samirelanduk/atomium issues and pull requests

#43 - PDB format output with numbers as chain ID

Issue - State: open - Opened by fwaibl over 1 year ago - 2 comments

#42 - Error with save

Issue - State: open - Opened by emarsh25 over 1 year ago - 1 comment

#41 - Standalone version of atomium

Issue - State: open - Opened by BradyAJohnston over 2 years ago - 2 comments

#40 - Auto-creation of bonds.

Issue - State: open - Opened by BradyAJohnston over 2 years ago - 11 comments

#39 - Adds atomic numbers

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

#38 - Add atomic number information

Issue - State: open - Opened by FilipeMaia over 2 years ago

#37 - Add chain annotation from COMPND and SOURCE records

Pull Request - State: closed - Opened by mnahinkhan over 2 years ago - 1 comment

#36 - Getting the Residue to which an Atom belongs

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

#35 - Atomimu should not depend on `strptime` for parse date in PDB

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

#34 - the "add_secondary_structure_to_polymers" function in the mmcif.py module only recognises single-letter chain identifiers

Issue - State: closed - Opened by FunkTipp over 3 years ago - 2 comments
Labels: bug

#33 - getting the residue details from an atom

Issue - State: closed - Opened by rbf22 over 3 years ago - 3 comments

#32 - Zero-pad pdb temperature factor

Issue - State: closed - Opened by hippolytej over 3 years ago - 1 comment

#31 - Loading 6LU7 from mmtf fails in decode_dict

Issue - State: closed - Opened by zacharyrs over 3 years ago - 1 comment

#30 - HETATM records change to ATOM when saving model

Issue - State: closed - Opened by hippolytej almost 4 years ago - 1 comment
Labels: bug

#29 - Unable to write atoms with negative residue id

Issue - State: closed - Opened by staszekdh almost 4 years ago - 2 comments

#28 - Calculate RMSD between sets of atoms as well as between structures

Issue - State: open - Opened by samirelanduk almost 4 years ago
Labels: enhancement

#27 - KeyError: 'branched' when fetching some pdb files

Issue - State: closed - Opened by NicoBio about 4 years ago - 2 comments
Labels: bug

#26 - gzip integration

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

#25 - TER line doesn't comply to PDB TER records spec

Issue - State: open - Opened by Koesed96 over 4 years ago - 3 comments

#24 - Add option for offline mirror of PDB

Issue - State: open - Opened by samirelanduk over 4 years ago - 1 comment
Labels: enhancement

#23 - Chains are not assigned to ligands in mmCIF files where label_asym_id and auth_asym_id are swapped

Issue - State: open - Opened by samirelanduk almost 5 years ago
Labels: bug

#22 - Converting PDB/mmft with a specific dict

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

#21 - Create conda package as well as pypi

Issue - State: closed - Opened by samirelanduk about 5 years ago - 5 comments
Labels: enhancement

#20 - Copying chains destroys connectivity information

Issue - State: closed - Opened by samirelanduk over 5 years ago
Labels: bug

#19 - Expression System should never be '?'

Issue - State: closed - Opened by samirelanduk over 5 years ago
Labels: bug

#18 - atomium breaks on RCSB generated assembly files

Issue - State: open - Opened by samirelanduk almost 6 years ago
Labels: bug, enhancement

#17 - Implement slots in class Atom to reduce memory usage in huge structures

Issue - State: closed - Opened by samirelanduk almost 6 years ago - 1 comment
Labels: enhancement

#16 - Get PDB files from remote machines

Issue - State: closed - Opened by gf712 about 6 years ago - 2 comments

#15 - Parsing the Rfree Value

Issue - State: closed - Opened by jonathanrd over 6 years ago - 1 comment
Labels: enhancement

#14 - README error

Issue - State: closed - Opened by jonathanrd over 6 years ago - 1 comment

#13 - Re-implement orientation to axes and planes

Issue - State: open - Opened by samirelanduk over 6 years ago
Labels: enhancement

#12 - Implement full residue names

Issue - State: closed - Opened by samirelanduk almost 7 years ago

#11 - Implement parallel processing

Issue - State: open - Opened by samirelanduk almost 7 years ago - 3 comments
Labels: enhancement

#10 - Site calculation should have option for ignoring main chain atoms

Issue - State: closed - Opened by samirelanduk almost 7 years ago

#9 - Create function to save string over multiple PDB records

Issue - State: closed - Opened by samirelanduk almost 7 years ago - 1 comment
Labels: enhancement

#8 - Add clustering of chains into complexes

Issue - State: closed - Opened by samirelanduk almost 7 years ago
Labels: enhancement

#7 - Saving TITLE records breaks in the middle of words

Issue - State: closed - Opened by samirelanduk almost 7 years ago
Labels: bug

#6 - Parser crashes when trying to fetch multi-file PDBs

Issue - State: closed - Opened by samirelanduk almost 7 years ago
Labels: bug

#5 - Structures can't handle negative temperature factors

Issue - State: closed - Opened by samirelanduk about 7 years ago
Labels: bug

#4 - PDB parser interprets numerical molecule names as integers and not strings

Issue - State: closed - Opened by samirelanduk about 7 years ago
Labels: bug

#3 - PDB file saving needs speeding up

Issue - State: closed - Opened by samirelanduk about 7 years ago - 3 comments
Labels: enhancement

#2 - implemented angle_with method

Pull Request - State: closed - Opened by gf712 about 7 years ago - 1 comment

#1 - Implement bond angles

Issue - State: closed - Opened by samirelanduk over 7 years ago
Labels: enhancement

GitHub / samirelanduk/atomium issues and pull requests