The extra property values are now saved into the mbsf files.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@553 a2be9bc6-48de-4e38-9406-05402d4bc13c

diff --git a/MolLib/Molecule.c b/MolLib/Molecule.c
index 8330455..408d3f6 100755 (executable)
--- a/MolLib/Molecule.c
+++ b/MolLib/Molecule.c
@@ -344,6 +344,7 @@ MoleculeInitWithAtoms(Molecule *mp, const Atom *atoms, int natoms)
 Molecule *
 MoleculeInitWithMolecule(Molecule *mp2, Molecule *mp)
 {
+       int i, n;
        MoleculeFlushFrames(mp);
        MoleculeInitWithAtoms(mp2, mp->atoms, mp->natoms);
        if (mp->nbonds > 0) {
@@ -387,6 +388,17 @@ MoleculeInitWithMolecule(Molecule *mp2, Molecule *mp)
                memmove(mp2->frame_cells, mp->frame_cells, sizeof(Vector) * 4 * mp->nframe_cells);
        }
        
+       if (mp->nmolprops > 0) {
+               if (NewArray(&mp2->molprops, &mp2->nmolprops, sizeof(MolProp), mp->nmolprops) == NULL)
+                       goto error;
+               n = MoleculeGetNumberOfFrames(mp);
+               for (i = 0; i < mp2->nmolprops; i++) {
+                       mp2->molprops[i].propname = strdup(mp->molprops[i].propname);
+                       mp2->molprops[i].propvals = (Double *)malloc(sizeof(Double) * n);
+                       memcpy(mp2->molprops[i].propvals, mp->molprops[i].propvals, sizeof(Double) * n);
+               }
+       }
+       
        /* FIXME: should bset (basis set info) and elpot be duplicated or not?  */
 
        if (mp->par != NULL)
@@ -1639,6 +1651,48 @@ MoleculeLoadMbsfFile(Molecule *mp, const char *fname, char **errbuf)
                                }
                        }
                        continue;
+               } else if (strcmp(buf, "!:property") == 0) {
+                       char dec[1024];
+                       i = 0;
+                       bufp = buf + 13;
+                       while (*bufp != 0 && *bufp != '\n' && bufp < (buf + sizeof buf - 3)) {
+                               if (*bufp == '%') {
+                                       dec[i] = bufp[1];
+                                       dec[i + 1] = bufp[2];
+                                       dec[i + 2] = 0;
+                                       dec[i++] = strtol(dec, NULL, 16);
+                                       bufp += 3;
+                               } else {
+                                       dec[i++] = *bufp++;
+                               }
+                               if (i >= 1000)
+                                       break;
+                       }
+                       if (i == 0)
+                               continue;
+                       dec[i] = 0;
+                       i = MoleculeCreateProperty(mp, dec);
+                       if (i < 0) {
+                               s_append_asprintf(errbuf, "line %d: warning: duplicate molecular property %s - ignored\n", lineNumber, dec);
+                               nwarnings++;
+                               continue;
+                       }
+                       j = 0;
+                       while (ReadLine(buf, sizeof buf, fp, &lineNumber) > 0) {
+                               if (buf[0] == '!')
+                                       continue;
+                               if (buf[0] == '\n')
+                                       break;
+                               if (j >= nframes) {
+                                       s_append_asprintf(errbuf, "line %d: warning: too many molecular property %s - ignored\n", lineNumber, dec);
+                                       nwarnings++;
+                                       break;
+                               }
+                               dbuf[0] = strtod(buf, NULL);
+                               mp->molprops[i].propvals[j] = dbuf[0];
+                               j++;
+                       }
+                       continue;
                }
                /*  Unknown sections are silently ignored  */
        }
@@ -4295,6 +4349,40 @@ MoleculeWriteToMbsfFile(Molecule *mp, const char *fname, char **errbuf)
                fprintf(fp, "\n");
        }
 
+       if (mp->nmolprops > 0) {
+               MolProp *prp;
+               for (i = 0, prp = mp->molprops; i < mp->nmolprops; i++, prp++) {
+                       /*  Encode the property name if necessary  */
+                       char *p;
+                       char enc[1024];
+                       n1 = n2 = 0;
+                       for (p = prp->propname; *p != 0 && n1 < 900; p++) {
+                               if (*p > ' ' && *p != '%' && *p < 0x7f) {
+                                       enc[n1++] = *p;
+                                       n2 = n1;
+                               } else {
+                                       sprintf(enc + n1, "%%%02x", *p);
+                                       n1 += 3;
+                               }
+                       }
+                       if (*p == 0)
+                               enc[n1] = 0;
+                       else {
+                               enc[n2] = 0; /* Truncate after last ASCII character */
+                               n1 = n2;
+                       }
+                       if (n1 == 0) {
+                               sprintf(enc, "prop_%d", i + 1);
+                               n1 = strlen(enc);
+                       }
+                       fprintf(fp, "!:property ; %s\n", enc);
+                       for (j = 0; j < nframes; j++) {
+                               fprintf(fp, "%.18g\n", prp->propvals[j]);
+                       }
+                       fprintf(fp, "\n");
+               }
+       }
+       
        fclose(fp);
        return 0;
 }