rino 0.1.0

data/ext/src/ichi_bns.h

@@ -0,0 +1,231 @@
+/*
+ * 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_BNS_H___
+#define __INCHI_BNS_H___
+
+#define BN_MAX_ALTP  16
+#define MAX_VERTEX 1024 /* including s; if vert[] has num_vert then MAX_VERTEX has (2*num_vert+2+FIRST_INDX) elements */
+
+/* forward declarations */
+
+struct BalancedNetworkStructure;
+struct BalancedNetworkData;
+struct tagTautomerGroupsInfo;
+struct tagChargeGroupsInfo;
+struct BN_AtomsAtTautGroup;
+struct tagSaltChargeCandidate;
+
+/* define BNS types */
+
+typedef S_SHORT  Vertex;
+typedef S_SHORT  EdgeIndex;
+typedef S_SHORT  Edge[2];         /* Edge[0] = vertex1, Edge[1] = iedge or -(1+vertex1) if vertex2 = s or t */
+typedef S_SHORT BNS_IEDGE;
+typedef S_SHORT EdgeFlow;
+typedef S_SHORT VertexFlow;
+
+
+#define BNS_EDGE_FORBIDDEN_MASK  1
+#define BNS_EDGE_FORBIDDEN_TEMP  2
+
+/**************************** BNS_EDGE ************************************/
+typedef struct BnsEdge {
+  AT_NUMB   neighbor1;                      /* the smaller neighbor */
+  AT_NUMB   neighbor12;                     /* neighbor1 ^ neighbor2 */
+  AT_NUMB   neigh_ord[2];                   /* ordering number of the neighbor: [0]: at<neighbor, [1]: at>neighbor */
+  EdgeFlow  cap;                            /* Edge capacity */
+  EdgeFlow  cap0;                           /* Initial edge capacity */
+  EdgeFlow  flow;                           /* Edge flow */
+  EdgeFlow  flow0;                          /* Initial flow */
+  /*S_CHAR    delta; */
+  S_CHAR    pass;                           /* number of times changed in AugmentEdge() */
+  S_CHAR    forbidden;
+} BNS_EDGE;
+
+/**************************** BNS_ST_EDGE ************************************/
+typedef struct BnsStEdge {
+  VertexFlow cap;                            /* Edge capacity */
+  VertexFlow cap0;                           /* Initial edge capacity */
+  VertexFlow flow;                           /* Edge flow */
+  VertexFlow flow0;                          /* Initial edge flow */
+  S_CHAR     pass;                           /* number of times changed in AugmentEdge() */
+  /*S_CHAR     delta; */
+} BNS_ST_EDGE;
+
+/**************************** BNS_VERTEX ************************************/
+typedef struct BnsVertex {
+
+  BNS_ST_EDGE st_edge;                     /* 0,1 capacity and flow of the edge to s or t */
+  AT_NUMB     type;                        /* 2, atom, t-group, or added atom: BNS_VERT_TYPE_TGROUP, etc. */
+  AT_NUMB     num_adj_edges;               /* 3, actual number of neighbors incl. t-groups, excl. s or t */
+  AT_NUMB     max_adj_edges;               /* 4, including reserved */
+  /*S_CHAR      path_neigh[2];*/               /* 5 found path information */
+  /* indexes of Edges */
+  BNS_IEDGE  *iedge;                       /* 6 a pointer to the array of edge indexes adjacent to this vertex */
+}BNS_VERTEX;
+
+/**************************** BNS_ALT_PATH ************************************/
+typedef union BnsAltPath {
+    VertexFlow   flow[2];
+    Vertex       number;
+    AT_NUMB      ineigh[2];
+} BNS_ALT_PATH;
+
+/**************************** BN_STRUCT ************************************/
+typedef struct BalancedNetworkStructure {
+
+    int num_atoms;        /* number of real atoms */
+    /*int len_atoms; */       /* size of filled with real atoms portion of the BNS_VERTEX data */
+    int num_added_atoms;  /* number of added fictitious atoms */
+    int nMaxAddAtoms;     /* max. number of atoms to add (not including t-groups) */
+    int num_c_groups;     /* number of added c-groups */
+    int num_t_groups;     /* number of added t-groups */
+    int num_vertices;     /* total number currently in effect; includes t-groups and added atoms */
+    /*int len_vertices; */    /* allocation size for BNS_VERTEX data */
+    int num_bonds;        /* number of real bonds/2 = number of edges between real atoms */
+    int num_edges;        /* number of currently in effect */
+    int num_added_edges;  /* number of added edges (not including edges to t-groups) */
+    int nMaxAddEdges;     /* max. number edges of add to each atom (not including edges to t-groups) */
+
+    int max_vertices;     /* allocation size for BNS_VERTEX structures */
+    int max_edges;        /* allocation size for edge[]; iedge has length 2*max_edges */
+    int max_iedges;       /* allocation size for iedge */
+
+    int tot_st_cap;       /* not used, only calculated */
+    int tot_st_flow;      /* not used, only calculated */
+
+    int len_alt_path;     /* length of alt_path[] */
+
+    int bNotASimplePath;  /* alternating path traversed same bond 2 times in opposite directions */
+    int bChangeFlow;      /* actually change flow */
+
+    BNS_VERTEX    *vert;  /* vertices */
+    BNS_EDGE      *edge;  /* edges */
+    BNS_IEDGE     *iedge;
+    BNS_ALT_PATH  *alt_path;           /* current altp[] element */
+    BNS_ALT_PATH  *altp[BN_MAX_ALTP];  /* keep alt. paths */
+
+    int            max_altp;
+    int            num_altp;
+
+    INCHI_MODE     *pbTautFlags;     /* carry it through all functions; never NULL */
+    INCHI_MODE     *pbTautFlagsDone; /* carry it through all functions; never NULL */
+    AT_NUMB        type_TACN; /* BNS_VERT_TYPE_ACID: if non-zero than only for it path type_T-type_TACN-type_CN allowed */
+    AT_NUMB        type_T;    /* BNS_VERT_TYPE_TGROUP */
+    AT_NUMB        type_CN;   /* BNS_VERT_TYPE_C_GROUP | BNS_VERT_TYPE_C_NEGATIVE */
+    S_CHAR         edge_forbidden_mask;
+
+} BN_STRUCT;
+
+/********************* BN_DATA *******************************************/
+typedef struct BalancedNetworkData {
+    Vertex          *BasePtr;    /*[MAX_VERTEX];  pointer toward the base of C(v) */
+    Edge            *SwitchEdge; /*[MAX_VERTEX];  a pair of vertices and an edge, implemented here as [*][2] array */
+    S_CHAR          *Tree;       /*[MAX_VERTEX];  indicates presence in ScanQ, T, T', s-reachability */
+    Vertex          *ScanQ;      /*[MAX_VERTEX];  contains the set S of s-reachable vertices */
+    int             QSize;       /* index of the  last element added to ScanQ */
+    Vertex          *Pu;         /*[MAX_VERTEX/2+1] */
+    Vertex          *Pv;         /*[MAX_VERTEX/2+1] */
+    int             max_num_vertices; /* allocation size of all except Pu, Pv */
+    int             max_len_Pu_Pv;    /* allocation size of Pu and Pv */
+
+} BN_DATA;
+
+/* internal array size */
+#define MAX_ALT_AATG_ARRAY_LEN 127
+/* detected endpoint markings */
+#define AATG_MARK_IN_PATH      1  /* atom in path detected by the BNS */
+#define AATG_MARK_WAS_IN_PATH  2  /* found to be in path before next level */
+/* output */
+#define AATG_MARK_MAIN_TYPE   4  /* atom O-"salt" */
+#define AATG_MARK_OTHER_TYPE  8  /* other atom to be tested */
+
+struct tagTautomerGroupsInfo;   /* forward declaration */
+
+/******************** atoms in alt path through taut group ****************/
+typedef struct BN_AtomsAtTautGroup {
+    int      nAllocLen;
+    int      nNumFound;
+    int      nNumMainAdj2Tgroup;
+    int      nNumOthersAdj2Tgroup;
+    AT_NUMB *nEndPoint;            /* original t-group number */
+    S_CHAR  *nMarkedAtom;          /* atom mark, see AATG_MARK_* */
+    int     *nAtTypeTotals;
+    struct tagTautomerGroupsInfo *t_group_info;
+} BN_AATG;
+
+
+/************ store changes in flow and capacity to test a bond ****************/
+
+typedef struct tagBNS_FLOW_CHANGES {
+    BNS_IEDGE  iedge;
+    EdgeFlow   flow;
+    EdgeFlow   cap;
+    Vertex     v1;
+    VertexFlow cap_st1;
+    VertexFlow flow_st1;
+    Vertex     v2;
+    VertexFlow cap_st2;
+    VertexFlow flow_st2;
+} BNS_FLOW_CHANGES;
+
+
+#define ALT_PATH_MODE_TAUTOM     1
+#define ALT_PATH_MODE_CHARGE     2
+#define ALT_PATH_MODE_4_SALT     3   /* mark alt bonds along the path */
+#define ALT_PATH_MODE_4_SALT2    4   /* mark alt bonds along the path, path to taut. group fict. vertex if exists */
+#define ALT_PATH_MODE_REM2H_CHG  5   /* remove 2 H along alt. path AH-=-BH => A=-=B and change bonds to alternating */
+#define ALT_PATH_MODE_ADD2H_CHG  6   /* add 2 H along alt. path A=-=B => AH-=-BH    and change bonds to alternating */
+#define ALT_PATH_MODE_REM2H_TST  7   /* test-remove 2 H along alt. path AH-=-BH => A=-=B; restore changed bonds */
+#define ALT_PATH_MODE_ADD2H_TST  8   /* test-add 2 H along alt. path A=-=B => AH-=-BH; restore changed bonds */
+#define ALT_PATH_MODE_REM_PROTON 9   /* remove proton, adjust bonds, charges, H-counts 2004-03-05 */
+
+#ifndef INCHI_ALL_CPP
+#ifdef __cplusplus
+extern "C" {
+#endif
+#endif
+
+
+int nExists2AtMoveAltPath( struct BalancedNetworkStructure *pBNS, struct BalancedNetworkData *pBD,
+                           struct BN_AtomsAtTautGroup *pAATG, inp_ATOM *at, int num_atoms,
+                           int jj2, int jj1, struct tagSaltChargeCandidate *s_candidate, int nNumCandidates,
+                           AT_NUMB *nForbiddenAtom, int nNumForbiddenAtoms);
+int bExistsAltPath( struct BalancedNetworkStructure *pBNS, struct BalancedNetworkData *pBD,
+                    struct BN_AtomsAtTautGroup *pAATG, inp_ATOM *at, int num_atoms, int nVertDoubleBond, int nVertSingleBond, int path_type );
+int bExistsAnyAltPath( struct BalancedNetworkStructure *pBNS, struct BalancedNetworkData *pBD,
+                       inp_ATOM *at, int num_atoms, int nVertDoubleBond, int nVertSingleBond, int path_type );
+int AddTGroups2BnStruct( struct BalancedNetworkStructure *pBNS, inp_ATOM *at, int num_atoms,
+                         struct tagTautomerGroupsInfo *tgi  );
+int AddSuperTGroup2BnStruct( struct BalancedNetworkStructure *pBNS, inp_ATOM *at, int num_atoms,
+                             struct tagTautomerGroupsInfo *tgi  );
+int AddCGroups2BnStruct( struct BalancedNetworkStructure *pBNS, inp_ATOM *at, int num_atoms,
+                         struct tagChargeGroupsInfo *cgi );
+
+int ReInitBnStruct( struct BalancedNetworkStructure *pBNS, inp_ATOM *at, int num_at, int bRemoveGroupsFromAtoms );
+int ReInitBnStructAddGroups( struct BalancedNetworkStructure *pBNS, inp_ATOM *at, int num_atoms,
+                             struct tagTautomerGroupsInfo *tgi, struct tagChargeGroupsInfo *cgi );
+
+
+int DisconnectTestAtomFromTGroup( struct BalancedNetworkStructure *pBNS, int v1, int *pv2, BNS_FLOW_CHANGES *fcd );
+int DisconnectTGroupFromSuperTGroup( struct BalancedNetworkStructure *pBNS, int v1, int *pv1, int *pv2,
+                                     BNS_FLOW_CHANGES *fcd );
+int ReconnectTestAtomToTGroup( struct BalancedNetworkStructure *pBNS, int v1, int v2, int ie, BNS_FLOW_CHANGES *fcd );
+
+int bIsHardRemHCandidate(  inp_ATOM *at, int i, int *cSubType );
+
+#ifndef INCHI_ALL_CPP
+#ifdef __cplusplus
+}
+#endif
+#endif
+
+
+#endif /* __INCHI_BNS_H___ */