mirror of
https://github.com/rdkit/rdkit.git
synced 2026-06-03 21:44:30 +08:00
Update SMARTS parsing syntax error to include bad token position (#8610)
This commit is contained in:
Hussein Faara
GitHub
@@ -23,7 +23,7 @@ if(FLEX_EXECUTABLE)
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COMPILE_FLAGS "-Pyysmiles_ --noline" )
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FLEX_TARGET(SmartsL smarts.ll
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${CMAKE_CURRENT_SOURCE_DIR}/lex.yysmarts.cpp
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COMPILE_FLAGS "-Pyysmarts_" )
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COMPILE_FLAGS "-Pyysmarts_ --noline" )
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SET(FLEX_OUTPUT_FILES ${FLEX_SmilesL_OUTPUTS} ${FLEX_SmartsL_OUTPUTS})
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else(FLEX_EXECUTABLE)
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CONFIGURE_FILE(${CMAKE_CURRENT_SOURCE_DIR}/lex.yysmiles.cpp.cmake
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@@ -39,7 +39,7 @@ if(BISON_EXECUTABLE)
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COMPILE_FLAGS "-pyysmiles_ --no-lines" )
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BISON_TARGET(SmartsY smarts.yy
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${CMAKE_CURRENT_SOURCE_DIR}/smarts.tab.cpp
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COMPILE_FLAGS "-pyysmarts_" )
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COMPILE_FLAGS "-pyysmarts_ --no-lines" )
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SET(BISON_OUTPUT_FILES ${BISON_SmilesY_OUTPUTS} ${BISON_SmartsY_OUTPUTS})
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if(FLEX_EXECUTABLE)
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ADD_FLEX_BISON_DEPENDENCY(SmilesL SmilesY)
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@@ -70,10 +70,10 @@ target_compile_definitions(SmilesParse PRIVATE RDKIT_SMILESPARSE_BUILD)
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rdkit_headers(SmartsWrite.h
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SmilesParse.h
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SmilesParseOps.h
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SmilesWrite.h
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SmilesWrite.h
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CanonicalizeStereoGroups.h
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SmilesJSONParsers.h DEST GraphMol/SmilesParse)
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rdkit_test(smiTest1 test.cpp LINK_LIBRARIES CIPLabeler FileParsers SmilesParse )
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rdkit_test(smiTest2 test2.cpp LINK_LIBRARIES SmilesParse )
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rdkit_catch_test(cxsmilesTest cxsmiles_test.cpp LINK_LIBRARIES FileParsers SmilesParse MarvinParser )
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@@ -63,38 +63,69 @@ namespace v2 {
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namespace SmilesParse {
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namespace {
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int smarts_parse_helper(const std::string &inp,
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std::vector<RDKit::RWMol *> &molVect, Atom *&atom,
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Bond *&bond, int start_tok) {
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std::list<unsigned int> branchPoints;
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template<int(*lex_init)(void**),
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size_t(*string_setup)(const std::string &, void *),
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int(*lex_destroy)(void*),
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typename T>
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int generic_parse_helper(T parser,
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const std::string &inp,
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std::vector<RDKit::RWMol *> &molVect,
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Atom *&atom,
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Bond *&bond,
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int start_tok,
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const std::string& input_type) {
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std::vector<std::pair<unsigned int, unsigned int>> branchPoints;
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void *scanner;
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int res = 1; // initialize with fail code
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TEST_ASSERT(!yysmarts_lex_init(&scanner));
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TEST_ASSERT(!lex_init(&scanner));
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size_t ltrim = 0;
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try {
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size_t ltrim = setup_smarts_string(inp, scanner);
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ltrim = string_setup(inp, scanner);
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unsigned numAtomsParsed = 0;
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unsigned numBondsParsed = 0;
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res = yysmarts_parse(inp.c_str() + ltrim, &molVect, atom, bond,
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numAtomsParsed, numBondsParsed, &branchPoints, scanner,
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start_tok);
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// NOTE: This variable will be used to point to the location of the
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// offending token if we encounter a syntax error
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unsigned int current_token_position = 0;
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res = parser(inp.c_str() + ltrim, &molVect, atom, bond,
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numAtomsParsed, numBondsParsed, branchPoints, scanner,
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start_tok, current_token_position);
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} catch (...) {
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yysmarts_lex_destroy(scanner);
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lex_destroy(scanner);
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throw;
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}
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yysmarts_lex_destroy(scanner);
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lex_destroy(scanner);
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if (res == 1) {
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std::stringstream errout;
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errout << "Failed parsing SMARTS '" << inp << "'";
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throw SmilesParseException(errout.str());
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}
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if (!branchPoints.empty()) {
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throw SmilesParseException("extra open parentheses");
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auto input = inp.c_str() + ltrim;
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// If there are multiple unclosed brackets, we want to report them all at
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// once.
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for (auto [_, open_bracket_position] : branchPoints) {
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SmilesParseOps::detail::printSyntaxErrorMessage(
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input, "extra open parentheses", open_bracket_position, input_type);
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}
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}
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if (res == 1 || !branchPoints.empty()) {
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throw SmilesParseException("Failed parsing " + input_type + " '" + inp + "'");
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}
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return res;
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}
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int smarts_parse_helper(const std::string &inp,
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std::vector<RDKit::RWMol *> &molVect, Atom *&atom,
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Bond *&bond, int start_tok) {
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return generic_parse_helper<yysmarts_lex_init,
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setup_smarts_string,
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yysmarts_lex_destroy>(yysmarts_parse,
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inp,
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molVect,
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atom,
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bond,
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start_tok,
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"SMARTS");
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}
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int smarts_bond_parse(const std::string &inp, Bond *&bond) {
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auto start_tok = static_cast<int>(START_BOND);
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std::vector<RWMol *> molVect;
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@@ -119,47 +150,15 @@ int smarts_parse(const std::string &inp, std::vector<RDKit::RWMol *> &molVect) {
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int smiles_parse_helper(const std::string &inp,
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std::vector<RDKit::RWMol *> &molVect, Atom *&atom,
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Bond *&bond, int start_tok) {
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std::vector<std::pair<unsigned int, unsigned int>> branchPoints;
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void *scanner;
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int res = 1; // initialize with fail code
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unsigned numAtomsParsed = 0;
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unsigned numBondsParsed = 0;
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TEST_ASSERT(!yysmiles_lex_init(&scanner));
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size_t ltrim = 0;
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try {
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ltrim = setup_smiles_string(inp, scanner);
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// NOTE: This variable will be used to point to the location of the
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// offending token if we encounter a syntax error
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unsigned int current_token_position = 0;
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res = yysmiles_parse(inp.c_str() + ltrim, &molVect, atom, bond,
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numAtomsParsed, numBondsParsed, branchPoints, scanner,
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start_tok, current_token_position);
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} catch (...) {
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yysmiles_lex_destroy(scanner);
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throw;
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}
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yysmiles_lex_destroy(scanner);
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if (res == 1) {
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std::stringstream errout;
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errout << "Failed parsing SMILES '" << inp << "'";
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throw SmilesParseException(errout.str());
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}
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if (!branchPoints.empty()) {
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auto input_smiles = inp.c_str() + ltrim;
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// If there are multiple unclosed brackets, we want to report them all at
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// once. e.g. CC(CC(CC
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for (auto [_, open_bracket_position] : branchPoints) {
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SmilesParseOps::detail::printSyntaxErrorMessage(
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input_smiles, "extra open parentheses", open_bracket_position);
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}
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std::stringstream errout;
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errout << "Failed parsing SMILES '" << inp << "'";
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throw SmilesParseException(errout.str());
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}
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return res;
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return generic_parse_helper<yysmiles_lex_init,
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setup_smiles_string,
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yysmiles_lex_destroy>(yysmiles_parse,
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inp,
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molVect,
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atom,
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bond,
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start_tok,
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"SMILES");
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}
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int smiles_bond_parse(const std::string &inp, Bond *&bond) {
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@@ -696,7 +696,8 @@ namespace detail {
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void printSyntaxErrorMessage(std::string_view input,
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std::string_view err_message,
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unsigned int bad_token_position) {
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unsigned int bad_token_position,
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std::string_view input_type) {
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// NOTE: If the input is very long, the pointer to the failed location
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// becomes less useful. We should truncate the length of the error message
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// to 41 chars.
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@@ -717,10 +718,10 @@ void printSyntaxErrorMessage(std::string_view input,
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(bad_token_position >= prefix_size ? prefix_size
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: bad_token_position - 1);
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BOOST_LOG(rdErrorLog) << "SMILES Parse Error: " << err_message
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BOOST_LOG(rdErrorLog) << input_type << " Parse Error: " << err_message
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<< " while parsing: " << input << std::endl;
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BOOST_LOG(rdErrorLog)
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<< "SMILES Parse Error: check for mistakes around position "
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<< input_type << " Parse Error: check for mistakes around position "
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<< bad_token_position << ":" << std::endl;
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BOOST_LOG(rdErrorLog) << truncate_input(input, bad_token_position - 1)
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<< std::endl;
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@@ -70,7 +70,8 @@ constexpr auto _needsDetectAtomStereo = "_needsDetectAtomStereo";
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void printSyntaxErrorMessage(std::string_view input,
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std::string_view err_message,
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unsigned int bad_token_position);
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unsigned int bad_token_position,
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std::string_view input_type);
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} // namespace detail
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} // namespace SmilesParseOps
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@@ -1,6 +1,3 @@
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#line 1 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/lex.yysmarts.cpp"
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#line 3 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/lex.yysmarts.cpp"
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#define YY_INT_ALIGNED short int
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@@ -794,8 +791,6 @@ static const flex_int16_t yy_chk[363] =
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#define yymore() yymore_used_but_not_detected
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#define YY_MORE_ADJ 0
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#define YY_RESTORE_YY_MORE_OFFSET
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#line 1 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
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#line 9 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
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//
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// Copyright (C) 2003-2018 Greg Landrum and Rational Discovery LLC
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@@ -820,7 +815,10 @@ extern "C" int fileno(FILE*);
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using namespace RDKit;
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//static PeriodicTable * gl_ptab = PeriodicTable::getTable();
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// This will be called every time we construct a token an will allow us to track
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// the position of the current token.
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#undef YY_USER_ACTION
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#define YY_USER_ACTION current_token_position += yyleng;
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#define YY_FATAL_ERROR(msg) smarts_lexer_error(msg)
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@@ -855,7 +853,6 @@ size_t setup_smarts_string(const std::string &text,yyscan_t yyscanner){
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n = _yybytes_len + 2;
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memcpy(buf, yybytes+start, _yybytes_len);
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buf[_yybytes_len] = buf[_yybytes_len+1] = YY_END_OF_BUFFER_CHAR;
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b = yysmarts__scan_buffer(buf,n ,yyscanner);
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@@ -867,16 +864,11 @@ size_t setup_smarts_string(const std::string &text,yyscan_t yyscanner){
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*/
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b->yy_is_our_buffer = 1;
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POSTCONDITION(b,"invalid buffer");
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return start;
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}
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#line 876 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/lex.yysmarts.cpp"
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#line 878 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/lex.yysmarts.cpp"
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#define INITIAL 0
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#define IN_ATOM_STATE 1
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#define IN_BRANCH_STATE 2
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@@ -1158,11 +1150,7 @@ YY_DECL
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}
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{
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#line 91 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
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#line 95 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
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if (start_token)
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{
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int t = start_token;
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@@ -1170,9 +1158,6 @@ YY_DECL
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return t;
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}
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#line 1174 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/lex.yysmarts.cpp"
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while ( /*CONSTCOND*/1 ) /* loops until end-of-file is reached */
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{
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yy_cp = yyg->yy_c_buf_p;
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@@ -1226,252 +1211,140 @@ do_action: /* This label is used only to access EOF actions. */
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case 1:
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YY_RULE_SETUP
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#line 103 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
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{ yylval->chiraltype = Atom::ChiralType::CHI_TETRAHEDRAL; return CHI_CLASS_TOKEN; }
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YY_BREAK
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case 2:
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YY_RULE_SETUP
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#line 104 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
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{ yylval->chiraltype = Atom::ChiralType::CHI_ALLENE; return CHI_CLASS_TOKEN; }
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YY_BREAK
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case 3:
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YY_RULE_SETUP
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#line 105 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
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{ yylval->chiraltype = Atom::ChiralType::CHI_SQUAREPLANAR; return CHI_CLASS_TOKEN; }
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YY_BREAK
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case 4:
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YY_RULE_SETUP
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#line 106 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
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{ yylval->chiraltype = Atom::ChiralType::CHI_TRIGONALBIPYRAMIDAL; return CHI_CLASS_TOKEN; }
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YY_BREAK
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case 5:
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YY_RULE_SETUP
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#line 107 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
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{ yylval->chiraltype = Atom::ChiralType::CHI_OCTAHEDRAL; return CHI_CLASS_TOKEN; }
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YY_BREAK
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case 6:
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YY_RULE_SETUP
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#line 109 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
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{ return AT_TOKEN; }
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YY_BREAK
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case 7:
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#line 113 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
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case 8:
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#line 114 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
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case 9:
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#line 115 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
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case 10:
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#line 116 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
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case 11:
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#line 117 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
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case 12:
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#line 118 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
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case 13:
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#line 119 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
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case 14:
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#line 120 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
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case 15:
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#line 121 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
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case 16:
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#line 122 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
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case 17:
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#line 123 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
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case 18:
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#line 124 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
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case 19:
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#line 125 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
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case 20:
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#line 126 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
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case 21:
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#line 127 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
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case 22:
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#line 128 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
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case 23:
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#line 129 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
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case 24:
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#line 130 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
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case 25:
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#line 131 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
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case 26:
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#line 132 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
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case 27:
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#line 133 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
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case 28:
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#line 134 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
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case 29:
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#line 135 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
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case 30:
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#line 136 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
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case 31:
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#line 137 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
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case 32:
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#line 138 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
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case 33:
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#line 139 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
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case 34:
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#line 140 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
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case 35:
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#line 141 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
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case 36:
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#line 142 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
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case 37:
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#line 143 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
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case 38:
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#line 144 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
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case 39:
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#line 145 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
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case 40:
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#line 146 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
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case 41:
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#line 147 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
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case 42:
|
||||
#line 148 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
case 43:
|
||||
#line 149 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
case 44:
|
||||
#line 150 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
case 45:
|
||||
#line 151 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
case 46:
|
||||
#line 152 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
case 47:
|
||||
#line 153 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
case 48:
|
||||
#line 154 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
case 49:
|
||||
#line 155 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
case 50:
|
||||
#line 156 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
case 51:
|
||||
#line 157 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
case 52:
|
||||
#line 158 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
case 53:
|
||||
#line 159 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
case 54:
|
||||
#line 160 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
case 55:
|
||||
#line 161 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
case 56:
|
||||
#line 162 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
case 57:
|
||||
#line 163 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
case 58:
|
||||
#line 164 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
case 59:
|
||||
#line 165 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
case 60:
|
||||
#line 166 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
case 61:
|
||||
#line 167 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
case 62:
|
||||
#line 168 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
case 63:
|
||||
#line 169 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
case 64:
|
||||
#line 170 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
case 65:
|
||||
#line 171 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
case 66:
|
||||
#line 172 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
case 67:
|
||||
#line 173 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
case 68:
|
||||
#line 174 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
case 69:
|
||||
#line 175 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
case 70:
|
||||
#line 176 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
case 71:
|
||||
#line 177 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
case 72:
|
||||
#line 178 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
case 73:
|
||||
#line 179 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
case 74:
|
||||
#line 180 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
case 75:
|
||||
#line 181 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
case 76:
|
||||
#line 182 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
case 77:
|
||||
#line 183 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
case 78:
|
||||
#line 184 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
case 79:
|
||||
#line 185 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
case 80:
|
||||
#line 186 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
case 81:
|
||||
#line 187 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
case 82:
|
||||
#line 188 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
case 83:
|
||||
#line 189 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
case 84:
|
||||
#line 190 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
case 85:
|
||||
#line 191 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
case 86:
|
||||
#line 192 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
case 87:
|
||||
#line 193 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
case 88:
|
||||
#line 194 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
case 89:
|
||||
#line 195 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
case 90:
|
||||
#line 196 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
case 91:
|
||||
#line 197 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
case 92:
|
||||
#line 198 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
case 93:
|
||||
#line 199 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
case 94:
|
||||
#line 200 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
case 95:
|
||||
#line 201 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
case 96:
|
||||
#line 202 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
case 97:
|
||||
#line 203 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
case 98:
|
||||
#line 204 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
case 99:
|
||||
#line 205 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
case 100:
|
||||
#line 206 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
case 101:
|
||||
#line 207 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
case 102:
|
||||
#line 208 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
case 103:
|
||||
#line 209 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
case 104:
|
||||
#line 210 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
case 105:
|
||||
#line 211 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
case 106:
|
||||
#line 212 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
case 107:
|
||||
#line 213 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
case 108:
|
||||
#line 214 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
case 109:
|
||||
#line 215 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
case 110:
|
||||
#line 216 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
case 111:
|
||||
YY_RULE_SETUP
|
||||
#line 216 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
{ yylval->atom = new QueryAtom( PeriodicTable::getTable()->getAtomicNumber( yytext ) );
|
||||
return ATOM_TOKEN;
|
||||
}
|
||||
YY_BREAK
|
||||
case 112:
|
||||
YY_RULE_SETUP
|
||||
#line 219 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
{
|
||||
yylval->atom = new QueryAtom();
|
||||
yylval->atom->setQuery(makeAtomExplicitDegreeQuery(1));
|
||||
@@ -1480,7 +1353,6 @@ YY_RULE_SETUP
|
||||
YY_BREAK
|
||||
case 113:
|
||||
YY_RULE_SETUP
|
||||
#line 224 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
{
|
||||
yylval->atom = new QueryAtom();
|
||||
yylval->atom->setQuery(makeAtomNonHydrogenDegreeQuery(1));
|
||||
@@ -1489,7 +1361,6 @@ YY_RULE_SETUP
|
||||
YY_BREAK
|
||||
case 114:
|
||||
YY_RULE_SETUP
|
||||
#line 230 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
{
|
||||
yylval->atom = new QueryAtom();
|
||||
yylval->atom->setQuery(makeAtomTotalDegreeQuery(1));
|
||||
@@ -1498,7 +1369,6 @@ YY_RULE_SETUP
|
||||
YY_BREAK
|
||||
case 115:
|
||||
YY_RULE_SETUP
|
||||
#line 236 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
{
|
||||
yylval->atom = new QueryAtom();
|
||||
yylval->atom->setQuery(makeAtomHasRingBondQuery());
|
||||
@@ -1507,7 +1377,6 @@ YY_RULE_SETUP
|
||||
YY_BREAK
|
||||
case 116:
|
||||
YY_RULE_SETUP
|
||||
#line 242 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
{
|
||||
yylval->atom = new QueryAtom();
|
||||
yylval->atom->setQuery(makeAtomTotalValenceQuery(1));
|
||||
@@ -1516,7 +1385,6 @@ YY_RULE_SETUP
|
||||
YY_BREAK
|
||||
case 117:
|
||||
YY_RULE_SETUP
|
||||
#line 248 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
{
|
||||
yylval->atom = new QueryAtom();
|
||||
yylval->atom->setQuery(makeAtomHasHeteroatomNbrsQuery());
|
||||
@@ -1525,7 +1393,6 @@ YY_RULE_SETUP
|
||||
YY_BREAK
|
||||
case 118:
|
||||
YY_RULE_SETUP
|
||||
#line 254 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
{
|
||||
yylval->atom = new QueryAtom();
|
||||
yylval->atom->setQuery(makeAtomHasAliphaticHeteroatomNbrsQuery());
|
||||
@@ -1534,7 +1401,6 @@ YY_RULE_SETUP
|
||||
YY_BREAK
|
||||
case 119:
|
||||
YY_RULE_SETUP
|
||||
#line 260 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
{
|
||||
yylval->atom = new QueryAtom();
|
||||
yylval->atom->setQuery(makeAtomHasImplicitHQuery());
|
||||
@@ -1543,7 +1409,6 @@ YY_RULE_SETUP
|
||||
YY_BREAK
|
||||
case 120:
|
||||
YY_RULE_SETUP
|
||||
#line 266 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
{
|
||||
yylval->atom = new QueryAtom();
|
||||
yylval->atom->setQuery(new AtomRingQuery(-1));
|
||||
@@ -1552,7 +1417,6 @@ YY_RULE_SETUP
|
||||
YY_BREAK
|
||||
case 121:
|
||||
YY_RULE_SETUP
|
||||
#line 272 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
{
|
||||
yylval->atom = new QueryAtom();
|
||||
yylval->atom->setQuery(makeAtomInRingQuery());
|
||||
@@ -1561,112 +1425,90 @@ YY_RULE_SETUP
|
||||
YY_BREAK
|
||||
case 122:
|
||||
YY_RULE_SETUP
|
||||
#line 278 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
{ return H_TOKEN; }
|
||||
YY_BREAK
|
||||
case 123:
|
||||
YY_RULE_SETUP
|
||||
#line 281 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
{ yylval->ival = 5; return ORGANIC_ATOM_TOKEN; }
|
||||
YY_BREAK
|
||||
case 124:
|
||||
YY_RULE_SETUP
|
||||
#line 283 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
{ yylval->ival = 6; return ORGANIC_ATOM_TOKEN; }
|
||||
YY_BREAK
|
||||
case 125:
|
||||
YY_RULE_SETUP
|
||||
#line 285 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
{ yylval->ival = 7; return ORGANIC_ATOM_TOKEN; }
|
||||
YY_BREAK
|
||||
case 126:
|
||||
YY_RULE_SETUP
|
||||
#line 287 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
{ yylval->ival = 8; return ORGANIC_ATOM_TOKEN; }
|
||||
YY_BREAK
|
||||
case 127:
|
||||
YY_RULE_SETUP
|
||||
#line 289 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
{ yylval->ival = 9; return ORGANIC_ATOM_TOKEN; }
|
||||
YY_BREAK
|
||||
case 128:
|
||||
YY_RULE_SETUP
|
||||
#line 291 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
{ yylval->ival = 15; return ORGANIC_ATOM_TOKEN; }
|
||||
YY_BREAK
|
||||
case 129:
|
||||
YY_RULE_SETUP
|
||||
#line 293 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
{ yylval->ival = 16; return ORGANIC_ATOM_TOKEN; }
|
||||
YY_BREAK
|
||||
case 130:
|
||||
YY_RULE_SETUP
|
||||
#line 295 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
{ yylval->ival = 17; return ORGANIC_ATOM_TOKEN; }
|
||||
YY_BREAK
|
||||
case 131:
|
||||
YY_RULE_SETUP
|
||||
#line 297 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
{ yylval->ival = 35; return ORGANIC_ATOM_TOKEN; }
|
||||
YY_BREAK
|
||||
case 132:
|
||||
YY_RULE_SETUP
|
||||
#line 299 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
{ yylval->ival = 53; return ORGANIC_ATOM_TOKEN; }
|
||||
YY_BREAK
|
||||
case 133:
|
||||
YY_RULE_SETUP
|
||||
#line 302 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
{ yylval->ival = 5; return AROMATIC_ATOM_TOKEN; }
|
||||
YY_BREAK
|
||||
case 134:
|
||||
YY_RULE_SETUP
|
||||
#line 304 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
{ yylval->ival = 6; return AROMATIC_ATOM_TOKEN; }
|
||||
YY_BREAK
|
||||
case 135:
|
||||
YY_RULE_SETUP
|
||||
#line 306 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
{ yylval->ival = 7; return AROMATIC_ATOM_TOKEN; }
|
||||
YY_BREAK
|
||||
case 136:
|
||||
YY_RULE_SETUP
|
||||
#line 308 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
{ yylval->ival = 8; return AROMATIC_ATOM_TOKEN; }
|
||||
YY_BREAK
|
||||
case 137:
|
||||
YY_RULE_SETUP
|
||||
#line 310 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
{ yylval->ival = 15; return AROMATIC_ATOM_TOKEN; }
|
||||
YY_BREAK
|
||||
case 138:
|
||||
YY_RULE_SETUP
|
||||
#line 312 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
{ yylval->ival = 16; return AROMATIC_ATOM_TOKEN; }
|
||||
YY_BREAK
|
||||
case 139:
|
||||
YY_RULE_SETUP
|
||||
#line 314 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
{ yylval->ival = 14; return AROMATIC_ATOM_TOKEN; }
|
||||
YY_BREAK
|
||||
case 140:
|
||||
YY_RULE_SETUP
|
||||
#line 316 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
{ yylval->ival = 33; return AROMATIC_ATOM_TOKEN; }
|
||||
YY_BREAK
|
||||
case 141:
|
||||
YY_RULE_SETUP
|
||||
#line 318 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
{ yylval->ival = 34; return AROMATIC_ATOM_TOKEN; }
|
||||
YY_BREAK
|
||||
case 142:
|
||||
YY_RULE_SETUP
|
||||
#line 320 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
{ yylval->ival = 52; return AROMATIC_ATOM_TOKEN; }
|
||||
YY_BREAK
|
||||
case 143:
|
||||
YY_RULE_SETUP
|
||||
#line 324 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
{
|
||||
yylval->atom = new QueryAtom();
|
||||
yylval->atom->setQuery(makeAtomNullQuery());
|
||||
@@ -1675,7 +1517,6 @@ YY_RULE_SETUP
|
||||
YY_BREAK
|
||||
case 144:
|
||||
YY_RULE_SETUP
|
||||
#line 330 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
{
|
||||
yylval->atom = new QueryAtom();
|
||||
yylval->atom->setQuery(makeAtomAromaticQuery());
|
||||
@@ -1685,7 +1526,6 @@ YY_RULE_SETUP
|
||||
YY_BREAK
|
||||
case 145:
|
||||
YY_RULE_SETUP
|
||||
#line 337 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
{
|
||||
yylval->atom = new QueryAtom();
|
||||
yylval->atom->setQuery(makeAtomAliphaticQuery());
|
||||
@@ -1694,43 +1534,36 @@ YY_RULE_SETUP
|
||||
YY_BREAK
|
||||
case 146:
|
||||
YY_RULE_SETUP
|
||||
#line 344 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
{ return COLON_TOKEN; }
|
||||
YY_BREAK
|
||||
case 147:
|
||||
YY_RULE_SETUP
|
||||
#line 346 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
{ return UNDERSCORE_TOKEN; }
|
||||
YY_BREAK
|
||||
case 148:
|
||||
YY_RULE_SETUP
|
||||
#line 348 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
{ return HASH_TOKEN; }
|
||||
YY_BREAK
|
||||
case 149:
|
||||
YY_RULE_SETUP
|
||||
#line 350 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
{ yylval->bond = new QueryBond(Bond::DOUBLE);
|
||||
yylval->bond->setQuery(makeBondOrderEqualsQuery(Bond::DOUBLE));
|
||||
return BOND_TOKEN; }
|
||||
YY_BREAK
|
||||
case 150:
|
||||
YY_RULE_SETUP
|
||||
#line 354 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
{ yylval->bond = new QueryBond();
|
||||
yylval->bond->setQuery(makeBondNullQuery());
|
||||
return BOND_TOKEN; }
|
||||
YY_BREAK
|
||||
case 151:
|
||||
YY_RULE_SETUP
|
||||
#line 358 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
{ yylval->bond = new QueryBond(Bond::QUADRUPLE);
|
||||
yylval->bond->setQuery(makeBondOrderEqualsQuery(Bond::QUADRUPLE));
|
||||
return BOND_TOKEN; }
|
||||
YY_BREAK
|
||||
case 152:
|
||||
YY_RULE_SETUP
|
||||
#line 362 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
{ yylval->bond = new QueryBond(Bond::SINGLE);
|
||||
yylval->bond->setBondDir(Bond::ENDDOWNRIGHT);
|
||||
yylval->bond->setQuery(makeSingleOrAromaticBondQuery());
|
||||
@@ -1738,15 +1571,13 @@ YY_RULE_SETUP
|
||||
YY_BREAK
|
||||
case 153:
|
||||
YY_RULE_SETUP
|
||||
#line 367 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
{ yylval->bond = new QueryBond(Bond::SINGLE);
|
||||
yylval->bond->setBondDir(Bond::ENDUPRIGHT);
|
||||
yylval->bond->setQuery(makeSingleOrAromaticBondQuery());
|
||||
yylval->bond->setQuery(makeSingleOrAromaticBondQuery());
|
||||
return BOND_TOKEN; }
|
||||
YY_BREAK
|
||||
case 154:
|
||||
YY_RULE_SETUP
|
||||
#line 372 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
{
|
||||
yylval->bond = new QueryBond(Bond::DATIVER);
|
||||
return BOND_TOKEN;
|
||||
@@ -1754,7 +1585,6 @@ YY_RULE_SETUP
|
||||
YY_BREAK
|
||||
case 155:
|
||||
YY_RULE_SETUP
|
||||
#line 376 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
{
|
||||
yylval->bond = new QueryBond(Bond::DATIVEL);
|
||||
return BOND_TOKEN;
|
||||
@@ -1762,57 +1592,46 @@ YY_RULE_SETUP
|
||||
YY_BREAK
|
||||
case 156:
|
||||
YY_RULE_SETUP
|
||||
#line 381 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
{ return MINUS_TOKEN; }
|
||||
YY_BREAK
|
||||
case 157:
|
||||
YY_RULE_SETUP
|
||||
#line 383 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
{ return PLUS_TOKEN; }
|
||||
YY_BREAK
|
||||
case 158:
|
||||
YY_RULE_SETUP
|
||||
#line 385 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
{ yy_push_state(IN_RECURSION_STATE,yyscanner); return BEGIN_RECURSE; }
|
||||
YY_BREAK
|
||||
case 159:
|
||||
YY_RULE_SETUP
|
||||
#line 387 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
{ yy_push_state(IN_BRANCH_STATE,yyscanner); return GROUP_OPEN_TOKEN; }
|
||||
YY_BREAK
|
||||
case 160:
|
||||
YY_RULE_SETUP
|
||||
#line 388 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
{ yy_pop_state(yyscanner); return GROUP_CLOSE_TOKEN; }
|
||||
YY_BREAK
|
||||
case 161:
|
||||
YY_RULE_SETUP
|
||||
#line 389 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
{ yy_pop_state(yyscanner); return END_RECURSE; }
|
||||
YY_BREAK
|
||||
case 162:
|
||||
YY_RULE_SETUP
|
||||
#line 391 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
{ return RANGE_OPEN_TOKEN; }
|
||||
YY_BREAK
|
||||
case 163:
|
||||
YY_RULE_SETUP
|
||||
#line 392 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
{ return RANGE_CLOSE_TOKEN; }
|
||||
YY_BREAK
|
||||
case 164:
|
||||
YY_RULE_SETUP
|
||||
#line 396 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
{ yy_push_state(IN_ATOM_STATE,yyscanner); return ATOM_OPEN_TOKEN; }
|
||||
YY_BREAK
|
||||
case 165:
|
||||
YY_RULE_SETUP
|
||||
#line 397 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
{ yy_pop_state(yyscanner); return ATOM_CLOSE_TOKEN; }
|
||||
YY_BREAK
|
||||
case 166:
|
||||
YY_RULE_SETUP
|
||||
#line 398 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
{ /* FIX: ???
|
||||
This rule is here because otherwise recursive SMARTS queries like:
|
||||
[$(C(=O)[O,N])] lex improperly (no ATOM_CLOSE token is returned).
|
||||
@@ -1824,47 +1643,38 @@ YY_RULE_SETUP
|
||||
YY_BREAK
|
||||
case 167:
|
||||
YY_RULE_SETUP
|
||||
#line 407 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
{ return SEPARATOR_TOKEN; }
|
||||
YY_BREAK
|
||||
case 168:
|
||||
YY_RULE_SETUP
|
||||
#line 409 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
{ return PERCENT_TOKEN; }
|
||||
YY_BREAK
|
||||
case 169:
|
||||
YY_RULE_SETUP
|
||||
#line 411 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
{ yylval->ival = 0; return ZERO_TOKEN; }
|
||||
YY_BREAK
|
||||
case 170:
|
||||
YY_RULE_SETUP
|
||||
#line 412 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
{ yylval->ival = yytext[0]-'0'; return NONZERO_DIGIT_TOKEN; }
|
||||
YY_BREAK
|
||||
case 171:
|
||||
YY_RULE_SETUP
|
||||
#line 414 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
{ return NOT_TOKEN; }
|
||||
YY_BREAK
|
||||
case 172:
|
||||
YY_RULE_SETUP
|
||||
#line 416 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
{ return SEMI_TOKEN; }
|
||||
YY_BREAK
|
||||
case 173:
|
||||
YY_RULE_SETUP
|
||||
#line 418 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
{ return AND_TOKEN; }
|
||||
YY_BREAK
|
||||
case 174:
|
||||
YY_RULE_SETUP
|
||||
#line 420 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
{ return OR_TOKEN; }
|
||||
YY_BREAK
|
||||
case 175:
|
||||
YY_RULE_SETUP
|
||||
#line 422 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
{
|
||||
yylval->atom = new QueryAtom();
|
||||
yylval->atom->setQuery(makeAtomHybridizationQuery(Atom::S));
|
||||
@@ -1873,7 +1683,6 @@ YY_RULE_SETUP
|
||||
YY_BREAK
|
||||
case 176:
|
||||
YY_RULE_SETUP
|
||||
#line 428 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
{
|
||||
yylval->atom = new QueryAtom();
|
||||
yylval->atom->setQuery(makeAtomHybridizationQuery(Atom::SP));
|
||||
@@ -1882,7 +1691,6 @@ YY_RULE_SETUP
|
||||
YY_BREAK
|
||||
case 177:
|
||||
YY_RULE_SETUP
|
||||
#line 434 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
{
|
||||
yylval->atom = new QueryAtom();
|
||||
yylval->atom->setQuery(makeAtomHybridizationQuery(Atom::SP2));
|
||||
@@ -1891,7 +1699,6 @@ YY_RULE_SETUP
|
||||
YY_BREAK
|
||||
case 178:
|
||||
YY_RULE_SETUP
|
||||
#line 440 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
{
|
||||
yylval->atom = new QueryAtom();
|
||||
yylval->atom->setQuery(makeAtomHybridizationQuery(Atom::SP3));
|
||||
@@ -1900,7 +1707,6 @@ YY_RULE_SETUP
|
||||
YY_BREAK
|
||||
case 179:
|
||||
YY_RULE_SETUP
|
||||
#line 445 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
{
|
||||
yylval->atom = new QueryAtom();
|
||||
yylval->atom->setQuery(makeAtomHybridizationQuery(Atom::SP3D));
|
||||
@@ -1909,7 +1715,6 @@ YY_RULE_SETUP
|
||||
YY_BREAK
|
||||
case 180:
|
||||
YY_RULE_SETUP
|
||||
#line 450 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
{
|
||||
yylval->atom = new QueryAtom();
|
||||
yylval->atom->setQuery(makeAtomHybridizationQuery(Atom::SP3D2));
|
||||
@@ -1919,27 +1724,22 @@ YY_RULE_SETUP
|
||||
case 181:
|
||||
/* rule 181 can match eol */
|
||||
YY_RULE_SETUP
|
||||
#line 455 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
return EOS_TOKEN;
|
||||
YY_BREAK
|
||||
case YY_STATE_EOF(INITIAL):
|
||||
case YY_STATE_EOF(IN_ATOM_STATE):
|
||||
case YY_STATE_EOF(IN_BRANCH_STATE):
|
||||
case YY_STATE_EOF(IN_RECURSION_STATE):
|
||||
#line 457 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
{ return EOS_TOKEN; }
|
||||
YY_BREAK
|
||||
case 182:
|
||||
YY_RULE_SETUP
|
||||
#line 458 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
return BAD_CHARACTER;
|
||||
YY_BREAK
|
||||
case 183:
|
||||
YY_RULE_SETUP
|
||||
#line 460 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
YY_FATAL_ERROR( "flex scanner jammed" );
|
||||
YY_BREAK
|
||||
#line 1942 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/lex.yysmarts.cpp"
|
||||
|
||||
case YY_END_OF_BUFFER:
|
||||
{
|
||||
@@ -3160,9 +2960,6 @@ void yyfree (void * ptr , yyscan_t yyscanner)
|
||||
|
||||
#define YYTABLES_NAME "yytables"
|
||||
|
||||
#line 460 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.ll"
|
||||
|
||||
|
||||
#undef yysmarts_wrap
|
||||
int yysmarts_wrap( void ) { return 1; }
|
||||
|
||||
|
||||
@@ -30,7 +30,11 @@ extern "C" int fileno(FILE*);
|
||||
|
||||
using namespace RDKit;
|
||||
|
||||
//static PeriodicTable * gl_ptab = PeriodicTable::getTable();
|
||||
// This will be called every time we construct a token an will allow us to track
|
||||
// the position of the current token.
|
||||
#undef YY_USER_ACTION
|
||||
#define YY_USER_ACTION current_token_position += yyleng;
|
||||
|
||||
|
||||
#define YY_FATAL_ERROR(msg) smarts_lexer_error(msg)
|
||||
|
||||
@@ -365,7 +369,7 @@ A {
|
||||
|
||||
[\/] { yylval->bond = new QueryBond(Bond::SINGLE);
|
||||
yylval->bond->setBondDir(Bond::ENDUPRIGHT);
|
||||
yylval->bond->setQuery(makeSingleOrAromaticBondQuery());
|
||||
yylval->bond->setQuery(makeSingleOrAromaticBondQuery());
|
||||
return BOND_TOKEN; }
|
||||
|
||||
\-\> {
|
||||
|
||||
File diff suppressed because it is too large
Load Diff
@@ -35,8 +35,8 @@
|
||||
especially those whose name start with YY_ or yy_. They are
|
||||
private implementation details that can be changed or removed. */
|
||||
|
||||
#ifndef YY_YYSMARTS_HOME_GLANDRUM_RDKIT_GIT_CODE_GRAPHMOL_SMILESPARSE_SMARTS_TAB_HPP_INCLUDED
|
||||
# define YY_YYSMARTS_HOME_GLANDRUM_RDKIT_GIT_CODE_GRAPHMOL_SMILESPARSE_SMARTS_TAB_HPP_INCLUDED
|
||||
#ifndef YY_YYSMARTS_USR_APP_RDKIT_CODE_GRAPHMOL_SMILESPARSE_SMARTS_TAB_HPP_INCLUDED
|
||||
# define YY_YYSMARTS_USR_APP_RDKIT_CODE_GRAPHMOL_SMILESPARSE_SMARTS_TAB_HPP_INCLUDED
|
||||
/* Debug traces. */
|
||||
#ifndef YYDEBUG
|
||||
# define YYDEBUG 0
|
||||
@@ -104,7 +104,6 @@ extern int yysmarts_debug;
|
||||
#if ! defined YYSTYPE && ! defined YYSTYPE_IS_DECLARED
|
||||
union YYSTYPE
|
||||
{
|
||||
#line 81 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.yy"
|
||||
|
||||
int moli;
|
||||
RDKit::QueryAtom * atom;
|
||||
@@ -112,7 +111,6 @@ union YYSTYPE
|
||||
RDKit::Atom::ChiralType chiraltype;
|
||||
int ival;
|
||||
|
||||
#line 116 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.tab.hpp"
|
||||
|
||||
};
|
||||
typedef union YYSTYPE YYSTYPE;
|
||||
@@ -123,16 +121,14 @@ typedef union YYSTYPE YYSTYPE;
|
||||
|
||||
|
||||
|
||||
int yysmarts_parse (const char *input, std::vector<RDKit::RWMol *> *molList, RDKit::Atom* &lastAtom, RDKit::Bond* &lastBond, unsigned &numAtomsParsed, unsigned &numBondsParsed, std::list<unsigned int> *branchPoints, void *scanner, int& start_token);
|
||||
int yysmarts_parse (const char *input, std::vector<RDKit::RWMol *> *molList, RDKit::Atom* &lastAtom, RDKit::Bond* &lastBond, unsigned &numAtomsParsed, unsigned &numBondsParsed, std::vector<std::pair<unsigned int, unsigned int>>& branchPoints, void *scanner, int& start_token, unsigned int& current_token_position);
|
||||
|
||||
/* "%code provides" blocks. */
|
||||
#line 74 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.yy"
|
||||
|
||||
#ifndef YY_DECL
|
||||
#define YY_DECL int yylex \
|
||||
(YYSTYPE * yylval_param , yyscan_t yyscanner, int& start_token)
|
||||
(YYSTYPE * yylval_param , yyscan_t yyscanner, int& start_token, unsigned int& current_token_position)
|
||||
#endif
|
||||
|
||||
#line 137 "/home/glandrum/RDKit_git/Code/GraphMol/SmilesParse/smarts.tab.hpp"
|
||||
|
||||
#endif /* !YY_YYSMARTS_HOME_GLANDRUM_RDKIT_GIT_CODE_GRAPHMOL_SMILESPARSE_SMARTS_TAB_HPP_INCLUDED */
|
||||
#endif /* !YY_YYSMARTS_USR_APP_RDKIT_CODE_GRAPHMOL_SMILESPARSE_SMARTS_TAB_HPP_INCLUDED */
|
||||
|
||||
@@ -7,6 +7,9 @@
|
||||
//
|
||||
#include <cstring>
|
||||
#include <iostream>
|
||||
#include <string>
|
||||
#include <string_view>
|
||||
#include <utility>
|
||||
#include <vector>
|
||||
|
||||
#include <GraphMol/RDKitBase.h>
|
||||
@@ -18,7 +21,7 @@
|
||||
#define YYDEBUG 1
|
||||
#include "smarts.tab.hpp"
|
||||
|
||||
extern int yysmarts_lex(YYSTYPE *,void *, int &);
|
||||
extern int yysmarts_lex(YYSTYPE *,void *, int &, unsigned int&);
|
||||
|
||||
using namespace RDKit;
|
||||
namespace {
|
||||
@@ -37,22 +40,35 @@ yysmarts_error( const char *input,
|
||||
std::vector<RDKit::RWMol *> *ms,
|
||||
RDKit::Atom* &,
|
||||
RDKit::Bond* &,
|
||||
unsigned int &,unsigned int &,
|
||||
std::list<unsigned int> *,
|
||||
void *,int , const char *msg )
|
||||
unsigned int &,
|
||||
unsigned int &,
|
||||
std::vector<std::pair<unsigned int, unsigned int>>&,
|
||||
void *,
|
||||
int,
|
||||
unsigned int bad_token_position,
|
||||
const char *msg )
|
||||
{
|
||||
yyErrorCleanup(ms);
|
||||
BOOST_LOG(rdErrorLog) << "SMARTS Parse Error: " << msg << " while parsing: " << input << std::endl;
|
||||
SmilesParseOps::detail::printSyntaxErrorMessage(input,
|
||||
msg,
|
||||
bad_token_position,
|
||||
"SMARTS");
|
||||
}
|
||||
|
||||
void
|
||||
yysmarts_error( const char *input,
|
||||
std::vector<RDKit::RWMol *> *ms,
|
||||
std::list<unsigned int> *,
|
||||
void *,int, const char * msg )
|
||||
std::vector<std::pair<unsigned int, unsigned int>>&,
|
||||
void *,
|
||||
int,
|
||||
unsigned int bad_token_position,
|
||||
const char * msg )
|
||||
{
|
||||
yyErrorCleanup(ms);
|
||||
BOOST_LOG(rdErrorLog) << "SMARTS Parse Error: " << msg << " while parsing: " << input << std::endl;
|
||||
SmilesParseOps::detail::printSyntaxErrorMessage(input,
|
||||
msg,
|
||||
bad_token_position,
|
||||
"SMARTS");
|
||||
}
|
||||
|
||||
|
||||
@@ -61,20 +77,22 @@ yysmarts_error( const char *input,
|
||||
%define api.pure full
|
||||
%lex-param {yyscan_t *scanner}
|
||||
%lex-param {int& start_token}
|
||||
%lex-param {unsigned int& current_token_position}
|
||||
%parse-param {const char *input}
|
||||
%parse-param {std::vector<RDKit::RWMol *> *molList}
|
||||
%parse-param {RDKit::Atom* &lastAtom}
|
||||
%parse-param {RDKit::Bond* &lastBond}
|
||||
%parse-param {unsigned &numAtomsParsed}
|
||||
%parse-param {unsigned &numBondsParsed}
|
||||
%parse-param {std::list<unsigned int> *branchPoints}
|
||||
%parse-param {std::vector<std::pair<unsigned int, unsigned int>>& branchPoints}
|
||||
%parse-param {void *scanner}
|
||||
%parse-param {int& start_token}
|
||||
%parse-param {unsigned int& current_token_position}
|
||||
|
||||
%code provides {
|
||||
#ifndef YY_DECL
|
||||
#define YY_DECL int yylex \
|
||||
(YYSTYPE * yylval_param , yyscan_t yyscanner, int& start_token)
|
||||
(YYSTYPE * yylval_param , yyscan_t yyscanner, int& start_token, unsigned int& current_token_position)
|
||||
#endif
|
||||
}
|
||||
|
||||
@@ -101,11 +119,11 @@ yysmarts_error( const char *input,
|
||||
%token NOT_TOKEN AND_TOKEN OR_TOKEN SEMI_TOKEN BEGIN_RECURSE END_RECURSE
|
||||
%token COLON_TOKEN UNDERSCORE_TOKEN
|
||||
%token <bond> BOND_TOKEN
|
||||
%token <chiraltype> CHI_CLASS_TOKEN
|
||||
%token <chiraltype> CHI_CLASS_TOKEN
|
||||
%type <moli> mol
|
||||
%type <atom> atomd simple_atom hydrogen_atom
|
||||
%type <atom> atom_expr point_query atom_query recursive_query possible_range_query
|
||||
%type <ival> ring_number nonzero_number number charge_spec digit
|
||||
%type <ival> ring_number nonzero_number number charge_spec digit branch_open_token
|
||||
%type <bond> bondd bond_expr bond_query
|
||||
%token BAD_CHARACTER
|
||||
%token EOS_TOKEN
|
||||
@@ -275,7 +293,7 @@ mol: atomd {
|
||||
|
||||
}
|
||||
|
||||
| mol GROUP_OPEN_TOKEN atomd {
|
||||
| mol branch_open_token atomd {
|
||||
RWMol *mp = (*molList)[$$];
|
||||
Atom *a1 = mp->getActiveAtom();
|
||||
int atomIdx1=a1->getIdx();
|
||||
@@ -289,10 +307,10 @@ mol: atomd {
|
||||
mp->addBond(newB);
|
||||
delete newB;
|
||||
|
||||
branchPoints->push_back(atomIdx1);
|
||||
branchPoints.push_back({atomIdx1, $2});
|
||||
}
|
||||
|
||||
| mol GROUP_OPEN_TOKEN bond_expr atomd {
|
||||
| mol branch_open_token bond_expr atomd {
|
||||
RWMol *mp = (*molList)[$$];
|
||||
int atomIdx1 = mp->getActiveAtom()->getIdx();
|
||||
int atomIdx2 = mp->addAtom($4,true,true);
|
||||
@@ -310,20 +328,20 @@ mol: atomd {
|
||||
}
|
||||
$3->setProp("_cxsmilesBondIdx",numBondsParsed++);
|
||||
mp->addBond($3,true);
|
||||
branchPoints->push_back(atomIdx1);
|
||||
branchPoints.push_back({atomIdx1, $2});
|
||||
|
||||
}
|
||||
|
||||
|
||||
| mol GROUP_CLOSE_TOKEN {
|
||||
if(branchPoints->empty()){
|
||||
yyerror(input,molList,branchPoints,scanner,start_token,"extra close parentheses");
|
||||
if(branchPoints.empty()){
|
||||
yyerror(input,molList,branchPoints,scanner,start_token, current_token_position, "extra close parentheses");
|
||||
yyErrorCleanup(molList);
|
||||
YYABORT;
|
||||
}
|
||||
RWMol *mp = (*molList)[$$];
|
||||
mp->setActiveAtom(branchPoints->back());
|
||||
branchPoints->pop_back();
|
||||
mp->setActiveAtom(branchPoints.back().first);
|
||||
branchPoints.pop_back();
|
||||
}
|
||||
|
||||
;
|
||||
@@ -774,10 +792,10 @@ number: ZERO_TOKEN
|
||||
|
||||
/* --------------------------------------------------------------- */
|
||||
nonzero_number: NONZERO_DIGIT_TOKEN
|
||||
| nonzero_number digit {
|
||||
if($1 >= std::numeric_limits<std::int32_t>::max()/10 ||
|
||||
| nonzero_number digit {
|
||||
if($1 >= std::numeric_limits<std::int32_t>::max()/10 ||
|
||||
$1*10 >= std::numeric_limits<std::int32_t>::max()-$2 ){
|
||||
yysmarts_error(input,molList,lastAtom,lastBond,numAtomsParsed,numBondsParsed,branchPoints,scanner,start_token,"number too large");
|
||||
yysmarts_error(input,molList,lastAtom,lastBond,numAtomsParsed,numBondsParsed,branchPoints,scanner,start_token, current_token_position, "number too large");
|
||||
YYABORT;
|
||||
}
|
||||
$$ = $1*10 + $2; }
|
||||
@@ -787,4 +805,7 @@ digit: NONZERO_DIGIT_TOKEN
|
||||
| ZERO_TOKEN
|
||||
;
|
||||
|
||||
// We'll use the token position for unclosed branch syntax error messages
|
||||
branch_open_token: GROUP_OPEN_TOKEN { $$ = current_token_position; };
|
||||
|
||||
%%
|
||||
|
||||
@@ -123,7 +123,10 @@ yysmiles_error( const char *input,
|
||||
void *,int, unsigned int bad_token_position, const char * msg )
|
||||
{
|
||||
yyErrorCleanup(ms);
|
||||
SmilesParseOps::detail::printSyntaxErrorMessage(input, msg, bad_token_position);
|
||||
SmilesParseOps::detail::printSyntaxErrorMessage(input,
|
||||
msg,
|
||||
bad_token_position,
|
||||
"SMILES");
|
||||
}
|
||||
|
||||
void
|
||||
@@ -133,7 +136,10 @@ yysmiles_error( const char *input,
|
||||
void *,int, unsigned int bad_token_position, const char * msg )
|
||||
{
|
||||
yyErrorCleanup(ms);
|
||||
SmilesParseOps::detail::printSyntaxErrorMessage(input, msg, bad_token_position);
|
||||
SmilesParseOps::detail::printSyntaxErrorMessage(input,
|
||||
msg,
|
||||
bad_token_position,
|
||||
"SMILES");
|
||||
}
|
||||
|
||||
|
||||
@@ -597,14 +603,14 @@ static const yytype_int8 yytranslate[] =
|
||||
/* YYRLINE[YYN] -- Source line where rule number YYN was defined. */
|
||||
static const yytype_int16 yyrline[] =
|
||||
{
|
||||
0, 121, 121, 124, 128, 131, 135, 139, 142, 147,
|
||||
152, 155, 163, 164, 165, 166, 174, 185, 196, 217,
|
||||
226, 232, 253, 277, 296, 306, 327, 335, 349, 352,
|
||||
353, 359, 360, 366, 374, 375, 376, 377, 378, 379,
|
||||
380, 384, 385, 386, 387, 388, 389, 390, 391, 392,
|
||||
396, 397, 398, 399, 400, 404, 405, 406, 407, 408,
|
||||
409, 413, 414, 418, 419, 420, 421, 422, 423, 424,
|
||||
428, 429, 433, 434, 445, 446
|
||||
0, 127, 127, 130, 134, 137, 141, 145, 148, 153,
|
||||
158, 161, 169, 170, 171, 172, 180, 191, 202, 223,
|
||||
232, 238, 259, 283, 302, 312, 333, 341, 355, 358,
|
||||
359, 365, 366, 372, 380, 381, 382, 383, 384, 385,
|
||||
386, 390, 391, 392, 393, 394, 395, 396, 397, 398,
|
||||
402, 403, 404, 405, 406, 410, 411, 412, 413, 414,
|
||||
415, 419, 420, 424, 425, 426, 427, 428, 429, 430,
|
||||
434, 435, 439, 440, 451, 452
|
||||
};
|
||||
#endif
|
||||
|
||||
|
||||
@@ -35,8 +35,8 @@
|
||||
especially those whose name start with YY_ or yy_. They are
|
||||
private implementation details that can be changed or removed. */
|
||||
|
||||
#ifndef YY_YYSMILES_HOME_GLANDRUM_RDKIT_GIT_CODE_GRAPHMOL_SMILESPARSE_SMILES_TAB_HPP_INCLUDED
|
||||
# define YY_YYSMILES_HOME_GLANDRUM_RDKIT_GIT_CODE_GRAPHMOL_SMILESPARSE_SMILES_TAB_HPP_INCLUDED
|
||||
#ifndef YY_YYSMILES_USR_APP_RDKIT_CODE_GRAPHMOL_SMILESPARSE_SMILES_TAB_HPP_INCLUDED
|
||||
# define YY_YYSMILES_USR_APP_RDKIT_CODE_GRAPHMOL_SMILESPARSE_SMILES_TAB_HPP_INCLUDED
|
||||
/* Debug traces. */
|
||||
#ifndef YYDEBUG
|
||||
# define YYDEBUG 0
|
||||
@@ -112,4 +112,4 @@ int yysmiles_parse (const char *input, std::vector<RDKit::RWMol *> *molList, RDK
|
||||
(YYSTYPE * yylval_param , yyscan_t yyscanner, int& start_token, unsigned int& current_token_position)
|
||||
|
||||
|
||||
#endif /* !YY_YYSMILES_HOME_GLANDRUM_RDKIT_GIT_CODE_GRAPHMOL_SMILESPARSE_SMILES_TAB_HPP_INCLUDED */
|
||||
#endif /* !YY_YYSMILES_USR_APP_RDKIT_CODE_GRAPHMOL_SMILESPARSE_SMILES_TAB_HPP_INCLUDED */
|
||||
|
||||
@@ -49,7 +49,10 @@ yysmiles_error( const char *input,
|
||||
void *,int, unsigned int bad_token_position, const char * msg )
|
||||
{
|
||||
yyErrorCleanup(ms);
|
||||
SmilesParseOps::detail::printSyntaxErrorMessage(input, msg, bad_token_position);
|
||||
SmilesParseOps::detail::printSyntaxErrorMessage(input,
|
||||
msg,
|
||||
bad_token_position,
|
||||
"SMILES");
|
||||
}
|
||||
|
||||
void
|
||||
@@ -59,7 +62,10 @@ yysmiles_error( const char *input,
|
||||
void *,int, unsigned int bad_token_position, const char * msg )
|
||||
{
|
||||
yyErrorCleanup(ms);
|
||||
SmilesParseOps::detail::printSyntaxErrorMessage(input, msg, bad_token_position);
|
||||
SmilesParseOps::detail::printSyntaxErrorMessage(input,
|
||||
msg,
|
||||
bad_token_position,
|
||||
"SMILES");
|
||||
}
|
||||
|
||||
|
||||
|
||||
Reference in New Issue
Block a user