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To use the Avalon Toolkit support in the RDKit, first download a copy of the
source from:
http://sourceforge.net/projects/avalontoolkit/files/AvalonToolkit_1.1_beta/AvalonToolkit_1.1_beta.source.tar/download
Note that the version number is important.
Extract the tar file somewhere; the source requred by the RDKit is in
the SourceDistribution directory.
Apply the following diff to the files
SourceDistribution/common/reaccsio.c and
SourceDistribution/common/smi2mol.c:
$ diff SourceDistribution/common ~/avalontoolkit_beta/SourceDistribution/common
diff SourceDistribution/common/reaccsio.c /cygdrive/c/Users/glandrum/avalontoolkit_beta/SourceDistribution/common/reaccsio.c
1400d1399
<
1414c1413
< MyFree((char *)tempdir);
---
> //MyFree((char *)tempdir);
1433d1431
<
1443c1441
<
---
> fprintf(stderr," returning\n");
diff SourceDistribution/common/smi2mol.c /cygdrive/c/Users/glandrum/avalontoolkit_beta/SourceDistribution/common/smi2mol.c
936c936
< fprintf(stderr, "2: opening branch '%s'\n", tmp);
---
> /* fprintf(stderr, "2: opening branch '%s'\n", tmp); */
1012c1012
< fprintf(stderr, "closing branch '%s'\n", tmp);
---
> /* fprintf(stderr, "closing branch '%s'\n", tmp); */
1543c1543
< fprintf(stderr, ".{%s:%d}", mp->atom_array[ibranch].atext, ibranch+1);
---
> /*fprintf(stderr, ".{%s:%d}", mp->atom_array[ibranch].atext, ibranch+1);*/
1550c1550
< fprintf(stderr, "{%s:%d}", mp->atom_array[ibranch].atext, ibranch+1);
---
> /*fprintf(stderr, "{%s:%d}", mp->atom_array[ibranch].atext, ibranch+1);*/
1574c1574
< fprintf(stderr, "1: opening branch '%s'\n", num_buf);
---
> /*fprintf(stderr, "1: opening branch '%s'\n", num_buf);*/
1592c1592
< fprintf(stderr, "{%s:%d}", mp->atom_array[ibranch].atext, ibranch+1);
---
> /*fprintf(stderr, "{%s:%d}", mp->atom_array[ibranch].atext, ibranch+1);*/
1596c1596
< fprintf(stderr, "\n");
---
> /*fprintf(stderr, "\n");*/
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