SPyCi-PDB

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:

1. PRE, NOE, J-Coupling, smFRET: Internal

2. Chemical shifts (CS): UCBShift

3. SAXS: CRYSOLv3

4. Hydrodynamic Radius (Rh): HullRad

5. Residual Dipolar Couplings (RDC): PALES

Please note for third-party software, installation instructions have been fully documented and tested for Linux Ubuntu Focal Fossa (20.04.X LTS) and Bionic Beaver (18.04.X 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.

Contents

• Installation
  • If you already have an idpconfgen environment
  • Standalone From Source
  • Updating SPyCi-PDB
  • Installing Third-party Software
• Usage
  • Command-Lines
  • Formatting for Input and Output Files
  • Basic Usage Examples
  • PRE, NOE, and JC Modules
  • CS Module - Using UCBShift
  • SAXS Module - Using CRYSOLv3
  • Rh Module - Using HullRad 8.1
• Contributing
  • Fork this repository
  • Install for developers
  • Make a new branch
  • Uniformed Tests with tox
• How to Cite
• Authors
  • Main Developers/Maintainers
  • Contributors
  • Acknowledgements
• Changelog
  • v0.3.13 (2023-07-27)
  • v0.3.12 (2023-07-27)
  • v0.3.11 (2023-07-27)
  • v0.3.10 (2023-05-11)
  • v0.3.9 (2023-05-10)
  • v0.3.8 (2023-05-10)
  • v0.3.7 (2023-05-10)
  • v0.3.6 (2023-05-10)
  • v0.3.5 (2023-05-02)
  • v0.3.4 (2023-04-26)
  • v0.3.3 (2023-04-15)
  • v0.3.2 (2023-04-13)
  • v0.3.1 (2023-04-12)
  • v0.3.0 (2023-04-10)
  • v0.2.3 (2023-03-27)
  • v0.2.2 (2023-03-07)
  • v0.2.1 (2023-03-06)
  • v0.2.0 (2023-01-27)
  • v0.1.16 (2023-01-18)
  • v0.1.15 (2023-01-16)
  • v0.1.14 (2022-11-28)
  • v0.1.13 (2022-09-30)
  • v0.1.12 (2022-09-29)
  • v0.1.11 (2022-09-28)
  • v0.1.10 (2022-09-20)
  • v0.1.9 (2022-09-20)
  • v0.1.8 (2022-09-19)
  • v0.1.7 (2022-09-19)
  • v0.1.6 (2022-09-14)
  • v0.1.5 (2022-09-08)
  • v0.1.4 (2022-09-01)
  • v0.1.3 (2022-09-01)
  • v0.1.2 (2022-08-31)
  • v0.1.1 (2022-08-31)
  • v0.1.0 (2022-08-24)
  • v0.0.15 (2022-08-24)
  • v0.0.14 (2022-08-23)
  • v0.0.13 (2022-08-22)
  • v0.0.12 (2022-08-12)
  • v0.0.11 (2022-08-12)
  • v0.0.10 (2022-08-12)
  • v0.0.9 (2022-08-10)
  • v0.0.8 (2022-08-10)
  • v0.0.7 (2022-08-10)
  • v0.0.6 (2022-08-10)
  • v0.0.5 (2022-08-09)
  • v0.0.4 (2022-08-08)
  • v0.0.3 (2022-08-08)
  • v0.0.2 (2022-08-08)
  • v0.0.1 (2022-07-28)

Indices and tables

• Index

• Module Index

• Search Page