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/ichinorm.h ADDED
@@ -0,0 +1,67 @@
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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 __INCHINORM_H__
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+ #define __INCHINORM_H__
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+
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+ #include "mode.h"
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+ #include "ichi_bns.h"
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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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+ /* main normalization procedure */
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+ int mark_alt_bonds_and_taut_groups ( inp_ATOM *at, inp_ATOM *at_fixed_bonds_out, int num_atoms,
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+ T_GROUP_INFO *t_group_info, INCHI_MODE *inpbTautFlags, INCHI_MODE *inpbTautFlagsDone );
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+
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+ int MarkTautomerGroups( inp_ATOM *at, int num_atoms, T_GROUP_INFO *t_group_info, C_GROUP_INFO *c_group_info,
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+ struct BalancedNetworkStructure *pBNS, struct BalancedNetworkData *pBD);
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+ int MarkChargeGroups ( inp_ATOM *at, int num_atoms, C_GROUP_INFO *c_group_info, T_GROUP_INFO *t_group_info,
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+ struct BalancedNetworkStructure *pBNS, struct BalancedNetworkData *pBD );
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+ int MarkSaltChargeGroups ( inp_ATOM *at, int num_atoms, S_GROUP_INFO *s_group_info,
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+ T_GROUP_INFO *t_group_info, C_GROUP_INFO *c_group_info,
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+ struct BalancedNetworkStructure *pBNS, struct BalancedNetworkData *pBD );
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+ int MarkSaltChargeGroups2 ( inp_ATOM *at, int num_atoms, S_GROUP_INFO *s_group_info,
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+ T_GROUP_INFO *t_group_info, C_GROUP_INFO *c_group_info,
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+ struct BalancedNetworkStructure *pBNS, struct BalancedNetworkData *pBD );
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+ int MergeSaltTautGroups( inp_ATOM *at, int num_atoms, S_GROUP_INFO *s_group_info,
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+ T_GROUP_INFO *t_group_info, C_GROUP_INFO *c_group_info,
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+ struct BalancedNetworkStructure *pBNS );
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+ int MakeIsotopicHGroup( inp_ATOM *at, int num_atoms, S_GROUP_INFO *s_group_info,
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+ T_GROUP_INFO *t_group_info );
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+
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+ int remove_terminal_HDT( int num_atoms, inp_ATOM *at );
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+ int RemoveExcessiveImplicitH( int num_atoms, int num_removed_H, inp_ATOM *at );
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+ int add_DT_to_num_H( int num_atoms, inp_ATOM *at );
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+ int MarkRingSystemsInp( inp_ATOM *at, int num_atoms );
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+ int free_t_group_info( T_GROUP_INFO *t_group_info );
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+ int make_a_copy_of_t_group_info( T_GROUP_INFO *t_group_info, T_GROUP_INFO *t_group_info_orig );
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+ int set_tautomer_iso_sort_keys( T_GROUP_INFO *t_group_info );
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+ int CountTautomerGroups( sp_ATOM *at, int num_atoms, T_GROUP_INFO *t_group_info );
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+ int SortTautomerGroupsAndEndpoints( T_GROUP_INFO *t_group_info, int num_atoms, int num_at_tg, AT_RANK *nRank );
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+ int FillIsotopicAtLinearCT( int num_atoms, sp_ATOM* at, const AT_RANK *nAtomNumber,
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+ AT_ISOTOPIC *LinearCTIsotopic, int nMaxLenLinearCTIsotopic, int *pnLenLinearCTIsotopic );
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+
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+ int FillTautLinearCT2( int num_atoms, int num_at_tg, int bIsoTaut,
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+ const AT_RANK *nRank, const AT_RANK *nAtomNumber, const AT_RANK *nSymmRank,
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+ const AT_RANK *nRankIso, const AT_RANK *nAtomNumberIso, const AT_RANK *nSymmRankIso,
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+ AT_TAUTOMER *LinearCTTautomer, int nMaxLenLinearCTTautomer, int *pnLenLinearCTTautomer,
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+ AT_ISO_TGROUP *LinearCTIsotopicTautomer, int nMaxLenLinearCTIsotopicTautomer, int *pnLenLinearCTIsotopicTautomer,
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+ T_GROUP_INFO *t_group_info );
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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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+ #endif /* __INCHINORM_H__ */
data/ext/src/ichiparm.c ADDED
@@ -0,0 +1,45 @@
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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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+ #include <stdio.h>
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+ #include <stdlib.h>
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+ #include <string.h>
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+ #include <ctype.h>
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+ #include <stdarg.h>
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+ /* #include <varargs.h> */
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+ #include <errno.h>
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+ #include <limits.h>
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+
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+ #include "mode.h" /* moved from below, suggestion by David Mosenkis */
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+
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+ #ifndef INCHI_ANSI_ONLY
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+ #include <conio.h>
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+ #endif
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+
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+ #include "inpdef.h"
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+ #include "ichi.h"
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+ #include "strutil.h"
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+ #include "util.h"
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+ #include "ichidrp.h"
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+ #include "ichierr.h"
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+ #include "ichimain.h"
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+ #include "extr_ct.h"
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+
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+ #ifdef INCHI_LIB
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+ #include "ichi_lib.h"
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+ #endif
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+
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+ #include "ichicomp.h"
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+
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+ #if( ADD_CMLPP == 1 )
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+ #include "readcml.hpp"
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+ #include "debug.h"
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+ #endif
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+
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+ #include "ichiparm.h"