111 lines
3.4 KiB
Diff
111 lines
3.4 KiB
Diff
Patches taken from the rdkit fork at this commit (there version
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AvalonToolkit_2.0.6-pre.2):
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https://github.com/rdkit/ava-formake/commit/d05bee0382b8f4696b2b4b05b0038fb7d559520a
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diff -ur a/src/main/C/common/reaccsio.c b/src/main/C/common/reaccsio.c
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--- a/src/main/C/common/reaccsio.c
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+++ b/src/main/C/common/reaccsio.c
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@@ -322,34 +322,49 @@
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fprintf(fp,"\n");
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}
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+#define MAX_BONDLINE_FIELDS 7
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+#define BONDLINE_FIELD_LEN 3
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+
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int ReadREACCSBond(Fortran_FILE *fp, struct reaccs_bond_t *bp)
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{
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- int nitems, i;
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- char buffer[MAX_BUFFER+1];
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+ int nitems, i, j, k;
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+ int bond_line_len, n_chars, pos;
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+ int *ptrarray[MAX_BONDLINE_FIELDS];
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+ char c;
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+ char buffer[BONDLINE_FIELD_LEN+1];
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if (fp->status != FORTRAN_NORMAL) return(fp->status);
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- strncpy(buffer,fp->buffer,MAX_BUFFER);
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- /* zero pad only atom numbers! */
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- for (i=0; i<6; i++) if (buffer[i] == ' ') buffer[i] = '0';
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-
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bp->stereo_symbol = 0;
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bp->dummy = 0;
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bp->topography = 0;
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bp->reaction_mark = NONE;
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- // make sure spaces are interpreted the Fortran-way
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- for (i=9; i<strlen(buffer) && i<21; i+=3)
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- {
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- if ((i+1)<strlen(buffer) && buffer[i+1]==' ') buffer[i+1] = '0';
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- if ((i+2)<strlen(buffer) && buffer[i+2]==' ') buffer[i+2] = '0';
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+ ptrarray[0] = &bp->atoms[0];
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+ ptrarray[1] = &bp->atoms[1];
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+ ptrarray[2] = &bp->bond_type;
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+ ptrarray[3] = &bp->stereo_symbol;
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+ ptrarray[4] = &bp->dummy;
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+ ptrarray[5] = &bp->topography;
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+ ptrarray[6] = &bp->reaction_mark;
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+ bond_line_len = strlen(fp->buffer);
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+ nitems = bond_line_len ? (bond_line_len - 1) / BONDLINE_FIELD_LEN + 1 : 0;
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+ if (nitems > MAX_BONDLINE_FIELDS)
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+ nitems = MAX_BONDLINE_FIELDS;
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+ for (i = 0; i < nitems; ++i)
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+ {
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+ pos = i * BONDLINE_FIELD_LEN;
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+ memset(buffer, 0, BONDLINE_FIELD_LEN + 1);
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+ n_chars = bond_line_len - pos;
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+ if (n_chars > BONDLINE_FIELD_LEN)
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+ n_chars = BONDLINE_FIELD_LEN;
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+ for (j = 0, k = 0; j < n_chars; ++j)
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+ {
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+ c = fp->buffer[pos + j];
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+ if (c != ' ')
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+ buffer[k++] = c;
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+ }
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+ sscanf(buffer, "%3d", ptrarray[i]);
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}
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- nitems = sscanf(buffer,
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- "%3d%3d%3d%3d%3d%3d%3d",
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- &bp->atoms[0], &bp->atoms[1],
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- &bp->bond_type, &bp->stereo_symbol,
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- &bp->dummy,
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- &bp->topography, &bp->reaction_mark);
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-
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if (nitems >= 3)
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{
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GetBuffer(fp);
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@@ -1582,6 +1597,8 @@
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PrintREACCSMolecule(fp, mp,"");
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+ fputc('\0', fp);
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+ fflush(fp);
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rewind(fp);
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MolStr = _ReadFile(fp);
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diff -ur a/src/main/C/programs/struchk.c b/src/main/C/programs/struchk.c
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--- a/src/main/C/programs/struchk.c
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+++ b/src/main/C/programs/struchk.c
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@@ -1581,6 +1581,22 @@
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if ((result & SIZE_CHECK_FAILED) == 0)
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{
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+ for (i = 0; i < mp->n_bonds; ++i) {
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+ for (j = 0; j < 2; ++j) {
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+ if (mp->bond_array[i].atoms[j] < 1 || mp->bond_array[i].atoms[j] > mp->n_atoms)
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+ {
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+ snprintf(msg_buffer, MAXMSG,
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+ "%10s : illegal atom # (%d, max allowed is %d) in bond %d",
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+ mp->name, mp->bond_array[i].atoms[j], mp->n_atoms, i + 1);
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+ AddMsgToList(msg_buffer);
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+ result |= SIZE_CHECK_FAILED;
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+ }
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+ }
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+ }
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+ }
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+
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+ if ((result & SIZE_CHECK_FAILED) == 0)
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+ {
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if (convert_atom_texts)
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{
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tmp = ConvertAtomAliases(mp);
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