Attribute table was not updated correctly after revert. Fixed.

[molby/Molby.git] / MolLib / Molecule.c

diff --git a/MolLib/Molecule.c b/MolLib/Molecule.c
index 52d3bfa..0d29d5c 100755 (executable)
--- a/MolLib/Molecule.c
+++ b/MolLib/Molecule.c
@@ -1045,7 +1045,7 @@ MoleculeLoadMbsfFile(Molecule *mp, const char *fname, char **errbuf)
                                        if (iibuf[0] < 0 || iibuf[0] >= mp->natoms || iibuf[1] < 0 || iibuf[1] >= mp->natoms || iibuf[2] < 0 || iibuf[2] >= mp->natoms || iibuf[0] == iibuf[1] || iibuf[1] == iibuf[2]) {
                                                s_append_asprintf(errbuf, "line %d: warning: bad angle specification (%d-%d-%d) - skipped\n", lineNumber, iibuf[0], iibuf[1], iibuf[2]);
                                                nwarnings++;
-                                       } else if (MoleculeAreAtomsConnected(mp, iibuf[0], iibuf[1]) == 0 || MoleculeAreAtomsConnected(mp, iibuf[1], iibuf[2]) == 0) {
+                                       } else if (MoleculeAreAtomsConnected(mp, iibuf[1], iibuf[0]) == 0 || MoleculeAreAtomsConnected(mp, iibuf[1], iibuf[2]) == 0) {
                                                s_append_asprintf(errbuf, "line %d: warning: angle with non-bonded atoms (%d-%d-%d) - skipped\n", lineNumber, iibuf[0], iibuf[1], iibuf[2]);
                                                nwarnings++;                                            
                                        } else if (MoleculeLookupAngle(mp, iibuf[0], iibuf[1], iibuf[2]) >= 0) {
@@ -1077,7 +1077,7 @@ MoleculeLoadMbsfFile(Molecule *mp, const char *fname, char **errbuf)
                                        if (iibuf[0] < 0 || iibuf[0] >= mp->natoms || iibuf[1] < 0 || iibuf[1] >= mp->natoms || iibuf[2] < 0 || iibuf[2] >= mp->natoms || iibuf[3] < 0 || iibuf[3] >= mp->natoms || iibuf[0] == iibuf[1] || iibuf[1] == iibuf[2] || iibuf[2] == iibuf[3] || iibuf[0] == iibuf[2] || iibuf[1] == iibuf[3] || iibuf[0] == iibuf[3]) {
                                                s_append_asprintf(errbuf, "line %d: warning: bad dihedral specification (%d-%d-%d-%d) - skipped\n", lineNumber, iibuf[0], iibuf[1], iibuf[2], iibuf[3]);
                                                nwarnings++;
-                                       } else if (MoleculeAreAtomsConnected(mp, iibuf[0], iibuf[1]) == 0 || MoleculeAreAtomsConnected(mp, iibuf[1], iibuf[2]) == 0 || MoleculeAreAtomsConnected(mp, iibuf[2], iibuf[3]) == 0) {
+                                       } else if (MoleculeAreAtomsConnected(mp, iibuf[1], iibuf[0]) == 0 || MoleculeAreAtomsConnected(mp, iibuf[1], iibuf[2]) == 0 || MoleculeAreAtomsConnected(mp, iibuf[2], iibuf[3]) == 0) {
                                                s_append_asprintf(errbuf, "line %d: warning: dihedral with non-bonded atoms (%d-%d-%d-%d) - skipped\n", lineNumber, iibuf[0], iibuf[1], iibuf[2], iibuf[3]);
                                                nwarnings++;                                            
                                        } else if (MoleculeLookupDihedral(mp, iibuf[0], iibuf[1], iibuf[2], iibuf[3]) >= 0) {
@@ -1109,7 +1109,7 @@ MoleculeLoadMbsfFile(Molecule *mp, const char *fname, char **errbuf)
                                        if (iibuf[0] < 0 || iibuf[0] >= mp->natoms || iibuf[1] < 0 || iibuf[1] >= mp->natoms || iibuf[2] < 0 || iibuf[2] >= mp->natoms || iibuf[3] < 0 || iibuf[3] >= mp->natoms || iibuf[0] == iibuf[1] || iibuf[1] == iibuf[2] || iibuf[2] == iibuf[3] || iibuf[0] == iibuf[2] || iibuf[1] == iibuf[3] || iibuf[0] == iibuf[3]) {
                                                s_append_asprintf(errbuf, "line %d: warning: bad improper specification (%d-%d-%d-%d) - skipped\n", lineNumber, iibuf[0], iibuf[1], iibuf[2], iibuf[3]);
                                                nwarnings++;
-                                       } else if (MoleculeAreAtomsConnected(mp, iibuf[0], iibuf[2]) == 0 || MoleculeAreAtomsConnected(mp, iibuf[1], iibuf[2]) == 0 || MoleculeAreAtomsConnected(mp, iibuf[2], iibuf[3]) == 0) {
+                                       } else if (MoleculeAreAtomsConnected(mp, iibuf[2], iibuf[0]) == 0 || MoleculeAreAtomsConnected(mp, iibuf[2], iibuf[1]) == 0 || MoleculeAreAtomsConnected(mp, iibuf[2], iibuf[3]) == 0) {
                                                s_append_asprintf(errbuf, "line %d: warning: improper with non-bonded atoms (%d-%d-%d-%d) - skipped\n", lineNumber, iibuf[0], iibuf[1], iibuf[2], iibuf[3]);
                                                nwarnings++;                                            
                                        } else if (MoleculeLookupImproper(mp, iibuf[0], iibuf[1], iibuf[2], iibuf[3]) >= 0) {
@@ -6624,8 +6624,10 @@ MoleculeAmendBySymmetry(Molecule *mp, IntGroup *group, IntGroup **groupout, Vect
                        free(vp);
                }
        } else {
-               *groupout = NULL;
-               *vpout = NULL;
+               if (groupout != NULL && vpout != NULL) {
+                       *groupout = NULL;
+                       *vpout = NULL;
+               }
        }
        return count;
 }
@@ -6828,11 +6830,18 @@ MoleculeCreateAnAtom(Molecule *mp, const Atom *ap, int pos)
                for (i = 0, api = ATOM_AT_INDEX(mp->atoms, i); i < mp->natoms; i++, api = ATOM_NEXT(api)) {
                        int j;
                        Int *cp;
+                       cp = AtomConnectData(&api->connect);
                        for (j = 0; j < api->connect.count; j++) {
-                               cp = AtomConnectData(&api->connect);
                                if (cp[j] >= pos)
                                        cp[j]++;
                        }
+                       if (api->anchor != NULL) {
+                               cp = AtomConnectData(&api->anchor->connect);
+                               for (j = 0; j < api->anchor->connect.count; j++) {
+                                       if (cp[j] >= pos)
+                                               cp[j]++;
+                               }
+                       }
                }
                for (i = 0; i < mp->nbonds * 2; i++) {
                        if (mp->bonds[i] >= pos)