rino 0.1.0

data/ext/src/ichi.h

@@ -0,0 +1,206 @@
+/*
+ * International Union of Pure and Applied Chemistry (IUPAC)
+ * International Chemical Identifier (InChI)
+ * Version 1
+ * Software version 1.00
+ * April 13, 2005
+ * Developed at NIST
+ */
+
+#ifndef __INCHI_H__
+#define __INCHI_H__
+
+#include "comdef.h"
+
+#define REQ_MODE_BASIC              0x000001    /* B    */
+#define REQ_MODE_TAUT               0x000002    /* T    */
+#define REQ_MODE_ISO                0x000004    /* I    */
+#define REQ_MODE_NON_ISO            0x000008    /* NI   */
+#define REQ_MODE_STEREO             0x000010    /* S    */
+#define REQ_MODE_ISO_STEREO         0x000020    /* IS   */
+#define REQ_MODE_NOEQ_STEREO        0x000040    /* SS   */
+#define REQ_MODE_REDNDNT_STEREO     0x000080    /* RS   */
+#define REQ_MODE_NO_ALT_SBONDS      0x000100    /* NASB */
+/* new 10-10-2003 */
+#define REQ_MODE_RELATIVE_STEREO    0x000200    /* REL All Relative Stereo */
+#define REQ_MODE_RACEMIC_STEREO     0x000400    /* RAC All Racemic Stereo */
+#define REQ_MODE_SC_IGN_ALL_UU      0x000800    /* IAUSC Ignore stereocenters if All Undef/Unknown */
+#define REQ_MODE_SB_IGN_ALL_UU      0x001000    /* IAUSC Ignore stereobonds if All Undef/Unknown */
+#define REQ_MODE_CHIR_FLG_STEREO    0x002000    /* SUCF  If Chiral flag then Abs otherwise Rel stereo */
+/* end of 10-10-2003 */
+#define REQ_MODE_MIN_SB_RING_MASK   0x0F0000    /* RSB  */
+#define REQ_MODE_MIN_SB_RING_SHFT      16
+
+#define REQ_MODE_DEFAULT  (REQ_MODE_BASIC | REQ_MODE_TAUT | REQ_MODE_ISO | REQ_MODE_NON_ISO | REQ_MODE_STEREO)
+
+#define WARN_FAILED_STEREO          0x0001
+#define WARN_FAILED_ISOTOPIC        0x0002
+#define WARN_FAILED_ISOTOPIC_STEREO 0x0004
+#define ERR_NO_CANON_RESULTS        0x0008
+
+/*********** compare components flags **********************************/
+#define CMP_COMPONENTS              0x0001     /* perform compare components */
+#define CMP_COMPONENTS_NONISO       0x0002     /* ignore isotopic */
+#define CMP_COMPONENTS_NONTAUT      0x0004     /* compare non-tautomeric */
+/****************** chemical identifier member definitions *************/
+typedef struct tagINChI_IsotopicAtom {
+    AT_NUMB   nAtomNumber;  /* Canonical atom number */
+    NUM_H     nIsoDifference; /* 0=non-isotopic; 1=only most abundant */
+    NUM_H     nNum_H;  /* number of 1H isotopic atoms attached */
+    NUM_H     nNum_D;  /* number of 2H isotopic atoms attached */
+    NUM_H     nNum_T;  /* number of 3H isotopic atoms attached */
+} INChI_IsotopicAtom;
+typedef struct tagINChI_IsotopicTGroup {
+    AT_NUMB   nTGroupNumber;  /* Tautomeric group number */
+    AT_NUMB   nNum_H;  /* number of 1H isotopic atoms */
+    AT_NUMB   nNum_D;  /* number of 2H isotopic atoms */
+    AT_NUMB   nNum_T;  /* number of 3H isotopic atoms */
+} INChI_IsotopicTGroup;
+typedef struct tagINChI_Stereo { /* [N] = allocated length */
+    /* ---- possibly tetrahedral stereogenic atoms */
+    int         nNumberOfStereoCenters;
+    AT_NUMB    *nNumber;      /* Canonical number of a possibly tetrahedral
+                               * stereogenic atom or allenes [nNumberOfAtoms] */
+    S_CHAR     *t_parity;     /* tetrahedral (relative, see nCompInv2Abs) atom parities [nNumberOfAtoms] */
+    /* ---- possibly tetrahedral stereogenic atoms of the iverted structure */
+    AT_NUMB    *nNumberInv;   /* Canonical number of a possibly tetrahedral
+                               * stereogenic atom or allene [nNumberOfAtoms] */
+    S_CHAR     *t_parityInv;  /* tetrahedral inverted atom parities [nNumberOfAtoms] */
+    /* bFlagAbsStereoIsInverted = nCompInv2Abs==-1: Abs stereo = Inverted  */
+    int         nCompInv2Abs; /* 0=>Inv = Abs stereo; -1=> Inv < Abs stereo, +1=> Inv > Abs stereo */
+    int         bTrivialInv;  /* 1=> nCompInv2Abs!= 0 && Inverted = Abs stereo with inverted parities 1<-->2 */
+    /* ---- possibly stereogenic bonds and tetrahedral cumuleles */
+    int         nNumberOfStereoBonds;
+    AT_NUMB    *nBondAtom1; /* Canonical number of a first atom 
+                             * [number of bonds] */
+    AT_NUMB    *nBondAtom2; /* Canonical number of a second atom
+                             * [number of bonds] */
+    S_CHAR     *b_parity;   /* possibly stereogenic bond parities
+                             * [number of bonds] */
+} INChI_Stereo;
+#define INCHI_FLAG_ACID_TAUT            0x0001   /* tautomerism of dissociated acid invoked */
+#define INCHI_FLAG_REL_STEREO           0x0002   /* requested relative stereo */
+#define INCHI_FLAG_RAC_STEREO           0x0004   /* requested racemic stereo */
+#define INCHI_FLAG_SC_IGN_ALL_UU        0x0008   /* ignored all undefined/unknown stereocenters, non-isotopic */
+#define INCHI_FLAG_SB_IGN_ALL_UU        0x0010   /* ignored all undefined/unknown stereocenters, non-isotopic */
+#define INCHI_FLAG_SC_IGN_ALL_ISO_UU    0x0020   /* ignored all undefined/unknown stereocenters, isotopic */
+#define INCHI_FLAG_SB_IGN_ALL_ISO_UU    0x0040   /* ignored all undefined/unknown stereocenters, isotopic */
+#define INCHI_FLAG_HARD_ADD_REM_PROTON  0x0080   /* in normalization a proton has been added or removed along alt path */
+
+#define INCHI_OUT_NO_AUX_INFO           0x0001   /* do not output Aux Info */
+#define INCHI_OUT_SHORT_AUX_INFO        0x0002   /* output short version of Aux Info */
+#define INCHI_OUT_ONLY_AUX_INFO         0x0004   /* output only Aux Info */
+#define INCHI_OUT_EMBED_REC             0x0008   /* embed reconnected INChI into disconnected INChI */
+#define INCHI_OUT_SDFILE_ONLY           0x0010   /* save input data in a Molfile instead of creating INChI */
+#define INCHI_OUT_XML                   0x0020   /* output xml INChI */
+#define INCHI_OUT_PLAIN_TEXT            0x0040   /* output plain text INChI */
+#define INCHI_OUT_PLAIN_TEXT_COMMENTS   0x0080   /* output plain text annotation */
+#define INCHI_OUT_XML_TEXT_COMMENTS     0x0100   /* output xml text annotation */
+#define INCHI_OUT_WINCHI_WINDOW         0x0200   /* output into wINChI text window */
+#define INCHI_OUT_TABBED_OUTPUT         0x0400   /* tab-delimited (only for plain text) */
+
+/*******REQ_MODE_SB_IGN_ALL_UU*************** chemical identifier definition *****************/
+typedef struct tagINChI {  /* [N] = allocated length */
+    
+    int        nErrorCode;  /* 0 = success */
+    INCHI_MODE  nFlags;      /* INCHI_FLAG_ACID_TAUT            tautomerism of dissociated acid invoked
+                                INCHI_FLAG_REL_STEREO           requested relative stereo
+                                INCHI_FLAG_RAC_STEREO           requested racemic stereo
+                                INCHI_FLAG_SC_IGN_ALL_UU        ignored all undefined/unknown stereocenters, non-isotopic
+                                INCHI_FLAG_SB_IGN_ALL_UU        ignored all undefined/unknown stereocenters, non-isotopic
+                                INCHI_FLAG_SC_IGN_ALL_ISO_UU    ignored all undefined/unknown stereocenters, isotopic
+                                INCHI_FLAG_SB_IGN_ALL_ISO_UU    ignored all undefined/unknown stereocenters, isotopic
+                                INCHI_FLAG_HARD_ADD_REM_PROTON  in normalization a proton has been added or removed along alt path
+                              */
+    /* ---- basic & tautomer layer */
+    int        nTotalCharge;
+    int        nNumberOfAtoms;
+    char      *szHillFormula;
+    U_CHAR    *nAtom;       /* atomic numbers [nNumberOfAtoms] from the Periodic Table */
+    int        lenConnTable;
+    AT_NUMB   *nConnTable;  /* Connection table [nNumberOfAtoms+NumberOfBonds] */
+    int        lenTautomer;
+    AT_NUMB   *nTautomer;   /* NumGroups; ((NumAt+1, NumH,         At1..AtNumAt),...); {INCHI_T_NUM_MOVABLE = 1} - old
+                             * NumGroups; ((NumAt+2, NumH, Num(-), At1..AtNumAt),...); {INCHI_T_NUM_MOVABLE = 2} - new
+                             * Allocated length: [5*nNumberOfAtoms/2+1], see Alloc_INChI(...) */
+    S_CHAR    *nNum_H;      /* number of terminal hydrogen atoms on each atom; in tautomeric
+                             * representation these H on tautomeric atoms are not included [nNumberOfAtoms] */
+    S_CHAR    *nNum_H_fixed;/* number of terminal hydrogen atoms on tautomeric atoms,
+                             * in non-atautomeric representation only [nNumberOfAtoms] */
+    /* ---- isotopic & isotopic tautomeric layer */
+    int                  nNumberOfIsotopicAtoms;
+    INChI_IsotopicAtom   *IsotopicAtom;              /* [nNumberOfIsotopicAtoms] */
+    int                  nNumberOfIsotopicTGroups;
+    INChI_IsotopicTGroup *IsotopicTGroup;             /* [nNumberOfIsotopicAtoms] */
+    /* ---- stereo layer */
+    INChI_Stereo *Stereo;
+    INChI_Stereo *StereoIsotopic;
+                                                /* not including mobile H groups */
+    AT_NUMB *nPossibleLocationsOfIsotopicH;     /* [0]=> length including 0th element, location1,...*/
+    int      bDeleted;
+#if( bREUSE_INCHI == 1 )
+    int nRefCount;
+#endif
+#if( bRELEASE_VERSION == 0 )
+    int bExtract;
+#endif
+
+} INChI;
+
+typedef INChI *PINChI2[TAUT_NUM];
+
+typedef struct tagOrigInfo {
+    S_CHAR cCharge;
+    S_CHAR cRadical;       /* 0=none, 1=doublet, 2=triplet, 3=unknown */
+    S_CHAR cUnusualValence; /* see get_unusual_el_valence() */
+} ORIG_INFO;
+/******************** auxiliary chemical identifier info **************/
+typedef struct tagINChI_Aux { /* [N] = allocated length */
+
+    int        nErrorCode;  /* 0 = success */
+    int        nNumberOfAtoms;
+    int        nNumberOfTGroups;   /* non-zero only in tautomeric representation */
+    int        bIsIsotopic;        /* filled out even though isotopic has not been requested */
+    int        bIsTautomeric;      /* filled out even though tautomeric has not been requested; non-zero if taut exists */
+    /* canonical numbers of the atoms: nOrigAtNosInCanonOrd[i-1]+1 =       */
+    /*                       input atom number for the canonical number i  */
+    AT_NUMB   *nOrigAtNosInCanonOrd;             /* [nNumberOfInputAtoms*1.5]; */
+    AT_NUMB   *nIsotopicOrigAtNosInCanonOrd;     /* [nNumberOfInputAtoms*1.5]; */
+    /* same for the inverted structure */
+    AT_NUMB   *nOrigAtNosInCanonOrdInv;          /* inveterted stereo [nNumberOfInputAtoms*1.5]; */
+    AT_NUMB   *nIsotopicOrigAtNosInCanonOrdInv;  /* [nNumberOfInputAtoms*1.5]; */
+    AT_NUMB   *nConstitEquNumbers;               /* [nNumberOfAtoms*1.5] */
+    AT_NUMB   *nConstitEquTGroupNumbers;         /* [nNumberOfAtoms/2] */
+    AT_NUMB   *nConstitEquIsotopicNumbers;       /* [nNumberOfAtoms*1.5] */
+    AT_NUMB   *nConstitEquIsotopicTGroupNumbers; /* [nNumberOfAtoms/2] */
+#if( bREUSE_INCHI == 1 )
+    int nRefCount;
+#endif
+#if( TEST_RENUMB_ATOMS == 1 )
+    unsigned long ulNormTime;
+    unsigned long ulCanonTime;
+#endif
+
+    ORIG_INFO *OrigInfo;
+    MOL_COORD *szOrigCoord;
+    NUM_H   nNumRemovedProtons;
+    NUM_H   nNumRemovedIsotopicH[NUM_H_ISOTOPES]; /* isotopic H that may be exchanged and considered
+                                                     randomly distributed, including removed protons */
+    int     bDeleted;
+    INCHI_MODE  bTautFlags;
+    INCHI_MODE  bTautFlagsDone;
+    INCHI_MODE  bNormalizationFlags;
+    int        nCanonFlags;
+} INChI_Aux;
+
+typedef INChI_Aux *PINChI_Aux2[TAUT_NUM];
+
+/********************* array of pointers for sorting components and INChI output *********/
+typedef struct tagINChIforSort {
+    INChI     *pINChI[TAUT_NUM];
+    INChI_Aux *pINChI_Aux[TAUT_NUM];
+    int      ord_number;    /* for stable sort */
+}INCHI_SORT;
+
+
+#endif /* __INCHI_H__ */