/src/formats/inchi103/ichiring.c

/*
 * International Chemical Identifier (InChI)
 * Version 1
 * Software version 1.03
 * May 9, 2010
 *
 * Originally developed at NIST
 * Modifications and additions by IUPAC and the InChI Trust
 *
 * The InChI library and programs are free software developed under the
 * auspices of the International Union of Pure and Applied Chemistry (IUPAC);
 * you can redistribute this software and/or modify it under the terms of 
 * the GNU Lesser General Public License as published by the Free Software 
 * Foundation:
 * http://www.opensource.org/licenses/lgpl-2.1.php
 */


#include <stdio.h>
#include <stdlib.h>
#include <string.h>

#include "mode.h"

#include "inpdef.h"
#include "extr_ct.h"
#include "ichiring.h"

/* local prototypes */
int GetMinRingSize( inp_ATOM* atom, QUEUE *q, AT_RANK *nAtomLevel, S_CHAR *cSource, AT_RANK nMaxRingSize );




/*******************************************************************/
/*  add to the queue */
int QueueAdd( QUEUE *q, QINT_TYPE *Val );
/*  read & remove from the queue */
int QueueGet( QUEUE *q, QINT_TYPE *Val );
/*  read from the queue */
int QueueGetAny( QUEUE *q, QINT_TYPE *, int ord );
/*  initialize the queue */
int QueueReinit( QUEUE *q );
/*  current queue length */
int QueueLength( QUEUE *q );
/*  number of used queue internal elements */
int QueueWrittenLength( QUEUE *q );


#if( QUEUE_QINT == 1 )  /* { */

QUEUE *QueueCreate( int nTotLength, int nSize )
{
    QUEUE     *q   = NULL;
    QINT_TYPE *Val = NULL;
    if ( nTotLength < 1 || nSize != (int)sizeof(QINT_TYPE) ||
         !(q   = (QUEUE     *) inchi_calloc( 1, sizeof(QUEUE)) ) ||
         !(Val = (QINT_TYPE *) inchi_calloc( nTotLength, nSize) )) {
        if ( q ) inchi_free(q);
        return NULL;
    }
    q->Val        = Val;
    /* q->nSize      = nSize; */
    q->nTotLength = nTotLength;
    return q;
}
int QueueAdd( QUEUE *q, QINT_TYPE *Val )
{
    if ( q && Val && q->nLength < q->nTotLength ) {
         q->Val[ (q->nFirst + q->nLength) % q->nTotLength ] = *Val;
         q->nLength ++;
         return q->nLength;
    }
    return -1;
}
int QueueGet( QUEUE *q, QINT_TYPE *Val )
{
    if ( q && Val && q->nLength > 0 ) {
        *Val = q->Val[ q->nFirst ];
        /* new: do not allow to overwrite the retrieved value */
        q->nFirst = (q->nFirst == q->nTotLength - 1)? 0 : q->nFirst + 1;
        q->nLength --;
        /* -- old --
        if ( -- q->nLength ) {
            q->nFirst = (q->nFirst == q->nTotLength - 1)? 0 : q->nFirst + 1;
        }
        */
        return q->nLength;
    }
    return -1;
}
int QueueGetAny( QUEUE *q, QINT_TYPE *Val, int ord )
{
    if ( 0 <= ord && ord < q->nTotLength ) {
        *Val = q->Val[ ord ];
        return  1; /*  success */
    } else {
        return -1; /*  error */
    }
}

#else  /* } QUEUE_QINT == 1 { */

QUEUE *QueueCreate( int nTotLength, int nSize )
{
    QUEUE     *q   = NULL;
    QINT_TYPE *Val = NULL;
    if ( nTotLength < 1 || nSize < 1 ||
         !(q   = (QUEUE     *) inchi_calloc( 1, sizeof(QUEUE)) ) ||
         !(Val = (QINT_TYPE *) inchi_calloc( nTotLength, nSize) )) {
        if ( q ) inchi_free(q);
        return NULL;
    }
    q->Val        = Val;
    q->nSize      = nSize;
    q->nTotLength = nTotLength;
    return q;
}
int QueueAdd( QUEUE *q, QINT_TYPE *Val )
{
    if ( q && Val && q->nLength < q->nTotLength ) {
         memcpy( (char*)q->Val + ((q->nFirst + q->nLength) % q->nTotLength)*q->nSize, Val, q->nSize);
         q->nLength ++;
         return q->nLength;
    }
    return -1;
}
int QueueGet( QUEUE *q, QINT_TYPE *Val )
{
    if ( q && Val && q->nLength > 0 ) {
        memcpy( Val, (char*)q->Val + q->nFirst * q->nSize, q->nSize);
        if ( -- q->nLength ) {
            q->nFirst = (q->nFirst == q->nTotLength - 1)? 0 : q->nFirst + 1;
        }
        return q->nLength;
    }
    return -1;
}
int QueueGetAny( QUEUE *q, QINT_TYPE *Val, int ord )
{
    if ( 0 <= ord && ord < q->nTotLength ) {
        memcpy( Val, (char*)q->Val + ord * q->nSize, q->nSize);
        return  1; /*  success */
    } else {
        return -1; /*  error */
    }
}

#endif /* } QUEUE_QINT == 1 */

QUEUE *QueueDelete( QUEUE *q )
{
    if ( q ) {
        if ( q->Val ) inchi_free(q->Val);
        inchi_free( q );
    }
    return NULL;
}
int QueueReinit( QUEUE *q )
{
    if ( q ) {
        q->nFirst  = 0;
        q->nLength = 0;
        /* memset( q->Val, 0, q->nTotLength*sizeof(q->Val[0])); */ /*  for debug only */
        return q->nTotLength;
    }
    return -1;
}
int QueueLength( QUEUE *q )
{
    if ( q ) {
        return q->nLength;
    } else {
        return 0;
    }
}
int QueueWrittenLength( QUEUE *q )
{
    if ( q ) {
        int len = q->nFirst+q->nLength;
        return (len > q->nTotLength)? q->nTotLength : len;
    } else {
        return 0;
    }
}

/**********************************************************************************/
/*  BFS: Breadth First Search */
int GetMinRingSize( inp_ATOM* atom, QUEUE *q, AT_RANK *nAtomLevel, S_CHAR *cSource, AT_RANK nMaxRingSize )
{
    int qLen, i, j;
    AT_RANK nCurLevel, nRingSize, nMinRingSize=MAX_ATOMS+1;
    qInt at_no, next;
    int  iat_no, inext;
    
    while ( qLen = QueueLength( q ) ) {
        /*  traverse the next level (next outer ring) */
        for ( i = 0; i < qLen; i ++ ) {
            if ( 0 <= QueueGet( q, &at_no ) ) {
                iat_no = (int)at_no;
                nCurLevel = nAtomLevel[iat_no] + 1;
                if ( 2*nCurLevel > nMaxRingSize + 4 ) {
                    /*  2*nCurLevel = nRingSize + 3 + k, k = 0 or 1  */
                    if ( nMinRingSize < MAX_ATOMS+1 ) {
                        return (nMinRingSize >= nMaxRingSize)? 0 : nMinRingSize;
                    }
                    return 0; /*  min. ring size > nMaxRingSize */
                }
                for ( j = 0; j < atom[iat_no].valence; j ++ ) {
                    next  = (qInt)atom[iat_no].neighbor[j];
                    inext = (int)next;
                    if ( !nAtomLevel[inext] ) {
                        /*  the at_no neighbor has not been traversed yet. Add it to the queue */
                        if ( 0 <= QueueAdd( q, &next ) ) {
                            nAtomLevel[inext] = nCurLevel;
                            cSource[inext] = cSource[iat_no]; /*  keep the path number */
                        } else {
                            return -1; /*  error */
                        }
                    } else
                    if ( nAtomLevel[inext]+1 >= nCurLevel &&
                         cSource[inext] != cSource[iat_no]
                         /*  && cSource[(int)next] != -1 */
                       ) {
                        /*  found a ring closure */
                        /*  debug */
                        if ( cSource[inext] == -1 ) {
                            return -1;  /*  error */
                        }
                        if ( (nRingSize = nAtomLevel[inext] + nCurLevel - 2) < nMinRingSize ) {
                            nMinRingSize = nRingSize;
                        }
                        /* return (nRingSize >= nMaxRingSize)? 0 : nRingSize; */
                    }
                }
            } else {
                return -1; /*  error */
            }
        }
    }

    if ( nMinRingSize < MAX_ATOMS+1 ) {
        return (nMinRingSize >= nMaxRingSize)? 0 : nMinRingSize;
    }

    return 0;
}
/*******************************************************************/
/* Return value:
     0:    nMaxRingSize < 3 or
           min. ring size >= nMaxRingSize or
           not a ring bond (the last is currently impossible: bond is known to belong to a ring system.
     n>0:  min. ring size < nMaxRingSize
     n<0:  error
   
  Input:
     atom[]
     at_no      number of the 1st atom adjacent to the bond
     neigh_ord  ordering number of the bond in question: at[at_no].bond_type[neigh_ord]
     q          queue structure
     nAtomLevel work array, DFS distance
     cSource    work array, origin mark
*/

int is_bond_in_Nmax_memb_ring( inp_ATOM* atom, int at_no, int neigh_ord, QUEUE *q, AT_RANK *nAtomLevel, S_CHAR *cSource, AT_RANK nMaxRingSize )
{
    int  nMinRingSize = -1, i;
    qInt n;
    int  nTotLen;

    if ( nMaxRingSize < 3 ) {
        return 0;
    }
    
    QueueReinit( q );

    /*  mark the starting atom */
    nAtomLevel[at_no] =  1;
    cSource[at_no]    = -1;
    /*  add neighbors */
    for ( i = 0; i < atom[at_no].valence; i ++ ) {
        n = (qInt)atom[at_no].neighbor[i];
        nAtomLevel[(int)n] = 2;
        cSource[(int)n]    = 1 + (i==neigh_ord);
        QueueAdd( q, &n );
    }

    nMinRingSize =  GetMinRingSize( atom, q, nAtomLevel, cSource, nMaxRingSize );
    /*  cleanup */
    nTotLen = QueueWrittenLength( q );
    for ( i = 0; i < nTotLen; i ++ ) {
        if ( 0 < QueueGetAny( q, &n, i ) ) {
            nAtomLevel[(int)n] = 0;
            cSource[(int)n]    = 0;
        }
    }
    nAtomLevel[at_no] = 0;
    cSource[at_no]    = 0;


/*
    if ( nAtomLevel )
        inchi_free ( nAtomLevel );
    if ( cSource )
        inchi_free ( cSource );
    QueueDelete( q );
*/
    return nMinRingSize;
}
/*******************************************************************/
int is_atom_in_3memb_ring( inp_ATOM* atom, int at_no )
{
    AT_NUMB   neigh_neigh;
    int       i, j, k, val, val_neigh, neigh;

    if ( atom[at_no].nNumAtInRingSystem < 3 ) {
        return 0;
    }
    
    for ( i = 0, val = atom[at_no].valence; i < val; i ++ ) {
        neigh = (int)atom[at_no].neighbor[i];
        if ( atom[at_no].nRingSystem != atom[neigh].nRingSystem )
            continue;
        for ( j = 0, val_neigh = atom[neigh].valence; j < val_neigh; j ++ ) {
            neigh_neigh = atom[neigh].neighbor[j];
            if ( (int)neigh_neigh == at_no )
                continue;
            for ( k = 0; k < val; k ++ ) {
                if ( atom[at_no].neighbor[k] == neigh_neigh ) {
                    return 1;
                }
            }
        }
    }
    return 0;
}