.. _file_formats: Table of available file formats =============================== .. note:: If you would like your data format to appear in the table below, please contact us via `GitHub `_. The following table contains the various different file formats currently implemented in ConKit. *Type* The type of information the file contains *Format* The source of the file *Keyword* The keyword to be used in ConKit *Parser* Hyperlink to the documentation of the relevant parser .. rst-class:: table-hover +--------------------+------------------------+-----------------------------------------------------------+-------------------------------------------------+ | Type | Format | Keyword | Parser | +====================+========================+===========================================================+=================================================+ | Contact Prediction | Al-eigen | ``aleigen`` | :obj:`~conkit.io.aleigen.AleigenParser` | + +------------------------+-----------------------------------------------------------+-------------------------------------------------+ | | Bbcontacts | ``bbcontacts``:sup:`*` | :obj:`~conkit.io.bbcontacts.BbcontactsParser` | + +------------------------+-----------------------------------------------------------+-------------------------------------------------+ | | BCLContacts | ``bclcontacts``:sup:`*` | :obj:`~conkit.io.bclcontact.BCLContactParser` | + +------------------------+-----------------------------------------------------------+-------------------------------------------------+ | | Casp RR | ``casp``, ``casprr`` | :obj:`~conkit.io.casp.CaspParser` | + +------------------------+-----------------------------------------------------------+-------------------------------------------------+ | | CCMpred | ``ccmpred`` | :obj:`~conkit.io.ccmpred.CCMpredParser` | + +------------------------+-----------------------------------------------------------+-------------------------------------------------+ | | COMSAT | ``comsat`` | :obj:`~conkit.io.comsat.ComsatParser` | + +------------------------+-----------------------------------------------------------+-------------------------------------------------+ | | EPCMap | ``epcmap`` | :obj:`~conkit.io.epcmap.EPCMapParser` | + +------------------------+-----------------------------------------------------------+-------------------------------------------------+ | | EVfold (EVcouplings) | ``evfold`` | :obj:`~conkit.io.evfold.EVfoldParser` | + +------------------------+-----------------------------------------------------------+-------------------------------------------------+ | | Flib | ``flib`` | :obj:`~conkit.io.pcons.PconsParser` | + +------------------------+-----------------------------------------------------------+-------------------------------------------------+ | | FreeContact | ``freecontact`` | :obj:`~conkit.io.freecontact.FreeContactParser` | + +------------------------+-----------------------------------------------------------+-------------------------------------------------+ | | GREMLIN | ``gremlin`` | :obj:`~conkit.io.gremlin.GremlinParser` | + +------------------------+-----------------------------------------------------------+-------------------------------------------------+ | | map_align | ``mapalign`` | :obj:`~conkit.io.mapalign.MapAlignParser` | + +------------------------+-----------------------------------------------------------+-------------------------------------------------+ | | MemBrain | ``membrain`` | :obj:`~conkit.io.membrain.MemBrainParser` | + +------------------------+-----------------------------------------------------------+-------------------------------------------------+ | | mmCIF | ``mmcif``:sup:`*` | :obj:`~conkit.io.pdb.MmCifParser` | + +------------------------+-----------------------------------------------------------+-------------------------------------------------+ | | Ncont | ``ncont``:sup:`*` | :obj:`~conkit.io.ncont.NcontParser` | + +------------------------+-----------------------------------------------------------+-------------------------------------------------+ | | NeBcon | ``nebcon`` | :obj:`~conkit.io.psicov.PsicovParser` | + +------------------------+-----------------------------------------------------------+-------------------------------------------------+ | | Pcons[C|C2|C3] | ``pconsc``, ``pconsc2``, ``pconsc3`` | :obj:`~conkit.io.pcons.PconsParser` | + +------------------------+-----------------------------------------------------------+-------------------------------------------------+ | | Protein DataBank (PDB) | ``pdb``:sup:`*` | :obj:`~conkit.io.pdb.PdbParser` | + +------------------------+-----------------------------------------------------------+-------------------------------------------------+ | | plmDCA | ``plmdca`` | :obj:`~conkit.io.plmdca.PlmDCAParser` | + +------------------------+-----------------------------------------------------------+-------------------------------------------------+ | | [Meta]PSICOV | ``psicov``, ``metapsicov`` | :obj:`~conkit.io.psicov.PsicovParser` | + +------------------------+-----------------------------------------------------------+-------------------------------------------------+ | | Rosetta | ``rosetta``:sup:`+` | :obj:`~conkit.io.rosetta.RosettaParser` | + +------------------------+-----------------------------------------------------------+-------------------------------------------------+ | | SAINT2 | ``saint2`` | :obj:`~conkit.io.pcons.PconsParser` | +--------------------+------------------------+-----------------------------------------------------------+-------------------------------------------------+ | Distance Prediction| AlphaFold2 | ``alphafold2``:sup:`*` | :obj:`~conkit.io.alphafold.AlphaFold2Parser` | + +------------------------+-----------------------------------------------------------+-------------------------------------------------+ | | Casp RR Mode 2 | ``caspmode2`` | :obj:`~conkit.io.caspmode2.CaspMode2Parser` | + +------------------------+-----------------------------------------------------------+-------------------------------------------------+ | | MapPred | ``mappred`` | :obj:`~conkit.io.mappred.MapPredParser` | + +------------------------+-----------------------------------------------------------+-------------------------------------------------+ | | Rosetta NPZ | ``rosetta_npz``:sup:`*` | :obj:`~conkit.io.rosetta_npz.RosettaNpzParser` | +--------------------+------------------------+-----------------------------------------------------------+-------------------------------------------------+ | Sequence Alignment | A2M | ``a2m`` | :obj:`~conkit.io.a2m.A2mParser` | + +------------------------+-----------------------------------------------------------+-------------------------------------------------+ | | A3M | ``a3m``, ``a3m-inserts``:sup:`a` | :obj:`~conkit.io.a3m.A3mParser` | + +------------------------+-----------------------------------------------------------+-------------------------------------------------+ | | Clustal | ``clustal`` | :obj:`~conkit.io.clustal.ClustalParser` | + +------------------------+-----------------------------------------------------------+-------------------------------------------------+ | | FASTA | ``fasta`` | :obj:`~conkit.io.fasta.FastaParser` | + +------------------------+-----------------------------------------------------------+-------------------------------------------------+ | | Jones | ``jones`` :sup:`b` | :obj:`~conkit.io.a2m.A2mParser` | + +------------------------+-----------------------------------------------------------+-------------------------------------------------+ | | Stockholm | ``stockholm`` | :obj:`~conkit.io.stockholm.StockholmParser` | +--------------------+------------------------+-----------------------------------------------------------+-------------------------------------------------+ | :sup:`*` These formats do not have a :func:`~conkit.io.write` function. | | | | :sup:`+` These formats do not have a :func:`~conkit.io.read` function. | | | | :sup:`a` The ``a3m-inserts`` keyword stores the alignment including insert states. | | | | :sup:`b` The ``jones`` format corresponds to the HH-suite A2M format. | | | +--------------------+------------------------+-----------------------------------------------------------+-------------------------------------------------+