mmtfPyspark.datasets.swissModelDataset module¶

References¶

• SWISS-MODEL API: https://swissmodel.expasy.org/docs/repository_help#smr_api
• Bienert S, Waterhouse A, de Beer TA, Tauriello G, Studer G, Bordoli L, Schwede T (2017). The SWISS-MODEL Repository - new features and functionality, Nucleic Acids Res. 45(D1):D313-D319. https://dx.doi.org/10.1093/nar/gkw1132
• Biasini M, Bienert S, Waterhouse A, Arnold K, Studer G, Schmidt T, Kiefer F, Gallo Cassarino T, Bertoni M, Bordoli L, Schwede T(2014). The SWISS-MODEL Repository - modelling protein tertiary and quaternary structure using evolutionary information, Nucleic Acids Res. 42(W1):W252–W258. https://doi.org/10.1093/nar/gku340

get_swiss_models(uniProtIds)[source]¶

Downloads metadata for SWISS-MODEL homology models for alist of UniProtIds. The original data schema is flatterened into a row-based schema.

Parameters:	uniProtIds : list list of UniProt Ids
Returns:	dataset SwissModel dataset

Examples

>>> uniProtIds = ["P36575", "P24539", "O00244"]
>>> ds = swissProtDataset.get_swiss_models(uniProtIds)
>>> ds.show()
+------+--------+----+---+-----+----------+----+--------+-----------+--------+--------+--------+----------+-----------+
|    ac|sequence|from| to|qmean|qmean_norm|gmqe|coverage|oligo-state|  method|template|identity|similarity|coordinates|
+------+--------+----+---+-----+----------+----+--------+-----------+--------+--------+-- -----+----------+-----------+
|P36575|MSKVF...|   2|371|-3.06|0.66345522|0.75|0.953608|    monomer|Homology|1suj.1.A|68.66484|0.50463312|https://...|
|P24539|MLSRV...|  76|249|-2.51|0.67113881|0.65|0.679687|    monomer|Homology|5ara.1.S|84.48275|0.54788881|https://...|
|O00244|MPKHE...|   1| 68| 1.04|0.84233218|0.98|     1.0| homo-2-mer|Homology|1fe4.1.A|   100.0|0.60686457|https://...|
+------+--------+----+---+-----+----------+----+--------+-----------+--------+--------+--------+----------+-----------+

get_swiss_models_raw_data(uniProtIds)[source]¶

Downloads the raw metadata for SWISS-MODEL homology models. This dataset is in the original data schema as downloaded from SWISS-MODEL.

Parameters:	uniProtIds : list list of UniProt Ids
Returns:	dataset SwissModel dataset in original data schema