pdbe issueshttps://gitlab.ebi.ac.uk/groups/pdbe/-/issues2018-03-28T06:56:43Zhttps://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/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/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 Smart