rino 0.1.0

data/ext/src/ichitaut.h

@@ -0,0 +1,387 @@
+/*
+ * 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 __INCHITAUT_H__
+#define __INCHITAUT_H__
+
+#include "inpdef.h"
+#include "ichi_bns.h"
+
+/*******************************************************
+  ---     Header of tautomers groups      ---
+  ---  Each entry is AT_TAUTOMER_HDR type ---
+          number of tautomer groups (nNumTautGroups)
+          index of the first tautomer group (#1)
+          ...
+          index of the last tautomer group  (#nNumTautGroups)
+  --- end of the Header of tautomers groups description ---
+  
+  ---  One endpoint group description  ---
+  ---  Each entry has AT_TAUTOMER type members ---
+    <fixed portion (6 entries)>
+          number of endpoints  (0=end of list)
+          number of mobile groups, including number of negative charges (=num(H)+num(-))
+          number of negative charges
+          number of 1H atoms
+          number of 2H (deuterium) atoms
+          number of 3H (tritium) atoms
+     <variable portion, sorted in ascending order>
+          atom rank #1 (ascending order)
+          ...
+          atom rank #endpoints
+  --- end of the endpoint group description ----
+
+  ----------------------------------------------
+     Note:
+     In the following Linear CT Tautomer descriptions
+     we assume the tautomeric groups and the endpoints
+     within them have been properly sorted
+  
+  --------- Linear CT Tautomer description -----
+    <for each tautomeric group>
+        -- fixed length part, non-isotopic --
+        number of endpoints        = t_group->nNumEndpoints
+        number of mobile atoms     = t_group->num[0]
+        ...
+        number of negative charges = t_group->num[T_NUM_NO_ISOTOPIC-1]
+        -- fixed length part, isotopic --
+        number of T (3H)           = t_group->num[T_NUM_NO_ISOTOPIC]
+        ...
+        number of 1H               = t_group->num[T_NUM_NO_ISOTOPIC+T_NUM_ISOTOPIC-1]
+        -- variable length part --
+        rank of the first endpoint = nRank[t_group_info->nEndpointAtomNumber[t_group->nFirstEndpointAtNoPos]];
+        ...
+        rank of the last endpoint  = nRank[t_group_info->nEndpointAtomNumber[t_group->nFirstEndpointAtNoPos+t_group->nNumEndpoints-1]];
+  
+  --------- Linear CT Isotopic Tautomer description -----
+    <for each isotopic tautomeric group>
+        number of T (3H)           = t_group->num[T_NUM_NO_ISOTOPIC]
+        ...
+        number of 1H               = t_group->num[T_NUM_NO_ISOTOPIC+T_NUM_ISOTOPIC-1]
+        t-group ordering number in the Linear CT Tautomer, starts from 1
+        
+***************************************************************/
+
+
+#define           T_NUM_NO_ISOTOPIC 2
+#define           T_NUM_ISOTOPIC    NUM_H_ISOTOPES /* was 2, now 3 */
+
+#define           T_GROUP_HDR_LEN   (1+T_NUM_NO_ISOTOPIC /*+T_NUM_ISOTOPIC*/) /* LinearCTTautomer */
+
+typedef AT_NUMB   AT_TAUTOMER;  /* LinearCTTautomer */
+
+typedef AT_ISO_SORT_KEY  T_GROUP_ISOWT; /* must hold value up to T_GROUP_ISOWT_MULT^3-1 */
+                                     /* similar to AT_ISO_SORT_KEY */
+/* = num_1H + T_GROUP_ISOWT_MULT*(num_D + T_GROUP_ISOWT_MULT*num_T) */
+
+
+#define T_GROUP_ISOWT_MULT   1024 /* (max. number of identical isotopic hydrogens in a taut. group) + 1 */
+                                   /* changed from 256U 9-12-2003 */
+                                   /* (similar to AT_ISO_SORT_KEY_MULT ) */
+/* note: (long)T_GROUP_ISOWT should always be positive (have zero sign bit) */
+
+typedef struct tagIsotopicTautomerGroup {
+    AT_NUMB  tgroup_num;  /* ordering number of a tautomer group with isotopes > 0 */
+    /*
+    union {
+        struct {
+            AT_NUMB num_T;
+            AT_NUMB num_D;
+            AT_NUMB num_1H;
+        };
+        AT_NUMB num[T_NUM_ISOTOPIC];
+    };
+    */
+    AT_NUMB  num[T_NUM_ISOTOPIC]; /* inverted order: num_T, num_D, num_1H */
+} AT_ISO_TGROUP;
+
+typedef enum tagTG_NumDA {  /* 2004-02-26 */
+    TG_Num_dH, /* number of H donors that have only H (all single bonds) */
+    TG_Num_dM, /* number of H donors that have (-)  (all single bonds) */
+    TG_Num_aH, /* number of H acceptors that have H and no (-) (+a double bond) */
+    TG_Num_aM, /* number of H acceptors that have (-) and possibly H (+ one double bond) */
+    TG_Num_dO, /* number of H donors =C-OH or =C-O(-) */
+    TG_Num_aO, /* number of H acceptors -C=O */
+    TG_NUM_DA  /* number of elements in an array */
+} TGNUMDA;
+
+typedef struct tagTautomerGroup {
+    /*
+    union {
+        struct {
+               // T_NUM_NO_ISOTOPIC = 2 elements:
+            AT_RANK num_Mobile; // Num_H+num_D+num_T+num_NegCharges
+            AT_RANK num_NegCharges;
+               // T_NUM_ISOTOPIC = 3 elements
+            AT_RANK num_T;      // here the isotopic part (num+T_NUM_NO_ISOTOPIC) starts
+            AT_RANK num_D;
+            AT_RANK num_1H;
+        };
+        AT_RANK num[T_NUM_NO_ISOTOPIC+T_NUM_ISOTOPIC];  // same size and meaning as num[] in T_ENDPOINT
+    };
+    */
+    AT_RANK num[T_NUM_NO_ISOTOPIC+T_NUM_ISOTOPIC];  /* same size and meaning as num[] in T_ENDPOINT */
+                                                    /* isotopic inv. order: num_T, num_D, num_1H */
+    AT_RANK num_DA[TG_NUM_DA];
+    T_GROUP_ISOWT iWeight;   /* isotopic "weight" = T_GROUP_ISOWT_MULT*(T_GROUP_ISOWT_MULT*num_T + num_D)+num_1H; */
+    AT_NUMB   nGroupNumber;  /* positive tautomer group ID = atom->endpoint */
+    AT_NUMB   nNumEndpoints; /* number of the atom numbers in T_GROUP_INFO::nEndpointAtomNumber[] */
+    AT_NUMB   nFirstEndpointAtNoPos; /* the first index of the atom number in T_GROUP_INFO::nEndpointAtomNumber[] */
+} T_GROUP;
+
+/* offsets/num_t_groups within T_GROUP_INFO::tGroupNumber  */
+#define TGSO_CURR_ORDER  0  /* tGroupNumber:     current sorting order */
+#define TGSO_PREV_ORDER  1  /* tPrevGroupNumber: previous sorting order; symmetry rank sorting order */
+/* #define TGSO_CURR_IORDER 1 */ /* tiGroupNumber:  isotopic sort order */
+#define TGSO_SYMM_RANK   2  /* tSymmRank:     symmetry ranks (no isotopes) = min. ordering number > 0. */
+#define TGSO_SORT_RANK   3  /* tSortRank:     current rank (positive ordering number) */
+#define TGSO_SYMM_IORDER 4  /* tiGroupNumber: isotopic symmetry rank sorting order */
+#define TGSO_SYMM_IRANK  5  /* tiSymmRank:    isotopic symmetry ranks */
+#define TGSO_SORT_IRANK  6  /* tiSortRank:    current isotopic rank (positive ordering number) */
+#define TGSO_MARK_IRANK  7  /* tiMarkGroup:   the min. canonical number has been mapped on the endpoint */
+#define TGSO_TOTAL_LEN   8
+
+/***************************************************/
+/* flags for t_group_info->tni.bNormalizationFlags */
+/***************************************************/
+#define FLAG_PROTON_NPO_SIMPLE_REMOVED 0x0001
+#define FLAG_PROTON_NP_HARD_REMOVED    0x0002
+#define FLAG_PROTON_AC_SIMPLE_ADDED    0x0004
+#define FLAG_PROTON_AC_SIMPLE_REMOVED  0x0008
+#define FLAG_PROTON_AC_HARD_REMOVED    0x0010
+#define FLAG_PROTON_AC_HARD_ADDED      0x0020
+#define FLAG_PROTON_CHARGE_CANCEL      0x0040
+#define FLAG_PROTON_SINGLE_REMOVED     0x0080
+
+/* signifies tautomeric structure even though no t-group discovered */
+#define FLAG_NORM_CONSIDER_TAUT      ( FLAG_PROTON_NPO_SIMPLE_REMOVED | \
+                                       FLAG_PROTON_NP_HARD_REMOVED    | \
+                                       FLAG_PROTON_AC_SIMPLE_ADDED    | \
+                                       FLAG_PROTON_AC_SIMPLE_REMOVED  | \
+                                       FLAG_PROTON_AC_HARD_REMOVED    | \
+                                       FLAG_PROTON_AC_HARD_ADDED      | \
+                                       FLAG_PROTON_SINGLE_REMOVED     | \
+                                       FLAG_PROTON_CHARGE_CANCEL    )
+
+/* force salt tautomerism exploration */
+#define FLAG_FORCE_SALT_TAUT         ( FLAG_PROTON_NP_HARD_REMOVED  | \
+                                       FLAG_PROTON_AC_HARD_REMOVED  | \
+                                       FLAG_PROTON_AC_HARD_ADDED    )
+
+typedef struct tagTautomerNormInfo {
+    NUM_H       nNumRemovedExplicitH; /* keeps track of explicit H */
+    NUM_H       nNumRemovedProtons;
+    NUM_H       nNumRemovedProtonsIsotopic[NUM_H_ISOTOPES];
+    INCHI_MODE   bNormalizationFlags;
+} TNI;
+
+/***************************************************/
+/*      t_group_info definition                    */
+/***************************************************/
+typedef struct tagTautomerGroupsInfo {
+    T_GROUP   *t_group;  /* max_num_t_groups elements */
+    AT_NUMB   *nEndpointAtomNumber; /* nNumEndpoints elements; also see comments to T_GROUP */
+    AT_NUMB   *tGroupNumber;
+    int       nNumEndpoints;
+    int       num_t_groups;
+    int       max_num_t_groups;
+    int       bIgnoreIsotopic;
+
+    AT_NUMB   *nIsotopicEndpointAtomNumber; /* [0]: number of the following atoms; [1...]: non-tautomeric atoms that may have isotopic H */
+    int       nNumIsotopicEndpoints;     /* allocated length of nIsotopicEndpointAtomNumber */
+    NUM_H     num_iso_H[NUM_H_ISOTOPES]; /* isotopic H on tautomeric atoms and those in nIsotopicEndpointAtomNumber */
+    
+    TNI       tni;
+    
+    INCHI_MODE bTautFlags;      
+    INCHI_MODE bTautFlagsDone;      
+} T_GROUP_INFO;
+
+#define CANON_FLAG_NO_H_RECANON           0x0001  /* iOther: second canonicalization of the no H structure */
+#define CANON_FLAG_NO_TAUT_H_DIFF         0x0002  /* iOther: NoTautH eq. partition differs from NoH */
+#define CANON_FLAG_ISO_ONLY_NON_TAUT_DIFF 0x0004  /* iOther: eq. partition in isotopic only non-taut differs from non-isotopic */
+#define CANON_FLAG_ISO_TAUT_DIFF          0x0008  /* iBase:  isotopic eq. partition in isotopic taut differs from non-isotopic taut */
+#define CANON_FLAG_ISO_FIXED_H_DIFF       0x0010  /* iOther: isotopic eq. partition in fixed H non-taut differs from non-isotopic fixed H */
+
+/* Note: rank of tautomer atom #i = Rank[nEndpointAtomNumber[i]] */
+/*       for each tautomer atom group (t_group) t_group.nFirstEndpointAtNoPos */
+/*       is the first index of the atom number in nEndpointAtomNumber[] */
+
+typedef struct tagTautomerEndpoint {
+    /*
+    union {
+        struct {
+            AT_RANK num_Mobile; // Num_H+num_D+num_T+num_NegCharges
+            AT_RANK num_NegCharges;
+            AT_RANK num_T;
+            AT_RANK num_D;
+        };
+        AT_RANK num[T_NUM_NO_ISOTOPIC+T_NUM_ISOTOPIC];    // same size and meaning as num[] in T_GROUP
+    };
+    */
+    AT_RANK num[T_NUM_NO_ISOTOPIC+T_NUM_ISOTOPIC];    /* same size and meaning as num[] in T_GROUP */
+    AT_RANK num_DA[TG_NUM_DA];
+    AT_NUMB nGroupNumber;
+    AT_NUMB nEquNumber;  /* same for endpoints connected by alt paths */
+    AT_NUMB nAtomNumber;
+    /*AT_NUMB neighbor_index; */
+} T_ENDPOINT;
+
+typedef struct tagTautomerBondLocation {
+    AT_NUMB nAtomNumber;
+    AT_NUMB neighbor_index;
+} T_BONDPOS;
+
+typedef struct tagEndpointInfo {
+    S_CHAR cMoveableCharge;
+    S_CHAR cNeutralBondsValence;
+    S_CHAR cMobile;
+    S_CHAR cDonor;
+    S_CHAR cAcceptor;
+} ENDPOINT_INFO;
+
+
+/* positive charge group (extended onium) */
+
+#define CHARGED_CPOINT(X,i) ((X)[i].charge==1)
+
+typedef struct tagChargeCandidate {
+    AT_NUMB   atnumber;
+    S_CHAR    type;
+    S_CHAR    subtype;
+} C_CANDIDATE;
+
+typedef struct tagChargeGroup {
+    AT_RANK   num[2]; /* [0]: number of (+), [1]: number atoms that have H, including H accessible through tautomerism */
+    AT_RANK   num_CPoints;
+    AT_NUMB   nGroupNumber;
+    U_CHAR    cGroupType;
+} C_GROUP;
+    
+typedef struct tagChargeGroupsInfo {
+    C_GROUP *c_group;
+    int     num_c_groups;
+    int     max_num_c_groups;
+    
+    C_CANDIDATE *c_candidate;
+    int          max_num_candidates;
+    int          num_candidates; /* 0=>unimitialized, -1=>no candidates found */
+} C_GROUP_INFO;
+
+/* salts */
+typedef struct tagSaltChargeCandidate {
+    AT_NUMB   atnumber;
+    S_CHAR    type;
+    S_CHAR    subtype;
+    AT_NUMB   endpoint; /* MAX_ATOMS+1 => found alt path to the candidate */
+} S_CANDIDATE;
+
+typedef struct tagSaltGroupInfo {
+    S_CANDIDATE *s_candidate;
+    int          max_num_candidates;
+    int          num_candidates; /* 0=>unimitialized, -1=>no candidates found */
+    int          num_other_candidates; /* num. non-"acidic O" candidates */
+    int          num_p_only_candidates; /* num. non-tautomeric p-donor/acceptor candidates like -CH2-SH */
+} S_GROUP_INFO;
+
+/********************* ATOM_SIZES *******************************/
+/* sizes of a component */
+typedef struct tagAtomSizes {
+    /* for tautomeric and non-tautomeric structures */
+    int nMaxNumStereoAtoms; /* max. number of stereo atoms in isotopic case */
+    int nMaxNumStereoBonds; /* max. number of stereo bonds in isotopic case */
+    int num_isotopic_atoms;  /* includes atoms that have isotopic tautomeric H */
+    int nLenCT;
+    int nLenBonds;
+    int nLenIsotopic;
+    int nLenCTAtOnly;
+    int nLenLinearCTStereoDble; /* max. number of stereo bonds in non-isotopic case */
+    int nLenLinearCTStereoCarb; /* max. number of stereo atoms in non-isotopic case */
+    /* int bHasIsotopicAtoms; */
+    int bMayHaveStereo;
+
+    int bIgnoreIsotopic;
+
+    /* tautomeric structure only; zeroes in non-tautomeric */
+    int nLenLinearCTTautomer;
+    int nLenLinearCTIsotopicTautomer;
+    int bHasIsotopicTautGroups;
+    int nLenIsotopicEndpoints;
+
+} ATOM_SIZES;
+
+
+typedef struct tagDfsPath {
+    AT_RANK       at_no;
+    AT_RANK       nDfsLevel;
+    U_CHAR        bond_type;
+    S_CHAR        bond_pos;
+} DFS_PATH;
+
+
+#ifndef INCHI_ALL_CPP
+#ifdef __cplusplus
+extern "C" {
+#endif
+#endif
+
+int is_centerpoint_elem( U_CHAR el_number );
+int is_centerpoint_elem_strict( U_CHAR el_number );
+
+int bIsCenterPointStrict( inp_ATOM *atom, int iat );
+
+int nGetEndpointInfo( inp_ATOM *atom, int iat, ENDPOINT_INFO *eif );
+void AddAtom2DA( AT_RANK num_DA[], inp_ATOM *atom, int at_no, int bSubtract );
+int AddAtom2num(  AT_RANK num[], inp_ATOM *atom, int at_no, int bSubtract );
+int AddEndPoint( T_ENDPOINT *pEndPoint, inp_ATOM *at, int iat );
+int bHasAcidicHydrogen( inp_ATOM *at, int i );
+int bHasOtherExchangableH ( inp_ATOM *at, int i );
+int bHasAcidicMinus( inp_ATOM *at, int i );
+
+
+int nGet15TautIn6MembAltRing( inp_ATOM *atom, int nStartAtom, AT_RANK  *nBfsTreePos,
+                              DFS_PATH *DfsPath, int nMaxLenBfsTree,
+                              T_ENDPOINT *EndPoint, int nMaxNumEndPoint,
+                              T_BONDPOS  *BondPos, int nMaxNumBondPos,
+                              int *pnNumEndPoint, int *pnNumBondPos,
+                              struct BalancedNetworkStructure *pBNS,
+                              struct BalancedNetworkData *pBD, int num_atoms );
+
+int nGet12TautIn5MembAltRing( inp_ATOM *atom, int nStartAtom, int nStartAtomNeighbor,
+                              AT_RANK  *nBfsTreePos, DFS_PATH *DfsPath, int nMaxLenBfsTree,
+                              T_ENDPOINT *EndPoint, int nMaxNumEndPoint,
+                              T_BONDPOS  *BondPos, int nMaxNumBondPos,
+                              int *pnNumEndPoint, int *pnNumBondPos,
+                              struct BalancedNetworkStructure *pBNS,
+                              struct BalancedNetworkData *pBD, int num_atoms );
+int nGet14TautIn7MembAltRing( inp_ATOM *atom, int nStartAtom, int nStartAtomNeighbor,
+                              int nStartAtomNeighborEndpoint, int nStartAtomNeighborNeighborEndpoint,
+                              AT_RANK  *nDfsPathPos, DFS_PATH *DfsPath, int nMaxLenDfsPath,
+                              T_ENDPOINT *EndPoint, int nMaxNumEndPoint,
+                              T_BONDPOS  *BondPos, int nMaxNumBondPos,
+                              int *pnNumEndPoint, int *pnNumBondPos,
+                              struct BalancedNetworkStructure *pBNS,
+                              struct BalancedNetworkData *pBD, int num_atoms );
+int nGet14TautIn5MembAltRing( inp_ATOM *atom, int nStartAtom, int nStartAtomNeighbor,
+                              int nStartAtomNeighborEndpoint, int nStartAtomNeighborNeighborEndpoint,
+                              AT_RANK  *nDfsPathPos, DFS_PATH *DfsPath, int nMaxLenDfsPath,
+                              T_ENDPOINT *EndPoint, int nMaxNumEndPoint,
+                              T_BONDPOS  *BondPos, int nMaxNumBondPos,
+                              int *pnNumEndPoint, int *pnNumBondPos,
+                              struct BalancedNetworkStructure *pBNS,
+                              struct BalancedNetworkData *pBD, int num_atoms );
+
+#ifndef INCHI_ALL_CPP
+#ifdef __cplusplus
+}
+#endif
+#endif
+
+#endif /* __INCHITAUT_H__ */
+

data/ext/src/ichitime.h

@@ -0,0 +1,74 @@
+/*
+ * 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 __ICHITIME_H__
+#define __ICHITIME_H__
+
+
+#ifdef INCHI_ANSI_ONLY
+
+#ifdef __FreeBSD__
+#include <sys/time.h>
+#endif
+
+/* get times() */
+#ifdef INCHI_USETIMES
+#include <sys/times.h>
+#endif
+
+/*#include <sys/timeb.h>*/
+
+#include <time.h>
+
+typedef struct tagInchiTime {
+    clock_t clockTime;
+} inchiTime;
+
+#else
+
+/* Win32 _ftime(): */
+#include <sys/timeb.h>
+
+typedef struct tagInchiTime {
+    unsigned long  clockTime; /* Time in seconds since midnight (00:00:00), January 1, 1970;
+                                 signed long overflow expected in 2038 */
+    long           millitime; /* milliseconds */
+
+} inchiTime;
+
+#endif
+
+
+#ifdef INCHI_MAIN
+
+#define InchiTimeGet           e_InchiTimeGet
+#define InchiTimeMsecDiff      e_InchiTimeMsecDiff
+#define InchiTimeAddMsec       e_InchiTimeAddMsec
+#define bInchiTimeIsOver       e_bInchiTimeIsOver
+#define InchiTimeElapsed       e_InchiTimeElapsed
+
+#define FullMaxClock           e_FullMaxClock
+#define HalfMaxClock           e_HalfMaxClock
+#define MaxPositiveClock       e_MaxPositiveClock
+#define MinNegativeClock       e_MinNegativeClock
+#define HalfMaxPositiveClock   e_HalfMaxPositiveClock
+#define HalfMinNegativeClock   e_HalfMinNegativeClock
+
+
+
+#endif
+
+void InchiTimeGet( inchiTime *TickEnd );
+long InchiTimeMsecDiff( inchiTime *TickEnd, inchiTime *TickStart );
+void InchiTimeAddMsec( inchiTime *TickEnd, unsigned long nNumMsec );
+int  bInchiTimeIsOver( inchiTime *TickEnd );
+long InchiTimeElapsed( inchiTime *TickStart );
+
+#endif /* __ICHITIME_H__ */
+