SBRG ssbio issues - Githubissues

SBRG / ssbio

A Python framework for structural systems biology

http://ssbio.readthedocs.io/en/latest/

MIT License

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issues

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ImportError: cannot import name 'one_to_three' from 'Bio.PDB.Polypeptide'

#57 miri-2000 opened 2 months ago
0
ImportError: cannot import name 'Mapping' from 'collections'

#56 wook2014 opened 6 months ago
0
MSMS installation on MacOS

#55 gcroci2 opened 9 months ago
0
Difficulty installing SSBIO package due to dependency conflicts

#54 MaryAnnBlaetke opened 12 months ago
0
tmhmm installtion and running

#53 kishor2019 opened 2 years ago
0
SIFTS map uniprot resnum to PDB function fix

#52 JoshuaMeyers opened 3 years ago
0
mapping pdb resnum to uniprot resnum

#51 JoshuaMeyers opened 3 years ago
0
Import Error - Bio.Alphabet has been removed from Biopython

#50 a-r-j opened 3 years ago
2
Use of .ix indexing is deprecated in pandas & no pandas version specified in requirements.

#49 a-r-j opened 3 years ago
0
characterize_residue_mutation will only return properties defined in EXTENDED_AA_PROPERTY_DICT_ONE

#48 pvphaneuf opened 4 years ago
0
Fail to read P00533

#47 bkellman opened 6 years ago
0
tmscore issue

#46 bkellman opened 6 years ago
1
Issues running the tutorial

#45 bkellman opened 6 years ago
1
Comprehensive calculation of amino acid composition

#44 nmih opened 6 years ago
0
Add runtime estimates for third party programs

#43 nmih opened 6 years ago
0
Some more complex updates, bug fixes

#42 nmih closed 6 years ago
0
Raise error when PDB file cannot be downloaded

#41 nmih closed 6 years ago
0
Update Protein class to match other changes

#40 nmih closed 6 years ago
0
Additional parallelization tests and some crucial bug fixes

#39 nmih closed 6 years ago
0
Remove webcolors from requirements

#38 nmih closed 6 years ago
0
Added example function to parallelize KEGG mapping.

#37 nmih closed 6 years ago
0
Update requirements.txt

#36 nmih closed 6 years ago
0
Update requirements.txt

#35 nmih closed 6 years ago
0
Fix notebook errors

#34 nmih closed 6 years ago
0
Fix notebook errors

#33 nmih closed 6 years ago
0
Fix notebook errors

#32 nmih closed 6 years ago
0
Fix notebook errors

#31 nmih closed 6 years ago
0
Fix notebook errors

#30 nmih closed 6 years ago
0
Fix notebook errors

#29 nmih closed 6 years ago
0
Add nbsphinx_allow_errors

#28 nmih closed 6 years ago
0
Develop

#27 nmih closed 6 years ago
0
Architectural change todo -- PDBProp objects with the same ID for a GEM-PRO should point to the same object rather than being created under different proteins

#26 nmih opened 6 years ago
1
Aquaria -- perhaps ssbio can have links to aquaria info pages

#25 nmih opened 6 years ago
0
Pyspark and parquet for sequences analysis to parallelize computations

#24 nmih opened 6 years ago
0
Virtual Jupyter notebooks (Everware, Binder) to have external software preinstalled for workflows would be much better for sustainability

#23 nmih closed 6 years ago
1
Revamp logging to disable at higher levels

#22 nmih opened 6 years ago
0
Tab completion issues on Jupyter notebook for a GEMPRO object

#21 nmih closed 6 years ago
3
Importing ssbio on python2.7 cobra environment

#20 nmih opened 6 years ago
1
COBRApy's newest release (0.6.1) moves json attributes into a new module

#19 nmih closed 7 years ago
2
json-tricks - saving a string with two forward slashes

#18 nmih opened 7 years ago
0
Problematic PDB files: list of IDs

#17 nmih opened 7 years ago
1
lxml etree doesn't work in Python 3.6?

#16 nmih opened 7 years ago
0
Cleaning mmtf files and saving as pdbs

#15 nmih closed 7 years ago
0
Issue saving PDB 5LZD

#14 nmih opened 7 years ago
0
pdb_file_type does not propagate when loading a GEM

#13 nmih closed 7 years ago
0
Intuitive coloring of protein structures

#12 nmih opened 7 years ago
1
Sequence to structure pairwise alignment parameter tuning

#11 nmih opened 7 years ago
3
Option to run QC/QA for all structures

#10 nmih opened 7 years ago
1
No module named json_r

#9 erolkavvas closed 7 years ago
2
AttributeError: 'module' object has no attribute 'urlretrieve'

#8 erolkavvas closed 7 years ago
3