scripts

PDBeChem pipeline

Script for PDBeChem backend infrastructure. Processes the wwPDB Chemical Components Dictionary file components.cif producing files for:

http://ftp.ebi.ac.uk/pub/databases/msd/pdbechem_v2/

To do this components.cif is split into individual PDB chemical component definitions cif files, sdf files, pdb files and image files. In addition creates chem_comp.xml and chem_comp.list for all components. More detailed description can be found here:

https://gitlab.ebi.ac.uk/pdbe/release/pdbechem

class pdbeccdutils.scripts.process_components_cif_cli.PDBeChemManager(pubchem_templates='', general_templates='/home/runner/work/ccdutils/ccdutils/pdbeccdutils/data/general_templates', library_path='/home/runner/work/ccdutils/ccdutils/pdbeccdutils/data/fragment_library.tsv', procedure='ccd')

Manager orchestrating computation and generation of all parts of the PDBeChem update process.

process_single_component(ccd_reader_result, out_dir, outfile_prefix)

Process single PDB-CCD component.

Parameters:

  • ccd_reader_result (CCDReaderResult) – pdbeccdutils parser output.

  • out_dir (Path) – Out directory

  • outfile_prefix – Prefix of output filename

Returns:

Whether or not all the files were succesfully written.

Return type:

bool

run(components_path, out_dir)

Process components

Parameters:

  • components_path (Path) – Path to the components.cif file.

  • out_dir (Path) – Path to the out_dir

pdbeccdutils.scripts.process_components_cif_cli.create_parser()

Sets up parse the command line options.

Returns:

argparse.Namespace parser

pdbeccdutils.scripts.process_components_cif_cli.main()

Runs the PDBeChem pipeline

Setup PubChem library

Small toolkit to update database with Pubchem depictions with within the pdbeccdutils. Based on the inchikey provided in the CCD a corresponding 2D layout is downloaded from PubChem database.

pdbeccdutils.scripts.setup_pubchem_library_cli.main()

Main method of the whole process.