Ecosyste.ms: Issues

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GitHub / DeepRank/pdb2sql issues and pull requests

#87 - pdb2sql.transform.rot_mat does not allow to set center

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

#86 - Refactor StructureSimilarity

Issue - State: open - Opened by NicoRenaud over 1 year ago - 2 comments
Labels: stale

#85 - compute_lrmsd_pdb2sql works only if there is no missing backbone atom

Issue - State: open - Opened by FarzanehParizi over 1 year ago - 9 comments
Labels: stale

#84 - add pdb matching function

Issue - State: open - Opened by LilySnow almost 2 years ago - 1 comment
Labels: stale

#83 - pdb2sql selects one alternative location for atoms

Issue - State: open - Opened by FarzanehParizi almost 2 years ago - 3 comments
Labels: stale

#82 - Fix lrmsd

Pull Request - State: closed - Opened by NicoRenaud almost 2 years ago - 3 comments
Labels: stale

#81 - Make the format of the PDB flexible so that we can read ZDOCK file

Pull Request - State: closed - Opened by NicoRenaud almost 2 years ago - 4 comments
Labels: stale

#80 - Iss76 nico

Pull Request - State: closed - Opened by NicoRenaud almost 2 years ago - 5 comments
Labels: stale

#79 - allow compute_irmsd_fast to process multiple chain pdbs

Pull Request - State: closed - Opened by LilySnow almost 2 years ago - 3 comments
Labels: stale

#78 - the atom order is independent of the returned values, which should not be the case

Issue - State: closed - Opened by DTRademaker almost 2 years ago - 4 comments
Labels: stale

#77 - compute_irmsd_fast() and compute_irmsd_pdb2sql() give very different RMSD

Issue - State: closed - Opened by LilySnow almost 2 years ago - 1 comment

#76 - compute_irmsd_fast() only works on two chains

Issue - State: open - Opened by LilySnow almost 2 years ago - 6 comments

#74 - pdb line is longer than 80

Issue - State: closed - Opened by LilySnow about 2 years ago - 7 comments
Labels: stale

#73 - Getting different results for irmsd, if the chain identifiers are in different order

Issue - State: closed - Opened by Smarti92 about 2 years ago - 3 comments
Labels: stale

#72 - Update pdb2sqlcore.py

Pull Request - State: closed - Opened by DTRademaker over 2 years ago - 16 comments
Labels: stale

#71 - Update pdb2sqlcore.py

Pull Request - State: closed - Opened by DTRademaker over 2 years ago

#70 - CITATION.cff fix and automatic validation of your citation metadata

Pull Request - State: closed - Opened by abelsiqueira over 2 years ago

#69 - Fix python errors in doc

Issue - State: closed - Opened by CunliangGeng over 2 years ago - 1 comment

#68 - Fix a bug in StructureSimilarity.py

Pull Request - State: closed - Opened by DarioMarzella about 3 years ago - 1 comment

#67 - Update StructureSimilarity.py

Pull Request - State: closed - Opened by manonreau about 3 years ago

#66 - enable missing residues at the interface in the rmsd calc

Pull Request - State: closed - Opened by manonreau about 3 years ago - 4 comments

#65 - Upgrade to GitHub-native Dependabot

Pull Request - State: closed - Opened by dependabot-preview[bot] about 3 years ago - 1 comment
Labels: dependencies

#64 - Update compute_CapriClass conditions

Pull Request - State: closed - Opened by CunliangGeng over 3 years ago

#63 - wrong assignment of CAPRI classes

Issue - State: closed - Opened by taras-stx over 3 years ago - 3 comments

#62 - Move to github actions

Pull Request - State: closed - Opened by CunliangGeng over 3 years ago

#60 - remove hardcoded chainIDs from StructureSimilarity.py

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

#59 - Issue55

Pull Request - State: closed - Opened by CunliangGeng about 4 years ago

#56 - Update doc on structureSimilarity methods

Issue - State: closed - Opened by CunliangGeng about 4 years ago - 3 comments
Labels: stale

#55 - Please add backbone selection to compute_lrmsd_pdb2sql()

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

#54 - small grammar changes and minor bib fix

Pull Request - State: closed - Opened by danielskatz about 4 years ago

#53 - Update version

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

#52 - Issue51

Pull Request - State: closed - Opened by CunliangGeng about 4 years ago - 2 comments

#51 - many2pdb arguments type check

Issue - State: closed - Opened by CunliangGeng about 4 years ago

#50 - Issue49

Pull Request - State: closed - Opened by NicoRenaud about 4 years ago

#48 - Add Paths to test folder

Pull Request - State: closed - Opened by joaomcteixeira about 4 years ago - 3 comments

#47 - Tests fail or not found

Issue - State: closed - Opened by joaomcteixeira about 4 years ago - 2 comments

#46 - [WIP] Many2SQL

Pull Request - State: closed - Opened by NicoRenaud about 4 years ago

#45 - updated doc

Pull Request - State: closed - Opened by NicoRenaud about 4 years ago - 3 comments

#43 - Issue41 : returns class instance

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

#42 - fix potential bug of column names in sql2pdb

Pull Request - State: closed - Opened by CunliangGeng about 4 years ago

#41 - returns class instance

Issue - State: closed - Opened by NicoRenaud about 4 years ago

#40 - Issue35-39

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

#39 - update commit method to private

Issue - State: closed - Opened by CunliangGeng about 4 years ago

#38 - Update docstring of pdb2sql.exportpdb

Issue - State: closed - Opened by CunliangGeng about 4 years ago

#37 - Update documentation about HETATM

Issue - State: closed - Opened by CunliangGeng about 4 years ago

#36 - improve print

Issue - State: closed - Opened by CunliangGeng about 4 years ago

#35 - provide info for help(pdb2sql)

Issue - State: closed - Opened by CunliangGeng about 4 years ago

#34 - Issue30 33 path as input

Pull Request - State: closed - Opened by CunliangGeng about 4 years ago

#33 - minor typo documentation

Issue - State: closed - Opened by joaomcteixeira about 4 years ago

#32 - Allow pdb2sql to read string data

Issue - State: closed - Opened by joaomcteixeira about 4 years ago

#31 - Proper error message when fetching CIF files

Issue - State: closed - Opened by joaomcteixeira about 4 years ago

#30 - pdb2sql read Path from pathlib

Issue - State: closed - Opened by joaomcteixeira about 4 years ago

#29 - update doc with the new align feature

Issue - State: closed - Opened by LilySnow about 4 years ago - 5 comments
Labels: stale

#28 - Orient

Issue - State: closed - Opened by NicoRenaud over 4 years ago - 1 comment

#27 - [WIP] Align

Pull Request - State: closed - Opened by NicoRenaud over 4 years ago

#26 - Update paper doc

Pull Request - State: closed - Opened by CunliangGeng over 4 years ago

#25 - Solve issue 21-24 and related ones

Pull Request - State: closed - Opened by CunliangGeng over 4 years ago - 1 comment

#24 - CONTRIBUTING.rst is not for this project

Issue - State: closed - Opened by JoaoRodrigues over 4 years ago

#22 - Unclear warning messages on PDB read.

Issue - State: closed - Opened by JoaoRodrigues over 4 years ago

#21 - Installation: unused dependencies in setup.py

Issue - State: closed - Opened by JoaoRodrigues over 4 years ago

#20 - add new badges

Pull Request - State: closed - Opened by CunliangGeng over 4 years ago

#19 - Create .zenodo.json

Pull Request - State: closed - Opened by jspaaks over 4 years ago

#18 - Create CITATION.cff

Pull Request - State: closed - Opened by jspaaks over 4 years ago

#17 - Paper

Pull Request - State: closed - Opened by NicoRenaud over 4 years ago - 1 comment

#16 - Update docstrings

Pull Request - State: closed - Opened by CunliangGeng over 4 years ago

#15 - add doc

Pull Request - State: closed - Opened by CunliangGeng over 4 years ago

#14 - Unittest structure similarity

Pull Request - State: closed - Opened by CunliangGeng over 4 years ago

#13 - Unittest interface

Pull Request - State: closed - Opened by CunliangGeng over 4 years ago

#12 - Unittest pdb2sql

Pull Request - State: closed - Opened by CunliangGeng over 4 years ago

#11 - update pdb2sqlcore and add unittests

Pull Request - State: closed - Opened by CunliangGeng over 4 years ago

#10 - Add unit test for transform

Pull Request - State: closed - Opened by CunliangGeng over 4 years ago

#9 - Use Codacy (or other code quality check)

Issue - State: closed - Opened by NicoRenaud over 4 years ago - 1 comment

#8 - Update read and write

Pull Request - State: closed - Opened by CunliangGeng over 4 years ago - 2 comments

#7 - Just formatting of code

Pull Request - State: closed - Opened by CunliangGeng over 4 years ago

#6 - refactor with base class

Pull Request - State: closed - Opened by NicoRenaud almost 5 years ago

#5 - Continuous integration

Issue - State: closed - Opened by NicoRenaud almost 5 years ago - 1 comment

#4 - pytest failed

Issue - State: closed - Opened by LilySnow about 5 years ago - 4 comments

#3 - Multiple interface

Pull Request - State: closed - Opened by NicoRenaud over 5 years ago

#2 - Import (rename pdb2sql.py)

Issue - State: closed - Opened by NicoRenaud almost 6 years ago - 1 comment

#1 - shall we write an installation instruction in the README?

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