pdbe issueshttps://gitlab.ebi.ac.uk/groups/pdbe/-/issues2017-09-21T14:18:05Zhttps://gitlab.ebi.ac.uk/pdbe/ccdutils/-/issues/15test PDB cif directory name should be clearer2017-09-21T14:18:05ZOliver Smarttest PDB cif directory name should be clearer## What
* currently the directory with test PDB CCD mmcif files is called `data/cif`
* lets rename it to `data/pdb_ccd_mmcif_test_files`
* Consider how many times does the directory name appear in the code?
* Read wikipedia page...## What
* currently the directory with test PDB CCD mmcif files is called `data/cif`
* lets rename it to `data/pdb_ccd_mmcif_test_files`
* Consider how many times does the directory name appear in the code?
* Read wikipedia page https://en.wikipedia.org/wiki/Don%27t_repeat_yourself
* Please improve the code.Improve PDBe Chemical Components backend infrastructure using RDKit: beta test version2017-05-31https://gitlab.ebi.ac.uk/pdbe/ccdutils/-/issues/52Overengineered images2019-06-27T09:16:56ZLukas PravdaOverengineered imagesThere are still some weird charges e.g. OEC, OEX
![OEC_500.svg](/uploads/3c9fb46d951ed22452d8d01e03c40241/OEC_500.svg) ![OEX_500.svg](/uploads/cedb45cdda3ffb5a1918a12f730ab2a7/OEX_500.svg)There are still some weird charges e.g. OEC, OEX
![OEC_500.svg](/uploads/3c9fb46d951ed22452d8d01e03c40241/OEC_500.svg) ![OEX_500.svg](/uploads/cedb45cdda3ffb5a1918a12f730ab2a7/OEX_500.svg)Lukas PravdaLukas Pravdahttps://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/49inspect changes to non-inchiable inchi generation2019-04-09T14:41:26ZLukas Pravdainspect changes to non-inchiable inchi generationThis is part of the https://github.com/rdkit/rdkit/issues/2176.This is part of the https://github.com/rdkit/rdkit/issues/2176.Lukas 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/11Display long name of ligands2019-02-05T14:50:42ZLukas PravdaDisplay long name of ligands@mvaradi said: "Perhaps you could also show the long ligand names on tooltip? HET code might not be clear for some more obscure ligands"@mvaradi said: "Perhaps you could also show the long ligand names on tooltip? HET code might not be clear for some more obscure ligands"Lukas PravdaLukas Pravdahttps://gitlab.ebi.ac.uk/pdbe/web-components/ligand-env/-/issues/10Display tooltips next to the place where they are relevant2019-02-05T14:49:07ZLukas PravdaDisplay tooltips next to the place where they are relevant@mvaradi said: "Maybe it would be more understandable if the tooltips for the details of interactions would appear right where the cursor is, instead of the top left corner"@mvaradi said: "Maybe it would be more understandable if the tooltips for the details of interactions would appear right where the cursor is, instead of the top left corner"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/5Bear color blind people in mind2019-01-28T14:26:39ZLukas PravdaBear color blind people in mindThe question is whether or not the colour-coding schema should reflect colour blind people all the time. It is a good practice to do so, however the price to pay is that we will not use the color coding people from chemistry and biology ...The question is whether or not the colour-coding schema should reflect colour blind people all the time. It is a good practice to do so, however the price to pay is that we will not use the color coding people from chemistry and biology background are used to.
https://www.color-blindness.com/coblis-color-blindness-simulator/Lukas PravdaLukas Pravdahttps://gitlab.ebi.ac.uk/pdbe/web-components/ligand-env/-/issues/4Add full-atom view of bound molecules2019-01-28T14:27:49ZLukas PravdaAdd full-atom view of bound moleculesExplore how to create bound molecules in RDkit, test a few examples and then possibly add these as a part of the interactions pipelineExplore how to create bound molecules in RDkit, test a few examples and then possibly add these as a part of the interactions pipelineLukas 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/2Set up a process and API to identify carbohydrates2019-01-03T17:29:02ZLukas PravdaSet up a process and API to identify carbohydratesPresently we rely on manually curated [list](https://www.ebi.ac.uk/seqdb/confluence/display/PDBE/LiteMol+3D+glycan+representation) created by Matt. This needs to be improved!
Ideally a process which is a part of PDBeChem pipeline is imp...Presently we rely on manually curated [list](https://www.ebi.ac.uk/seqdb/confluence/display/PDBE/LiteMol+3D+glycan+representation) created by Matt. This needs to be improved!
Ideally a process which is a part of PDBeChem pipeline is implemented to find sugars and stores results in the database.Lukas PravdaLukas Pravda