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gnu: avalon-toolkit: Update to 2.0.5a.

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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>
This commit is contained in:
David Elsing 2024-01-28 23:02:00 +00:00 • committed by Christopher Baines
parent baa711441a
commit 52cca41c6f
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3 changed files with 166 additions and 77 deletions
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110
gnu/packages/patches/avalon-toolkit-rdkit-fixes.patch Normal file
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@ -0,0 +1,110 @@
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);