rino 0.1.0

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Files changed (87) hide show
  1. data/README +44 -0
  2. data/Rakefile +123 -0
  3. data/ext/extconf.rb +26 -0
  4. data/ext/ruby_inchi_main.so +0 -0
  5. data/ext/src/aux2atom.h +2786 -0
  6. data/ext/src/comdef.h +148 -0
  7. data/ext/src/e_0dstereo.c +3014 -0
  8. data/ext/src/e_0dstereo.h +31 -0
  9. data/ext/src/e_comdef.h +57 -0
  10. data/ext/src/e_ctl_data.h +147 -0
  11. data/ext/src/e_ichi_io.c +498 -0
  12. data/ext/src/e_ichi_io.h +40 -0
  13. data/ext/src/e_ichi_parms.c +37 -0
  14. data/ext/src/e_ichi_parms.h +41 -0
  15. data/ext/src/e_ichicomp.h +50 -0
  16. data/ext/src/e_ichierr.h +40 -0
  17. data/ext/src/e_ichimain.c +593 -0
  18. data/ext/src/e_ichisize.h +43 -0
  19. data/ext/src/e_inchi_atom.c +75 -0
  20. data/ext/src/e_inchi_atom.h +33 -0
  21. data/ext/src/e_inpdef.h +41 -0
  22. data/ext/src/e_mode.h +706 -0
  23. data/ext/src/e_mol2atom.c +649 -0
  24. data/ext/src/e_readinch.c +58 -0
  25. data/ext/src/e_readmol.c +54 -0
  26. data/ext/src/e_readmol.h +180 -0
  27. data/ext/src/e_readstru.c +251 -0
  28. data/ext/src/e_readstru.h +33 -0
  29. data/ext/src/e_util.c +284 -0
  30. data/ext/src/e_util.h +61 -0
  31. data/ext/src/extr_ct.h +251 -0
  32. data/ext/src/ichi.h +206 -0
  33. data/ext/src/ichi_bns.c +7999 -0
  34. data/ext/src/ichi_bns.h +231 -0
  35. data/ext/src/ichican2.c +5000 -0
  36. data/ext/src/ichicano.c +2195 -0
  37. data/ext/src/ichicano.h +49 -0
  38. data/ext/src/ichicans.c +1625 -0
  39. data/ext/src/ichicant.h +379 -0
  40. data/ext/src/ichicomn.h +260 -0
  41. data/ext/src/ichicomp.h +50 -0
  42. data/ext/src/ichidrp.h +119 -0
  43. data/ext/src/ichierr.h +124 -0
  44. data/ext/src/ichiisot.c +101 -0
  45. data/ext/src/ichilnct.c +286 -0
  46. data/ext/src/ichimain.h +132 -0
  47. data/ext/src/ichimak2.c +1189 -0
  48. data/ext/src/ichimake.c +3812 -0
  49. data/ext/src/ichimake.h +205 -0
  50. data/ext/src/ichimap1.c +851 -0
  51. data/ext/src/ichimap2.c +2856 -0
  52. data/ext/src/ichimap4.c +1609 -0
  53. data/ext/src/ichinorm.c +741 -0
  54. data/ext/src/ichinorm.h +67 -0
  55. data/ext/src/ichiparm.c +45 -0
  56. data/ext/src/ichiparm.h +1441 -0
  57. data/ext/src/ichiprt1.c +3612 -0
  58. data/ext/src/ichiprt2.c +1511 -0
  59. data/ext/src/ichiprt3.c +3011 -0
  60. data/ext/src/ichiqueu.c +1003 -0
  61. data/ext/src/ichiring.c +326 -0
  62. data/ext/src/ichiring.h +49 -0
  63. data/ext/src/ichisize.h +35 -0
  64. data/ext/src/ichisort.c +539 -0
  65. data/ext/src/ichister.c +3538 -0
  66. data/ext/src/ichister.h +35 -0
  67. data/ext/src/ichitaut.c +3843 -0
  68. data/ext/src/ichitaut.h +387 -0
  69. data/ext/src/ichitime.h +74 -0
  70. data/ext/src/inchi_api.h +670 -0
  71. data/ext/src/inchi_dll.c +1480 -0
  72. data/ext/src/inchi_dll.h +34 -0
  73. data/ext/src/inchi_dll_main.c +23 -0
  74. data/ext/src/inchi_dll_main.h +31 -0
  75. data/ext/src/inpdef.h +328 -0
  76. data/ext/src/lreadmol.h +1246 -0
  77. data/ext/src/mode.h +706 -0
  78. data/ext/src/ruby_inchi_main.c +558 -0
  79. data/ext/src/runichi.c +4179 -0
  80. data/ext/src/strutil.c +3861 -0
  81. data/ext/src/strutil.h +182 -0
  82. data/ext/src/util.c +1130 -0
  83. data/ext/src/util.h +85 -0
  84. data/lib/clean_tempfile.rb +220 -0
  85. data/lib/rino.rb +111 -0
  86. data/test/test.rb +386 -0
  87. metadata +130 -0
data/ext/src/ichimain.h ADDED
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+ /*
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+ * International Union of Pure and Applied Chemistry (IUPAC)
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+ * International Chemical Identifier (InChI)
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+ * Version 1
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+ * Software version 1.00
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+ * April 13, 2005
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+ * Developed at NIST
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+ */
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+
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+ #ifndef __INCHIMAIN_H__
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+ #define __INCHIMAIN_H__
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+
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+ #define ESC_KEY 27
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+
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+ /********************************************************************/
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+ typedef struct tagStructData {
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+ unsigned long ulStructTime;
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+ int nErrorCode;
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+ int nErrorType;
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+ int nStructReadError;
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+ char pStrErrStruct[STR_ERR_LEN];
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+ long fPtrStart;
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+ long fPtrEnd;
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+ int bXmlStructStarted;
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+ int bUserQuit;
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+ int bUserQuitComponent;
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+ int bUserQuitComponentDisplay;
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+ int bChiralFlag;
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+ /* information related to normal or disconnected layers */
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+ int num_taut[INCHI_NUM];
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+ int num_non_taut[INCHI_NUM];
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+ INCHI_MODE bTautFlags[INCHI_NUM]; /* reconnected does not have TG_FLAG_DISCONNECT_COORD_DONE flag */
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+ INCHI_MODE bTautFlagsDone[INCHI_NUM]; /* reconnected does not have TG_FLAG_DISCONNECT_COORD_DONE flag */
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+ int num_components[INCHI_NUM]; /* number of allocated INChI, INChI_Aux data structures */
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+ /* debugging info */
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+ #if( bRELEASE_VERSION == 0 )
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+ int bExtract;
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+ #endif
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+
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+ } STRUCT_DATA;
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+
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+ #ifndef INCHI_ALL_CPP
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+ #ifdef __cplusplus
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+ extern "C" {
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+ #endif
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+ #endif
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+
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+ int ReadCommandLineParms( int argc, const char *argv[], INPUT_PARMS *ip, char *szSdfDataValue,
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+ unsigned long *ulDisplTime, int bReleaseVersion, INCHI_FILE *log_file );
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+ void HelpCommandLineParms( INCHI_FILE *f );
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+ int OpenFiles( FILE **inp_file, FILE **output_file, FILE **log_file, FILE **prb_file, INPUT_PARMS *ip );
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+ #ifndef INCHI_ANSI_ONLY
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+ int DisplayStructure( inp_ATOM *at, int num_at, int num_removed_H, int nNumRemovedProtons, NUM_H nNumRemovedProtonsIsotopic[],
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+ int bIsotopic, int j /*bTautomeric*/, INChI **cur_INChI, INChI_Aux **cur_INChI_Aux,
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+ int bAbcNumbers, DRAW_PARMS *dp, INCHI_MODE nMode, char *szTitle );
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+ void FillTableParms( SET_DRAW_PARMS *sdp, INChI **cur_INChI, INChI_Aux **cur_INChI_Aux, INCHI_MODE nMode, int bShowIsotopic, int bShowTaut );
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+ void FillCompositeTableParms( SET_DRAW_PARMS *sdp, AT_NUMB StereoFlags,
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+ INCHI_MODE nMode, int bShowIsotopic, int bShowTaut );
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+ #endif
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+ int PrintInputParms( INCHI_FILE *log_file, INPUT_PARMS *ip );
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+ const char *ErrMsg( int nErrorCode );
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+ int SortAndPrintINChI( INCHI_FILE *output_file, char *pStr, int nStrLen, INCHI_FILE *log_file,
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+ INPUT_PARMS *ip, ORIG_ATOM_DATA *orig_inp_data, ORIG_ATOM_DATA *prep_inp_data,
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+ COMP_ATOM_DATA composite_norm_data[INCHI_NUM][TAUT_NUM+1],
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+ ORIG_STRUCT *pOrigStruct, int num_components[INCHI_NUM],
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+ int num_non_taut[INCHI_NUM], int num_taut[INCHI_NUM],
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+ INCHI_MODE bTautFlags[INCHI_NUM], INCHI_MODE bTautFlagsDone[INCHI_NUM],
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+ NORM_CANON_FLAGS *pncFlags, int num_inp,
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+ PINChI2 *pINChI[INCHI_NUM], PINChI_Aux2 *pINChI_Aux[INCHI_NUM], int *bSortPrintINChIFlags );
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+ void FreeAllINChIArrays( PINChI2 *pINChI[INCHI_NUM], PINChI_Aux2 *pINChI_Aux[INCHI_NUM], int num_components[2] );
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+ void FreeINChIArrays( PINChI2 *pINChI, PINChI_Aux2 *pINChI_Aux, int num_components );
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+ void SplitTime( unsigned long ulTotalTime, int *hours, int *minutes, int *seconds, int *mseconds );
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+
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+ int ReadTheStructure( STRUCT_DATA *sd, INPUT_PARMS *ip, FILE *inp_file, ORIG_ATOM_DATA *orig_inp_data,
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+ int inp_index, int *out_index );
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+ int TreatReadTheStructureErrors( STRUCT_DATA *sd, INPUT_PARMS *ip, int nLogMask,
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+ FILE *inp_file, INCHI_FILE *log_file, INCHI_FILE *output_file, INCHI_FILE *prb_file,
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+ ORIG_ATOM_DATA *orig_inp_data, int *num_inp, char *pStr, int nStrLen );
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+
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+ int GetOneComponent( STRUCT_DATA *sd, INPUT_PARMS *ip, INCHI_FILE *log_file, INCHI_FILE *output_file,
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+ INP_ATOM_DATA *inp_cur_data,
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+ ORIG_ATOM_DATA *orig_inp_data, int i, int num_inp, char *pStr, int nStrLen );
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+ int CreateOneComponentINChI( STRUCT_DATA *sd, INPUT_PARMS *ip, INP_ATOM_DATA *inp_cur_data, ORIG_ATOM_DATA *orig_inp_data,
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+ PINChI2 *pINChI, PINChI_Aux2 *pINChI_Aux, int iINChI,
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+ int i, int num_inp, INP_ATOM_DATA **inp_norm_data,
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+ NORM_CANON_FLAGS *pncFlags, INCHI_FILE *log_file );
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+ int TreatCreateOneComponentINChIError(STRUCT_DATA *sd, INPUT_PARMS *ip, ORIG_ATOM_DATA *orig_inp_data,
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+ int i, int num_inp,
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+ FILE *inp_file, INCHI_FILE *log_file, INCHI_FILE *output_file, INCHI_FILE *prb_file,
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+ char *pStr, int nStrLen );
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+ int TreatCreateINChIWarning(STRUCT_DATA *sd, INPUT_PARMS *ip, ORIG_ATOM_DATA *orig_inp_data, int num_inp,
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+ FILE *inp_file, INCHI_FILE *log_file, INCHI_FILE *output_file, INCHI_FILE *prb_file,
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+ char *pStr, int nStrLen );
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+
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+ #if( TEST_RENUMB_ATOMS == 1 ) /* { */
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+ int CompareINChI( INChI *i1, INChI *i2, INChI_Aux *a1, INChI_Aux *a2 );
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+ #endif
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+
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+ void eat_keyboard_input( void );
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+ int user_quit( const char *msg, unsigned long ulMaxTime );
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+
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+ int GetOneStructure( STRUCT_DATA *sd, INPUT_PARMS *ip, char *szTitle,
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+ FILE *inp_file, INCHI_FILE *log_file, INCHI_FILE *output_file, INCHI_FILE *prb_file,
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+ ORIG_ATOM_DATA *orig_inp_data, int *num_inp, char *pStr, int nStrLen, STRUCT_FPTRS *struct_fptrs );
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+ int ProcessOneStructure( STRUCT_DATA *sd, INPUT_PARMS *ip, char *szTitle,
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+ PINChI2 *pINChI2[INCHI_NUM], PINChI_Aux2 *pINChI_Aux2[INCHI_NUM],
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+ FILE *inp_file, INCHI_FILE *log_file, INCHI_FILE *output_file, INCHI_FILE *prb_file,
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+ ORIG_ATOM_DATA *orig_inp_data, ORIG_ATOM_DATA *prep_inp_data,
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+ int num_inp, char *pStr, int nStrLen );
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+
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+ int CreateOneStructureINChI( STRUCT_DATA *sd, INPUT_PARMS *ip, char *szTitle,
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+ PINChI2 *pINChI2[INCHI_NUM], PINChI_Aux2 *pINChI_Aux2[INCHI_NUM], int iINChI,
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+ FILE *inp_file, INCHI_FILE *log_file, INCHI_FILE *output_file, INCHI_FILE *prb_file,
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+ ORIG_ATOM_DATA *orig_inp_data, ORIG_ATOM_DATA *prep_inp_data,
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+ COMP_ATOM_DATA composite_norm_data2[][TAUT_NUM+1],
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+ int num_inp, char *pStr, int nStrLen, NORM_CANON_FLAGS *pncFlags );
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+
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+ int bIsStructChiral( PINChI2 *pINChI2[INCHI_NUM], int num_components[] );
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+
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+ int PreprocessOneStructure( STRUCT_DATA *sd, INPUT_PARMS *ip, ORIG_ATOM_DATA *orig_inp_data, ORIG_ATOM_DATA *prep_inp_data );
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+
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+ int FillOutOrigStruct( ORIG_ATOM_DATA *orig_inp_data, ORIG_STRUCT *pOrigStruct, STRUCT_DATA *sd );
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+ void FreeOrigStruct( ORIG_STRUCT *pOrigStruct);
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+
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+ #ifndef INCHI_ALL_CPP
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+ #ifdef __cplusplus
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+ }
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+ #endif
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+ #endif
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+
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+
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+ #endif /* __INCHIMAIN_H__ */