- changed compound::is_known_peptide/is_know_base
- Add audit_conform only if file is really valid - Added reconstruction code for PDBx
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test/reconstruct/1cbs-stripped-2.cif
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test/reconstruct/1cbs-stripped.cif
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test/reconstruct/cif2fasta-1cbs_insert.cif
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test/reconstruct/cif2fasta-1cbs_mutate.cif
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test/reconstruct/phenix.cif
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test/reconstruction-test.cpp
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