Implementation of enhanced stereochemistry

INCHI-1-SRC/INCHI_BASE/src/ichimake.c

@@ -608,22 +608,21 @@ int GetSp3RelRacAbs(const INChI* pINChI, INChI_Stereo* Stereo)
                 nRet = SP3_REL;
 #endif
             }
-            else
-                if (pINChI->nFlags & INCHI_FLAG_RAC_STEREO)
-                {
+            else if (pINChI->nFlags & INCHI_FLAG_RAC_STEREO)
+            {
 #if ( REL_RAC_STEREO_IGN_1_SC == 1 )
-                    if (1 < Stereo->nNumberOfStereoCenters)
-                    {
-                        nRet = SP3_REL;
-                    }
-#else
-                    nRet = SP3_RAC;
-#endif
-                }
-                else
+                if (1 < Stereo->nNumberOfStereoCenters)
                 {
-                    nRet = SP3_ABS;
+                    nRet = SP3_REL;
                 }
+#else
+                nRet = SP3_RAC;
+#endif
+            }
+            else
+            {
+                nRet = SP3_ABS;
+            }
         }
         else
 #if ( REL_RAC_STEREO_IGN_1_SC == 1 )

INCHI-1-SRC/INCHI_BASE/src/ichiprt1.c

@@ -150,11 +150,11 @@ static int OutputINCHI_PolymerLayer( CANON_GLOBALS *pCG, INCHI_IOSTREAM *out_fil
                                      INCHI_OUT_CTL *io, char *pLF, char *pTAB );
 static int OutputINCHI_PolymerLayer_SingleUnit( OAD_PolymerUnit *u,
                                                 int bPolymers,
-                                                int total_star_atoms, 
+                                                int total_star_atoms,
                                                 int *n_used_stars,
-                                                OAD_AtProps *aprops, 
+                                                OAD_AtProps *aprops,
                                                 int *cano_nums,
-                                                ORIG_ATOM_DATA *orig_inp_data, 
+                                                ORIG_ATOM_DATA *orig_inp_data,
                                                 ORIG_STRUCT *pOrigStruct,
                                                 INCHI_IOS_STRING *strbuf );
 static int OutputAUXINFO_HeaderAndNormalization_type( CANON_GLOBALS *pCG,
@@ -1160,7 +1160,7 @@ int OutputINChI1( CANON_GLOBALS *pCG,
             io.n_pzz = orig_inp_data->polymer->n_pzz;
         }
     }
-    
+
 
     io.bPolymers = ip->bPolymers;
 
@@ -2640,7 +2640,7 @@ int WriteOrigBonds( CANON_GLOBALS *pCG,
             num_trans = 0; /* djb-rwth: ignoring LLVM warning: variable used to store function return value */
             nNeighOrder[0] = 0;
         }
-        for (kk = 0; kk < at[j].valence; kk++) 
+        for (kk = 0; kk < at[j].valence; kk++)
         {
             k = nNeighOrder[kk];
             j2 = at[j].neighbor[k];
@@ -3121,7 +3121,7 @@ void set_line_separators( int bINChIOutputOptions, char **pLF, char **pTAB )
         int  bPlainTabbedOutput = 0 != ( bINChIOutputOptions & INCHI_OUT_TABBED_OUTPUT ) &&
             bPlainText && !bPlainTextCommnts;
 
-        *pTAB = bPlainTabbedOutput ? "\t" : "\n";
+        *pTAB = bPlainTabbedOutput ? (char*)"\t" : (char*)"\n";
     }
 #else
     *pTAB = "\n";
@@ -3359,11 +3359,9 @@ int OutputINCHI_StereoLayer( CANON_GLOBALS    *pCG,
                              char             *pTAB )
 {
 
-    {
-        int i;
-        i = INChI_SegmentAction( io->sDifSegs[io->nCurINChISegment][DIFS_t_SATOMS] ); /* djb-rwth: ignoring LLVM warning: variable used to store function return value */
-        /* djb-rwth: removing redundant code */
-    }
+    // int i;
+    // i = INChI_SegmentAction( io->sDifSegs[io->nCurINChISegment][DIFS_t_SATOMS] ); /* djb-rwth: ignoring LLVM warning: variable used to store function return value */
+    // /* djb-rwth: removing redundant code */
 
     if (INChI_SegmentAction( io->sDifSegs[io->nCurINChISegment][DIFS_b_SBONDS] ) ||
          INChI_SegmentAction( io->sDifSegs[io->nCurINChISegment][DIFS_t_SATOMS] ) ||
@@ -3432,7 +3430,10 @@ int OutputINCHI_StereoLayer( CANON_GLOBALS    *pCG,
         }
         else
         {
-            if (io->bPlainTextTags == 1) inchi_ios_print_nodisplay( out_file, "/" ); /* sp3 */
+            if (io->bPlainTextTags == 1)
+            {
+                inchi_ios_print_nodisplay( out_file, "/" ); /* sp3 */
+            }
         }
 
         /* bStereoAbsInverted[io->iCurTautMode]  */
@@ -3490,7 +3491,10 @@ int OutputINCHI_StereoLayer( CANON_GLOBALS    *pCG,
     }
     else
     {
-        if (io->bPlainTextTags == 1) inchi_ios_print_nodisplay( out_file, "////" ); /* sp3, sp2, abs-inv, stereo.type */
+        if (io->bPlainTextTags == 1)
+        {
+            inchi_ios_print_nodisplay( out_file, "////" ); /* sp2, sp3, abs-inv, stereo.type */
+        }
     }
 
     return 0;
@@ -3908,7 +3912,7 @@ static int OutputINCHI_PolymerLayer( CANON_GLOBALS *pCG,
     nat = orig_inp_data->num_inp_atoms;
     num_inp_bonds = orig_inp_data->num_inp_bonds;
 
-    
+
     if (pOrigStruct && !pOrigStruct->polymer)
     {
         return 0;
@@ -4145,7 +4149,7 @@ static int OutputINCHI_PolymerLayer_SingleUnit( OAD_PolymerUnit *u,
         a2 = u->blist[1];
         a3 = u->blist[2];
         a4 = u->blist[3];
-        
+
         if (is_in_the_ilist( u->alist, a1, u->na ))
         {
             tmp = a2;
@@ -4172,7 +4176,7 @@ static int OutputINCHI_PolymerLayer_SingleUnit( OAD_PolymerUnit *u,
             /* The first printed is the crossing bond pointing to more senior CRU end ("head")    */
             swap = (OAD_Polymer_IsFirstAtomRankLower(a2, a4, aprops) == 1);
         }
-        
+
         if (swap)
         {
             inchi_strbuf_printf( strbuf, "(%-d-%-d,%-d-%-d)", a3, a4, a1, a2 );
@@ -4288,8 +4292,8 @@ static int OutputINCHI_PolymerLayer_SingleUnit( OAD_PolymerUnit *u,
                         here
                         at1, at2 is the most senior bond, and at1 is more senior than at2
                         all other pairs at3,at4,  at5,at6, ... are sorted just in increasing
-                        order of first number in pair, then second one, e.g.: at3<at4; at3<=at5 
-                        (and if at3==at5 then at4<at6) 
+                        order of first number in pair, then second one, e.g.: at3<at4; at3<=at5
+                        (and if at3==at5 then at4<at6)
                     */
 
                     if (p->frame_shift_scheme != FSS_NONE && u->nbkbonds >= 1 && u->cap1 >= 1 && u->cap2 >= 1)
@@ -5046,7 +5050,7 @@ void EditINCHI_HidePolymerZz(INCHI_IOSTREAM *out, int n_pzz, int n_zy)
         eol_was_consumed = 0, pre_eol = 0,
         nonprt_sym = 0, nonprt_prev = 0;
 
-    if (n_zy > 0) 
+    if (n_zy > 0)
     {
         /* We have some placeholder pseudo atoms which should not be removed below (if anyway they are allowed) */
         if (n_pzz == 0)
@@ -5131,7 +5135,7 @@ void EditINCHI_HidePolymerZz(INCHI_IOSTREAM *out, int n_pzz, int n_zy)
                 AT_NUMB ia = (AT_NUMB) inchi_strtol(p, &q, 10); /* make compiler happy: */ /* djb-rwth: removing redundant code; ignoring LLVM warning: variable used to store function return value */
                 if (*q != '-')
                 {
-                    skip = 1; 
+                    skip = 1;
                 }
             }
         }
@@ -5283,16 +5287,16 @@ int CountPseudoElementInFormula( const char *pseudo, char *s ) /* djb-rwth: igno
     char prev = '/';
 
     /*
-        format is 
+        format is
         [sequence of] [.[int_mult[Zz[int_index]]]]
     */
 
     if (!s)
     {
         return 0;
     }
-    
-    p = s; 
+
+    p = s;
     while (*p)
     /*for (p = s ; *p; p++)*/
     {
@@ -5317,7 +5321,7 @@ int CountPseudoElementInFormula( const char *pseudo, char *s ) /* djb-rwth: igno
             {
                 mult = (int)inchi_strtol(p, &q, 10);
                 p = q;
-                prev = *q--; 
+                prev = *q--;
                 continue;
             }
             else
@@ -5326,7 +5330,7 @@ int CountPseudoElementInFormula( const char *pseudo, char *s ) /* djb-rwth: igno
             }
             if (!mult)
             {
-                break; 
+                break;
             }
         }
         else if (*p== pseudo[1] && prev== pseudo[0])
@@ -5446,7 +5450,7 @@ int MergeZzInHillFormula(INCHI_IOS_STRING *strbuf)
     {
         inchi_free(scopy); /* djb-rwth: avoiding memory leak */
         return -1; /* failed */
-    }    
+    }
     memcpy(scopy, strbuf->pStr, strbuf->nAllocatedLength);
     stmp = (char *)inchi_calloc((long long)strbuf->nAllocatedLength + 1, sizeof(char)); /* djb-rwth: cast operator added */
     if (!stmp)
@@ -5458,7 +5462,7 @@ int MergeZzInHillFormula(INCHI_IOS_STRING *strbuf)
     inchi_strbuf_reset(strbuf);
     p0 = scopy;
     p = p0;
-    do 
+    do
     {
         /* djb-rwth: removing redundant code */
         pend = strchr(p, '.');

INCHI-1-TEST/tests/test_unit/test_ichimain.cpp

@@ -191,7 +191,6 @@ TEST(test_ichimain, test_CalcAndPrintINCHIAndINCHIKEY) {
     PINChI_Aux2* pINChI_Aux[INCHI_NUM] = {};
     ORIG_ATOM_DATA prep_inp_data = {};
     INCHI_IOS_STRING *strbuf = new INCHI_IOS_STRING;
-    memset(strbuf, 0, sizeof(*strbuf));
     inchi_strbuf_init(strbuf, INCHI_STRBUF_INITIAL_SIZE, INCHI_STRBUF_SIZE_INCREMENT);
 
     unsigned long pulTotalProcessingTime = 0;

INCHI-1-TEST/tests/test_unit/test_ichimake.cpp

@@ -0,0 +1,90 @@
+#include <gtest/gtest.h>
+#include <gmock/gmock.h>
+#include <unistd.h>
+#include <sys/stat.h>
+#include <fstream>
+#include <filesystem>
+#include <vector>
+
+extern "C"
+{
+#include "../../../INCHI-1-SRC/INCHI_BASE/src/ichimake.c"
+#include "../../../INCHI-1-SRC/INCHI_BASE/src/ichi_io.h"
+}
+
+TEST(test_ichimake, test_GetSp3RelRacAbs_none)
+{
+
+    INChI inchi = {0};
+    INChI_Stereo stereo = {0};
+
+    stereo.nNumberOfStereoCenters = 0;
+
+    // pINChI->bDeleted
+    // Stereo->nCompInv2Abs
+    // 0: No inversion (structure unchanged by inversion)
+    // Positive integer (>0): Indicates inversion changes the structure (normal/absolute stereo)
+    // Negative integer (<0): Indicates inversion changes the structure (inverted/absolute stereo)
+
+    //int GetSp3RelRacAbs(const INChI* pINChI, INChI_Stereo* Stereo);
+
+    int result = GetSp3RelRacAbs(&inchi, &stereo);
+
+    EXPECT_EQ(result, SP3_NONE);
+
+}
+
+TEST(test_ichimake, test_GetSp3RelRacAbs_sp3)
+{
+    INChI inchi = {0};
+    INChI_Stereo stereo = {0};
+
+    stereo.nNumberOfStereoCenters = 1;
+    stereo.nCompInv2Abs = 0;
+
+    int result = GetSp3RelRacAbs(&inchi, &stereo);
+
+    EXPECT_EQ(result, SP3_ONLY);
+}
+
+TEST(test_ichimake, test_GetSp3RelRacAbs_rel)
+{
+    INChI inchi = {0};
+    INChI_Stereo stereo = {0};
+
+    inchi.nFlags = INCHI_FLAG_REL_STEREO;
+    stereo.nNumberOfStereoCenters = 1;
+    stereo.nCompInv2Abs = 1;
+
+    int result = GetSp3RelRacAbs(&inchi, &stereo);
+
+    EXPECT_EQ(result, SP3_REL);
+}
+
+TEST(test_ichimake, test_GetSp3RelRacAbs_rac)
+{
+    INChI inchi = {0};
+    INChI_Stereo stereo = {0};
+
+    inchi.nFlags = INCHI_FLAG_RAC_STEREO;
+    stereo.nNumberOfStereoCenters = 1;
+    stereo.nCompInv2Abs = 1;
+
+    int result = GetSp3RelRacAbs(&inchi, &stereo);
+
+    EXPECT_EQ(result, SP3_RAC);
+}
+
+TEST(test_ichimake, test_GetSp3RelRacAbs_abs)
+{
+    INChI inchi = {0};
+    INChI_Stereo stereo = {0};
+
+    inchi.nFlags = 0x0111;
+    stereo.nNumberOfStereoCenters = 1;
+    stereo.nCompInv2Abs = 1;
+
+    int result = GetSp3RelRacAbs(&inchi, &stereo);
+
+    EXPECT_EQ(result, SP3_ABS);
+}