pdbe issueshttps://gitlab.ebi.ac.uk/groups/pdbe/-/issues2018-10-13T09:14:48Zhttps://gitlab.ebi.ac.uk/pdbe/ccdutils/-/issues/23PDBeChem ftp Output: Supply divided directory2018-10-13T09:14:48ZOliver SmartPDBeChem ftp Output: Supply divided directory* From issue #13
* Currently it is difficult to navigate the ftp site because it takes around 40 seconds to see http://ftp.ebi.ac.uk/pub/databases/msd/pdbechem/images/large/ as it contains 24936 files.
* Instead provide a divided direct...* From issue #13
* Currently it is difficult to navigate the ftp site because it takes around 40 seconds to see http://ftp.ebi.ac.uk/pub/databases/msd/pdbechem/images/large/ as it contains 24936 files.
* Instead provide a divided directory with all the files for an individual chemical component.
* so for ATP directory `divided/A/ATP` would contain:
```
divided/A/ATP/ATP.cif
divided/A/ATP/coordinates/ideal/ATP.sdf
divided/A/ATP/coordinates/ideal/ATP.pdb
divided/A/ATP/coordinates/ideal/ATP_no_hydrogen.sdf
divided/A/ATP/coordinates/ideal/ATP.xml
divided/A/ATP/coordinates/model/ATP.sdf
divided/A/ATP/coordinates/model/ATP.pdb
divided/A/ATP/coordinates/model/ATP_no_hydrogen.sdf
divided/A/ATP/2Dimages/with_labels/ATP.xml
divided/A/ATP/2Dimages/with_labels/ATP.png
divided/A/ATP/2Dimages/without_labels/ATP.xml
divided/A/ATP/2Dimages/without_labels/ATP.png
```
* this will enable users to quickly find what they want (hopefully?)PDBeChem Backend Processing: get into preproductionhttps://gitlab.ebi.ac.uk/pdbe/ccdutils/-/issues/42Method duplicitation in the file test_process_components_cif_cli.py2018-05-10T12:46:39ZIjaz AhmadMethod duplicitation in the file test_process_components_cif_cli.pyThe method `test_subdir_in_files_created(output_dir, subdir)` is defined twice in the fileThe method `test_subdir_in_files_created(output_dir, subdir)` is defined twice in the filerefactor ccd_utils with better class structure.Oliver SmartOliver Smarthttps://gitlab.ebi.ac.uk/pdbe/ccdutils/-/issues/41Get process_components_cif_cli working in refactoring branch2018-10-13T09:17:51ZOliver SmartGet process_components_cif_cli working in refactoring branchIssue #38 *Add process_components_cif script to back refactoring branch in stub form* now finished.
So functionality developed and tested in milestone %1 can now be added back to refactoring branch using the unit test [test_process_comp...Issue #38 *Add process_components_cif script to back refactoring branch in stub form* now finished.
So functionality developed and tested in milestone %1 can now be added back to refactoring branch using the unit test [test_process_components_cif_cli.py](pdbeccdutils/tests/test_process_components_cif_cli.py) taken from current master.refactor ccd_utils with better class structure.https://gitlab.ebi.ac.uk/pdbe/ccdutils/-/issues/40Docstring format and automatic python API documenation generation2018-04-18T10:10:49ZOliver SmartDocstring format and automatic python API documenation generationIt would be useful to agree on docstring format.It would be useful to agree on docstring format.refactor ccd_utils with better class structure.Lukas PravdaLukas Pravdahttps://gitlab.ebi.ac.uk/pdbe/ccdutils/-/issues/39Agree coding standards2018-06-01T08:36:42ZOliver SmartAgree coding standardsFor the refactoring work it would be a good idea to agree on coding standards.
* Code to PEP8 compliant.
* Unit tests to use pytest rather than nose as this is much easier to use in practice (and not out of date)
although pytest suppor...For the refactoring work it would be a good idea to agree on coding standards.
* Code to PEP8 compliant.
* Unit tests to use pytest rather than nose as this is much easier to use in practice (and not out of date)
although pytest supports yield in tests (currently used a lot) this is deprecated and some this will be replaced by parameterised tests. refactor ccd_utils with better class structure.https://gitlab.ebi.ac.uk/pdbe/ccdutils/-/issues/38Add process_components_cif script to back refactoring branch in stub form2018-03-31T14:35:20ZOliver SmartAdd process_components_cif script to back refactoring branch in stub formThe script `process_components_cif` was the major product of the initial ccd_utils project milestone \#1 %1 that was completed in September 2017.
Project milestone \#3 %3 is to completely replace the code in the initial project but p...The script `process_components_cif` was the major product of the initial ccd_utils project milestone \#1 %1 that was completed in September 2017.
Project milestone \#3 %3 is to completely replace the code in the initial project but process_components_cif` is a well considered script that achieved its aims:
```
Script for PDBeChem backend infrastructure.
Processes the wwPDB Chemical Components Dictionary file components.cif
producing files for
http://ftp.ebi.ac.uk/pub/databases/msd/pdbechem/
To do this components.cif is split into individual PDB chemical component
definitions cif files, sdf files, pdb files and image files.
In addition creates chem_comp.xml and chem_comp.list for all components.
```
The unit tests [test_process_components_cif_cli.py](pdbeccdutils/tests/test_process_components_cif_cli.py) are worth updating and preservingrefactor ccd_utils with better class structure.Oliver SmartOliver Smarthttps://gitlab.ebi.ac.uk/pdbe/ccdutils/-/issues/51have a look at the SVGs generated if anything has changed with the new release.2019-04-10T11:13:54ZLukas Pravdahave a look at the SVGs generated if anything has changed with the new release.Lukas PravdaLukas Pravdahttps://gitlab.ebi.ac.uk/pdbe/ccdutils/-/issues/50Add bond information to the component annotation json file2019-05-20T22:07:36ZLukas PravdaAdd bond information to the component annotation json fileLukas PravdaLukas Pravdahttps://gitlab.ebi.ac.uk/pdbe/ccdutils/-/issues/48Improve CIF export2019-06-27T09:13:16ZLukas PravdaImprove CIF exportnew features exported as a part of the CIF file.
* properties
* scaffolds
* fragments
* 2D coordinates
* version of ccdutils and rdkit (for transparency reasons)new features exported as a part of the CIF file.
* properties
* scaffolds
* fragments
* 2D coordinates
* version of ccdutils and rdkit (for transparency reasons)Lukas PravdaLukas Pravdahttps://gitlab.ebi.ac.uk/pdbe/ccdutils/-/issues/47Fix collision bond detection when bonds are completelly overlapping2019-04-10T11:14:01ZLukas PravdaFix collision bond detection when bonds are completelly overlappinghttp://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/show/CPThttp://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/show/CPTLukas PravdaLukas Pravdahttps://gitlab.ebi.ac.uk/pdbe/web-components/ligand-env/-/issues/14make sure text does not clip the border of elements2019-02-05T17:10:33ZLukas Pravdamake sure text does not clip the border of elements@mvaradi said: "I would try to ensure that the text never clips with the shape outline - currently with circle shaped nodes you have text overlapping with the borders"@mvaradi said: "I would try to ensure that the text never clips with the shape outline - currently with circle shaped nodes you have text overlapping with the borders"Lukas PravdaLukas Pravdahttps://gitlab.ebi.ac.uk/pdbe/web-components/ligand-env/-/issues/13rethink border color of the graphical elements2019-03-21T17:02:34ZLukas Pravdarethink border color of the graphical elements@mvaradi said: "I'm not sure why some circles have grey borders, and others are black - the legends don't mention reasons for this"@mvaradi said: "I'm not sure why some circles have grey borders, and others are black - the legends don't mention reasons for this"Lukas PravdaLukas Pravdahttps://gitlab.ebi.ac.uk/pdbe/web-components/ligand-env/-/issues/12Change pointer based on the context2019-02-05T17:10:36ZLukas PravdaChange pointer based on the context@mvaradi said: "When going one level below the main (i.e. clicking on something that is part of the ligand), it would be nice to have a quick and obvious way of going back. It was not clear to me that the home button would do the trick. ...@mvaradi said: "When going one level below the main (i.e. clicking on something that is part of the ligand), it would be nice to have a quick and obvious way of going back. It was not clear to me that the home button would do the trick. I also didn't know what happened when I suddenly got down to the sub-level after merrily clicking around :) (I.e. I first clicked nodes that didn't take me anywhere, and then suddenly I clicked on a node that did, and I was like "damn, how do I get back")"Lukas PravdaLukas Pravdahttps://gitlab.ebi.ac.uk/pdbe/web-components/ligand-env/-/issues/9Make legend visible at the begining2019-02-19T23:05:28ZLukas PravdaMake legend visible at the begining@mvaradi said: "I would find it better to have the legends visible at all time, without (first trying to find and then) turning it on with the ? button"@mvaradi said: "I would find it better to have the legends visible at all time, without (first trying to find and then) turning it on with the ? button"Lukas PravdaLukas Pravdahttps://gitlab.ebi.ac.uk/pdbe/web-components/ligand-env/-/issues/8Highlight bound molecule2019-03-21T17:03:13ZLukas PravdaHighlight bound molecule@mvaradi said: "It would be helpful if somehow it would be more apparent which nodes are actually part of the ligand. Something like making the edges of the ligand wider perhaps?"@mvaradi said: "It would be helpful if somehow it would be more apparent which nodes are actually part of the ligand. Something like making the edges of the ligand wider perhaps?"Lukas PravdaLukas Pravdahttps://gitlab.ebi.ac.uk/pdbe/web-components/ligand-env/-/issues/7zoom issues on all devices2019-03-21T16:47:07ZLukas Pravdazoom issues on all devicesThis has been introduced after the cetenring functionality has been implementedThis has been introduced after the cetenring functionality has been implementedLukas PravdaLukas Pravdahttps://gitlab.ebi.ac.uk/pdbe/web-components/ligand-env/-/issues/6Glycans are broken on firefox2019-02-04T09:41:23ZLukas PravdaGlycans are broken on firefoxFor some reason the graphical primitives on firefox (mac os) are not displayed at all.
![Screenshot_2019-01-29_at_09.39.51](/uploads/a0fc5a17a86b35741ed88d9b628dfefa/Screenshot_2019-01-29_at_09.39.51.png)For some reason the graphical primitives on firefox (mac os) are not displayed at all.
![Screenshot_2019-01-29_at_09.39.51](/uploads/a0fc5a17a86b35741ed88d9b628dfefa/Screenshot_2019-01-29_at_09.39.51.png)Lukas PravdaLukas Pravdahttps://gitlab.ebi.ac.uk/pdbe/web-components/ligand-env/-/issues/3Distinguish sidechain vs. mainchain interactions2020-02-24T12:00:51ZLukas PravdaDistinguish sidechain vs. mainchain interactionsGraphically distinguis sidechain and mainchain interactionsGraphically distinguis sidechain and mainchain interactionsLukas PravdaLukas Pravdahttps://gitlab.ebi.ac.uk/pdbe/web-components/ligand-env/-/issues/1Draw all sugar classes2019-01-28T14:18:14ZLukas PravdaDraw all sugar classesglycans.xml needs to be extended! The list to use can be found here: https://www.ncbi.nlm.nih.gov/glycans/snfg.html
Presently only these classes are drawn:
* Hexose
* HexNAc
* Hexosamine
* Hexuronate
* Deoxyhexose
These needs to be ad...glycans.xml needs to be extended! The list to use can be found here: https://www.ncbi.nlm.nih.gov/glycans/snfg.html
Presently only these classes are drawn:
* Hexose
* HexNAc
* Hexosamine
* Hexuronate
* Deoxyhexose
These needs to be added:
* DeoxyhexNAc
* Di-deoxyhexose
* Pentose
* Deoxynonulosonate
* Di-deoxynonulosonate
* Unkwnown
* AssignedLukas PravdaLukas Pravdahttps://gitlab.ebi.ac.uk/pdbe/ccdutils/-/issues/46Ring MatPlotLib code causes crash in Linux.2018-05-08T15:42:49ZOliver SmartRing MatPlotLib code causes crash in Linux.From issue #36From issue #36