52cca41c6f
The bug freeing static memory and the makefile have been improved upstream, so we don't have to work around them anymore. Now, two static libraries are built instead. * gnu/packages/chemistry.scm (avalon-toolkit): Update to 2.0.5a. [source]: Switch to git reference from GitHub. Adjust snippet. Add patch from the RDKit fork. [arguments]: Remove 'dont-free-static-memory phase. Use provided makefile. Adjust 'install phase. * gnu/packages/patches/avalon-toolkit-rdkit-fixes.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. Signed-off-by: Christopher Baines <mail@cbaines.net>
111 lines
3.4 KiB
Diff
111 lines
3.4 KiB
Diff
Patches taken from the rdkit fork at this commit (there version
|
|
AvalonToolkit_2.0.6-pre.2):
|
|
https://github.com/rdkit/ava-formake/commit/d05bee0382b8f4696b2b4b05b0038fb7d559520a
|
|
|
|
diff -ur a/src/main/C/common/reaccsio.c b/src/main/C/common/reaccsio.c
|
|
--- a/src/main/C/common/reaccsio.c
|
|
+++ b/src/main/C/common/reaccsio.c
|
|
@@ -322,34 +322,49 @@
|
|
fprintf(fp,"\n");
|
|
}
|
|
|
|
+#define MAX_BONDLINE_FIELDS 7
|
|
+#define BONDLINE_FIELD_LEN 3
|
|
+
|
|
int ReadREACCSBond(Fortran_FILE *fp, struct reaccs_bond_t *bp)
|
|
{
|
|
- int nitems, i;
|
|
- char buffer[MAX_BUFFER+1];
|
|
+ int nitems, i, j, k;
|
|
+ int bond_line_len, n_chars, pos;
|
|
+ int *ptrarray[MAX_BONDLINE_FIELDS];
|
|
+ char c;
|
|
+ char buffer[BONDLINE_FIELD_LEN+1];
|
|
|
|
if (fp->status != FORTRAN_NORMAL) return(fp->status);
|
|
|
|
- strncpy(buffer,fp->buffer,MAX_BUFFER);
|
|
- /* zero pad only atom numbers! */
|
|
- for (i=0; i<6; i++) if (buffer[i] == ' ') buffer[i] = '0';
|
|
-
|
|
bp->stereo_symbol = 0;
|
|
bp->dummy = 0;
|
|
bp->topography = 0;
|
|
bp->reaction_mark = NONE;
|
|
- // make sure spaces are interpreted the Fortran-way
|
|
- for (i=9; i<strlen(buffer) && i<21; i+=3)
|
|
- {
|
|
- if ((i+1)<strlen(buffer) && buffer[i+1]==' ') buffer[i+1] = '0';
|
|
- if ((i+2)<strlen(buffer) && buffer[i+2]==' ') buffer[i+2] = '0';
|
|
+ ptrarray[0] = &bp->atoms[0];
|
|
+ ptrarray[1] = &bp->atoms[1];
|
|
+ ptrarray[2] = &bp->bond_type;
|
|
+ ptrarray[3] = &bp->stereo_symbol;
|
|
+ ptrarray[4] = &bp->dummy;
|
|
+ ptrarray[5] = &bp->topography;
|
|
+ ptrarray[6] = &bp->reaction_mark;
|
|
+ bond_line_len = strlen(fp->buffer);
|
|
+ nitems = bond_line_len ? (bond_line_len - 1) / BONDLINE_FIELD_LEN + 1 : 0;
|
|
+ if (nitems > MAX_BONDLINE_FIELDS)
|
|
+ nitems = MAX_BONDLINE_FIELDS;
|
|
+ for (i = 0; i < nitems; ++i)
|
|
+ {
|
|
+ pos = i * BONDLINE_FIELD_LEN;
|
|
+ memset(buffer, 0, BONDLINE_FIELD_LEN + 1);
|
|
+ n_chars = bond_line_len - pos;
|
|
+ if (n_chars > BONDLINE_FIELD_LEN)
|
|
+ n_chars = BONDLINE_FIELD_LEN;
|
|
+ for (j = 0, k = 0; j < n_chars; ++j)
|
|
+ {
|
|
+ c = fp->buffer[pos + j];
|
|
+ if (c != ' ')
|
|
+ buffer[k++] = c;
|
|
+ }
|
|
+ sscanf(buffer, "%3d", ptrarray[i]);
|
|
}
|
|
- nitems = sscanf(buffer,
|
|
- "%3d%3d%3d%3d%3d%3d%3d",
|
|
- &bp->atoms[0], &bp->atoms[1],
|
|
- &bp->bond_type, &bp->stereo_symbol,
|
|
- &bp->dummy,
|
|
- &bp->topography, &bp->reaction_mark);
|
|
-
|
|
if (nitems >= 3)
|
|
{
|
|
GetBuffer(fp);
|
|
@@ -1582,6 +1597,8 @@
|
|
|
|
PrintREACCSMolecule(fp, mp,"");
|
|
|
|
+ fputc('\0', fp);
|
|
+ fflush(fp);
|
|
rewind(fp);
|
|
|
|
MolStr = _ReadFile(fp);
|
|
diff -ur a/src/main/C/programs/struchk.c b/src/main/C/programs/struchk.c
|
|
--- a/src/main/C/programs/struchk.c
|
|
+++ b/src/main/C/programs/struchk.c
|
|
@@ -1581,6 +1581,22 @@
|
|
|
|
if ((result & SIZE_CHECK_FAILED) == 0)
|
|
{
|
|
+ for (i = 0; i < mp->n_bonds; ++i) {
|
|
+ for (j = 0; j < 2; ++j) {
|
|
+ if (mp->bond_array[i].atoms[j] < 1 || mp->bond_array[i].atoms[j] > mp->n_atoms)
|
|
+ {
|
|
+ snprintf(msg_buffer, MAXMSG,
|
|
+ "%10s : illegal atom # (%d, max allowed is %d) in bond %d",
|
|
+ mp->name, mp->bond_array[i].atoms[j], mp->n_atoms, i + 1);
|
|
+ AddMsgToList(msg_buffer);
|
|
+ result |= SIZE_CHECK_FAILED;
|
|
+ }
|
|
+ }
|
|
+ }
|
|
+ }
|
|
+
|
|
+ if ((result & SIZE_CHECK_FAILED) == 0)
|
|
+ {
|
|
if (convert_atom_texts)
|
|
{
|
|
tmp = ConvertAtomAliases(mp);
|