ccdutils issueshttps://gitlab.ebi.ac.uk/pdbe/ccdutils/-/issues2017-11-18T16:36:27Zhttps://gitlab.ebi.ac.uk/pdbe/ccdutils/-/issues/20Proof of concept: Mogul report on PDB-CCD ideal coordinates2017-11-18T16:36:27ZOliver SmartProof of concept: Mogul report on PDB-CCD ideal coordinates# idea
* For a given wwPDB chemical components definition (PDB-CCD) run the [Mogul tool](https://www.ccdc.cam.ac.uk/solutions/csd-system/components/mogul/using) the chemical description from PDB-CCD
* Produce an html format report for th...# idea
* For a given wwPDB chemical components definition (PDB-CCD) run the [Mogul tool](https://www.ccdc.cam.ac.uk/solutions/csd-system/components/mogul/using) the chemical description from PDB-CCD
* Produce an html format report for the PDB-CCD ideal coordinates
* Use [Global Phasing Buster-Report](https://www.globalphasing.com/buster/wiki/index.cgi?BusterReport) detailed ligand report [example](http://grade.globalphasing.org/tut/erice_workshop/introtutorial/buster/00_MapOnly.report/ligand/detailedreport_A_501_.html#atableBOND) as a starting point - want coloured 2D diagrams to show which bonds/angles/torsions/rings are outliers.
* use ccd_utils with rdkit code
* for Mogul use the [CSD Python API](https://downloads.ccdc.cam.ac.uk/documentation/API/) rather than directly running MogulOliver SmartOliver Smarthttps://gitlab.ebi.ac.uk/pdbe/ccdutils/-/issues/19Develop utility command line script to read single cif and write coordinate f...2017-09-27T13:21:16ZOliver SmartDevelop utility command line script to read single cif and write coordinate files/images etc.## What
* Want a command line script so a user can read in any ccd cif and
* write a sdf if they want to - with options for ideal/model coordinates, hydrogen, alias on off
* write a pdb file with options ...
* write an image w...## What
* Want a command line script so a user can read in any ccd cif and
* write a sdf if they want to - with options for ideal/model coordinates, hydrogen, alias on off
* write a pdb file with options ...
* write an image with options ....
* Display properties about the molecule - lipinski things - num rings, rotable bonds etc. etc.
## How
* The command line arguments and the help text for each must be proposed as a comment on this page. **The proposal must be agreed to before any coding is done!**
* Script is to use argparse
* All points except 2 in https://ajminich.com/2013/08/01/10-things-i-wish-every-python-script-did/ must be followed.
* Can you unit test a command line script?
* If there are exceptions (file does not exist etc.) catch them produce a sensible error message to the user and call `sys.exit(1)` to indicate to the calling process there was problem.PDBeChem Backend Processing: get into preproductionOliver SmartOliver Smarthttps://gitlab.ebi.ac.uk/pdbe/ccdutils/-/issues/8Write CML files: *needs to be checked*2017-10-01T19:13:29ZOliver SmartWrite CML files: *needs to be checked** PDBeChem produces CML files.
* CML http://www.xml-cml.org/ might be a bit unpopular
* Should be fairly easy to write using standard xml library?
* But if difficult we could drop CML but it should be easy.* PDBeChem produces CML files.
* CML http://www.xml-cml.org/ might be a bit unpopular
* Should be fairly easy to write using standard xml library?
* But if difficult we could drop CML but it should be easy.PDBeChem Backend Processing: get into preproductionOliver SmartOliver Smart