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; iatoms[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); ts/publish.scm?id=37402ecb4379d7199dd4b3386488261938edc780'>tests: Use unbuffered input ports when decompressing from 'guix publish'....Ludovic Courtès 2016-07-20publish: Handle '/file' URLs, for content-addressed files....Ludovic Courtès 2016-07-19publish: Add '--compression'....Ludovic Courtès 2016-06-08publish: Encore URIs that appear in narinfos....Ludovic Courtès 2016-04-03build: Add a Guile custom test driver using SRFI-64....Mathieu Lirzin 2016-02-25publish: Do not publish nars for invalid store items....Ludovic Courtès 2016-01-22tests: Prevent 'http_proxy' from breaking Web server tests....Ludovic Courtès 2015-07-18tests: Fix 'publish' test for nix-base32 format....Alex Kost 2015-04-04scripts: Add 'publish' command....David Thompson