diff options
Diffstat (limited to 'gnu/packages/patches')
| -rw-r--r-- | gnu/packages/patches/avalon-toolkit-rdkit-fixes.patch | 110 |
1 files changed, 110 insertions, 0 deletions
diff --git a/gnu/packages/patches/avalon-toolkit-rdkit-fixes.patch b/gnu/packages/patches/avalon-toolkit-rdkit-fixes.patch new file mode 100644 index 0000000000..c93a9869ed --- /dev/null +++ b/gnu/packages/patches/avalon-toolkit-rdkit-fixes.patch @@ -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); |