Commit Graph

9 Commits

Author SHA1 Message Date
Greg Landrum
2ed6df962e allow default radii in the DCLV calculation (#8836) 2025-10-31 13:45:17 +01:00
Ricardo Rodriguez
e3f2e4651e Refactor iostreams includes (#8846)
* refactor iostreams includes

* restore ostream to MonomerInfo.cpp
2025-10-31 13:42:16 +01:00
Rachael Pirie
2e1d946f6d DCLV updates (#8756)
* first pass speed up of DCLV method

* drop to 320 surface points, add polar surface area v1

* suggested changes

* add John's GridKey implementation

* revert standard dots to float array

* pass simple variables by value

* stable pass radii as param

* final DCLV updates

- update max radius
- includeHs flag for polar surface area/volume
- fix silly include ligand mistake in checkExcludeAtoms
- update tests

* add missing break statements

* missing ;

* Greg changes 1

Co-authored-by: Greg Landrum <greg.landrum@gmail.com>

* Greg changes 2

Co-authored-by: Greg Landrum <greg.landrum@gmail.com>

* Greg changes 3

Co-authored-by: Greg Landrum <greg.landrum@gmail.com>

* Greg changes 4

Co-authored-by: Greg Landrum <greg.landrum@gmail.com>

* Greg changes 5

Co-authored-by: Greg Landrum <greg.landrum@gmail.com>

* Greg changes 6

Co-authored-by: Greg Landrum <greg.landrum@gmail.com>

* Greg changes 7

Co-authored-by: Greg Landrum <greg.landrum@gmail.com>

* Greg changes 7

Co-authored-by: Greg Landrum <greg.landrum@gmail.com>

* missing return false

* Greg changes 8

Co-authored-by: Greg Landrum <greg.landrum@gmail.com>

* fix incomplete doc string

* fix pytests

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Co-authored-by: greg landrum <greg.landrum@gmail.com>
2025-09-26 16:40:11 +02:00
David Cosgrove
79403df1b0 Synthon space bad chiral count (#8550)
* Count chiral atoms just counts tetrahedral atoms.

* Put an actual check in.

* Randomly fix some unconnected warnings.

* Curb my enthusiasm for std::cmp_less.

* Trigger Build

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Co-authored-by: David Cosgrove <david@cozchemix.co.uk>
2025-06-03 13:09:09 +02:00
Hussein Faara
44364fd982 remove no-op macros and dead code (pt 4) (#8037)
* remove no-op macros and dead code (pt 4)

* review comments
2025-01-26 07:49:50 +01:00
Greg Landrum
da6cd73168 Run clang-format across everything (#7849)
* run clang-format-18 across Code/*.cpp and Code/*.h

* run clang-format-18 across External
2024-09-26 13:39:02 +02:00
Rachael Pirie
c651ca61de Dclv fix (#7480)
* fix for ligand only DCLV calcs

* formatting suggestion from review

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Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
2024-06-04 16:14:05 +02:00
Greg Landrum
eebad845f5 fix a leak in the new DCLV code (#7279) 2024-03-21 12:56:41 +01:00
Rachael Pirie
58023dd3b8 Add Double Cubic Lattice Volume (DCLV). (#7234)
* Add Double Cubic Lattice Volume (DCLV).

Method to compute the solvent accessible surface area and volume, van der Waals volume, compactness and packing density of a protein. Implemented from:  Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander and Michael Scharf, "The Double Cubic Lattice Method: Efficient Approaches to Numerical Integration of Surface Area and Volume and to Dot Surface Contouring of Molecular Assemblies", Journal of Computational Chemistry, Vol. 16, No. 3, pp. 273-284, 1995.

* refactor

* DCLV is no longer a configuration option

* add to the docs

* standalone test has been removed

* reduce use of pointers as args

* DCLV to catch_tests

* update python wrapper

* add copyright statements

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Co-authored-by: greg landrum <greg.landrum@gmail.com>
2024-03-20 13:35:54 +01:00