https://github.com/nbehrnd/structurfinder_cif_export

A concept study to retrieve at least some of the .cif-relevant data from structurefinder's .sqlite database file.
https://github.com/nbehrnd/structurfinder_cif_export

cif datawarrior python structurefinder

Last synced: 6 days ago
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A concept study to retrieve at least some of the .cif-relevant data from structurefinder's .sqlite database file.

• Host: GitHub
• URL: https://github.com/nbehrnd/structurfinder_cif_export
• Owner: nbehrnd
• Created: 2020-05-07T17:01:21.000Z (over 4 years ago)
• Default Branch: master
• Last Pushed: 2020-05-11T18:17:34.000Z (over 4 years ago)
• Last Synced: 2024-11-14T15:49:01.942Z (2 months ago)
• Topics: cif, datawarrior, python, structurefinder
• Language: Python
• Size: 55.7 KB
• Stars: 0
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: readme.md

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README

        
This script, `sf_reader.py`, written for the CLI of Python 3, retrieves

information from the .sqlite data base StructureFinder (by Kratzert and

Krossing) writes.

StructureFinder (https://www.xs3.uni-freiburg.de/research/structurefinder,

https://github.com/dkratzert/StructureFinder) provides the infrastructure

to set up a local database of crystallographic data in .cif files.  It

is desirable to complement structural information with applications like

DataWarrior (http://openmolecules.org/datawarrior/index.html) already

offering access to the Crystallographic Open Database

(http://www.crystallography.net/cod/index.php) with a snapshot (

http://www.openmolecules.org/datawarrior/datafiles.html) with model data

not yet in the public, too 

(https://github.com/dkratzert/StructureFinder/issues/3).

By a call of

`python sf_reader.py example.sqlite`

the script will retrieve a _minimal subset_ of data from the .sqlite data

base StructureFinder writes: lattice constants, space group

symmetry, symmetry operators; atom label, atom label and atom coordinates.

The script does not consider additional crystallographic information

such as site occupancy factors used to describe positional disorder,

or anisotropic displacement parameters.

Note that script restores the file name of the `.cif`, rather than

the model name of the within the script.  This reflects that more

often than wanted `.cif` provided as supporting information do not

provide a (as possibly meaningful) name to the structure model, and

publishers include in the name the `.cif` accessible e.g. a part

of the doi of the corresponding publication.

Equally note that the retrieval should be restricted to `.cif` which

originally (i.e., when read by StructureFinder) contained only one

single model _per file_.

As a training, the repository contains test data.  File

`three_data.sqlite` is a test data base written by StructureFinder

(version 47) while accessing structure models `ACSALA01.cif`,

`ADRENL.cif`, and `BAPLOT01.cif`; these files are part of CCDC's freely

accessible [teaching subset](https://www.ccdc.cam.ac.uk/Community/educationalresources/teaching-database/),

section [Drug molecules](https://www.ccdc.cam.ac.uk/structures/search?compound=drug%20molecules), 

and are copied in sub-folder `input`.

Running `python sf_reader.py three_data.sqlite` restores the three

`.cif` files deposit in sub-folder `output`.

Additional paramaters the script accepts are

-h    to access the help screen

-v    to access the version information