kripodb.dive

kripodb.dive.dense_dump(inputfile, outputfile, frag1only)

Dump dense matrix with zeros included

Parameters:

• inputfile (str) – Filename of dense similarity matrix
• outputfile (file) – Writeable file object
• frag1only (bool) – Only dump frag1 fragments

Returns:

kripodb.dive.dense_dump_iter(matrix, frag1only)

Iterate dense matrix with zeros

Parameters:

• matrix (FrozenSimilarityMatrix) – Dense similarity matrix
• frag1only (bool) – True to iterate over *frag1 only

Yields:

(str, str, float) – Fragment label pair and score

kripodb.dive.dive_export(fragmentsdb, uniprot_annot, pdbtags, propnames, props)

Writes metdata props for DiVE visualization

Parameters:

• fragmentsdb (str) – Filename fo fragments db file
• uniprot_annot (file) – Readable file object with uniprot gene and family mapping as tsv
• pdbtags (list) – List of readable file objects to tag pdb by filename
• propnames (file) – Writable file object to write prop names to
• props (file) – Writeable file object to write props to

kripodb.dive.dive_sphere(inputfile, outputfile, onlyfrag1)

Export fragments as DiVE formatted sphere

Parameters:

• inputfile (str) – fragments db input file
• outputfile (file) – fragments dive output file
• onlyfrag1 (bool) – Only *_frag1