williamgilpin pypdb issues

williamgilpin / pypdb

A Python API for the RCSB Protein Data Bank (PDB)

MIT License

309 stars 77 forks source link

issues

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pypdb is failing in [recent] jupyterlab notebook document

#67 perllaghu opened 2 months ago
1
Ask for JSON to avoid HTTP 415 error.

#66 jbenjoseph closed 2 months ago
0
Add JSON Content-Type header to request

#65 ajm13 closed 2 months ago
0
Remove pandas usage and dependency.

#64 jbenjoseph closed 6 months ago
1
how to search PDBID via smiles of ligands

#63 jhxu003 opened 11 months ago
0
Data module

#62 sodiumnitrate closed 1 year ago
2
search by uniprot id

#61 echen1214 closed 1 year ago
3
Irems updates

#60 sodiumnitrate closed 1 year ago
2
Change 'is' to '==', RangeOperator now functioning

#59 jthornton-0 closed 1 year ago
1
Added verbose bools to optionally suppress printing output to screen

#58 jthornton-0 closed 1 year ago
2
Searching field which returns a list of words

#57 inthesomeday000 closed 1 year ago
1
Searching via EC number

#56 erfantoloue opened 1 year ago
0
Adapt the describe_chemical function to the new api

#55 davidoskky closed 1 year ago
1
AttributeError: 'NoneType' object has no attribute 'status_code'

#54 chuliangcui closed 2 years ago
3
get_ligands

#53 pauljmclaughlin opened 2 years ago
5
RCSB Search API V1 has been removed

#52 noahharrison64 closed 2 years ago
2
Negating Arbitrary Text Operators

#51 tarungog opened 2 years ago
1
Chemical description retrieval / new RCSB API

#50 zrqiao closed 1 year ago
4
Access structure pH

#49 stepdasha closed 6 months ago
3
TypeError: 'NoneType' object is not subscriptable AND json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)

#48 kfuku52 closed 1 year ago
7
fix basic search requests

#47 samuelstanton closed 2 years ago
1
Cannot perform the first query from the jupyter notebook

#46 YannRoussel closed 2 years ago
3
Chain IDs

#45 ynskoroglu opened 3 years ago
1
Problem with the search() function trying to run the examples.

#44 marcosleke closed 3 years ago
0
Trouble with executing sample codes from section "New API for advanced search"

#43 marketapavlikova closed 3 years ago
2
PyPDB for fetching .sdf (or .mol2) ligand coordinate

#42 areyesromero opened 3 years ago
2
Fixes small error in comparions types

#41 kalinni closed 3 years ago
2
Fix small typo in README.md

#40 amorehead closed 3 years ago
1
How to get ligand SMILES from Protein?

#39 kexul opened 3 years ago
0
RangeOperator dict needs updating

#38 dtriand closed 3 years ago
2
[BugFix] Closes issue #36

#37 tux2603 closed 3 years ago
0
Calling search on a Query that returns no results causes an AttributeError exception to be raised

#36 tux2603 closed 3 years ago
3
[Bugfix] - Added chemical operator to search service inference function.

#35 lacoperon closed 3 years ago
0
[Formatting] - Formatted whole repo to follow PEP8 using YAPF

#34 lacoperon closed 3 years ago
0
[RCSB Search + PDB] - Added chemical search, fixed bug in pdb client

#33 lacoperon closed 3 years ago
0
Added chemical search, formatted all code files with YAPF

#32 lacoperon closed 3 years ago
0
[`get_pdb_file`] - Factored out `get_pdb_file` logic from `pypdb.py`.

#31 lacoperon closed 3 years ago
1
Get rid of `SearchService` and `QueryNode` concepts in Public Search API

#30 lacoperon closed 3 years ago
2
Implemented FASTA fetching, autoresolving sequence type for `SequenceOperator` searches

#29 lacoperon closed 3 years ago
0
[RCSB SeqMotif Search] - Implemented SeqMotif Search

#28 lacoperon closed 3 years ago
0
Implemented Sequence and Structure RCSB Search Services

#27 lacoperon closed 3 years ago
1
Trouble with the function get_blast

#26 Levi-Magny closed 3 years ago
9
Installation problems

#25 Talianash closed 3 years ago
3
[RCSB Search API] - Added support for `NOT_EQUAL` comparison type

#24 lacoperon closed 3 years ago
0
[RCSB Search: Text Service] - Added full support

#23 lacoperon closed 3 years ago
3
[RCSB Search] - Added support for "terminal" node queries against the Text search service

#22 lacoperon closed 3 years ago
3
[Testing/Bugfix] - Fixed pathing issues to allow for testing of PyPDB

#21 lacoperon closed 3 years ago
4
[API Refactor / Update] - Factored out HTTP Methods into separate file, added tests

#20 lacoperon closed 3 years ago
2
Can't Retrieve PDB Release Date

#19 inthesomeday000 closed 3 years ago
3
[Feature Request] Advanced search that pairs sequences with number of distinct entities

#18 williamgilpin closed 3 years ago
4