xchem/fragalysis-api

Issues

• Need an API access token for authenticated uploads

  #106 opened a year ago by alanbchristie
  0

• Allow for multiple conformations for those particularly tricky systems.

  #102 opened 2 years ago by TJGorrie
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• Expand crystal symmetry around a ligand and include that in the alignment

  #101 opened 2 years ago by TJGorrie
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• Add downsampling for maps

  #100 opened 2 years ago by TJGorrie
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• Building docker is missing environment.yml file

  #99 opened 2 years ago by OleinikovasV
  1

• Provide new mol file to sdf writer.

  #98 opened 2 years ago by TJGorrie
  0

• aligned / unaligned ligand crisscross

  #97 opened 3 years ago by TJGorrie
  0

• Create checks for inappropriate usage of rrf mode...

  #95 opened 3 years ago by TJGorrie
  0

• Change the mol conversion in non-rrf mode to add chain names to ligands.

  #88 opened 3 years ago by TJGorrie
  1

• Create png/jpg for SMILES files for reasons...

  #93 opened 3 years ago by TJGorrie
  0

• Generate Centre of Mass Cites from a fragalysis output

  #94 opened 3 years ago by TJGorrie
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• Change monomerisation to be more groovy in general.

  #79 opened 3 years ago by TJGorrie
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• Create functional spec that does entire step in memory instead of using various file steps

  #92 opened 3 years ago by TJGorrie
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• Use gemmi map mask instead of ccp4 map mask

  #91 opened 3 years ago by TJGorrie
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• Fragalysis API should append biomol remark to pdbs

  #57 opened 3 years ago by TJGorrie
  1

• Fragalysis API needs to perform covalent conversion on mol files

  #58 opened 3 years ago by TJGorrie
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• Create method to align single model to a reference.

  #50 opened 3 years ago by TJGorrie
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• Make align more versatile

  #27 opened 3 years ago by TobiasHeOl
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• Tests for align

  #26 opened 3 years ago by TobiasHeOl
  1

• HOH's being removed from _apo.pdb using monomer mode.

  #56 opened 3 years ago by TJGorrie
  0

• Look into alternatives to setting space group of map?

  #89 opened 3 years ago by TJGorrie
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• Figure out why certain pdb files do not align

  #87 opened 3 years ago by TJGorrie
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• Enable Multicore processing

  #86 opened 3 years ago by TJGorrie
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• Frank's Stuff (To be ticketed)

  #85 opened 3 years ago by TJGorrie
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• can probably un-nest this a bit?Combine I and j into a list of tuples or something? - not important now

  #62 opened 3 years ago by TJGorrie
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• Maybe put this in a json file like ``non_ligs.json``?

  #63 opened 3 years ago by TJGorrie
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• Add all to a list and use ``if line.startswith(tuple(list)):``

  #61 opened 3 years ago by TJGorrie
  0

• Is this repeated from ``align_to_reference``? if it is - separate out into a new function that can be called in both places. Do the same for anywhere else you've copied and pasted code

  #64 opened 3 years ago by TJGorrie
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• Might be also useful to return the file path of the reference as a string, in case someone wants to use this bit of code in isolation

  #65 opened 3 years ago by TJGorrie
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• Add pandda_gemmi - it'll pick up that the user hasn't installed it, I think? Give it a go.

  #60 opened 3 years ago by TJGorrie
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• We will need to adapt the tests in the future to check the content of the output. Another suggestion: dump the contents of all of the files you've added to a json file/object. If an object, you can use it in the test itself and write it to a temp file or using ``stringIO`` (better). Some examples here: https://stackoverflow.com/questions/3942820/how-to-do-unit-testing-of-functions-writing-files-using-python-unittest

  #59 opened 3 years ago by TJGorrie
  0

• Can't get xcimporter to work

  #53 opened 3 years ago by tdudgeon
  2

• Wrap target upload to allow curl/CLI upload

  #84 opened 3 years ago by reskyner
  0

• Run xcimporter as a python function instead of calling script in pipelines

  #83 opened 3 years ago by reskyner
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• Warn user when structure contains really small chain

  #82 opened 3 years ago by reskyner
  0

• Optional argument to reference Fragalysis-api endpoints and add input to set?

  #81 opened 3 years ago by TJGorrie
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• Some project data cannot be downloaded

  #76 opened 4 years ago by rsanchezgarc
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• get_blast2 removed from pypdb in version 2

  #72 opened 4 years ago by reskyner
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• ANISOU LIG patterns not being removed from _apo.pdb files post alignment.

  #55 opened 4 years ago by TJGorrie
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• Add map cutting and alignment

  #46 opened 4 years ago by reskyner
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• Monomerization mode requires better handling of Ligands in own Chain

  #49 opened 4 years ago by TJGorrie
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• remove pipelines folder

  #41 opened 4 years ago by reskyner
  1