Structural Python (Back) Calculator Interface for PDBs
Goal: User friendly Python3 based interface to generate back-calculated experimental data for singular and multiple (ensembles of) PDB structures.
Back-Calculators: The current back calculators integrated are:
- NOE, J-Coupling, smFRET: Internal
- Paramagnetic Relaxation Enhancement (PRE): distance-based and DEERPREdict
- Chemical shifts (CS): UCBShift
- SAXS: CRYSOLv3
- Hydrodynamic Radius (Rh): HullRadSAS
- Residual Dipolar Couplings (RDC): PALES
Please note for third-party software, installation instructions have been fully documented and tested for the following Linux Ubuntu versions: 24.04 LTS, 22.04 LTS, 20.04 LTS, and 18.04 LTS.
To make new requests and/or additions, please see docs/contributing.rst.
Developer Notes: project CI based on @joaomcteixeira's Python-Project-Skeleton template. Developed as a standalone program with integration into the IDPConformerGenerator platform in mind.
More detailed documentation can be found at: https://spyci-pdb.readthedocs.io/en/stable/
Within the repository you can find:
- Installation instructions in
docs/installation.rst. - Usage instructions in
docs/usage.rst. - See also the examples in the
example/folder.
If you use SPyCi-PDB, please cite:
Liu et al., (2023). SPyCi-PDB: A modular command-line interface for back-calculating experimental datatypes of protein structures.. Journal of Open Source Software, 8(85), 4861, https://doi.org/10.21105/joss.04861
v0.5.3