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Setting up CSD‐Theory Web
This section of the wiki contains information on the setup options for CSD-Theory Web. CSD-Theory Web requires two databases:
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A CSD-Theory metadata database containing additional theoretical data. This must be named CSPDatabase.db.
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A CSD-Theory landscape database for initial searching of landscape structures, e.g. CSPLandscape.csdsqlx
These two databases are used in conjunction to create the CSD-Theory charts and reports.
To create or update a CSD-Theory Landscape Database, you will need the Python Utilities. These can be downloaded from the CCDC Downloads page under CSD Python API > Python CSD Python API Utilities. If you do not see the CSD Python API listed in the available downloads, you may need to sign in.
Relevant scripts can be found under ccdc > utitities > csp.
Use the import_csp_landscape.py script to import the CIFs. This script can build a new database or update an existing one.
| argument | description | examples |
|---|---|---|
| landscape_database | URL of the landscape database server (the same as the URL you use in your web browser) |
https://csd-theory.ccdc.cam.ac.uk https://csd-theory.ccdc.cam.ac.uk:8080 |
| structure_database | crystal structure database (.csdsqlx). Either point to an existing database via the filepath, or give it a name to build it directly. |
E:\CSP_Upload\existingLandscapeDatabaseName.csdsqlx newLandscapeDatabaseName.csdsqlx |
| cif_files | CIF file(s) for structure(s) to be imported to the landscape and structure databases (.cif) | E:\CSP_Upload\CSP_enriched_CIFs\singlestructurelandscape.cif E:\CSP_Upload\CSP_enriched_CIFs*.cif |
| -n LANDSCAPE_NAME | The name of the CSP landscape. If not included, landscape name will be generated from the CIFs |
|
| -v, --validate | Validate, rather than add, that the CIF files have been added to a CSP landscape |
Some sample commands include:
Validate importing a single CIF into an existing database at https://csd-theory.ccdc.cam.ac.uk :
import_csp_landscape.py https://csd-theory.ccdc.cam.ac.uk E:\CSP_Upload\existingLandscapeDatabaseName.csdsqlx E:\CSP_Upload\CSP_enriched_CIFs\singlestructurelandscape.cif -v
Import a folder of CIFs into a new database called "NewDatabase.csdsqlx" at https://csd-theory.ccdc.cam.ac.uk:8080/, with landscape name “NewLandscape”:
import_csp_landscape.py https://csd-theory.ccdc.cam.ac.uk:8080 NewDatabase.csdsqlx E:\CSP_Upload\CSP_enriched_CIFs\*.cif -n NewLandscape
The CSD-Theory Landscape database needs to be added to the /csd-data/ folder.
If you are copying the database via an SCP command to transfer the file between a local host and a remote host, you may need to run chown on the /csd-data/ folder to change it to the owner who is running SCP, such as onsiteadmin.
Ensure once the SCP command is complete, you change the owner of /csd-data/ and all databases inside back to ccdc.
Ensure you have copied the blank CSPDatabase.db to your /csd-data/ folder and ensure the name is CSPDatabase.db
Containers run as the ccdc user, so run chown ccdc.ccdc on the CSPDatabase.db file. The user "ccdc" must have read access to any in-house or CSP databases, as indicated in link.
Start by taking down the instance of the WebCSD docker container and update the docker-compose.database.yml file. You can start from docker-compose.sample-csd-theory-db-config.yml. Updates should include:
Update locations and names in the the webcsdbackend volumes and environment sections, e.g.
webcsdbackend:
volumes:
- ./csd-data/LandscapeDatabaseName.csdsqlx:/csd-data
environment:
- ServiceSettings__Databases__2__Name=LandscapeDatabaseName
- ServiceSettings__Databases__2__ConnectionString=/csd-data/LandscapeDatabaseName.csdsqlx
the volumes of the webcsd-theory section and optional settings in the environment section (described below), e.g.
volumes:
- ./csd-data/CSPDatabase.db:/app/CSPDatabase.db
- ./csd-data/LandscapeDatabaseName.csdsqlx:/app/databases/CSPLandscape.csdsqlx
environment:
- ReportSettings__CspStructureDatabaseConnectionString=/app/databases/CSPLandscape.csdsqlx
- ReverseProxy__Clusters__csdtheory__Destinations__csdtheory/destination1__Address=http://webcsd-theory:${WEBCSD_PORT}
Once you have edited and saved the docker-compose.database.yml file, restart the docker container. You should now be able to access all the basic CSD-Theory functionality.
If you wish to run reports, the Landscape Database needs to be mapped to CSPLandscape.csdsqlx and you need to include the ReportSettings environment information.
If you are running on a port other than 80, ensure the ConnectionString environment detail (ReverseProxy) includes the port information. Do not include a backslash on the CSP url.
Once a CSP landscape has been ingested into CSD-Theory there are additional steps that can be taken to add extra information.
To compare structures within a landscape, the script csp_similar_structures.py will produce a heatplot showing the similarity between (up to) the 25 lowest energy structures. The script has a syntax
python csp_similar_structures.py http://my.landscape.server:12345 wonder_drug.csdsqlx wonder_drug --pxrd_threshold 0.98
This will run similar structures calculations in the CSP landscape wonder_drug. The optional argument --pxrd_threshold sets the PXRD similarity threshold.
Structures within a landscape can also be compared to experimental data from an in-house database. This requires the script csp_cross_reference.py with the syntax
python csp_cross_reference.py http://my.landscape.server:12345 wonder_drug.csdsqlx my_in-house_database.csdsql
This will cross reference all structures in the CSP database "wonder_drug" with observed structures in the my_inhouse_database of experimental structures. If no in-house database is referenced the script will run a comparison against the CSD.