pdbe issueshttps://gitlab.ebi.ac.uk/groups/pdbe/-/issues2018-03-28T06:56:43Zhttps://gitlab.ebi.ac.uk/pdbe/ccdutils/-/issues/1Class to parse PDB chemical component cif definitions: initial version2018-03-28T06:56:43ZOliver SmartClass to parse PDB chemical component cif definitions: initial versionRequirement is to produce a class that parses PDB chemical components cif files.
It should not be coupled to any cif parser (PDBeCIF or the one used in OneDep) but instead use any and provide a user interface that does not vary so tha...Requirement is to produce a class that parses PDB chemical components cif files.
It should not be coupled to any cif parser (PDBeCIF or the one used in OneDep) but instead use any and provide a user interface that does not vary so that same code can be shared between validator and PDBeChem processes.Improve PDBe Chemical Components backend infrastructure using RDKit: beta test versionOliver SmartOliver Smarthttps://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/2Initial version of class to create RDKit molecule from a PDB CCD definition2017-05-29T14:47:22ZOliver SmartInitial version of class to create RDKit molecule from a PDB CCD definitionIdea create daughter class of [pdb_chemical_components.py](pdb_chemical_components.py) that would parse CCD cif file but afterwards create an RDKit molecule. By keeping functionality separate can use the original [pdb_chemical_component...Idea create daughter class of [pdb_chemical_components.py](pdb_chemical_components.py) that would parse CCD cif file but afterwards create an RDKit molecule. By keeping functionality separate can use the original [pdb_chemical_components.py](pdb_chemical_components.py) without importing RDKit if desired.Improve PDBe Chemical Components backend infrastructure using RDKit: beta test versionOliver SmartOliver Smarthttps://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 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/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/ccdutils/-/issues/14Document the current installation procedure2017-09-21T14:18:05ZOliver SmartDocument the current installation procedure* Currently the ccd_utils project needs a parallel check out of PDBeCIF project. https://github.com/glenveegee/PDBeCIF.git
* How to do this should be explained in the [README.md](README.md) file.
* Add a section *Installation instructions** Currently the ccd_utils project needs a parallel check out of PDBeCIF project. https://github.com/glenveegee/PDBeCIF.git
* How to do this should be explained in the [README.md](README.md) file.
* Add a section *Installation instructions*Improve PDBe Chemical Components backend infrastructure using RDKit: beta test versionhttps://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/ccdutils/-/issues/12Add DMSO and Sildenafil to list of test CCD cif files2017-09-21T14:18:05ZOliver SmartAdd DMSO and Sildenafil to list of test CCD cif files* In previous work I found that SOx groups could cause problems.
* Please look up [DMSO](https://en.wikipedia.org/wiki/Dimethyl_sulfoxide) and [Sildenafil (Viagra)](https://en.wikipedia.org/wiki/Sildenafil) in PDBeChem and add to directo...* In previous work I found that SOx groups could cause problems.
* Please look up [DMSO](https://en.wikipedia.org/wiki/Dimethyl_sulfoxide) and [Sildenafil (Viagra)](https://en.wikipedia.org/wiki/Sildenafil) in PDBeChem and add to directory with test cif files.
* How do the molecules perform in current tests?
* When committing the files you must include where the files were obtained (exact url) in the commit message.
* Include reference to this issue number in the commit message. See https://docs.gitlab.com/ee/user/project/issues/automatic_issue_closing.htmlImprove PDBe Chemical Components backend infrastructure using RDKit: beta test versionhttps://gitlab.ebi.ac.uk/pdbe/ccdutils/-/issues/6Write 2D images of PDB CCD molecule2017-10-01T19:13:29ZOliver SmartWrite 2D images of PDB CCD moleculeImprove PDBe Chemical Components backend infrastructure using RDKit: beta test versionOliver SmartOliver Smarthttps://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/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/ccdutils/-/issues/3Use RDKit to write sdf file for PDB CCD2018-03-28T06:56:43ZOliver SmartUse RDKit to write sdf file for PDB CCD## What
* mol and the related sdf file formats are the standard way to pass molecules with chemical information between application
* Currently pdbechem provides 4 different molfile/sdf for each chemical component (with/without hydrogen ...## What
* mol and the related sdf file formats are the standard way to pass molecules with chemical information between application
* Currently pdbechem provides 4 different molfile/sdf for each chemical component (with/without hydrogen atoms and ideal/model coordinates), see http://ftp.ebi.ac.uk/pub/databases/msd/pdbechem/readme.htm
* This feature request to get RDKit to be able to write each of the 4 different sdf files.
* It is possible to include atom names and other information in sdf files. This may be useful. For an example see rcsb:
## How
* should be relatively easy method in [pdb_chemical_components_rdkit.py](pdb_chemical_components_rdkit.py)
* Note that the adding/removing hydrogen atoms should not effect the main self.rdkit_mol object in the class
## tasks
This is a big issue so lets separate out into checklist:
- [x] write sdf ideal with hydrogen atoms and alias
- [x] write different sdf model and ideal
- [x] write sdf without hydrogen atoms
- [x] turn on/off atom alias in the sdf.Improve PDBe Chemical Components backend infrastructure using RDKit: beta test versionhttps://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/ccdutils/-/issues/4Write pdb files for PDB CCD2017-09-21T14:18:05ZOliver SmartWrite pdb files for PDB CCD# What
* See #3 for sdf files
* in addition we need method to write old style PDB format files.
# How
* RDKit includes code to write PDB files
* Note that it is important the PDB files produce are well formed with correct atom nam...# What
* See #3 for sdf files
* in addition we need method to write old style PDB format files.
# How
* RDKit includes code to write PDB files
* Note that it is important the PDB files produce are well formed with correct atom names and residue names.
* In addition the occupancy and temperature factors should be well formed.
* probably also neccessary to include dummy CRYST1 card
* Testing should include comparison to existing files at PDBeChem as well as loading in coot, pymol, litemol.Improve PDBe Chemical Components backend infrastructure using RDKit: beta test versionOliver SmartOliver Smarthttps://gitlab.ebi.ac.uk/pdbe/ccdutils/-/issues/9Split wwPDB chemical component dictionary file into separate cif file for eac...2017-09-11T14:57:41ZOliver SmartSplit wwPDB chemical component dictionary file into separate cif file for each component## What
* The wwPDB chemical component dictionary is available as a single big (around 215MB) file each week.
* download link ftp://ftp.wwpdb.org/pub/pdb/data/monomers/components.cif
* details https://www.wwpdb.org/data/ccd
* this needs...## What
* The wwPDB chemical component dictionary is available as a single big (around 215MB) file each week.
* download link ftp://ftp.wwpdb.org/pub/pdb/data/monomers/components.cif
* details https://www.wwpdb.org/data/ccd
* this needs to be split into individual CCD files - one for each chemical component.
* these then need to be processed to sdf/pdb and images.
## How
* It might be sensible to do this by parsing the complete file using a cif parser - could then process each component using the tools developed to write sdf, pdb files and images. If so could address issue #10 at same time.
* Or it might be necessary to split the file into individual small files in a separate program without using cif parser each component starts with line `data_ABC` where `ABC` is the chem_comp.id (aka residue name).
** for instance http://ftp.ebi.ac.uk/pub/databases/msd/pdbechem/files/mmcif/001.cif
```
data_001
#
_chem_comp.id 001
_chem_comp.name "1-[2,2-DIFLUORO-2-(3,4,5-TRIMETHOXY-PHENYL)-ACETYL]-PIPERIDINE-2-CARBOXYLIC ACID 4-PHENYL-1-(3-PYRIDIN-3-YL-PROPYL)-BUTYL ESTER"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C35 H42 F2 N2 O6"
```
* could simply read file and look for lines starting `data_...` when line found close previous file and open a new one for the code `...`Improve PDBe Chemical Components backend infrastructure using RDKit: beta test versionOliver SmartOliver Smarthttps://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/ccdutils/-/issues/10Create chem.xml for all components2017-08-29T17:00:52ZOliver SmartCreate chem.xml for all components# What
Currently http://ftp.ebi.ac.uk/pub/databases/msd/pdbechem/chem.xml lists in xml format information for every PDB chemical component. For instance for ATP and ATQ:
```xml
<chemComp>
<id>ATP</id>
<name>ADENOSINE-5'-TRIPHOSPHATE</...# What
Currently http://ftp.ebi.ac.uk/pub/databases/msd/pdbechem/chem.xml lists in xml format information for every PDB chemical component. For instance for ATP and ATQ:
```xml
<chemComp>
<id>ATP</id>
<name>ADENOSINE-5'-TRIPHOSPHATE</name>
<formula>C10 H16 N5 O13 P3</formula>
<systematicName>[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl] phosphono hydrogen phosphate</systematicName>
<stereoSmiles>Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O</stereoSmiles>
<nonStereoSmiles>Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O</nonStereoSmiles>
<InChi>InChI=1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(26-10)1-25-30(21,22)28-31(23,24)27-29(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1</InChi>
</chemComp>
<chemComp>
<id>ATQ</id>
<name>2-AMINOTHIAZOLINE</name><formula>C3 H6 N2 S</formula>
<systematicName>4,5-dihydro-1,3-thiazol-2-amine</systematicName>
<stereoSmiles>NC1=NCCS1</stereoSmiles>
<nonStereoSmiles>NC1=NCCS1</nonStereoSmiles>
<InChi>InChI=1S/C3H6N2S/c4-3-5-1-2-6-3/h1-2H2,(H2,4,5)</InChi>
</chemComp>
```
the process developed needs to be able to produce this file.
N.B. file starts:
```
<chemCompList>
<chemComp>
<id>000</id>
<name>methyl hydrogen carbonate</name>
<formula>C2 H4 O3</formula>
<systematicName>methyl hydrogen carbonate</systematicName>
<stereoSmiles>COC(O)=O</stereoSmiles>
<nonStereoSmiles>COC(O)=O</nonStereoSmiles>
<InChi>InChI=1S/C2H4O3/c1-5-2(3)4/h1H3,(H,3,4)</InChi>
</chemComp>
```
and ends with ```</chemCompList>```
# How
* related to issue #9 if the cif file could be processed and split creating `chem.xml` this would be good.
```Improve PDBe Chemical Components backend infrastructure using RDKit: beta test versionOliver SmartOliver Smarthttps://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/ccdutils/-/issues/11Tool for finding "fragments" in each CCD molecule.2017-09-14T15:35:12ZOliver SmartTool for finding "fragments" in each CCD molecule.## What
Requirements From PDBe confluence: **16 June 2016**
SV wants a tool to produce a file that lists the fragments present in each of the chemical compounds:
* read in the chemical component definition cif file.
* read in...## What
Requirements From PDBe confluence: **16 June 2016**
SV wants a tool to produce a file that lists the fragments present in each of the chemical compounds:
* read in the chemical component definition cif file.
* read in file smi.txt that contains lines like:
```
cyclopentane:C1CCCC1
cyclopropane:C1CC1
cytosine:C1=CNC(NC1N)O
```
* use rdkit to find which of the fragments is in the ccd.
* write results as a csv format file with the contents:
3 letter code eg. "ATP", fragment name from smi.txt, atom names comma delimited e.g. "C1,C2,C3,C4,O5"
* Producing this tool is a priority.
* name for tool ccd_find_fragments.py (provisional)Improve PDBe Chemical Components backend infrastructure using RDKit: beta test versionOliver SmartOliver Smart