pychemovality

pychemovality is a python library for estimating the ovality of molecules.

The library consists of three parts:

1. Input File Generation: This part creates an XYZR file necessary for the calculations downstream. XYZ refers to coordinates and R refers to the vanderwaals radii.
2. Calculating SES Area and Volume: The SES area and volume calculation takes place inside a Fortran executable that is created by compiling a modified version of the original Gepol93 Fortran script. This script provides the possibility to calculate various molecular surface area such as the Vanderwaals surface area, the molecular surface area and solvent-excluding surface (SES) area and the corresponding volume. For the ovality calculation we use the SES area.
3. Calculate Ovality: Utilize area and volume to calculate ovality

Modifications made to the original Fortran 77 code:

• Bug fixes
• Modified the fortran code to accept sys args from upstream python script
• Modified the fortran code to log all relevant details into a file instead of stdout
• Made the fortran code compatible with latest gfortran for compilation into an executable

Usage

Clone the repo and cd into root dir:

git clone https://github.com/vandan-revanur/pychemovality 
cd pychemovality

Three types of coordinate files can be used as input for calculating ovality.

• XYZ file
• PDB file
• MOL file

To get the ovality of the molecule in your coordinate file run the following:

python pychemovality --coord-file-path <path-to-your-coord-file>

Fortran Code Compilation

If you would like to compile the Fortran code residing in the Fortran directory of the repo, instructions are available in the Compilation Instructions

Authors

• Vandan Revanur

License

This project is licensed under the BSD License - see the LICENSE.txt file for details

References

[1] Pascual-ahuir, J.L., Silla, E. and Tuñon, I. (1994), GEPOL: An improved description of molecular surfaces. III. A new algorithm for the computation of a solvent-excluding surface. J. Comput. Chem., 15: 1127-1138. https://doi.org/10.1002/jcc.540151009

[2] X-Ability Co. Ltd, 6.19.6 Molecular Surface Area & Volume, Winmostar™ User Manual, Release 11.4.2, Feb 2023, pp 199-200

[3] Pirika, Y. (2011) Properties Estimation: Density: Volume, Surface Area and Ovality estimation with HTML5 program, Density, volume, surface tension and ovality estimation with HTML5 program. Available at: https://www.pirika.com/ENG/TCPE/Den-H5.html (Accessed: March 3, 2023).

[4] Pirika, Y. (2011) Properties Estimation: Estimation of density and volumetric properties, Estimation of density and volumetric properties. Available at: https://pirika.com/ENG/TCPE/Den-Theory.html (Accessed: March 3, 2023).