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AstraZeneca / kallisto

Efficiently calculate 3D-features for quantitative structure-activity relationship approaches.
https://ehjc.gitbook.io/kallisto/
Apache License 2.0
61 stars 21 forks source link

Feature request: solvent accessible surface area (SASA) #10

Open f3rmion opened 3 years ago

f3rmion commented 3 years ago

Describe the solution you'd like Implement solvent accessible surface area (SASA) using an angular Lebedev-Laikov grid as described in "A quadrature formula for the sphere of the 131st algebraic order of accuracy", Doklady Mathematics, Vol. 59, No. 3, 1999, pp. 477-481. Extend present grid implementation in src/grid.py to cover finer grids and use the defined gridpoints to construct a SASA.

awvwgk commented 3 years ago

Note that most Lebedev-Laikov grid implementations carry either the LGPL (inherited from J. Burkardt's version) or originate from the CCL announcement of the original implementation of D. Laikov, which has somewhat unclear licensing conditions but might be considered public domain (?).

f3rmion commented 3 years ago

Note that most Lebedev-Laikov grid implementations carry either the LGPL (inherited from J. Burkardt's version) or originate from the CCL announcement of the original implementation of D. Laikov, which has somewhat unclear licensing conditions but might be considered public domain (?).

That's right, using Burkardt's version would force an LGPL license on the project. Laikov's original version does not seem to be properly licensed, especially since the linked Fortran version was not implemented by Laikov himself, but rather by Christoph van Wuellen depending on an initial C-version written by Laikov.

awvwgk commented 3 years ago

My xtb and DFTB+ implementation of the grids are based on J. Burkhardt's version due to the clearer and compatible licensing.

Every other implementation (C, Matlab, Python, ...) I have been able to find so far at some point goes back to J. Burkhardt's version or C. van Wuellen's version of the C implementation by D. Laikov. The original C code seems to be lost, at least I wasn't able to find it up to now.

Montana commented 3 years ago

Thank you @awvwgk!