williamgilpin/pypdb issues and pull requests

#67 - pypdb is failing in [recent] jupyterlab notebook document

Issue - State: open - Opened by perllaghu 2 months ago - 1 comment

#66 - Ask for JSON to avoid HTTP 415 error.

Pull Request - State: closed - Opened by jbenjoseph 4 months ago

#65 - Add JSON Content-Type header to request

Pull Request - State: closed - Opened by ajm13 4 months ago

#64 - Remove pandas usage and dependency.

Pull Request - State: closed - Opened by jbenjoseph 7 months ago - 1 comment

#63 - how to search PDBID via smiles of ligands

Issue - State: open - Opened by jhxu003 11 months ago

#62 - Data module

Pull Request - State: closed - Opened by sodiumnitrate about 1 year ago - 2 comments

#61 - search by uniprot id

Pull Request - State: closed - Opened by echen1214 about 1 year ago - 3 comments

#60 - Irems updates

Pull Request - State: closed - Opened by sodiumnitrate about 1 year ago - 2 comments

#59 - Change 'is' to '==', RangeOperator now functioning

Pull Request - State: closed - Opened by jthornton-0 over 1 year ago - 1 comment

#58 - Added verbose bools to optionally suppress printing output to screen

Pull Request - State: closed - Opened by jthornton-0 over 1 year ago - 2 comments

#57 - Searching field which returns a list of words

Issue - State: closed - Opened by inthesomeday000 over 1 year ago - 1 comment

#56 - Searching via EC number

Issue - State: open - Opened by erfantoloue over 1 year ago

#55 - Adapt the describe_chemical function to the new api

Pull Request - State: closed - Opened by davidoskky over 1 year ago - 1 comment

#54 - AttributeError: 'NoneType' object has no attribute 'status_code'

Issue - State: closed - Opened by chuliangcui about 2 years ago - 3 comments

#53 - get_ligands

Issue - State: open - Opened by pauljmclaughlin about 2 years ago - 5 comments

#52 - RCSB Search API V1 has been removed

Issue - State: closed - Opened by noahharrison64 about 2 years ago - 2 comments

#51 - Negating Arbitrary Text Operators

Issue - State: open - Opened by tarungog over 2 years ago - 1 comment

#50 - Chemical description retrieval / new RCSB API

Issue - State: closed - Opened by zrqiao over 2 years ago - 4 comments

#49 - Access structure pH

Issue - State: closed - Opened by stepdasha over 2 years ago - 3 comments

#48 - TypeError: 'NoneType' object is not subscriptable AND json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)

Issue - State: closed - Opened by kfuku52 almost 3 years ago - 7 comments

#47 - fix basic search requests

Pull Request - State: closed - Opened by samuelstanton almost 3 years ago - 1 comment

#46 - Cannot perform the first query from the jupyter notebook

Issue - State: closed - Opened by YannRoussel about 3 years ago - 3 comments
Labels: bug, help wanted

#45 - Chain IDs

Issue - State: open - Opened by ynskoroglu about 3 years ago - 1 comment
Labels: enhancement

#44 - Problem with the search() function trying to run the examples.

Issue - State: closed - Opened by marcosleke about 3 years ago

#43 - Trouble with executing sample codes from section "New API for advanced search"

Issue - State: closed - Opened by marketapavlikova about 3 years ago - 2 comments

#42 - PyPDB for fetching .sdf (or .mol2) ligand coordinate

Issue - State: open - Opened by areyesromero over 3 years ago - 2 comments
Labels: enhancement, help wanted

#41 - Fixes small error in comparions types

Pull Request - State: closed - Opened by kalinni over 3 years ago - 2 comments

#40 - Fix small typo in README.md

Pull Request - State: closed - Opened by amorehead over 3 years ago - 1 comment

#39 - How to get ligand SMILES from Protein?

Issue - State: open - Opened by kexul over 3 years ago
Labels: enhancement, help wanted

#38 - RangeOperator dict needs updating

Issue - State: closed - Opened by dtriand over 3 years ago - 2 comments

#37 - [BugFix] Closes issue #36

Pull Request - State: closed - Opened by tux2603 almost 4 years ago

#36 - Calling search on a Query that returns no results causes an AttributeError exception to be raised

Issue - State: closed - Opened by tux2603 almost 4 years ago - 3 comments

#35 - [Bugfix] - Added chemical operator to search service inference function.

Pull Request - State: closed - Opened by lacoperon almost 4 years ago

#34 - [Formatting] - Formatted whole repo to follow PEP8 using YAPF

Pull Request - State: closed - Opened by lacoperon almost 4 years ago

#33 - [RCSB Search + PDB] - Added chemical search, fixed bug in pdb client

Pull Request - State: closed - Opened by lacoperon almost 4 years ago

#32 - Added chemical search, formatted all code files with YAPF

Pull Request - State: closed - Opened by lacoperon almost 4 years ago

#31 - [`get_pdb_file`] - Factored out `get_pdb_file` logic from `pypdb.py`.

Pull Request - State: closed - Opened by lacoperon almost 4 years ago - 1 comment

#30 - Get rid of `SearchService` and `QueryNode` concepts in Public Search API

Pull Request - State: closed - Opened by lacoperon almost 4 years ago - 2 comments

#29 - Implemented FASTA fetching, autoresolving sequence type for `SequenceOperator` searches

Pull Request - State: closed - Opened by lacoperon almost 4 years ago

#28 - [RCSB SeqMotif Search] - Implemented SeqMotif Search

Pull Request - State: closed - Opened by lacoperon almost 4 years ago

#27 - Implemented Sequence and Structure RCSB Search Services

Pull Request - State: closed - Opened by lacoperon almost 4 years ago - 1 comment

#26 - Trouble with the function get_blast

Issue - State: closed - Opened by Levi-Magny almost 4 years ago - 9 comments

#25 - Installation problems

Issue - State: closed - Opened by Talianash almost 4 years ago - 3 comments

#24 - [RCSB Search API] - Added support for `NOT_EQUAL` comparison type

Pull Request - State: closed - Opened by lacoperon almost 4 years ago

#23 - [RCSB Search: Text Service] - Added full support

Pull Request - State: closed - Opened by lacoperon almost 4 years ago - 3 comments

#22 - [RCSB Search] - Added support for "terminal" node queries against the Text search service

Pull Request - State: closed - Opened by lacoperon almost 4 years ago - 3 comments

#21 - [Testing/Bugfix] - Fixed pathing issues to allow for testing of PyPDB

Pull Request - State: closed - Opened by lacoperon almost 4 years ago - 4 comments

#20 - [API Refactor / Update] - Factored out HTTP Methods into separate file, added tests

Pull Request - State: closed - Opened by lacoperon almost 4 years ago - 2 comments

#19 - Can't Retrieve PDB Release Date

Issue - State: closed - Opened by inthesomeday000 almost 4 years ago - 3 comments

#18 - [Feature Request] Advanced search that pairs sequences with number of distinct entities

Issue - State: closed - Opened by williamgilpin almost 4 years ago - 4 comments

#17 - [API Refactor] - Would love to help

Issue - State: closed - Opened by lacoperon almost 4 years ago - 4 comments

#16 - get_all_info isn't working

Issue - State: closed - Opened by ynskoroglu almost 4 years ago - 6 comments

#15 - ETA on new release?

Issue - State: closed - Opened by jaimergp about 4 years ago - 7 comments

#14 - Fix for Requirements Missing 'Requests' Pkg

Pull Request - State: closed - Opened by rlangefe about 4 years ago - 1 comment

#13 - Searching

Issue - State: closed - Opened by Chokerino about 4 years ago - 8 comments

#12 - get_all_info results in TypeError

Issue - State: closed - Opened by Shkev over 4 years ago - 6 comments

#11 - Search by taxonomy

Issue - State: closed - Opened by mirix over 4 years ago - 8 comments

#10 - Getting BLAST scores from PyPDB

Issue - State: closed - Opened by danolson1 about 5 years ago - 2 comments

#9 - do_search gives bad pdbid's when using MotifQuery search

Issue - State: closed - Opened by GMC1997 over 5 years ago - 5 comments

#8 - get_pdb_file leads to broken link

Issue - State: closed - Opened by gustalima over 5 years ago - 3 comments

#7 - Adding instructions to compile the conda package

Pull Request - State: closed - Opened by dprada over 5 years ago - 3 comments

#6 - Adding PDB chain functionality: Chain Sequence, Chain Description, Chain Name, Taxonomy etc.

Issue - State: closed - Opened by lacoperon over 5 years ago - 1 comment

#5 - Add querytype for pubmed id search in make_query

Pull Request - State: closed - Opened by dataroo about 8 years ago - 2 comments

#4 - PDBs have 0 atoms

Issue - State: closed - Opened by dmyersturnbull over 8 years ago - 2 comments

#3 - find_authors() throws URLError: <urlopen error [Errno 60] Operation timed out>

Issue - State: closed - Opened by williamgilpin almost 9 years ago - 1 comment

#2 - KeyError when using list_types() and lists_taxa()

Issue - State: closed - Opened by williamgilpin almost 9 years ago - 1 comment

#1 - Add init file and alter import statements

Pull Request - State: closed - Opened by jonathan-wells almost 9 years ago - 2 comments

GitHub / williamgilpin/pypdb issues and pull requests