# smiles_parser.nim const libPath = "/home/pahl/anaconda3/pkgs/rdkit-2017.03.3-np111py36_1/lib/" libSmiles = "libRDKitSmilesParse.so" srcPath = "/home/pahl/dev/github/rdkit/Code/GraphMol/SmilesParse/" srcSmiles = "SmilesParse.h" {.link: libPath & libSmiles.} discard "forward decl of RWMol" type stdStringObj {.header: "<string.h>", importcpp: "std::string".} = object stdString* = ptr stdStringObj RWMolObj {.final, header: srcPath & srcSmiles, importcpp: "RDKit::RWMol".} = object RWMol* = ptr RWMolObj SmilesParserParams* {.header: srcPath & srcSmiles, importcpp: "RDKit::SmilesParserParams", bycopy.} = object sanitize* {.importc: "sanitize".}: bool proc constructString*(s: cstring): stdStringObj {.header: "<string.h>", importcpp: "std::string(@)", constructor.} proc constructSmilesParserParams*(): SmilesParserParams {.constructor, importcpp: "RDKit::SmilesParserParams(@)", header: srcPath & srcSmiles.} proc smilesToMol*(smi: stdStringObj; params: SmilesParserParams): RWMol {.header: srcPath & srcSmiles, importcpp: "RDKit::SmilesToMol(@)".}

# test_smiles.nim.cfg cincludes:"/home/pahl/dev/github/rdkit/Code/" # l:"-lstdc++" t:"-D_GLIBCXX_USE_CXX11_ABI=0"

/* test_smiles.cpp */ /* Generated by Nim Compiler v0.17.3 */ /* (c) 2017 Andreas Rumpf */ /* The generated code is subject to the original license. */ /* Compiled for: Linux, amd64, gcc */ /* Command for C compiler: g++ -c -w -w -fpermissive -D_GLIBCXX_USE_CXX11_ABI=0 -I/home/pahl/progs/nim/lib -I/home/pahl/dev/github/rdkit/Code/ -o /home/pahl/dev/nim/rdkit/nimcache/test_smiles.o /home/pahl/dev/nim/rdkit/nimcache/test_smiles.cpp */ #define NIM_NEW_MANGLING_RULES #define NIM_INTBITS 64 #include "nimbase.h" #include <string.h> #include "/home/pahl/dev/github/rdkit/Code/GraphMol/SmilesParse/SmilesParse.h" #include "/home/pahl/dev/github/rdkit/Code/GraphMol/GraphMol.h" #undef LANGUAGE_C #undef MIPSEB #undef MIPSEL #undef PPC #undef R3000 #undef R4000 #undef i386 #undef linux #undef mips #undef near #undef powerpc #undef unix struct NimStringDesc; struct TGenericSeq; struct TNimType; struct TNimNode; struct tyObject_Cell_1zcF9cV8XIAtbN8h5HRUB8g; struct tyObject_CellSeq_Axo1XVm9aaQueTOldv8le5w; struct tyObject_GcHeap_1TRH1TZMaVZTnLNcIHuNFQ; struct tyObject_GcStack_7fytPA5bBsob6See21YMRA; struct tyObject_MemRegion_x81NhDv59b8ercDZ9bi85jyg; struct tyObject_SmallChunk_tXn60W2f8h3jgAYdEmy5NQ; struct tyObject_LLChunk_XsENErzHIZV9bhvyJx56wGw; struct tyObject_BigChunk_Rv9c70Uhp2TytkX7eH78qEg; struct tyObject_IntSet_EZObFrE3NC9bIb3YMkY9crZA; struct tyObject_Trunk_W0r8S0Y3UGke6T9bIUWnnuw; struct tyObject_AvlNode_IaqjtwKhxLEpvDS9bct9blEw; struct tyObject_HeapLinks_PDV1HBZ8CQSQJC9aOBFNRSg; struct tyTuple_ujsjpB2O9cjj3uDHsXbnSzg; struct tyObject_GcStat_0RwLoVBHZPfUAcLczmfQAg; struct tyObject_CellSet_jG87P0AI9aZtss9ccTYBIISQ; struct tyObject_PageDesc_fublkgIY4LG3mT51LU2WHg; struct tyObject_BaseChunk_Sdq7WpT6qAH858F5ZEdG3w; struct tyObject_FreeCell_u6M5LHprqzkn9axr04yg9bGQ; struct TGenericSeq { NI len; NI reserved; }; struct NimStringDesc : public TGenericSeq { NIM_CHAR data[SEQ_DECL_SIZE]; }; typedef NU8 tyEnum_TNimKind_jIBKr1ejBgsfM33Kxw4j7A; typedef NU8 tySet_tyEnum_TNimTypeFlag_v8QUszD1sWlSIWZz7mC4bQ; typedef N_NIMCALL_PTR(void, tyProc_ojoeKfW4VYIm36I9cpDTQIg) (void* p, NI op); typedef N_NIMCALL_PTR(void*, tyProc_WSm2xU5ARYv9aAR4l0z9c9auQ) (void* p); struct TNimType { NI size; tyEnum_TNimKind_jIBKr1ejBgsfM33Kxw4j7A kind; tySet_tyEnum_TNimTypeFlag_v8QUszD1sWlSIWZz7mC4bQ flags; TNimType* base; TNimNode* node; void* finalizer; tyProc_ojoeKfW4VYIm36I9cpDTQIg marker; tyProc_WSm2xU5ARYv9aAR4l0z9c9auQ deepcopy; }; typedef NU8 tyEnum_TNimNodeKind_unfNsxrcATrufDZmpBq4HQ; struct TNimNode { tyEnum_TNimNodeKind_unfNsxrcATrufDZmpBq4HQ kind; NI offset; TNimType* typ; NCSTRING name; NI len; TNimNode** sons; }; typedef N_NIMCALL_PTR(void, tyProc_T4eqaYlFJYZUv9aG9b1TV0bQ) (void); struct tyObject_Cell_1zcF9cV8XIAtbN8h5HRUB8g { NI refcount; TNimType* typ; }; struct tyObject_GcStack_7fytPA5bBsob6See21YMRA { void* bottom; }; struct tyObject_CellSeq_Axo1XVm9aaQueTOldv8le5w { NI len; NI cap; tyObject_Cell_1zcF9cV8XIAtbN8h5HRUB8g** d; }; typedef tyObject_SmallChunk_tXn60W2f8h3jgAYdEmy5NQ* tyArray_SiRwrEKZdLgxqz9a9aoVBglg[512]; typedef tyObject_Trunk_W0r8S0Y3UGke6T9bIUWnnuw* tyArray_lh2A89ahMmYg9bCmpVaplLbA[256]; struct tyObject_IntSet_EZObFrE3NC9bIb3YMkY9crZA { tyArray_lh2A89ahMmYg9bCmpVaplLbA data; }; typedef tyObject_AvlNode_IaqjtwKhxLEpvDS9bct9blEw* tyArray_0aOLqZchNi8nWtMTi8ND8w[2]; struct tyObject_AvlNode_IaqjtwKhxLEpvDS9bct9blEw { tyArray_0aOLqZchNi8nWtMTi8ND8w link; NI key; NI upperBound; NI level; }; struct tyTuple_ujsjpB2O9cjj3uDHsXbnSzg { tyObject_BigChunk_Rv9c70Uhp2TytkX7eH78qEg* Field0; NI Field1; }; typedef tyTuple_ujsjpB2O9cjj3uDHsXbnSzg tyArray_LzOv2eCDGiceMKQstCLmhw[30]; struct tyObject_HeapLinks_PDV1HBZ8CQSQJC9aOBFNRSg { NI len; tyArray_LzOv2eCDGiceMKQstCLmhw chunks; tyObject_HeapLinks_PDV1HBZ8CQSQJC9aOBFNRSg* next; }; struct tyObject_MemRegion_x81NhDv59b8ercDZ9bi85jyg { NI minLargeObj; NI maxLargeObj; tyArray_SiRwrEKZdLgxqz9a9aoVBglg freeSmallChunks; tyObject_LLChunk_XsENErzHIZV9bhvyJx56wGw* llmem; NI currMem; NI maxMem; NI freeMem; NI lastSize; tyObject_BigChunk_Rv9c70Uhp2TytkX7eH78qEg* freeChunksList; tyObject_IntSet_EZObFrE3NC9bIb3YMkY9crZA chunkStarts; tyObject_AvlNode_IaqjtwKhxLEpvDS9bct9blEw* root; tyObject_AvlNode_IaqjtwKhxLEpvDS9bct9blEw* deleted; tyObject_AvlNode_IaqjtwKhxLEpvDS9bct9blEw* last; tyObject_AvlNode_IaqjtwKhxLEpvDS9bct9blEw* freeAvlNodes; NIM_BOOL locked; NIM_BOOL blockChunkSizeIncrease; NI nextChunkSize; tyObject_AvlNode_IaqjtwKhxLEpvDS9bct9blEw bottomData; tyObject_HeapLinks_PDV1HBZ8CQSQJC9aOBFNRSg heapLinks; }; struct tyObject_GcStat_0RwLoVBHZPfUAcLczmfQAg { NI stackScans; NI cycleCollections; NI maxThreshold; NI maxStackSize; NI maxStackCells; NI cycleTableSize; NI64 maxPause; }; struct tyObject_CellSet_jG87P0AI9aZtss9ccTYBIISQ { NI counter; NI max; tyObject_PageDesc_fublkgIY4LG3mT51LU2WHg* head; tyObject_PageDesc_fublkgIY4LG3mT51LU2WHg** data; }; struct tyObject_GcHeap_1TRH1TZMaVZTnLNcIHuNFQ { tyObject_GcStack_7fytPA5bBsob6See21YMRA stack; NI cycleThreshold; tyObject_CellSeq_Axo1XVm9aaQueTOldv8le5w zct; tyObject_CellSeq_Axo1XVm9aaQueTOldv8le5w decStack; tyObject_CellSeq_Axo1XVm9aaQueTOldv8le5w tempStack; NI recGcLock; tyObject_MemRegion_x81NhDv59b8ercDZ9bi85jyg region; tyObject_GcStat_0RwLoVBHZPfUAcLczmfQAg stat; tyObject_CellSet_jG87P0AI9aZtss9ccTYBIISQ marked; tyObject_CellSeq_Axo1XVm9aaQueTOldv8le5w additionalRoots; }; struct tyObject_BaseChunk_Sdq7WpT6qAH858F5ZEdG3w { NI prevSize; NI size; }; struct tyObject_SmallChunk_tXn60W2f8h3jgAYdEmy5NQ : public tyObject_BaseChunk_Sdq7WpT6qAH858F5ZEdG3w { tyObject_SmallChunk_tXn60W2f8h3jgAYdEmy5NQ* next; tyObject_SmallChunk_tXn60W2f8h3jgAYdEmy5NQ* prev; tyObject_FreeCell_u6M5LHprqzkn9axr04yg9bGQ* freeList; NI free; NI acc; NF data; }; struct tyObject_LLChunk_XsENErzHIZV9bhvyJx56wGw { NI size; NI acc; tyObject_LLChunk_XsENErzHIZV9bhvyJx56wGw* next; }; struct tyObject_BigChunk_Rv9c70Uhp2TytkX7eH78qEg : public tyObject_BaseChunk_Sdq7WpT6qAH858F5ZEdG3w { tyObject_BigChunk_Rv9c70Uhp2TytkX7eH78qEg* next; tyObject_BigChunk_Rv9c70Uhp2TytkX7eH78qEg* prev; NF data; }; typedef NI tyArray_9a8QARi5WsUggNU9bom7kzTQ[8]; struct tyObject_Trunk_W0r8S0Y3UGke6T9bIUWnnuw { tyObject_Trunk_W0r8S0Y3UGke6T9bIUWnnuw* next; NI key; tyArray_9a8QARi5WsUggNU9bom7kzTQ bits; }; struct tyObject_PageDesc_fublkgIY4LG3mT51LU2WHg { tyObject_PageDesc_fublkgIY4LG3mT51LU2WHg* next; NI key; tyArray_9a8QARi5WsUggNU9bom7kzTQ bits; }; struct tyObject_FreeCell_u6M5LHprqzkn9axr04yg9bGQ { tyObject_FreeCell_u6M5LHprqzkn9axr04yg9bGQ* next; NI zeroField; }; N_NIMCALL(void, nimGCvisit)(void* d, NI op); static N_NIMCALL(void, TM_Am5Z4BpJc7OwUgoAEME44g_2)(void); N_NIMCALL(void, nimRegisterGlobalMarker)(tyProc_T4eqaYlFJYZUv9aG9b1TV0bQ markerProc); N_NIMCALL(NimStringDesc*, copyStringRC1)(NimStringDesc* src); static N_INLINE(void, nimGCunrefNoCycle)(void* p); static N_INLINE(tyObject_Cell_1zcF9cV8XIAtbN8h5HRUB8g*, usrToCell_yB9aH5WIlwd0xkYrcdPeXrQsystem)(void* usr); static N_INLINE(void, nimFrame)(TFrame* s); N_NOINLINE(void, stackOverflow_II46IjNZztN9bmbxUD8dt8g)(void); static N_INLINE(void, popFrame)(void); static N_INLINE(void, rtlAddZCT_MV4BBk6J1qu70IbBxwEn4w_2system)(tyObject_Cell_1zcF9cV8XIAtbN8h5HRUB8g* c); N_NOINLINE(void, addZCT_fCDI7oO1NNVXXURtxSzsRw)(tyObject_CellSeq_Axo1XVm9aaQueTOldv8le5w& s, tyObject_Cell_1zcF9cV8XIAtbN8h5HRUB8g* c); static N_INLINE(void, initStackBottomWith)(void* locals); N_NOINLINE(void, setStackBottom)(void* theStackBottom); NIM_EXTERNC N_NOINLINE(void, systemInit000)(void); NIM_EXTERNC N_NOINLINE(void, systemDatInit000)(void); NIM_EXTERNC N_NOINLINE(void, unknown_rdmolInit000)(void); NIM_EXTERNC N_NOINLINE(void, unknown_rdmolDatInit000)(void); NIM_EXTERNC N_NOINLINE(void, unknown_smiles_parserInit000)(void); NIM_EXTERNC N_NOINLINE(void, unknown_smiles_parserDatInit000)(void); NIM_EXTERNC N_NOINLINE(void, NimMainModule)(void); NIM_EXTERNC N_NOINLINE(void, test_smilesDatInit000)(void); NimStringDesc* sp_K5kyEubSVpZuAGSTh8im9cQ; extern TNimType NTI_77mFvmsOLKik79ci2hXkHEg_; extern TFrame* framePtr_HRfVMH3jYeBJz6Q6X9b6Ptw; extern tyObject_GcHeap_1TRH1TZMaVZTnLNcIHuNFQ gch_IcYaEuuWivYAS86vFMTS3Q; std::string s_QAI3Ojvcqbr3MIZceDYakg; RDKit::SmilesParserParams p_YnMGxqjt4oqe2M6ZTaHLVg; RDKit::RWMol* m_g8Ov9a9ceGsqVAYZVR9cUmruw; STRING_LITERAL(TM_Am5Z4BpJc7OwUgoAEME44g_3, "c1ccccc1", 8); static N_NIMCALL(void, TM_Am5Z4BpJc7OwUgoAEME44g_2)(void) { nimGCvisit((void*)sp_K5kyEubSVpZuAGSTh8im9cQ, 0); } static N_INLINE(void, nimFrame)(TFrame* s) { NI T1_; T1_ = (NI)0; { if (!(framePtr_HRfVMH3jYeBJz6Q6X9b6Ptw == NIM_NIL)) goto LA4_; { T1_ = ((NI) 0); } } goto LA2_; LA4_: ; { T1_ = ((NI) ((NI16)((*framePtr_HRfVMH3jYeBJz6Q6X9b6Ptw).calldepth + ((NI16) 1)))); } LA2_: ; (*s).calldepth = ((NI16) (T1_)); (*s).prev = framePtr_HRfVMH3jYeBJz6Q6X9b6Ptw; framePtr_HRfVMH3jYeBJz6Q6X9b6Ptw = s; { if (!((*s).calldepth == ((NI16) 2000))) goto LA9_; { stackOverflow_II46IjNZztN9bmbxUD8dt8g(); } } LA9_: ; } static N_INLINE(void, popFrame)(void) { framePtr_HRfVMH3jYeBJz6Q6X9b6Ptw = (*framePtr_HRfVMH3jYeBJz6Q6X9b6Ptw).prev; } static N_INLINE(tyObject_Cell_1zcF9cV8XIAtbN8h5HRUB8g*, usrToCell_yB9aH5WIlwd0xkYrcdPeXrQsystem)(void* usr) { tyObject_Cell_1zcF9cV8XIAtbN8h5HRUB8g* result; nimfr_("usrToCell", "gc.nim"); result = (tyObject_Cell_1zcF9cV8XIAtbN8h5HRUB8g*)0; nimln_(138, "gc.nim"); result = ((tyObject_Cell_1zcF9cV8XIAtbN8h5HRUB8g*) ((NI)((NU64)(((NI) (usr))) - (NU64)(((NI)sizeof(tyObject_Cell_1zcF9cV8XIAtbN8h5HRUB8g)))))); popFrame(); return result; } static N_INLINE(void, rtlAddZCT_MV4BBk6J1qu70IbBxwEn4w_2system)(tyObject_Cell_1zcF9cV8XIAtbN8h5HRUB8g* c) { nimfr_("rtlAddZCT", "gc.nim"); nimln_(216, "gc.nim"); addZCT_fCDI7oO1NNVXXURtxSzsRw(gch_IcYaEuuWivYAS86vFMTS3Q.zct, c); popFrame(); } static N_INLINE(void, nimGCunrefNoCycle)(void* p) { nimfr_("nimGCunrefNoCycle", "gc.nim"); nimln_(255, "gc.nim"); tyObject_Cell_1zcF9cV8XIAtbN8h5HRUB8g* c = usrToCell_yB9aH5WIlwd0xkYrcdPeXrQsystem(p); nimln_(257, "gc.nim"); { (*c).refcount -= ((NI) 8); if (!((NU64)((*c).refcount) < (NU64)(((NI) 8)))) goto LA3_; { nimln_(258, "gc.nim"); rtlAddZCT_MV4BBk6J1qu70IbBxwEn4w_2system(c); } } LA3_: ; popFrame(); } static N_INLINE(void, initStackBottomWith)(void* locals) { setStackBottom(locals); } void PreMainInner(void) { systemInit000(); unknown_rdmolDatInit000(); unknown_smiles_parserDatInit000(); test_smilesDatInit000(); unknown_rdmolInit000(); unknown_smiles_parserInit000(); } void PreMain(void) { void (*volatile inner)(void); systemDatInit000(); inner = PreMainInner; initStackBottomWith((void *)&inner); (*inner)(); } int cmdCount; char** cmdLine; char** gEnv; N_CDECL(void, NimMainInner)(void) { NimMainModule(); } N_CDECL(void, NimMain)(void) { void (*volatile inner)(void); PreMain(); inner = NimMainInner; initStackBottomWith((void *)&inner); (*inner)(); } int main(int argc, char** args, char** env) { cmdLine = args; cmdCount = argc; gEnv = env; NimMain(); return nim_program_result; } NIM_EXTERNC N_NOINLINE(void, NimMainModule)(void) { NimStringDesc* T1_; nimfr_("test_smiles", "test_smiles.nim"); nimRegisterGlobalMarker(TM_Am5Z4BpJc7OwUgoAEME44g_2); nimln_(4, "test_smiles.nim"); T1_ = (NimStringDesc*)0; T1_ = sp_K5kyEubSVpZuAGSTh8im9cQ; sp_K5kyEubSVpZuAGSTh8im9cQ = copyStringRC1(((NimStringDesc*) &TM_Am5Z4BpJc7OwUgoAEME44g_3)); if (T1_) nimGCunrefNoCycle(T1_); nimln_(7, "test_smiles.nim"); s_QAI3Ojvcqbr3MIZceDYakg = std::string(sp_K5kyEubSVpZuAGSTh8im9cQ->data); nimln_(8, "test_smiles.nim"); p_YnMGxqjt4oqe2M6ZTaHLVg = RDKit::SmilesParserParams(); nimln_(9, "test_smiles.nim"); m_g8Ov9a9ceGsqVAYZVR9cUmruw = RDKit::SmilesToMol(s_QAI3Ojvcqbr3MIZceDYakg, p_YnMGxqjt4oqe2M6ZTaHLVg); popFrame(); } NIM_EXTERNC N_NOINLINE(void, test_smilesDatInit000)(void) { }