ccdutils issueshttps://gitlab.ebi.ac.uk/pdbe/ccdutils/-/issues2017-09-28T10:55:02Zhttps://gitlab.ebi.ac.uk/pdbe/ccdutils/-/issues/27process_components_cif improve logging output with a summary at the end of th...2017-09-28T10:55:02ZOliver Smartprocess_components_cif improve logging output with a summary at the end of the run.From issue #17 **need to improve logging output - would be good to list number of unsuccessful sdf, pdb, images etc.**From issue #17 **need to improve logging output - would be good to list number of unsuccessful sdf, pdb, images etc.**PDBeChem Backend Processing: get into preproductionhttps://gitlab.ebi.ac.uk/pdbe/ccdutils/-/issues/28process_components_cif separate out functionality to split into individual cif2017-09-28T11:40:31ZOliver Smartprocess_components_cif separate out functionality to split into individual cif* from discussion with Sameer.
* for production want to be able to start processes that just depend on the split PDB-CCD mmcif as soon as possible
* so add command line options to process_components cif
| option | what |
| -------- | --...* from discussion with Sameer.
* for production want to be able to start processes that just depend on the split PDB-CCD mmcif as soon as possible
* so add command line options to process_components cif
| option | what |
| -------- | -------- |
| `--just_mmcif` | does the split into individual mmcif files but no further processing. The `--output_dir` must be specified with this option. |
| `--apart_from_mmcif` | used after `--just_mmcif` to do the rest of the processing into coordinate files images `chem.xml` etc. The `--output_dir` option must be specified with this option. `--clean` must not be. |
| `--clean` | remove any existing `output_dir` completely |
* not sure whether this is necessary need to sort out #29 #30 first.PDBeChem Backend Processing: get into preproductionhttps://gitlab.ebi.ac.uk/pdbe/ccdutils/-/issues/31Produce images of named fragments2017-10-01T09:52:34ZOliver SmartProduce images of named fragments* Have got the named fragment searching working but the fragments used have to improved see #24
* in the current PDBeChem web interface there is a Fragments `edit` popup:
![pdbe_chem_fragment_search](/uploads/7451398b8da99eae92051496eb...* Have got the named fragment searching working but the fragments used have to improved see #24
* in the current PDBeChem web interface there is a Fragments `edit` popup:
![pdbe_chem_fragment_search](/uploads/7451398b8da99eae92051496ebf88101/pdbe_chem_fragment_search.png)
* this shows a picture of the fragment (to the right) on a mouse over of the fragment name (here `oxazolidinedione`)
* this issue is provide nice images of the new fragments to replace the old ones.PDBeChem Backend Processing: get into preproductionhttps://gitlab.ebi.ac.uk/pdbe/ccdutils/-/issues/32write a document about porphryin remediation2017-09-29T08:37:43ZOliver Smartwrite a document about porphryin remediationWork on heme #5 reveals some inconsistency in how porphryin-like rings are described in the PDB-CCD. Should work up a document to propose a remediation.
Not a %2 issue but keep on board so as not to forget :elephant: Work on heme #5 reveals some inconsistency in how porphryin-like rings are described in the PDB-CCD. Should work up a document to propose a remediation.
Not a %2 issue but keep on board so as not to forget :elephant: PDBeChem Backend Processing: get into preproduction