PDB-Profiling: a programmatic interface integrating rich metadata of protein structures with flexible data accessibility

version: 0.3.3

Incorporating features from large-scale genome studies with precise molecular phenotypes still poses a challenging task in the context of data accessibility and flexibility. Many tools have been developed to provide genomic-protein coordinates mapping portal and integrate various functions, but within some specific datasets and go no further than displaying features and perform some in-house analysis which obstacles further batch analysis. PDB-Profiling, a programmatic interface, offers a broader range of metadata collected in real-time to perform accurate identifier-level or residue-level mapping of protein structures while organizing annotations at the same time. It also can retrieve the best-quality representative structure set of a target protein or protein-pair with collected features and introduced bs-score that contribute to scoring and ranking.

PDB-Profiling is released as a Python package with a command-line interface. It can be used as a Python module or command-line tool. The documentation and source code are freely available at https://github.com/naturegeorge/pdb-profiling.

Sync With PyPI: better fix_range

🤹‍♂️towards v0.2.12 (#13)

* 🐎standardize e-r-m output

* 🐃fix bug report

* 🧶add header for unp api

* strange

* 🦺Impl UniProtTXT

* 🎫add SMRModel table

* 🛒add MappedMutation table

* 🧦fix err

* 🎃fix stream_txt retry

* 🧶check whether uniprot api recover

* 🤹‍♂️towards v0.2.12

Sync With PyPI: With Selected Residue-Mapping Results

0.2.10

🧭del init command

Sync With PyPI: Impl Cy & Trim Edge

0.2.7

🚦v0.2.7a1

Sync With PyPI: Command Line Update & API Update

pdb_id = '3hl2'
PDB(pdb_id).fetch_from_rcsb_data_api(
        'graphql',
        query='{entry(entry_id:"%s"){rcsb_entry_container_identifiers{assembly_ids}}}' % pdb_id,
        then_func=a_load_json,
        json=True).result()

Sync With PyPI: Latest Update

0.1.16

🎶Fix Bugs & Prepare for docs

Sync With PyPI: Implement Score&Sele (fix import error)

0.1.8a0

✈Implement new Score&Select (Single only)

Sync With PyPI: Implement Score&Sele

from pdb_profiling.processors import SIFTS, SIFTSs
SIFTS('O15350').pipe_select_mo().result()

SIFTSs(('O15350', 'O15350-2', 'Q8N2K1-3')).fetch('pipe_select_mo').run().result()

Sync With PyPI: Implement Chain Stats

pec_df, nec_df = PDB('2hvr').stats_chain().result()

Sync With PyPI: Implement More API

Examples

EutilsAPI

EutilsAPI.single_retrieve('efetch.fcgi', dict(db='sequences', id='NP_689699.2', rettype='fasta'), yourfolder, Base.get_web_semaphore()).then(a_seq_reader).result()