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  • pdbe
  • ccdutilsccdutils
  • Milestones
  • Improve PDBe Chemical Components backend infrastructure using RDKit: beta test version

Closed
Milestone May 24, 2017–Oct 1, 2017

Improve PDBe Chemical Components backend infrastructure using RDKit: beta test version

Project aims

  • The current process(es) to produce the data for PDBeChem pages is out of date and needs replacement. This project will produce software to process the wwPDB Chemical Component Dictionary into individual PDB chemical component definitions files and then processing these into sdf file (aka mol), pdb files and 2D svg images (possibly). * A list of chemical fragments in each of the chemical components should also be produced.
  • The project should produce files to replace those in the PDBeChem ftp area:
    • Description http://ftp.ebi.ac.uk/pub/databases/msd/pdbechem/readme.htm
    • browse files: http://ftp.ebi.ac.uk/pub/databases/msd/pdbechem/
    • the fragment list should include information to be used for a replacement of the PDBeChem search http://www.ebi.ac.uk/pdbe-srv/pdbechem/ Fragments feature.
  • Issues 18
  • Merge requests 0
  • Participants 1
  • Labels 4
100% complete
100%
Start date
May 24, 2017
May 24
-
Oct 1 2017
Due date
Oct 1, 2017 (Past due)
18
Issues 18 New issue
Open: 0 Closed: 18
None
Total issue weight
None
1
Merge requests 1
Open: 0 Closed: 1 Merged: 0
0
Releases
None
Reference: pdbe/ccdutils%"Improve PDBe Chemical Components backend infrastructure using RDKit: beta test version"