samirelanduk atomium issues

samirelanduk / atomium

Python macromolecular parsing (with .pdb/.cif/.mmtf parsing and production)

https://atomium.bio

MIT License

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issues

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PDB format output with numbers as chain ID

#43 fwaibl opened 1 year ago
2
Error with save

#42 emarsh25 opened 1 year ago
1
Standalone version of atomium

#41 BradyAJohnston opened 2 years ago
2
Auto-creation of bonds.

#40 BradyAJohnston opened 2 years ago
11
Adds atomic numbers

#39 FilipeMaia closed 2 years ago
2
Add atomic number information

#38 FilipeMaia opened 2 years ago
0
Add chain annotation from COMPND and SOURCE records

#37 mnahinkhan closed 2 years ago
1
Getting the Residue to which an Atom belongs

#36 mnahinkhan closed 2 years ago
2
Atomimu should not depend on `strptime` for parse date in PDB

#35 Czaki opened 2 years ago
1
the "add_secondary_structure_to_polymers" function in the mmcif.py module only recognises single-letter chain identifiers

#34 FunkTipp closed 3 years ago
2
getting the residue details from an atom

#33 rbf22 closed 3 years ago
3
Zero-pad pdb temperature factor

#32 hippolytej closed 3 years ago
1
Loading 6LU7 from mmtf fails in decode_dict

#31 zacharyrs closed 3 years ago
1
HETATM records change to ATOM when saving model

#30 hippolytej closed 3 years ago
1
Unable to write atoms with negative residue id

#29 staszekdh closed 4 years ago
2
Calculate RMSD between sets of atoms as well as between structures

#28 samirelanduk opened 4 years ago
0
KeyError: 'branched' when fetching some pdb files

#27 NicoBio closed 4 years ago
2
gzip integration

#26 juvilius closed 4 years ago
1
TER line doesn't comply to PDB TER records spec

#25 Koesed96 opened 4 years ago
3
Add option for offline mirror of PDB

#24 samirelanduk opened 4 years ago
1
Chains are not assigned to ligands in mmCIF files where label_asym_id and auth_asym_id are swapped

#23 samirelanduk opened 5 years ago
0
Converting PDB/mmft with a specific dict

#22 chaconlab closed 3 years ago
2
Create conda package as well as pypi

#21 samirelanduk closed 4 years ago
5
Copying chains destroys connectivity information

#20 samirelanduk closed 5 years ago
0
Expression System should never be '?'

#19 samirelanduk closed 5 years ago
0
atomium breaks on RCSB generated assembly files

#18 samirelanduk opened 6 years ago
0
Implement slots in class Atom to reduce memory usage in huge structures

#17 samirelanduk closed 6 years ago
1
Get PDB files from remote machines

#16 gf712 closed 6 years ago
2
Parsing the Rfree Value

#15 jonathanrd closed 6 years ago
1
README error

#14 jonathanrd closed 6 years ago
1
Re-implement orientation to axes and planes

#13 samirelanduk opened 6 years ago
0
Implement full residue names

#12 samirelanduk closed 6 years ago
0
Implement parallel processing

#11 samirelanduk opened 7 years ago
3
Site calculation should have option for ignoring main chain atoms

#10 samirelanduk closed 6 years ago
0
Create function to save string over multiple PDB records

#9 samirelanduk closed 6 years ago
1
Add clustering of chains into complexes

#8 samirelanduk closed 6 years ago
0
Saving TITLE records breaks in the middle of words

#7 samirelanduk closed 6 years ago
0
Parser crashes when trying to fetch multi-file PDBs

#6 samirelanduk closed 7 years ago
0
Structures can't handle negative temperature factors

#5 samirelanduk closed 7 years ago
0
PDB parser interprets numerical molecule names as integers and not strings

#4 samirelanduk closed 7 years ago
0
PDB file saving needs speeding up

#3 samirelanduk closed 7 years ago
3
implemented angle_with method

#2 gf712 closed 7 years ago
1
Implement bond angles

#1 samirelanduk closed 7 years ago
0