DeepRank pdb2sql issues

DeepRank / pdb2sql

Fast and versatile biomolecular structure PDB file parser using SQL queries

https://pdb2sql.readthedocs.io

Apache License 2.0

24 stars 12 forks source link

issues

Newest

Newest Most commented Recently updated Oldest Least commented Least recently updated

superpose() does not work when chain IDs are different and the residue numbering are different

#88 LilySnow opened 2 months ago
0
pdb2sql.transform.rot_mat does not allow to set center

#87 LilySnow opened 1 year ago
0
Refactor StructureSimilarity

#86 NicoRenaud opened 2 years ago
2
compute_lrmsd_pdb2sql works only if there is no missing backbone atom

#85 FarzanehParizi opened 2 years ago
9
add pdb matching function

#84 LilySnow opened 2 years ago
1
pdb2sql selects one alternative location for atoms

#83 FarzanehParizi opened 2 years ago
3
Fix lrmsd

#82 NicoRenaud closed 1 year ago
3
Make the format of the PDB flexible so that we can read ZDOCK file

#81 NicoRenaud closed 2 years ago
4
Iss76 nico

#80 NicoRenaud closed 2 years ago
5
allow compute_irmsd_fast to process multiple chain pdbs

#79 LilySnow closed 2 years ago
3
the atom order is independent of the returned values, which should not be the case

#78 DTRademaker closed 2 years ago
4
compute_irmsd_fast() and compute_irmsd_pdb2sql() give very different RMSD

#77 LilySnow closed 2 years ago
1
compute_irmsd_fast() only works on two chains

#76 LilySnow opened 2 years ago
6
when superposing without defining the chainID, the error 'NameError: name 'warnings' is not defined', instead of printing the warning itself

#75 reneejoosten closed 2 years ago
3
pdb line is longer than 80

#74 LilySnow closed 2 years ago
7
Getting different results for irmsd, if the chain identifiers are in different order

#73 Smarti92 closed 2 years ago
3
Update pdb2sqlcore.py

#72 DTRademaker closed 2 years ago
16
Update pdb2sqlcore.py

#71 DTRademaker closed 2 years ago
0
CITATION.cff fix and automatic validation of your citation metadata

#70 abelsiqueira closed 2 years ago
0
Fix python errors in doc

#69 CunliangGeng closed 2 years ago
1
Fix a bug in StructureSimilarity.py

#68 DarioMarzella closed 3 years ago
1
Update StructureSimilarity.py

#67 manonreau closed 3 years ago
0
enable missing residues at the interface in the rmsd calc

#66 manonreau closed 3 years ago
4
Upgrade to GitHub-native Dependabot

#65 dependabot-preview[bot] closed 2 years ago
1
Update compute_CapriClass conditions

#64 CunliangGeng closed 3 years ago
0
wrong assignment of CAPRI classes

#63 taras-stx closed 3 years ago
3
Move to github actions

#62 CunliangGeng closed 3 years ago
0
Dependabot couldn't authenticate with https://pypi.python.org/simple/

#61 dependabot-preview[bot] closed 4 years ago
0
remove hardcoded chainIDs from StructureSimilarity.py

#60 CunliangGeng closed 4 years ago
0
Issue55

#59 CunliangGeng closed 4 years ago
0
StructureSimilarity "Matrix don't have the same number of points" between two matched files

#58 DarioMarzella closed 4 years ago
3
StructureSimilarity.compute_lrmsd_fast() and StructureSimilarity.compute_lrmsd_fast() provide different results

#57 DarioMarzella closed 2 years ago
3
Update doc on structureSimilarity methods

#56 CunliangGeng closed 2 years ago
3
Please add backbone selection to compute_lrmsd_pdb2sql()

#55 DarioMarzella closed 4 years ago
4
small grammar changes and minor bib fix

#54 danielskatz closed 4 years ago
0
Update version

#53 CunliangGeng closed 4 years ago
1
Issue51

#52 CunliangGeng closed 4 years ago
2
many2pdb arguments type check

#51 CunliangGeng closed 4 years ago
0
Issue49

#50 NicoRenaud closed 4 years ago
0
structure similarity fails if the chains are not called A and B

#49 NicoRenaud closed 4 years ago
0
Add Paths to test folder

#48 joaomcteixeira closed 4 years ago
3
Tests fail or not found

#47 joaomcteixeira closed 4 years ago
2
[WIP] Many2SQL

#46 NicoRenaud closed 4 years ago
0
updated doc

#45 NicoRenaud closed 4 years ago
3
compute_lrmsd_fast() does not report proper error message on pdb files with non-amino acids in ATOM section

#44 LilySnow closed 2 years ago
4
Issue41 : returns class instance

#43 NicoRenaud closed 4 years ago
1
fix potential bug of column names in sql2pdb

#42 CunliangGeng closed 4 years ago
0
returns class instance

#41 NicoRenaud closed 4 years ago
0
Issue35-39

#40 CunliangGeng closed 4 years ago
1
update commit method to private

#39 CunliangGeng closed 4 years ago
0