefs2="a14 a16" order="2"/><bond id="b16" atomRefs2="a3 a17" order="1"/><bond id="b17" atomRefs2="a17 a18" order="1"/><bond id="b18" atomRefs2="a17 a19" order="1"/><bond id="b19" atomRefs2="a17 a20" order="1"/><bond id="b20" atomRefs2="a20 a21" order="1"/><bond id="b21" atomRefs2="a21 a22" order="1"/><bond id="b22" atomRefs2="a22 a2" order="1"/></bondArray></molecule></MChemicalStruct></MDocument></cml>
|
||||
@@ -0,0 +1,56 @@
|
||||
|
||||
RDKit 2D
|
||||
|
||||
0 0 0 0 0 0 0 0 0 0999 V3000
|
||||
M V30 BEGIN CTAB
|
||||
M V30 COUNTS 22 22 0 0 0
|
||||
M V30 BEGIN ATOM
|
||||
M V30 1 C 3.000000 0.000000 0.000000 0
|
||||
M V30 2 C 1.500000 0.000000 0.000000 0
|
||||
M V30 3 C 0.750000 -1.299038 0.000000 0
|
||||
M V30 4 C 1.500000 -2.598076 0.000000 0
|
||||
M V30 5 C 3.000000 -2.598076 0.000000 0
|
||||
M V30 6 C 3.750000 -3.897114 0.000000 0
|
||||
M V30 7 C 3.000000 -5.196152 0.000000 0
|
||||
M V30 8 C 5.250000 -3.897114 0.000000 0
|
||||
M V30 9 C 6.000000 -5.196152 0.000000 0
|
||||
M V30 10 C 7.500000 -5.196152 0.000000 0
|
||||
M V30 11 C 8.250000 -6.495191 0.000000 0
|
||||
M V30 12 C 7.500000 -7.794229 0.000000 0
|
||||
M V30 13 C 9.750000 -6.495191 0.000000 0
|
||||
M V30 14 C 10.500000 -5.196152 0.000000 0
|
||||
M V30 15 O 12.000000 -5.196152 0.000000 0
|
||||
M V30 16 O 9.750000 -3.897114 0.000000 0
|
||||
M V30 17 C -0.750000 -1.299038 0.000000 0
|
||||
M V30 18 C -0.489528 -2.776250 0.000000 0
|
||||
M V30 19 C -2.159539 -1.812068 0.000000 0
|
||||
M V30 20 C -1.500000 0.000000 0.000000 0
|
||||
M V30 21 C -0.750000 1.299038 0.000000 0
|
||||
M V30 22 C 0.750000 1.299038 0.000000 0
|
||||
M V30 END ATOM
|
||||
M V30 BEGIN BOND
|
||||
M V30 1 1 1 2
|
||||
M V30 2 2 2 3
|
||||
M V30 3 1 3 4
|
||||
M V30 4 2 4 5
|
||||
M V30 5 1 5 6
|
||||
M V30 6 1 6 7
|
||||
M V30 7 2 6 8
|
||||
M V30 8 1 8 9
|
||||
M V30 9 2 9 10
|
||||
M V30 10 1 10 11
|
||||
M V30 11 1 11 12
|
||||
M V30 12 2 11 13
|
||||
M V30 13 1 13 14
|
||||
M V30 14 1 14 15
|
||||
M V30 15 2 14 16
|
||||
M V30 16 1 3 17
|
||||
M V30 17 1 17 18
|
||||
M V30 18 1 17 19
|
||||
M V30 19 1 17 20
|
||||
M V30 20 1 20 21
|
||||
M V30 21 1 21 22
|
||||
M V30 22 1 22 2
|
||||
M V30 END BOND
|
||||
M V30 END CTAB
|
||||
M END
|
||||
@@ -0,0 +1 @@
|
||||
CC1=C(/C=C/C(C)=C/C=C/C(C)=C\C(O)=O)C(C)(C)CCC1
|
||||
1
Code/GraphMol/MarvinParse/test_data/DoubleBondChain.mrv
Normal file
1
Code/GraphMol/MarvinParse/test_data/DoubleBondChain.mrv
Normal file
@@ -0,0 +1 @@
|
||||
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||||
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||||
|
||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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|
||||
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|
||||
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|
||||
M V30 2 2 2 3
|
||||
M V30 3 1 3 4
|
||||
M V30 4 2 4 5
|
||||
M V30 5 1 5 6
|
||||
M V30 6 1 6 7
|
||||
M V30 7 2 6 8
|
||||
M V30 8 1 8 9
|
||||
M V30 9 2 9 10
|
||||
M V30 10 1 10 11
|
||||
M V30 11 1 11 12
|
||||
M V30 12 2 11 13
|
||||
M V30 13 1 13 14
|
||||
M V30 14 1 14 15
|
||||
M V30 15 2 14 16
|
||||
M V30 16 1 3 17
|
||||
M V30 17 1 17 18
|
||||
M V30 18 1 17 19
|
||||
M V30 19 1 17 20
|
||||
M V30 20 1 20 21
|
||||
M V30 21 1 21 22
|
||||
M V30 22 1 22 2
|
||||
M V30 END BOND
|
||||
M V30 END CTAB
|
||||
M END
|
||||
56
Code/GraphMol/MarvinParse/test_data/DoubleBondChain.sdf
Normal file
56
Code/GraphMol/MarvinParse/test_data/DoubleBondChain.sdf
Normal file
@@ -0,0 +1,56 @@
|
||||
|
||||
RDKit 2D
|
||||
|
||||
0 0 0 0 0 0 0 0 0 0999 V3000
|
||||
M V30 BEGIN CTAB
|
||||
M V30 COUNTS 22 22 0 0 0
|
||||
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|
||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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|
||||
M V30 22 C 0.750000 1.299040 0.000000 0
|
||||
M V30 END ATOM
|
||||
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|
||||
M V30 1 1 1 2
|
||||
M V30 2 2 2 3
|
||||
M V30 3 1 3 4
|
||||
M V30 4 2 4 5
|
||||
M V30 5 1 5 6
|
||||
M V30 6 1 6 7
|
||||
M V30 7 2 6 8
|
||||
M V30 8 1 8 9
|
||||
M V30 9 2 9 10
|
||||
M V30 10 1 10 11
|
||||
M V30 11 1 11 12
|
||||
M V30 12 2 11 13
|
||||
M V30 13 1 13 14
|
||||
M V30 14 1 14 15
|
||||
M V30 15 2 14 16
|
||||
M V30 16 1 3 17
|
||||
M V30 17 1 17 18
|
||||
M V30 18 1 17 19
|
||||
M V30 19 1 17 20
|
||||
M V30 20 1 20 21
|
||||
M V30 21 1 21 22
|
||||
M V30 22 1 22 2
|
||||
M V30 END BOND
|
||||
M V30 END CTAB
|
||||
M END
|
||||
@@ -0,0 +1 @@
|
||||
CC1=C(/C=C/C(C)=C/C=C/C(C)=C\C(=O)O)C(C)(C)CCC1 |(3,0,;1.5,0,;0.75,-1.29904,;1.5,-2.59808,;3,-2.59808,;3.75,-3.89711,;3,-5.19615,;5.25,-3.89711,;6,-5.19615,;7.5,-5.19615,;8.25,-6.49519,;7.5,-7.79423,;9.75,-6.49519,;10.5,-5.19615,;9.75,-3.89711,;12,-5.19615,;-0.75,-1.29904,;-0.489528,-2.77625,;-2.15954,-1.81207,;-1.5,0,;-0.75,1.29904,;0.75,1.29904,)|
|
||||
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|
||||
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||||
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||||
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||||
|
||||
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||||
|
||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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|
||||
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||||
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||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
M V30 21 1 21 22
|
||||
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|
||||
M V30 END BOND
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||||
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|
||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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||||
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||||
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||||
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|
||||
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|
||||
|
||||
RDKit 2D
|
||||
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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||||
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||||
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||||
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||||
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|
||||
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||||
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|
||||
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|
||||
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|
||||
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||||
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|
||||
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|
||||
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|
||||
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||||
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|
||||
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|
||||
M V30 END ATOM
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
M V30 13 1 11 10
|
||||
M V30 14 1 13 14
|
||||
M V30 15 1 13 12
|
||||
M V30 16 1 15 16
|
||||
M V30 17 1 15 14
|
||||
M V30 END BOND
|
||||
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|
||||
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|
||||
M V30 LABEL=tBu
|
||||
M V30 2 MUL 0 ATOMS=(8 9 10 11 12 13 14 15 16) XBONDS=(2 9 11) -
|
||||
M V30 PATOMS=(2 9 10) MULT=4
|
||||
M V30 END SGROUP
|
||||
M V30 END CTAB
|
||||
M END
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||||
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||||
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||||
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|
||||
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|
||||
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|
||||
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|
||||
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||||
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||||
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||||
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||||
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||||
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|
||||
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|
||||
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|
||||
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|
||||
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||||
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||||
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||||
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||||
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||||
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|
||||
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||||
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||||
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|
||||
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|
||||
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|
||||
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||||
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||||
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||||
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|
||||
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|
||||
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|
||||
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|
||||
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||||
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|
||||
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||||
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||||
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||||
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||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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||||
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||||
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||||
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|
||||
@@ -0,0 +1,36 @@
|
||||
|
||||
RDKit 2D
|
||||
|
||||
0 0 0 0 0 0 0 0 0 0999 V3000
|
||||
M V30 BEGIN CTAB
|
||||
M V30 COUNTS 10 10 2 0 0
|
||||
M V30 BEGIN ATOM
|
||||
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|
||||
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||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
M V30 END ATOM
|
||||
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|
||||
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|
||||
M V30 2 1 1 3
|
||||
M V30 3 1 2 4
|
||||
M V30 4 1 3 5
|
||||
M V30 5 1 4 5
|
||||
M V30 6 1 1 7
|
||||
M V30 7 1 3 6
|
||||
M V30 8 1 7 8
|
||||
M V30 9 1 7 9
|
||||
M V30 10 1 7 10
|
||||
M V30 END BOND
|
||||
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|
||||
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|
||||
M V30 2 SUP 0 ATOMS=(4 7 8 9 10) XBONDS=(1 6) LABEL=tBu
|
||||
M V30 END SGROUP
|
||||
M V30 END CTAB
|
||||
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||||
@@ -0,0 +1,44 @@
|
||||
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||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
<molecule molID="m3" id="sg2" role="SuperatomSgroup" title="tBu">
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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||||
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||||
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|
||||
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|
||||
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|
||||
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||||
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||||
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||||
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||||
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||||
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||||
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|
||||
@@ -0,0 +1,38 @@
|
||||
|
||||
RDKit 2D
|
||||
|
||||
0 0 0 0 0 0 0 0 0 0999 V3000
|
||||
M V30 BEGIN CTAB
|
||||
M V30 COUNTS 10 10 2 0 0
|
||||
M V30 BEGIN ATOM
|
||||
M V30 1 C 15.225000 -9.862500 0.000000 0
|
||||
M V30 2 C 16.442041 -10.746733 0.000000 0
|
||||
M V30 3 C 14.007959 -10.746733 0.000000 0
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||||
M V30 4 C 15.977165 -12.177408 0.000000 0
|
||||
M V30 5 C 14.472835 -12.177408 0.000000 0
|
||||
M V30 6 Cl 13.000000 -10.700000 0.000000 0
|
||||
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|
||||
M V30 8 C 16.527900 -9.149444 0.000000 0
|
||||
M V30 9 C 13.922200 -9.149444 0.000000 0
|
||||
M V30 10 C 15.225000 -6.892944 0.000000 0
|
||||
M V30 END ATOM
|
||||
M V30 BEGIN BOND
|
||||
M V30 1 1 1 2
|
||||
M V30 2 1 1 3
|
||||
M V30 3 1 2 4
|
||||
M V30 4 1 3 5
|
||||
M V30 5 1 4 5
|
||||
M V30 6 1 1 7
|
||||
M V30 7 1 3 6
|
||||
M V30 8 1 7 8
|
||||
M V30 9 1 7 9
|
||||
M V30 10 1 7 10
|
||||
M V30 END BOND
|
||||
M V30 BEGIN SGROUP
|
||||
M V30 1 DAT 0 ATOMS=(9 1 2 3 4 5 7 8 9 10) FIELDNAME=TestFrag -
|
||||
M V30 FIELDDISP=" -0.6668 1.5400 DRU ALL 0 0" QUERYTYPE=mQ -
|
||||
M V30 QUERYOP=<> FIELDDATA="qqwwq"
|
||||
M V30 2 SUP 0 ATOMS=(4 7 8 9 10) XBONDS=(1 6) LABEL=tBu
|
||||
M V30 END SGROUP
|
||||
M V30 END CTAB
|
||||
M END
|
||||
@@ -0,0 +1,48 @@
|
||||
<cml xmlns="http://www.chemaxon.com" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" version="ChemAxon file format v20.20.0, generated by vunknown" xsi:schemaLocation="http://www.chemaxon.com http://www.chemaxon.com/marvin/schema/mrvSchema_20_20_0.xsd">
|
||||
<MDocument xmlns="">
|
||||
<MChemicalStruct>
|
||||
<molecule molID="m1">
|
||||
<atomArray>
|
||||
<atom id="a1" elementType="C" x2="15.225000000000001" y2="-9.8625" sgroupRef="sg1"/>
|
||||
<atom id="a2" elementType="C" x2="16.44204126014696" y2="-10.746732882803618" sgroupRef="sg1"/>
|
||||
<atom id="a3" elementType="C" x2="14.00795873985304" y2="-10.746732882803618" sgroupRef="sg1"/>
|
||||
<atom id="a4" elementType="C" x2="15.977164515862558" y2="-12.17740840219622" sgroupRef="sg1"/>
|
||||
<atom id="a5" elementType="C" x2="14.472835484137445" y2="-12.17740840219622" sgroupRef="sg1"/>
|
||||
<atom id="a6" elementType="R" x2="15.225000000000001" y2="-8.397244449618395" sgroupRef="sg2"/>
|
||||
<atom id="a11" elementType="Cl" x2="13.0" y2="-10.7"/>
|
||||
<atom id="a18" elementType="X" x2="-0.85261" y2="-2.7923"/>
|
||||
<atom id="a19" elementType="Br" x2="1.1125000000000005" y2="-0.6337518310926612"/>
|
||||
|
||||
</atomArray>
|
||||
<bondArray>
|
||||
<bond id="b1" atomRefs2="a1 a2" order="1"/>
|
||||
<bond id="b2" atomRefs2="a1 a3" order="1"/>
|
||||
<bond id="b3" atomRefs2="a2 a4" order="1"/>
|
||||
<bond id="b4" atomRefs2="a3 a5" order="1"/>
|
||||
<bond id="b5" atomRefs2="a4 a5" order="1"/>
|
||||
<bond id="b6" atomRefs2="a1 a6" order="1"/>
|
||||
<bond id="b10" atomRefs2="a3 a11" order="1"/>
|
||||
<bond id="b10" atomRefs2="a18 a19" order="1"/>
|
||||
</bondArray>
|
||||
<molecule id="sg1" role="MulticenterSgroup" molID="m2" atomRefs="a1 a2 a3 a4 a5" center="a18" >
|
||||
<molecule molID="m3" id="sg2" role="SuperatomSgroup" title="tBu">
|
||||
<atomArray>
|
||||
<atom id="a7" elementType="C" x2="15.225" y2="-8.3972" sgroupAttachmentPoint="1"/>
|
||||
<atom id="a8" elementType="C" x2="16.5279" y2="-9.1494"/>
|
||||
<atom id="a9" elementType="C" x2="13.9222" y2="-9.1494"/>
|
||||
<atom id="a10" elementType="C" x2="15.225" y2="-6.8929"/>
|
||||
</atomArray>
|
||||
<bondArray>
|
||||
<bond id="b7" atomRefs2="a7 a8" order="1"/>
|
||||
<bond id="b8" atomRefs2="a7 a9" order="1"/>
|
||||
<bond id="b9" atomRefs2="a7 a10" order="1"/>
|
||||
</bondArray>
|
||||
<AttachmentPointArray>
|
||||
<AttachmentPoint atom="a7" order="1" bond="b6"/>
|
||||
</AttachmentPointArray>
|
||||
</molecule>
|
||||
</molecule>
|
||||
</molecule>
|
||||
</MChemicalStruct>
|
||||
</MDocument>
|
||||
</cml>
|
||||
@@ -0,0 +1,2 @@
|
||||
<?xml version="1.0" encoding="utf-8"?>
|
||||
<cml xmlns="http://www.chemaxon.com" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.chemaxon.com http://www.chemaxon.com/marvin/schema/mrvSchema_20_20_0.xsd"><MDocument><MChemicalStruct><molecule molID="m1"><atomArray><atom id="a1" elementType="C" x2="15.225" y2="-9.8625"/><atom id="a2" elementType="C" x2="16.442" y2="-10.7467"/><atom id="a3" elementType="C" x2="14.008" y2="-10.7467"/><atom id="a4" elementType="C" x2="15.9772" y2="-12.1774"/><atom id="a5" elementType="C" x2="14.4728" y2="-12.1774"/><atom id="a6" elementType="Cl" x2="13" y2="-10.7"/><atom id="a7" elementType="Br" x2="1.1125" y2="-0.633752"/><atom id="a8" elementType="R" x2="15.225" y2="-8.39724" sgroupRef="sg1"/></atomArray><bondArray><bond id="b1" atomRefs2="a1 a2" order="1"/><bond id="b2" atomRefs2="a1 a3" order="1"/><bond id="b3" atomRefs2="a2 a4" order="1"/><bond id="b4" atomRefs2="a3 a5" order="1"/><bond id="b5" atomRefs2="a4 a5" order="1"/><bond id="b6" atomRefs2="a1 a8" order="1"/><bond id="b7" atomRefs2="a3 a6" order="1"/></bondArray><molecule molID="m2" id="sg1" role="SuperatomSgroup" title="tBu"><atomArray><atom id="a9" elementType="C" x2="15.225" y2="-8.39724" sgroupAttachmentPoint="1"/><atom id="a10" elementType="C" x2="16.5279" y2="-9.14944"/><atom id="a11" elementType="C" x2="13.9222" y2="-9.14944"/><atom id="a12" elementType="C" x2="15.225" y2="-6.89294"/></atomArray><bondArray><bond id="b8" atomRefs2="a9 a10" order="1"/><bond id="b9" atomRefs2="a9 a11" order="1"/><bond id="b10" atomRefs2="a9 a12" order="1"/></bondArray><AttachmentPointArray><attachmentPoint atom="a9" order="1" bond="b6"/></AttachmentPointArray></molecule></molecule></MChemicalStruct></MDocument></cml>
|
||||
@@ -0,0 +1,36 @@
|
||||
|
||||
RDKit 2D
|
||||
|
||||
0 0 0 0 0 0 0 0 0 0999 V3000
|
||||
M V30 BEGIN CTAB
|
||||
M V30 COUNTS 11 10 1 0 0
|
||||
M V30 BEGIN ATOM
|
||||
M V30 1 C 15.225000 -9.862500 0.000000 0
|
||||
M V30 2 C 16.442041 -10.746733 0.000000 0
|
||||
M V30 3 C 14.007959 -10.746733 0.000000 0
|
||||
M V30 4 C 15.977165 -12.177408 0.000000 0
|
||||
M V30 5 C 14.472835 -12.177408 0.000000 0
|
||||
M V30 6 Cl 13.000000 -10.700000 0.000000 0
|
||||
M V30 7 Br 1.112500 -0.633752 0.000000 0
|
||||
M V30 8 C 15.225000 -8.397244 0.000000 0
|
||||
M V30 9 C 16.527900 -9.149444 0.000000 0
|
||||
M V30 10 C 13.922200 -9.149444 0.000000 0
|
||||
M V30 11 C 15.225000 -6.892944 0.000000 0
|
||||
M V30 END ATOM
|
||||
M V30 BEGIN BOND
|
||||
M V30 1 1 1 2
|
||||
M V30 2 1 1 3
|
||||
M V30 3 1 2 4
|
||||
M V30 4 1 3 5
|
||||
M V30 5 1 4 5
|
||||
M V30 6 1 1 8
|
||||
M V30 7 1 3 6
|
||||
M V30 8 1 8 9
|
||||
M V30 9 1 8 10
|
||||
M V30 10 1 8 11
|
||||
M V30 END BOND
|
||||
M V30 BEGIN SGROUP
|
||||
M V30 1 SUP 0 ATOMS=(4 8 9 10 11) XBONDS=(1 6) LABEL=tBu
|
||||
M V30 END SGROUP
|
||||
M V30 END CTAB
|
||||
M END
|
||||
335
Code/GraphMol/MarvinParse/test_data/EmbeddedSgroupMUL_MUL.mrv
Normal file
335
Code/GraphMol/MarvinParse/test_data/EmbeddedSgroupMUL_MUL.mrv
Normal file
@@ -0,0 +1,335 @@
|
||||
<cml xmlns="http://www.chemaxon.com" version="ChemAxon file format v20.20.0, generated by vunknown" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.chemaxon.com http://www.chemaxon.com/marvin/schema/mrvSchema_20_20_0.xsd">
|
||||
<MDocument>
|
||||
<MChemicalStruct>
|
||||
<molecule molID="m1">
|
||||
<atomArray>
|
||||
<atom id="a1" elementType="O" x2="-12.766083333333338" y2="14.681350000000004" lonePair="2" sgroupRef="sg1"/>
|
||||
<atom id="a2" elementType="C" x2="-11.432383333333338" y2="15.451350000000003" sgroupRef="sg1"/>
|
||||
<atom id="a3" elementType="C" x2="-10.098583333333337" y2="14.681350000000004" sgroupRef="sg1"/>
|
||||
<atom id="a4" elementType="N" x2="-8.765083333333337" y2="15.451350000000003" lonePair="1" sgroupRef="sg1"/>
|
||||
<atom id="a5" elementType="C" x2="-7.431383333333336" y2="14.681350000000004" sgroupRef="sg1"/>
|
||||
<atom id="a6" elementType="C" x2="-6.097583333333338" y2="15.451350000000003" sgroupRef="sg1"/>
|
||||
<atom id="a7" elementType="C" x2="-9.328583333333338" y2="13.347650000000003" sgroupRef="sg1"/>
|
||||
<atom id="a8" elementType="C" x2="-10.098583333333337" y2="12.013950000000001" sgroupRef="sg1"/>
|
||||
<atom id="a9" elementType="N" x2="-9.328583333333338" y2="10.680150000000001" lonePair="1" sgroupRef="sg1"/>
|
||||
<atom id="a10" elementType="C" x2="-10.098583333333337" y2="9.34665" sgroupRef="sg1"/>
|
||||
<atom id="a11" elementType="C" x2="-9.328583333333338" y2="8.012950000000002" sgroupRef="sg1"/>
|
||||
<atom id="a12" elementType="N" x2="-10.098583333333337" y2="6.679150000000002" lonePair="1" sgroupRef="sg1"/>
|
||||
<atom id="a13" elementType="C" x2="-9.328583333333338" y2="5.345650000000001" sgroupRef="sg1"/>
|
||||
<atom id="a14" elementType="C" x2="-10.098583333333337" y2="4.011850000000002" sgroupRef="sg1"/>
|
||||
<atom id="a15" elementType="N" x2="-9.328583333333338" y2="2.6781500000000014" lonePair="1" sgroupRef="sg1"/>
|
||||
<atom id="a16" elementType="C" x2="-10.098583333333337" y2="1.344450000000002" sgroupRef="sg1"/>
|
||||
<atom id="a17" elementType="O" x2="-11.432383333333338" y2="16.991350000000004" lonePair="2" sgroupRef="sg1"/>
|
||||
<atom id="a18" elementType="O" x2="-7.431383333333336" y2="13.141350000000001" lonePair="2" sgroupRef="sg1"/>
|
||||
<atom id="a19" elementType="C" x2="-4.763883333333338" y2="14.681350000000004" sgroupRef="sg1"/>
|
||||
<atom id="a20" elementType="N" x2="-3.4303833333333373" y2="15.451350000000003" lonePair="1" sgroupRef="sg1"/>
|
||||
<atom id="a21" elementType="C" x2="-3.9938833333333386" y2="13.347650000000003" sgroupRef="sg1"/>
|
||||
<atom id="a22" elementType="N" x2="-4.763883333333338" y2="12.013950000000001" lonePair="1" sgroupRef="sg1"/>
|
||||
<atom id="a23" elementType="C" x2="-3.9938833333333386" y2="10.680150000000001" sgroupRef="sg1"/>
|
||||
<atom id="a24" elementType="C" x2="-4.763883333333338" y2="9.34665" sgroupRef="sg1"/>
|
||||
<atom id="a25" elementType="N" x2="-3.9938833333333386" y2="8.012950000000002" lonePair="1" sgroupRef="sg1"/>
|
||||
<atom id="a26" elementType="C" x2="-4.763883333333338" y2="6.679150000000002" sgroupRef="sg1"/>
|
||||
<atom id="a27" elementType="C" x2="-3.9938833333333386" y2="5.345650000000001" sgroupRef="sg1"/>
|
||||
<atom id="a28" elementType="N" x2="-4.763883333333338" y2="4.011850000000002" lonePair="1" sgroupRef="sg1"/>
|
||||
<atom id="a29" elementType="C" x2="-3.9938833333333386" y2="2.6781500000000014" sgroupRef="sg1"/>
|
||||
<atom id="a30" elementType="C" x2="-4.763883333333338" y2="1.344450000000002" sgroupRef="sg1"/>
|
||||
<atom id="a31" elementType="O" x2="-11.638583333333337" y2="12.013950000000001" lonePair="2" sgroupRef="sg1"/>
|
||||
<atom id="a32" elementType="O" x2="-2.453883333333336" y2="13.347650000000003" lonePair="2" sgroupRef="sg1"/>
|
||||
<atom id="a33" elementType="C" x2="-9.328583333333338" y2="0.010850000000002247" sgroupRef="sg1"/>
|
||||
<atom id="a34" elementType="C" x2="-10.098583333333337" y2="-1.322849999999998" sgroupRef="sg1"/>
|
||||
<atom id="a35" elementType="O" x2="-9.328583333333338" y2="-2.6565499999999984" lonePair="2" sgroupRef="sg1"/>
|
||||
<atom id="a36" elementType="C" x2="-10.098583333333337" y2="-3.990149999999998" sgroupRef="sg1"/>
|
||||
<atom id="a37" elementType="C" x2="-9.328583333333338" y2="-5.323849999999998" sgroupRef="sg1"/>
|
||||
<atom id="a38" elementType="O" x2="-10.098583333333337" y2="-6.6576499999999985" lonePair="2" sgroupRef="sg1"/>
|
||||
<atom id="a39" elementType="C" x2="-3.9938833333333386" y2="0.010850000000002247" sgroupRef="sg1"/>
|
||||
<atom id="a40" elementType="O" x2="-4.763883333333338" y2="-1.322849999999998" lonePair="2" sgroupRef="sg1"/>
|
||||
<atom id="a41" elementType="C" x2="-3.9938833333333386" y2="-2.6565499999999984" sgroupRef="sg1"/>
|
||||
<atom id="a42" elementType="C" x2="-4.763883333333338" y2="-3.990149999999998" sgroupRef="sg1"/>
|
||||
<atom id="a43" elementType="O" x2="-3.9938833333333386" y2="-5.323849999999998" lonePair="2" sgroupRef="sg1"/>
|
||||
<atom id="a44" elementType="C" x2="-4.763883333333338" y2="-6.6576499999999985" sgroupRef="sg1"/>
|
||||
<atom id="a45" elementType="O" x2="-11.638583333333337" y2="-1.322849999999998" lonePair="2" sgroupRef="sg1"/>
|
||||
<atom id="a46" elementType="C" x2="-9.328583333333338" y2="-7.991349999999999" sgroupRef="sg1"/>
|
||||
<atom id="a47" elementType="O" x2="-2.453883333333336" y2="0.010850000000002247" lonePair="2" sgroupRef="sg1"/>
|
||||
<atom id="a48" elementType="C" x2="2.097416666666662" y2="15.121350000000001"/>
|
||||
<atom id="a49" elementType="C" x2="3.431116666666662" y2="14.351350000000002"/>
|
||||
<atom id="a50" elementType="N" x2="4.764916666666663" y2="15.121350000000001" lonePair="1"/>
|
||||
<atom id="a51" elementType="C" x2="6.0984166666666635" y2="14.351350000000002"/>
|
||||
<atom id="a52" elementType="C" x2="7.432216666666664" y2="15.121350000000001"/>
|
||||
<atom id="a53" elementType="C" x2="8.765916666666664" y2="14.351350000000002"/>
|
||||
<atom id="a54" elementType="O" x2="2.097416666666662" y2="16.66155" lonePair="2"/>
|
||||
<atom id="a55" elementType="C" x2="3.431116666666662" y2="12.811550000000002"/>
|
||||
<atom id="a56" elementType="O" x2="6.0984166666666635" y2="12.811550000000002" lonePair="2"/>
|
||||
<atom id="a57" elementType="N" x2="10.099416666666665" y2="15.121350000000001" lonePair="1"/>
|
||||
<atom id="a58" elementType="C" x2="8.765916666666664" y2="12.811550000000002"/>
|
||||
<atom id="a59" elementType="O" x2="10.099416666666665" y2="12.041350000000001" lonePair="2"/>
|
||||
<atom id="a60" elementType="N" x2="7.432216666666664" y2="12.041350000000001" lonePair="1"/>
|
||||
<atom id="a61" elementType="C" x2="7.432216666666664" y2="10.501350000000002"/>
|
||||
<atom id="a62" elementType="C" x2="2.097416666666662" y2="12.041350000000001"/>
|
||||
<atom id="a63" elementType="N" x2="2.097416666666662" y2="10.501350000000002" lonePair="1"/>
|
||||
<atom id="a64" elementType="O" x2="0.763916666666661" y2="12.811550000000002" lonePair="2"/>
|
||||
<atom id="a65" elementType="C" x2="3.431116666666662" y2="9.731550000000002"/>
|
||||
<atom id="a66" elementType="C" x2="3.431116666666662" y2="8.191550000000001"/>
|
||||
<atom id="a67" elementType="C" x2="6.0984166666666635" y2="9.731550000000002"/>
|
||||
<atom id="a68" elementType="C" x2="6.0984166666666635" y2="8.191550000000001"/>
|
||||
<atom id="a69" elementType="C" x2="7.432216666666664" y2="7.421350000000002"/>
|
||||
<atom id="a70" elementType="C" x2="7.432216666666664" y2="5.881550000000002"/>
|
||||
<atom id="a71" elementType="C" x2="8.765916666666664" y2="5.111550000000001"/>
|
||||
<atom id="a72" elementType="C" x2="2.097416666666662" y2="7.421350000000002"/>
|
||||
<atom id="a73" elementType="C" x2="2.097416666666662" y2="5.881550000000002"/>
|
||||
<atom id="a74" elementType="C" x2="0.763916666666661" y2="5.111550000000001"/>
|
||||
<atom id="a75" elementType="C" x2="0.763916666666661" y2="3.5713500000000016"/>
|
||||
<atom id="a76" elementType="C" x2="-14.306083333333337" y2="14.681350000000004"/>
|
||||
</atomArray>
|
||||
<bondArray>
|
||||
<bond id="b1" atomRefs2="a1 a2" order="1"/>
|
||||
<bond id="b2" atomRefs2="a2 a3" order="1"/>
|
||||
<bond id="b3" atomRefs2="a2 a17" order="2"/>
|
||||
<bond id="b4" atomRefs2="a3 a4" order="1"/>
|
||||
<bond id="b5" atomRefs2="a3 a7" order="1"/>
|
||||
<bond id="b6" atomRefs2="a4 a5" order="1"/>
|
||||
<bond id="b7" atomRefs2="a5 a6" order="1"/>
|
||||
<bond id="b8" atomRefs2="a5 a18" order="2"/>
|
||||
<bond id="b9" atomRefs2="a6 a19" order="1"/>
|
||||
<bond id="b10" atomRefs2="a7 a8" order="1"/>
|
||||
<bond id="b11" atomRefs2="a8 a9" order="1"/>
|
||||
<bond id="b12" atomRefs2="a8 a31" order="2"/>
|
||||
<bond id="b13" atomRefs2="a9 a10" order="1"/>
|
||||
<bond id="b14" atomRefs2="a10 a11" order="1"/>
|
||||
<bond id="b15" atomRefs2="a11 a12" order="1"/>
|
||||
<bond id="b16" atomRefs2="a12 a13" order="1"/>
|
||||
<bond id="b17" atomRefs2="a13 a14" order="1"/>
|
||||
<bond id="b18" atomRefs2="a14 a15" order="1"/>
|
||||
<bond id="b19" atomRefs2="a15 a16" order="1"/>
|
||||
<bond id="b20" atomRefs2="a16 a33" order="1"/>
|
||||
<bond id="b21" atomRefs2="a19 a20" order="1"/>
|
||||
<bond id="b22" atomRefs2="a19 a21" order="1"/>
|
||||
<bond id="b23" atomRefs2="a21 a22" order="1"/>
|
||||
<bond id="b24" atomRefs2="a21 a32" order="2"/>
|
||||
<bond id="b25" atomRefs2="a22 a23" order="1"/>
|
||||
<bond id="b26" atomRefs2="a23 a24" order="1"/>
|
||||
<bond id="b27" atomRefs2="a24 a25" order="1"/>
|
||||
<bond id="b28" atomRefs2="a25 a26" order="1"/>
|
||||
<bond id="b29" atomRefs2="a26 a27" order="1"/>
|
||||
<bond id="b30" atomRefs2="a27 a28" order="1"/>
|
||||
<bond id="b31" atomRefs2="a28 a29" order="1"/>
|
||||
<bond id="b32" atomRefs2="a29 a30" order="1"/>
|
||||
<bond id="b33" atomRefs2="a30 a39" order="1"/>
|
||||
<bond id="b34" atomRefs2="a33 a34" order="1"/>
|
||||
<bond id="b35" atomRefs2="a34 a35" order="1"/>
|
||||
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File diff suppressed because one or more lines are too long
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||||
M V30 61 C -7.431383 14.681350 0.000000 0
|
||||
M V30 62 C -6.097583 15.451350 0.000000 0
|
||||
M V30 63 C -9.328583 13.347650 0.000000 0
|
||||
M V30 64 C -10.098583 12.013950 0.000000 0
|
||||
M V30 65 N -9.328583 10.680150 0.000000 0
|
||||
M V30 66 C -10.098583 9.346650 0.000000 0
|
||||
M V30 67 C -9.328583 8.012950 0.000000 0
|
||||
M V30 68 N -10.098583 6.679150 0.000000 0
|
||||
M V30 69 C -9.328583 5.345650 0.000000 0
|
||||
M V30 70 C -10.098583 4.011850 0.000000 0
|
||||
M V30 71 N -9.328583 2.678150 0.000000 0
|
||||
M V30 72 C -10.098583 1.344450 0.000000 0
|
||||
M V30 73 O -11.432383 16.991350 0.000000 0
|
||||
M V30 74 O -7.431383 13.141350 0.000000 0
|
||||
M V30 75 C -4.763883 14.681350 0.000000 0
|
||||
M V30 76 N -3.430383 15.451350 0.000000 0
|
||||
M V30 77 C -3.993883 13.347650 0.000000 0
|
||||
M V30 78 N -4.763883 12.013950 0.000000 0
|
||||
M V30 79 C -3.993883 10.680150 0.000000 0
|
||||
M V30 80 C -4.763883 9.346650 0.000000 0
|
||||
M V30 81 N -3.993883 8.012950 0.000000 0
|
||||
M V30 82 C -4.763883 6.679150 0.000000 0
|
||||
M V30 83 C -3.993883 5.345650 0.000000 0
|
||||
M V30 84 N -4.763883 4.011850 0.000000 0
|
||||
M V30 85 C -3.993883 2.678150 0.000000 0
|
||||
M V30 86 C -4.763883 1.344450 0.000000 0
|
||||
M V30 87 O -11.638583 12.013950 0.000000 0
|
||||
M V30 88 O -2.453883 13.347650 0.000000 0
|
||||
M V30 89 C -9.328583 0.010850 0.000000 0
|
||||
M V30 90 C -10.098583 -1.322850 0.000000 0
|
||||
M V30 91 O -9.328583 -2.656550 0.000000 0
|
||||
M V30 92 C -10.098583 -3.990150 0.000000 0
|
||||
M V30 93 C -9.328583 -5.323850 0.000000 0
|
||||
M V30 94 O -10.098583 -6.657650 0.000000 0
|
||||
M V30 95 C -3.993883 0.010850 0.000000 0
|
||||
M V30 96 O -4.763883 -1.322850 0.000000 0
|
||||
M V30 97 C -3.993883 -2.656550 0.000000 0
|
||||
M V30 98 C -4.763883 -3.990150 0.000000 0
|
||||
M V30 99 O -3.993883 -5.323850 0.000000 0
|
||||
M V30 100 C -4.763883 -6.657650 0.000000 0
|
||||
M V30 101 O -11.638583 -1.322850 0.000000 0
|
||||
M V30 102 C -10.098583 -1.322850 0.000000 0
|
||||
M V30 103 O -9.328583 -2.656550 0.000000 0
|
||||
M V30 104 O -11.638583 -1.322850 0.000000 0
|
||||
M V30 105 C -10.098583 -1.322850 0.000000 0
|
||||
M V30 106 O -9.328583 -2.656550 0.000000 0
|
||||
M V30 107 O -11.638583 -1.322850 0.000000 0
|
||||
M V30 108 C -10.098583 -1.322850 0.000000 0
|
||||
M V30 109 O -9.328583 -2.656550 0.000000 0
|
||||
M V30 110 O -11.638583 -1.322850 0.000000 0
|
||||
M V30 111 C -9.328583 -7.991350 0.000000 0
|
||||
M V30 112 O -2.453883 0.010850 0.000000 0
|
||||
M V30 113 C 2.097417 15.121350 0.000000 0
|
||||
M V30 114 C 3.431117 14.351350 0.000000 0
|
||||
M V30 115 N 4.764917 15.121350 0.000000 0
|
||||
M V30 116 C 6.098417 14.351350 0.000000 0
|
||||
M V30 117 C 7.432217 15.121350 0.000000 0
|
||||
M V30 118 C 8.765917 14.351350 0.000000 0
|
||||
M V30 119 O 2.097417 16.661550 0.000000 0
|
||||
M V30 120 C 3.431117 12.811550 0.000000 0
|
||||
M V30 121 O 6.098417 12.811550 0.000000 0
|
||||
M V30 122 N 10.099417 15.121350 0.000000 0
|
||||
M V30 123 C 8.765917 12.811550 0.000000 0
|
||||
M V30 124 O 10.099417 12.041350 0.000000 0
|
||||
M V30 125 N 7.432217 12.041350 0.000000 0
|
||||
M V30 126 C 7.432217 10.501350 0.000000 0
|
||||
M V30 127 C 2.097417 12.041350 0.000000 0
|
||||
M V30 128 N 2.097417 10.501350 0.000000 0
|
||||
M V30 129 O 0.763917 12.811550 0.000000 0
|
||||
M V30 130 C 3.431117 9.731550 0.000000 0
|
||||
M V30 131 C 3.431117 8.191550 0.000000 0
|
||||
M V30 132 C 6.098417 9.731550 0.000000 0
|
||||
M V30 133 C 6.098417 8.191550 0.000000 0
|
||||
M V30 134 C 7.432217 7.421350 0.000000 0
|
||||
M V30 135 C 7.432217 5.881550 0.000000 0
|
||||
M V30 136 C 8.765917 5.111550 0.000000 0
|
||||
M V30 137 C 2.097417 7.421350 0.000000 0
|
||||
M V30 138 C 2.097417 5.881550 0.000000 0
|
||||
M V30 139 C 0.763917 5.111550 0.000000 0
|
||||
M V30 140 C 0.763917 3.571350 0.000000 0
|
||||
M V30 141 C -14.306083 14.681350 0.000000 0
|
||||
M V30 END ATOM
|
||||
M V30 BEGIN BOND
|
||||
M V30 1 1 1 2
|
||||
M V30 2 1 2 3
|
||||
M V30 3 2 2 17
|
||||
M V30 4 1 3 4
|
||||
M V30 5 1 3 7
|
||||
M V30 6 1 4 5
|
||||
M V30 7 1 5 6
|
||||
M V30 8 2 5 18
|
||||
M V30 9 1 6 19
|
||||
M V30 10 1 7 8
|
||||
M V30 11 1 8 9
|
||||
M V30 12 2 8 31
|
||||
M V30 13 1 9 10
|
||||
M V30 14 1 10 11
|
||||
M V30 15 1 11 12
|
||||
M V30 16 1 12 13
|
||||
M V30 17 1 13 14
|
||||
M V30 18 1 14 15
|
||||
M V30 19 1 15 16
|
||||
M V30 20 1 16 33
|
||||
M V30 21 1 19 20
|
||||
M V30 22 1 19 21
|
||||
M V30 23 1 21 22
|
||||
M V30 24 2 21 32
|
||||
M V30 25 1 22 23
|
||||
M V30 26 1 23 24
|
||||
M V30 27 1 24 25
|
||||
M V30 28 1 25 26
|
||||
M V30 29 1 26 27
|
||||
M V30 30 1 27 28
|
||||
M V30 31 1 28 29
|
||||
M V30 32 1 29 30
|
||||
M V30 33 1 30 39
|
||||
M V30 34 1 33 34
|
||||
M V30 35 1 34 35
|
||||
M V30 36 2 34 45
|
||||
M V30 37 1 36 53
|
||||
M V30 38 1 36 37
|
||||
M V30 39 1 37 38
|
||||
M V30 40 1 38 55
|
||||
M V30 41 1 39 40
|
||||
M V30 42 2 39 56
|
||||
M V30 43 1 40 41
|
||||
M V30 44 1 41 42
|
||||
M V30 45 1 42 43
|
||||
M V30 46 1 43 44
|
||||
M V30 47 1 113 114
|
||||
M V30 48 2 113 119
|
||||
M V30 49 1 114 115
|
||||
M V30 50 1 114 120
|
||||
M V30 51 1 115 116
|
||||
M V30 52 1 116 117
|
||||
M V30 53 2 116 121
|
||||
M V30 54 1 117 118
|
||||
M V30 55 1 118 122
|
||||
M V30 56 1 118 123
|
||||
M V30 57 1 120 127
|
||||
M V30 58 2 123 124
|
||||
M V30 59 1 123 125
|
||||
M V30 60 1 125 126
|
||||
M V30 61 1 126 132
|
||||
M V30 62 1 127 128
|
||||
M V30 63 2 127 129
|
||||
M V30 64 1 128 130
|
||||
M V30 65 1 130 131
|
||||
M V30 66 1 131 137
|
||||
M V30 67 1 132 133
|
||||
M V30 68 1 133 134
|
||||
M V30 69 1 134 135
|
||||
M V30 70 1 135 136
|
||||
M V30 71 1 137 138
|
||||
M V30 72 1 138 139
|
||||
M V30 73 1 139 140
|
||||
M V30 74 1 20 113
|
||||
M V30 75 1 141 57
|
||||
M V30 76 1 46 47
|
||||
M V30 77 2 46 48
|
||||
M V30 78 1 46 35
|
||||
M V30 79 1 49 50
|
||||
M V30 80 2 49 51
|
||||
M V30 81 1 49 47
|
||||
M V30 82 1 52 53
|
||||
M V30 83 2 52 54
|
||||
M V30 84 1 52 50
|
||||
M V30 85 1 57 58
|
||||
M V30 86 1 58 59
|
||||
M V30 87 2 58 73
|
||||
M V30 88 1 59 60
|
||||
M V30 89 1 59 63
|
||||
M V30 90 1 60 61
|
||||
M V30 91 1 61 62
|
||||
M V30 92 2 61 74
|
||||
M V30 93 1 62 75
|
||||
M V30 94 1 63 64
|
||||
M V30 95 1 64 65
|
||||
M V30 96 2 64 87
|
||||
M V30 97 1 65 66
|
||||
M V30 98 1 66 67
|
||||
M V30 99 1 67 68
|
||||
M V30 100 1 68 69
|
||||
M V30 101 1 69 70
|
||||
M V30 102 1 70 71
|
||||
M V30 103 1 71 72
|
||||
M V30 104 1 72 89
|
||||
M V30 105 1 75 76
|
||||
M V30 106 1 75 77
|
||||
M V30 107 1 77 78
|
||||
M V30 108 2 77 88
|
||||
M V30 109 1 78 79
|
||||
M V30 110 1 79 80
|
||||
M V30 111 1 80 81
|
||||
M V30 112 1 81 82
|
||||
M V30 113 1 82 83
|
||||
M V30 114 1 83 84
|
||||
M V30 115 1 84 85
|
||||
M V30 116 1 85 86
|
||||
M V30 117 1 86 95
|
||||
M V30 118 1 89 90
|
||||
M V30 119 1 90 91
|
||||
M V30 120 2 90 101
|
||||
M V30 121 1 92 109
|
||||
M V30 122 1 92 93
|
||||
M V30 123 1 93 94
|
||||
M V30 124 1 94 111
|
||||
M V30 125 1 95 96
|
||||
M V30 126 2 95 112
|
||||
M V30 127 1 96 97
|
||||
M V30 128 1 97 98
|
||||
M V30 129 1 98 99
|
||||
M V30 130 1 99 100
|
||||
M V30 131 1 102 103
|
||||
M V30 132 2 102 104
|
||||
M V30 133 1 102 91
|
||||
M V30 134 1 105 106
|
||||
M V30 135 2 105 107
|
||||
M V30 136 1 105 103
|
||||
M V30 137 1 108 109
|
||||
M V30 138 2 108 110
|
||||
M V30 139 1 108 106
|
||||
M V30 140 1 76 1
|
||||
M V30 END BOND
|
||||
M V30 BEGIN SGROUP
|
||||
M V30 1 MUL 0 -
|
||||
M V30 ATOMS=(112 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 -
|
||||
M V30 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 -
|
||||
M V30 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 -
|
||||
M V30 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 -
|
||||
M V30 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112) -
|
||||
M V30 XBONDS=(2 74 75) -
|
||||
M V30 PATOMS=(56 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 -
|
||||
M V30 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 -
|
||||
M V30 48 49 50 51 52 53 54 55 56) MULT=2
|
||||
M V30 2 MUL 0 ATOMS=(12 90 91 101 102 103 104 105 106 107 108 109 110) -
|
||||
M V30 PATOMS=(3 90 91 101) MULT=4
|
||||
M V30 3 MUL 0 ATOMS=(12 34 35 45 46 47 48 49 50 51 52 53 54) -
|
||||
M V30 XBONDS=(2 34 37) PATOMS=(3 34 35 45) MULT=4
|
||||
M V30 END SGROUP
|
||||
M V30 END CTAB
|
||||
M END
|
||||
@@ -0,0 +1 @@
|
||||
<cml xmlns="http://www.chemaxon.com" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.chemaxon.com http://www.chemaxon.com/marvin/schema/mrvSchema_20_20_0.xsd"><MDocument><MChemicalStruct><molecule molID="m1"><atomArray><atom id="a1" elementType="C" x2="6.1" y2="-4.9"/><atom id="a2" elementType="C" x2="6.966" y2="-5.4" sgroupRef="sg1"/><atom id="a3" elementType="C" x2="7.8321" y2="-4.9" sgroupRef="sg1"/><atom id="a4" elementType="C" x2="8.6981" y2="-5.4"/><atom id="a5" elementType="C" x2="6.7072" y2="-6.3659"/><atom id="a6" elementType="C" x2="7.4143" y2="-7.073"/><atom id="a7" elementType="O" x2="7.1555" y2="-8.039" sgroupRef="sg1"/></atomArray><bondArray><bond id="b1" atomRefs2="a1 a2" order="1"/><bond id="b2" atomRefs2="a2 a3" order="1"/><bond id="b3" atomRefs2="a4 a3" order="1"/><bond id="b4" atomRefs2="a2 a5" order="1"/><bond id="b5" atomRefs2="a5 a6" order="1"/><bond id="b6" atomRefs2="a7 a6" order="1"/></bondArray><molecule molID="m2" id="sg1" role="MultipleSgroup" atomRefs="a2 a3 a5 a6 a7" title="3"><molecule molID="m3" id="sg2" role="MultipleSgroup" atomRefs="a5 a6" title="2"></molecule></molecule></molecule></MChemicalStruct></MDocument></cml>
|
||||
@@ -0,0 +1,2 @@
|
||||
<?xml version="1.0" encoding="utf-8"?>
|
||||
<cml xmlns="http://www.chemaxon.com" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.chemaxon.com http://www.chemaxon.com/marvin/schema/mrvSchema_20_20_0.xsd"><MDocument><MChemicalStruct><molecule molID="m1"><atomArray><atom id="a1" elementType="C" x2="6.1" y2="-4.9"/><atom id="a2" elementType="C" x2="6.966" y2="-5.4" sgroupRef="sg1"/><atom id="a3" elementType="C" x2="7.8321" y2="-4.9" sgroupRef="sg1"/><atom id="a4" elementType="C" x2="8.6981" y2="-5.4"/><atom id="a5" elementType="C" x2="6.7072" y2="-6.3659" sgroupRef="sg2"/><atom id="a6" elementType="C" x2="7.4143" y2="-7.073" sgroupRef="sg2"/><atom id="a7" elementType="O" x2="7.1555" y2="-8.039" sgroupRef="sg1"/></atomArray><bondArray><bond id="b1" atomRefs2="a1 a2" order="1"/><bond id="b2" atomRefs2="a2 a3" order="1"/><bond id="b3" atomRefs2="a4 a3" order="1"/><bond id="b4" atomRefs2="a2 a5" order="1"/><bond id="b5" atomRefs2="a5 a6" order="1"/><bond id="b6" atomRefs2="a7 a6" order="1"/></bondArray><molecule molID="m2" id="sg1" role="MultipleSgroup" atomRefs="a2 a3 a5 a6 a7" title="3"><molecule molID="m3" id="sg2" role="MultipleSgroup" atomRefs="a5 a6" title="2"/></molecule></molecule></MChemicalStruct></MDocument></cml>
|
||||
@@ -0,0 +1,65 @@
|
||||
|
||||
RDKit 2D
|
||||
|
||||
0 0 0 0 0 0 0 0 0 0999 V3000
|
||||
M V30 BEGIN CTAB
|
||||
M V30 COUNTS 23 22 4 0 0
|
||||
M V30 BEGIN ATOM
|
||||
M V30 1 C 6.100000 -4.900000 0.000000 0
|
||||
M V30 2 C 6.966000 -5.400000 0.000000 0
|
||||
M V30 3 C 7.832100 -4.900000 0.000000 0
|
||||
M V30 4 C 8.698100 -5.400000 0.000000 0
|
||||
M V30 5 C 6.707200 -6.365900 0.000000 0
|
||||
M V30 6 C 7.414300 -7.073000 0.000000 0
|
||||
M V30 7 C 6.707200 -6.365900 0.000000 0
|
||||
M V30 8 C 7.414300 -7.073000 0.000000 0
|
||||
M V30 9 O 7.155500 -8.039000 0.000000 0
|
||||
M V30 10 C 6.966000 -5.400000 0.000000 0
|
||||
M V30 11 C 7.832100 -4.900000 0.000000 0
|
||||
M V30 12 C 6.707200 -6.365900 0.000000 0
|
||||
M V30 13 C 7.414300 -7.073000 0.000000 0
|
||||
M V30 14 C 6.707200 -6.365900 0.000000 0
|
||||
M V30 15 C 7.414300 -7.073000 0.000000 0
|
||||
M V30 16 O 7.155500 -8.039000 0.000000 0
|
||||
M V30 17 C 6.966000 -5.400000 0.000000 0
|
||||
M V30 18 C 7.832100 -4.900000 0.000000 0
|
||||
M V30 19 C 6.707200 -6.365900 0.000000 0
|
||||
M V30 20 C 7.414300 -7.073000 0.000000 0
|
||||
M V30 21 C 6.707200 -6.365900 0.000000 0
|
||||
M V30 22 C 7.414300 -7.073000 0.000000 0
|
||||
M V30 23 O 7.155500 -8.039000 0.000000 0
|
||||
M V30 END ATOM
|
||||
M V30 BEGIN BOND
|
||||
M V30 1 1 1 2
|
||||
M V30 2 1 2 3
|
||||
M V30 3 1 4 18
|
||||
M V30 4 1 2 5
|
||||
M V30 5 1 5 6
|
||||
M V30 6 1 9 8
|
||||
M V30 7 1 7 8
|
||||
M V30 8 1 7 6
|
||||
M V30 9 1 10 11
|
||||
M V30 10 1 10 12
|
||||
M V30 11 1 12 13
|
||||
M V30 12 1 16 15
|
||||
M V30 13 1 14 15
|
||||
M V30 14 1 14 13
|
||||
M V30 15 1 10 3
|
||||
M V30 16 1 17 18
|
||||
M V30 17 1 17 19
|
||||
M V30 18 1 19 20
|
||||
M V30 19 1 23 22
|
||||
M V30 20 1 21 22
|
||||
M V30 21 1 21 20
|
||||
M V30 22 1 17 11
|
||||
M V30 END BOND
|
||||
M V30 BEGIN SGROUP
|
||||
M V30 1 MUL 0 -
|
||||
M V30 ATOMS=(21 2 3 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23) -
|
||||
M V30 XBONDS=(2 1 3) PATOMS=(7 2 3 5 6 7 8 9) MULT=3
|
||||
M V30 2 MUL 0 ATOMS=(4 12 13 14 15) PATOMS=(2 12 13) MULT=2
|
||||
M V30 3 MUL 0 ATOMS=(4 19 20 21 22) PATOMS=(2 19 20) MULT=2
|
||||
M V30 4 MUL 0 ATOMS=(4 5 6 7 8) XBONDS=(2 4 6) PATOMS=(2 5 6) MULT=2
|
||||
M V30 END SGROUP
|
||||
M V30 END CTAB
|
||||
M END
|
||||
349
Code/GraphMol/MarvinParse/test_data/EmbeddedSgroupMUL_SUP.mrv
Normal file
349
Code/GraphMol/MarvinParse/test_data/EmbeddedSgroupMUL_SUP.mrv
Normal file
@@ -0,0 +1,349 @@
|
||||
<cml xmlns="http://www.chemaxon.com" version="ChemAxon file format v20.20.0, generated by vunknown" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.chemaxon.com http://www.chemaxon.com/marvin/schema/mrvSchema_20_20_0.xsd">
|
||||
<MDocument>
|
||||
<MChemicalStruct>
|
||||
<molecule molID="m1">
|
||||
<atomArray>
|
||||
<atom id="a1" elementType="O" x2="-10.621083333333337" y2="12.09801666666667" lonePair="2" sgroupRef="sg1"/>
|
||||
<atom id="a2" elementType="C" x2="-9.287383333333336" y2="12.86801666666667" sgroupRef="sg1"/>
|
||||
<atom id="a3" elementType="C" x2="-7.953583333333336" y2="12.09801666666667" sgroupRef="sg1"/>
|
||||
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|
||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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||||
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||||
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||||
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|
||||
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|
||||
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|
||||
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|
||||
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||||
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||||
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||||
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||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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||||
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||||
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||||
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|
||||
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||||
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||||
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||||
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|
||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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|
||||
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|
||||
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|
||||
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||||
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|
||||
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|
||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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|
||||
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M V30 72 1 72 73
|
||||
M V30 73 1 73 74
|
||||
M V30 74 1 20 47
|
||||
M V30 75 1 75 80
|
||||
M V30 76 1 76 77
|
||||
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|
||||
M V30 78 1 76 79
|
||||
M V30 79 1 80 81
|
||||
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|
||||
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|
||||
M V30 82 1 82 83
|
||||
M V30 83 1 82 86
|
||||
M V30 84 1 83 84
|
||||
M V30 85 1 84 85
|
||||
M V30 86 2 84 97
|
||||
M V30 87 1 85 98
|
||||
M V30 88 1 86 87
|
||||
M V30 89 1 87 88
|
||||
M V30 90 2 87 110
|
||||
M V30 91 1 88 89
|
||||
M V30 92 1 89 90
|
||||
M V30 93 1 90 91
|
||||
M V30 94 1 91 92
|
||||
M V30 95 1 92 93
|
||||
M V30 96 1 93 94
|
||||
M V30 97 1 94 95
|
||||
M V30 98 1 95 112
|
||||
M V30 99 1 98 99
|
||||
M V30 100 1 98 100
|
||||
M V30 101 1 100 101
|
||||
M V30 102 2 100 111
|
||||
M V30 103 1 101 102
|
||||
M V30 104 1 102 103
|
||||
M V30 105 1 103 104
|
||||
M V30 106 1 104 105
|
||||
M V30 107 1 105 106
|
||||
M V30 108 1 106 107
|
||||
M V30 109 1 107 108
|
||||
M V30 110 1 108 109
|
||||
M V30 111 1 109 118
|
||||
M V30 112 1 112 113
|
||||
M V30 113 1 113 114
|
||||
M V30 114 2 113 124
|
||||
M V30 115 1 114 115
|
||||
M V30 116 1 115 116
|
||||
M V30 117 1 116 117
|
||||
M V30 118 1 117 126
|
||||
M V30 119 1 118 119
|
||||
M V30 120 2 118 125
|
||||
M V30 121 1 119 120
|
||||
M V30 122 1 120 121
|
||||
M V30 123 1 121 122
|
||||
M V30 124 1 122 123
|
||||
M V30 125 1 126 127
|
||||
M V30 126 1 126 128
|
||||
M V30 127 1 126 129
|
||||
M V30 128 1 99 1
|
||||
M V30 END BOND
|
||||
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|
||||
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|
||||
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|
||||
M V30 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 76 -
|
||||
M V30 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100-
|
||||
M V30 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118-
|
||||
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|
||||
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|
||||
M V30 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 76 -
|
||||
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|
||||
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|
||||
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|
||||
M V30 END SGROUP
|
||||
M V30 END CTAB
|
||||
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|
||||
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|
||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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||||
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||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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|
||||
|
||||
RDKit 2D
|
||||
|
||||
0 0 0 0 0 0 0 0 0 0999 V3000
|
||||
M V30 BEGIN CTAB
|
||||
M V30 COUNTS 10 10 2 0 0
|
||||
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||||
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|
||||
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||||
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||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
M V30 END ATOM
|
||||
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|
||||
M V30 1 1 1 2
|
||||
M V30 2 1 1 3
|
||||
M V30 3 1 2 4
|
||||
M V30 4 1 3 5
|
||||
M V30 5 1 4 5
|
||||
M V30 6 1 1 7
|
||||
M V30 7 1 3 6
|
||||
M V30 8 1 7 8
|
||||
M V30 9 1 7 9
|
||||
M V30 10 1 7 10
|
||||
M V30 END BOND
|
||||
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|
||||
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|
||||
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|
||||
M V30 END SGROUP
|
||||
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|
||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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|
||||
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|
||||
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||||
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|
||||
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|
||||
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||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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||||
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|
||||
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||||
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||||
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|
||||
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|
||||
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||||
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|
||||
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|
||||
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||||
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|
||||
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|
||||
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|
||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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|
||||
@@ -0,0 +1,36 @@
|
||||
|
||||
RDKit 2D
|
||||
|
||||
0 0 0 0 0 0 0 0 0 0999 V3000
|
||||
M V30 BEGIN CTAB
|
||||
M V30 COUNTS 10 10 2 0 0
|
||||
M V30 BEGIN ATOM
|
||||
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|
||||
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||||
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||||
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|
||||
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||||
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|
||||
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|
||||
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||||
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|
||||
M V30 10 C 15.225000 -6.892944 0.000000 0
|
||||
M V30 END ATOM
|
||||
M V30 BEGIN BOND
|
||||
M V30 1 1 1 2
|
||||
M V30 2 1 1 3
|
||||
M V30 3 1 2 4
|
||||
M V30 4 1 3 5
|
||||
M V30 5 1 4 5
|
||||
M V30 6 1 1 7
|
||||
M V30 7 1 3 6
|
||||
M V30 8 1 7 8
|
||||
M V30 9 1 7 9
|
||||
M V30 10 1 7 10
|
||||
M V30 END BOND
|
||||
M V30 BEGIN SGROUP
|
||||
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|
||||
M V30 2 SUP 0 ATOMS=(4 7 8 9 10) XBONDS=(1 6) LABEL=tBu
|
||||
M V30 END SGROUP
|
||||
M V30 END CTAB
|
||||
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||||
@@ -0,0 +1,44 @@
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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||||
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||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
<molecule molID="m3" id="sg2" role="SuperatomSgroup" title="tBu">
|
||||
<atomArray>
|
||||
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|
||||
<atom id="a8" elementType="C" x2="16.5279" y2="-9.1494"/>
|
||||
<atom id="a9" elementType="C" x2="13.9222" y2="-9.1494"/>
|
||||
<atom id="a10" elementType="C" x2="15.225" y2="-6.8929"/>
|
||||
</atomArray>
|
||||
<bondArray>
|
||||
<bond id="b7" atomRefs2="a7 a8" order="1"/>
|
||||
<bond id="b8" atomRefs2="a7 a9" order="1"/>
|
||||
<bond id="b9" atomRefs2="a7 a10" order="1"/>
|
||||
</bondArray>
|
||||
<AttachmentPointArray>
|
||||
<AttachmentPoint atom="a7" order="1" bond="b6"/>
|
||||
</AttachmentPointArray>
|
||||
</molecule>
|
||||
</molecule>
|
||||
</molecule>
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
<?xml version="1.0" encoding="utf-8"?>
|
||||
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|
||||
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|
||||
|
||||
RDKit 2D
|
||||
|
||||
0 0 0 0 0 0 0 0 0 0999 V3000
|
||||
M V30 BEGIN CTAB
|
||||
M V30 COUNTS 10 10 2 0 0
|
||||
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|
||||
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||||
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||||
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||||
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|
||||
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||||
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||||
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||||
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||||
M V30 9 C 13.922200 -9.149444 0.000000 0
|
||||
M V30 10 C 15.225000 -6.892944 0.000000 0
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||||
M V30 END ATOM
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||||
M V30 BEGIN BOND
|
||||
M V30 1 1 1 2
|
||||
M V30 2 1 1 3
|
||||
M V30 3 1 2 4
|
||||
M V30 4 1 3 5
|
||||
M V30 5 1 4 5
|
||||
M V30 6 1 1 7
|
||||
M V30 7 1 3 6
|
||||
M V30 8 1 7 8
|
||||
M V30 9 1 7 9
|
||||
M V30 10 1 7 10
|
||||
M V30 END BOND
|
||||
M V30 BEGIN SGROUP
|
||||
M V30 1 SUP 0 ATOMS=(9 1 2 3 4 5 7 8 9 10) LABEL=Chain
|
||||
M V30 2 SUP 0 ATOMS=(4 7 8 9 10) XBONDS=(1 6) LABEL=tBu
|
||||
M V30 END SGROUP
|
||||
M V30 END CTAB
|
||||
M END
|
||||
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|
||||
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||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
<bondArray>
|
||||
<bond id="b1" atomRefs2="a1 a2" order="1"></bond>
|
||||
<bond id="b2" atomRefs2="a2 a3" order="1"></bond>
|
||||
</bondArray>
|
||||
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|
||||
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|
||||
<bondArray>
|
||||
<bond id="b3" atomRefs2="a10 a11" order="1"></bond>
|
||||
<bond id="b4" atomRefs2="a6 a7" order="1"></bond>
|
||||
<bond id="b5" atomRefs2="a7 a8" order="1"></bond>
|
||||
<bond id="b6" atomRefs2="a8 a9" order="1"></bond>
|
||||
<bond id="b7" atomRefs2="a9 a4" order="1">
|
||||
<bondStereo>W</bondStereo>
|
||||
</bond>
|
||||
<bond id="b8" atomRefs2="a9 a5" order="1"></bond>
|
||||
<bond id="b9" atomRefs2="a5 a12" order="2"></bond>
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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||||
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||||
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|
||||
<?xml version="1.0" encoding="utf-8"?>
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||||
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|
||||
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|
||||
|
||||
RDKit 2D
|
||||
|
||||
0 0 0 0 0 0 0 0 0 0999 V3000
|
||||
M V30 BEGIN CTAB
|
||||
M V30 COUNTS 10 8 1 0 0
|
||||
M V30 BEGIN ATOM
|
||||
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|
||||
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|
||||
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|
||||
M V30 4 C 2.873700 0.000000 0.000000 0
|
||||
M V30 5 C 0.206300 4.620000 0.000000 0
|
||||
M V30 6 C 0.206300 3.080000 0.000000 0
|
||||
M V30 7 C 1.540000 2.310000 0.000000 0
|
||||
M V30 8 C 1.540000 0.770000 0.000000 0
|
||||
M V30 9 C 3.183100 2.695000 0.000000 0
|
||||
M V30 10 O 2.873700 -1.540000 0.000000 0
|
||||
M V30 END ATOM
|
||||
M V30 BEGIN BOND
|
||||
M V30 1 1 1 3
|
||||
M V30 2 1 4 2
|
||||
M V30 3 1 5 6
|
||||
M V30 4 1 6 7
|
||||
M V30 5 1 7 8
|
||||
M V30 6 1 8 3 CFG=1
|
||||
M V30 7 1 8 4
|
||||
M V30 8 2 4 10
|
||||
M V30 END BOND
|
||||
M V30 BEGIN SGROUP
|
||||
M V30 1 SUP 0 ATOMS=(8 3 4 5 6 7 8 9 10) XBONDS=(2 1 2) LABEL=Xle
|
||||
M V30 END SGROUP
|
||||
M V30 END CTAB
|
||||
M END
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||||
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|
||||
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||||
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||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
<bondArray>
|
||||
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|
||||
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|
||||
<bond id="b6" atomRefs2="a8 a9" order="1"></bond>
|
||||
<bond id="b7" atomRefs2="a9 a4" order="1">
|
||||
<bondStereo>W</bondStereo>
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
<molecule molID="m3" id="sg2" role="SuperatomSgroup" title="tBu">
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
<atom id="a30" elementType="C" x2="15.225" y2="-6.8929"/>
|
||||
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|
||||
<bondArray>
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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||||
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|
||||
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|
||||
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|
||||
|
||||
|
||||
@@ -0,0 +1,2 @@
|
||||
<?xml version="1.0" encoding="utf-8"?>
|
||||
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||||
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|
||||
|
||||
RDKit 2D
|
||||
|
||||
0 0 0 0 0 0 0 0 0 0999 V3000
|
||||
M V30 BEGIN CTAB
|
||||
M V30 COUNTS 12 11 2 0 0
|
||||
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|
||||
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|
||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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|
||||
M V30 END ATOM
|
||||
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|
||||
M V30 1 1 1 3
|
||||
M V30 2 1 4 2
|
||||
M V30 3 1 9 5
|
||||
M V30 4 1 5 6
|
||||
M V30 5 1 6 7
|
||||
M V30 6 1 7 3 CFG=1
|
||||
M V30 7 1 7 4
|
||||
M V30 8 2 4 8
|
||||
M V30 9 2 9 10
|
||||
M V30 10 1 9 11
|
||||
M V30 11 1 9 12
|
||||
M V30 END BOND
|
||||
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|
||||
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|
||||
M V30 2 SUP 0 ATOMS=(4 9 10 11 12) XBONDS=(1 3) LABEL=tBu
|
||||
M V30 END SGROUP
|
||||
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|
||||
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||||
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|
||||
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||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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|
||||
<bond id="b3" atomRefs2="a2 a4" order="1"/>
|
||||
<bond id="b4" atomRefs2="a3 a5" order="1"/>
|
||||
<bond id="b5" atomRefs2="a4 a5" order="1"/>
|
||||
<bond id="b6" atomRefs2="a1 a6" order="1"/>
|
||||
</bondArray>
|
||||
<molecule molID="m2" id="sg1" role="SuperatomSgroup" title="tBu">
|
||||
<atomArray>
|
||||
<atom id="a7" elementType="C" x2="15.225" y2="-8.3972" sgroupAttachmentPoint="1"/>
|
||||
<atom id="a8" elementType="C" x2="16.5279" y2="-9.1494"/>
|
||||
<atom id="a9" elementType="C" x2="13.9222" y2="-9.1494"/>
|
||||
<atom id="a10" elementType="R" x2="15.225" y2="-6.8929" sgroupRef="sg2"/>
|
||||
</atomArray>
|
||||
<bondArray>
|
||||
<bond id="b7" atomRefs2="a7 a8" order="1"/>
|
||||
<bond id="b8" atomRefs2="a7 a9" order="1"/>
|
||||
<bond id="b9" atomRefs2="a7 a10" order="1"/>
|
||||
</bondArray>
|
||||
<AttachmentPointArray>
|
||||
<AttachmentPoint atom="a7" order="1" bond="b6"/>
|
||||
</AttachmentPointArray>
|
||||
<molecule molID="m3" id="sg2" role="SuperatomSgroup" title="nBu">
|
||||
<atomArray>
|
||||
<atom id="a17" elementType="C" x2="15.225" y2="-8.3972" sgroupAttachmentPoint="1"/>
|
||||
<atom id="a18" elementType="C" x2="16.5279" y2="-9.1494"/>
|
||||
<atom id="a19" elementType="C" x2="13.9222" y2="-9.1494"/>
|
||||
<atom id="a20" elementType="C" x2="15.225" y2="-6.8929"/>
|
||||
</atomArray>
|
||||
<bondArray>
|
||||
<bond id="b17" atomRefs2="a17 a18" order="1"/>
|
||||
<bond id="b18" atomRefs2="a18 a19" order="1"/>
|
||||
<bond id="b19" atomRefs2="a19 a20" order="1"/>
|
||||
</bondArray>
|
||||
<AttachmentPointArray>
|
||||
<AttachmentPoint atom="a17" order="1" bond="b9"/>
|
||||
</AttachmentPointArray>
|
||||
</molecule>
|
||||
</molecule>
|
||||
</molecule>
|
||||
</MChemicalStruct>
|
||||
</MDocument>
|
||||
</cml>
|
||||
@@ -0,0 +1,2 @@
|
||||
<?xml version="1.0" encoding="utf-8"?>
|
||||
<cml xmlns="http://www.chemaxon.com" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.chemaxon.com http://www.chemaxon.com/marvin/schema/mrvSchema_20_20_0.xsd"><MDocument><MChemicalStruct><molecule molID="m1"><atomArray><atom id="a1" elementType="C" x2="15.225" y2="-9.8625"/><atom id="a2" elementType="C" x2="16.442" y2="-10.7467"/><atom id="a3" elementType="C" x2="14.008" y2="-10.7467"/><atom id="a4" elementType="C" x2="15.9772" y2="-12.1774"/><atom id="a5" elementType="C" x2="14.4728" y2="-12.1774"/><atom id="a6" elementType="R" x2="15.225" y2="-8.39724" sgroupRef="sg1"/></atomArray><bondArray><bond id="b1" atomRefs2="a1 a2" order="1"/><bond id="b2" atomRefs2="a1 a3" order="1"/><bond id="b3" atomRefs2="a2 a4" order="1"/><bond id="b4" atomRefs2="a3 a5" order="1"/><bond id="b5" atomRefs2="a4 a5" order="1"/><bond id="b6" atomRefs2="a1 a6" order="1"/></bondArray><molecule molID="m2" id="sg1" role="SuperatomSgroup" title="tBu"><atomArray><atom id="a7" elementType="C" x2="15.225" y2="-8.39724" sgroupAttachmentPoint="1"/><atom id="a8" elementType="C" x2="16.5279" y2="-9.14944"/><atom id="a9" elementType="C" x2="13.9222" y2="-9.14944"/><atom id="a10" elementType="R" x2="15.225" y2="-6.89294" sgroupRef="sg2"/></atomArray><bondArray><bond id="b7" atomRefs2="a7 a8" order="1"/><bond id="b8" atomRefs2="a7 a9" order="1"/><bond id="b9" atomRefs2="a7 a10" order="1"/></bondArray><AttachmentPointArray><attachmentPoint atom="a7" order="1" bond="b6"/></AttachmentPointArray><molecule molID="m3" id="sg2" role="SuperatomSgroup" title="nBu"><atomArray><atom id="a11" elementType="C" x2="15.225" y2="-6.89294" sgroupAttachmentPoint="1"/><atom id="a12" elementType="C" x2="16.5279" y2="-7.64514"/><atom id="a13" elementType="C" x2="13.9222" y2="-7.64514"/><atom id="a14" elementType="C" x2="15.225" y2="-5.38864"/></atomArray><bondArray><bond id="b10" atomRefs2="a11 a12" order="1"/><bond id="b11" atomRefs2="a12 a13" order="1"/><bond id="b12" atomRefs2="a13 a14" order="1"/></bondArray><AttachmentPointArray><attachmentPoint atom="a11" order="1" bond="b9"/></AttachmentPointArray></molecule></molecule></molecule></MChemicalStruct></MDocument></cml>
|
||||
Some files were not shown because too many files have changed in this diff Show More
Reference in New Issue
Block a user