search

biomadeira / pyPDBeREST

A python wrapper for the PDBe REST API
https://pypi.python.org/pypi/pyPDBeREST/0.1.0
Other
6 stars 1 forks source link

Update the config to match the 'latest' API changes #1

Open biomadeira opened 7 years ago

biomadeira commented 7 years ago

Since 17/Nov/2015, there were a few updates:

"You can see the list of changes below. Every attribute is preceded by a symbol which is either + (addition), - (removal) or ~ (modification)."

14/Mar/2016 Changelog 1.2 

/pdb/entry/molecules/  
/pdb/entry/entities/  
    + pdb_sequence  
    + pdb_sequence_indices_with_multiple_residues  
/pdb/entry/polymer_coverage/:pdbid/chain/:chainid  
    + new call  
/pdb/entry/observed_residues_ratio/  
    + new call  
/mappings/uniprot_to_pfam/  
    + new call

15/Aug/2016 Changelog 1.3 

/pdb/entry/assembly  
    + new call  
/mappings/uniprot_segments  
    + new call

30/Nov/2016 Changelog EMDB endpoints

The EMDB call 'analysis' has been updated: some string will become numbers. The fields modified are: 'fsc' section ('x', 'y', 'threshold_x', 'threshold_half_bit', 'threshold_3_sigma'), 'sample_weight', and 'volume_based_on_weight'.
Additionally, we fixed a bug in the FSC that caused some duplication in the 'x' values.

05/Apr/2017 Changelog 1.4 

/validation/nmr_cyrange_cores/entry  
    + new call  
/validation/nmr_ensemble_clustering/entry  
    + new call  
/pdb/entry/electron_density_statistics  
    + new call  
/mappings/isoforms/  
    + new call  
/mappings/all_isoforms/  
    + new call  
/mappings/uniref90/  
    + new call  
/mappings/homologene_uniref90/  
    + new call

10/May/2017 Changelog 1.5 

/pdb/entry/files/  
    ~ addition of 'map' category
biomadeira commented 7 years ago

Bump API version to 1.2 https://github.com/biomadeira/pyPDBeREST/commit/51d3440a51c6f4a4088fdf36beb292bb08fa2ac3 Bump API version to 1.3 https://github.com/biomadeira/pyPDBeREST/commit/871c46a3b94fcd0c1d4ac2286ecf7429cd1a8048 Bump API version to 1.4 https://github.com/biomadeira/pyPDBeREST/commit/0f04e5f4378aa3b9e5220773c4cce5d95220485c Bump API version to 1.5 https://github.com/biomadeira/pyPDBeREST/commit/0c72239307a5cb14223da1d069bf07e23afd8d07

biomadeira commented 6 years ago

06/Nov/2017 Changelog 1.7 

/pdb/entry/assembly
    + polymeric_count field

/pdb/entry/experiment/
    ~ specimen_preparation (dictionary -> list of dictionaries)

/mappings/ensembl/
    + new call

/mappings/
    ~ Ensembl mappings added

/pdb/entry/related_publications/
    ~ uniprot_publications section added

07/Mar/2018 Changelog 1.7 

/validation/rama_sidechain_listing/entry/
    ~ cis_peptide field added

/pdb/entry/related_experiment_data/
    + new call

/nucleic_mappings/
    + new call

/nucleic_mappings/rfam/
    + new call

/nucleic_mappings/sequence_domains/
    + new call

/compound/cofactors
    + new call

/compound/cofactors/het/:id
    + new call

/compound/mappings/:id
    + new call

/pdb/entry/drugbank/:pdbid
    + new call

/pdb/entry/cofactor/:pdbid
    + new call

/mappings/hmmer/
    + new call

/mappings/
    ~ HMMER mappings added

09/Aug/2018 Changelog 1.8 

/mappings/hmmer/
   + description field added.

/mappings/all_isoforms/
   + is_canonical field added (true if the UniProt sequence is the canonical
   one, false otherwise).
   + The call now accepts UniProt accessions as input, including isoforms
   (e.g. P83949-5).

/pdb/entry/related_publications/
   + UniProt accession added to uniprot_publications.

/mappings/
/mappings/pfam/
   + coverage field added for Pfam mappings.