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  • pdbe
  • Issues

  • Open 20
  • Closed 43
  • All 63
  • Priority Created date Updated date Milestone due date Due date Popularity Label priority Manual Title Weight Blocking
  • PDBeChem ftp Output: Supply divided directory
    ccdutils#23 · created Sep 08, 2017 by Oliver Smart   PDBeChem Backend Processing: get into preproduction   proposals
    • CLOSED
    • 1
    updated Oct 13, 2018
  • chem.xml add useful rdkit descriptors like number of rotatable bonds
    ccdutils#22 · created Aug 29, 2017 by Oliver Smart
    • 2
    updated Nov 22, 2018
  • write xyz format file for PDB-CCD
    ccdutils#21 · created Aug 25, 2017 by Oliver Smart   Improve PDBe Chemical Components backend infrastructure using RDKit: beta test version
    • CLOSED
    • 0
    updated Aug 25, 2017
  • Proof of concept: Mogul report on PDB-CCD ideal coordinates
    ccdutils#20 · created Jul 13, 2017 by Oliver Smart   development
    • 21
    updated Nov 18, 2017
  • Develop utility command line script to read single cif and write coordinate files/images etc.
    ccdutils#19 · created Jun 07, 2017 by Oliver Smart   PDBeChem Backend Processing: get into preproduction   Shelved development started
    • 4
    updated Sep 27, 2017
  • Package code so it can be installed with pip
    ccdutils#18 · created Jun 01, 2017 by Oliver Smart   Improve PDBe Chemical Components backend infrastructure using RDKit: beta test version
    • CLOSED
    • 9
    updated Sep 19, 2017
  • process_components_cif script to read complete components.cif and produce PDBeChem ftp area   4 of 5 tasks completed
    ccdutils#17 · created Jun 01, 2017 by Oliver Smart   Improve PDBe Chemical Components backend infrastructure using RDKit: beta test version   development
    • CLOSED
    • 26
    updated Sep 27, 2017
  • Test fails in directories other than ccd_utils
    ccdutils#16 · created May 31, 2017 by Ijaz Ahmad   Improve PDBe Chemical Components backend infrastructure using RDKit: beta test version   Qi project bug
    • CLOSED
    • 0
    updated Sep 21, 2017
  • test PDB cif directory name should be clearer
    ccdutils#15 · created May 31, 2017 by Oliver Smart   Improve PDBe Chemical Components backend infrastructure using RDKit: beta test version   May 31, 2017   Qi project enhancement
    • CLOSED
    • 0
    updated Sep 21, 2017
  • Document the current installation procedure
    ccdutils#14 · created May 29, 2017 by Oliver Smart   Improve PDBe Chemical Components backend infrastructure using RDKit: beta test version   Qi project development
    • CLOSED
    • 0
    updated Sep 21, 2017
  • Script to read wwPDB chemical component dictionary and split it to produce PDBeChem outputs   17 of 18 tasks completed
    ccdutils#13 · created May 29, 2017 by Oliver Smart   Improve PDBe Chemical Components backend infrastructure using RDKit: beta test version   development
    • CLOSED
    • 21
    updated Sep 08, 2017
  • Add DMSO and Sildenafil to list of test CCD cif files
    ccdutils#12 · created May 29, 2017 by Oliver Smart   Improve PDBe Chemical Components backend infrastructure using RDKit: beta test version   Qi project enhancement
    • CLOSED
    • 1
    updated Sep 21, 2017
  • Tool for finding "fragments" in each CCD molecule.
    ccdutils#11 · created May 29, 2017 by Oliver Smart   Improve PDBe Chemical Components backend infrastructure using RDKit: beta test version   development
    • CLOSED
    • 8
    updated Sep 14, 2017
  • Create chem.xml for all components
    ccdutils#10 · created May 29, 2017 by Oliver Smart   Improve PDBe Chemical Components backend infrastructure using RDKit: beta test version   development
    • CLOSED
    • 4
    updated Aug 29, 2017
  • Split wwPDB chemical component dictionary file into separate cif file for each component
    ccdutils#9 · created May 29, 2017 by Oliver Smart   Improve PDBe Chemical Components backend infrastructure using RDKit: beta test version   development
    • CLOSED
    • 7
    updated Sep 11, 2017
  • Write CML files: *needs to be checked*
    ccdutils#8 · created May 29, 2017 by Oliver Smart   PDBeChem Backend Processing: get into preproduction   Qi project Shelved development
    • 8
    updated Oct 01, 2017
  • Write 2D images of PDB CCD molecule
    ccdutils#6 · created May 29, 2017 by Oliver Smart   Improve PDBe Chemical Components backend infrastructure using RDKit: beta test version   Qi project development
    • CLOSED
    • 11
    updated Oct 01, 2017
  • Handling heme
    ccdutils#5 · created May 29, 2017 by Oliver Smart   Improve PDBe Chemical Components backend infrastructure using RDKit: beta test version   bug
    • CLOSED
    • 16
    updated Sep 29, 2017
  • Write pdb files for PDB CCD
    ccdutils#4 · created May 29, 2017 by Oliver Smart   Improve PDBe Chemical Components backend infrastructure using RDKit: beta test version   Qi project development
    • CLOSED
    • 7
    updated Sep 21, 2017
  • Use RDKit to write sdf file for PDB CCD   4 of 4 tasks completed
    ccdutils#3 · created May 29, 2017 by Oliver Smart   Improve PDBe Chemical Components backend infrastructure using RDKit: beta test version   Qi project development
    • CLOSED
    • 5
    updated Mar 28, 2018
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