Parsing mmCIF crashes if struct_conn table present

[Tom Goddard]

Calling pdbio.parse_mmCIF_file() on 1a0m.cif from Python causes a crash due to an uncaught C++ exception, reported to the shell as

libc++abi.dylib: terminating with uncaught exception of type std::runtime_error: missing category: audit_conform on line 1065

There error does not seem to have anything to do with the audit_conform table. The file is parsed without errors if I remove the struct_conn table from 1a0m.cif. Also if I open a file without a struct_conn table such as 1a0k.cif then it works correctly. Also if I comment out

register_category("struct_conn",

[this] (bool in) {

parse_struct_conn(in/*_loop*/);

}, { "atom_site" });

in pdbio/pdbio/mmcif.cpp the files are read correctly. The error is not specific to 1a0m, any file with a struct_conn table crashes with the same error, for example, I tried 1jj2.cif.

[Greg Couch]

Fixed. Bug was in molecular library used to return molecules.

[Eric Pettersen]

reducing # of categories, so lumping into I/O category