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

---------

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

2025-09-26 16:40:11 +02:00

..

test_data

DCLV updates (#8756)

2025-09-26 16:40:11 +02:00

Wrap

DCLV updates (#8756)

2025-09-26 16:40:11 +02:00

AtomFeat.cpp

Replace GetImplicitValence() and GetExplicitValence() with GetValence() (#7926)

2025-01-28 21:09:03 +01:00

AtomFeat.h

Run clang-format against header files (#4143)

2021-06-08 07:57:51 +02:00

AUTOCORR2D.cpp

Run clang-format across everything (#7849)

2024-09-26 13:39:02 +02:00

AUTOCORR2D.h

clang-tidy-7 pass (#2408)

2019-04-16 12:05:47 -04:00

AUTOCORR3D.cpp

Run clang-format across everything (#7849)

2024-09-26 13:39:02 +02:00

AUTOCORR3D.h

clang-tidy-7 pass (#2408)

2019-04-16 12:05:47 -04:00

BCUT.cpp

Fixes #7364 (#7657)

2024-07-24 12:51:57 -04:00

BCUT.h

Run clang-format against header files (#4143)

2021-06-08 07:57:51 +02:00

catch_tests.cpp

DCLV updates (#8756)

2025-09-26 16:40:11 +02:00

CMakeLists.txt

Add Double Cubic Lattice Volume (DCLV). (#7234)

2024-03-20 13:35:54 +01:00

ConnectivityDescriptors.cpp

Add Kier Phi descriptor (#3864)

2021-03-06 09:40:27 -05:00

ConnectivityDescriptors.h

a few doxygen comment fixes (#4368)

2021-08-09 04:58:01 +02:00

CoulombMat.cpp

Run clang-format against cpp (#4358)

2021-10-20 04:25:27 +02:00

CoulombMat.h

Run clang-format against header files (#4143)

2021-06-08 07:57:51 +02:00

Crippen.cpp

Run clang-format against cpp (#4358)

2021-10-20 04:25:27 +02:00

Crippen.h

Run clang-format against header files (#4143)

2021-06-08 07:57:51 +02:00

Data3Ddescriptors.cpp

Run clang-format across everything (#7849)

2024-09-26 13:39:02 +02:00

Data3Ddescriptors.h

Run clang-format across everything (#7849)

2024-09-26 13:39:02 +02:00

datas.cpp

another clang-format run

2017-10-12 06:42:15 +02:00

DCLV_dots.h

DCLV updates (#8756)

2025-09-26 16:40:11 +02:00

DCLV.cpp

DCLV updates (#8756)

2025-09-26 16:40:11 +02:00

DCLV.h

DCLV updates (#8756)

2025-09-26 16:40:11 +02:00

EEM.cpp

Run clang-format against cpp (#4358)

2021-10-20 04:25:27 +02:00

EEM.h

clang-tidy-7 pass (#2408)

2019-04-16 12:05:47 -04:00

GETAWAY.cpp

Fixes #7264 (#8696)

2025-08-12 16:27:18 +02:00

GETAWAY.h

clang-tidy-7 pass (#2408)

2019-04-16 12:05:47 -04:00

Lipinski.cpp

Run clang-format across everything (#7849)

2024-09-26 13:39:02 +02:00

Lipinski.h

a few doxygen comment fixes (#4368)

2021-08-09 04:58:01 +02:00

MolData3Ddescriptors.cpp

Run clang-format across everything (#7849)

2024-09-26 13:39:02 +02:00

MolData3Ddescriptors.h

Run clang-format across everything (#7849)

2024-09-26 13:39:02 +02:00

MolDescriptors3D.h

Add CoulombMat calculator (#2993)

2020-03-15 17:38:21 +01:00

MolDescriptors.cpp

Remove Descriptors as a dependency of many other RDKit libraries (#7700)

2024-08-13 13:22:43 +02:00

MolDescriptors.h

support getNumAtoms and getNumHeavyAtoms in descriptors (#4200)

2021-06-04 11:48:07 -04:00

MolSurf.cpp

Fixes #5941 (#5942)

2023-01-14 08:54:30 -05:00

MolSurf.h

Modernization: use nullptr (#3143)

2020-05-25 09:40:01 +02:00

MORSE.cpp

clear up some compiler warnings (#6627)

2023-08-15 04:43:51 +02:00

MORSE.h

clang-tidy-7 pass (#2408)

2019-04-16 12:05:47 -04:00

MQN.cpp

Run clang-format across everything (#7849)

2024-09-26 13:39:02 +02:00

MQN.h

clang-tidy-7 pass (#2408)

2019-04-16 12:05:47 -04:00

OxidationNumbers.cpp

fix bond check (#6271)

2023-04-05 19:10:58 +02:00

OxidationNumbers.h

Fix oxidation numbers calculation (#6266)

2023-04-03 09:55:59 +02:00

PBF.cpp

Remove boost::foreach from public headers (#3820)

2021-02-17 14:15:48 +01:00

PBF.h

Run clang-format across everything (#7849)

2024-09-26 13:39:02 +02:00

PMI.cpp

Run clang-format across everything (#7849)

2024-09-26 13:39:02 +02:00

PMI.h

Run clang-format across everything (#7849)

2024-09-26 13:39:02 +02:00

Property.cpp

One final round of mem errors (#7943)

2024-10-29 06:46:43 +01:00

Property.h

One final round of mem errors (#7943)

2024-10-29 06:46:43 +01:00

RDF.cpp

Run clang-format across everything (#7849)

2024-09-26 13:39:02 +02:00

RDF.h

clang-tidy-7 pass (#2408)

2019-04-16 12:05:47 -04:00

RegisterDescriptor.h

One final round of mem errors (#7943)

2024-10-29 06:46:43 +01:00

test3D_old.py

Numpy 2 Support (#7531)

2024-06-19 07:54:50 +02:00

test3D.cpp

Update CI, remove some warnings (#6882)

2023-11-09 13:14:00 -05:00

test3D.py

Numpy 2 Support (#7531)

2024-06-19 07:54:50 +02:00

test.cpp

Fixes #6757 (#7664)

2024-07-25 15:26:22 +02:00

testATF.cpp

run clang_format (#5676)

2022-11-01 04:14:26 +01:00

testAUTOCORR2D.cpp

Fixes #3806 (#3823)

2021-02-22 13:32:17 +01:00

testAUTOCORR3D.cpp

Address compile warnings & trivial improvements (#2097)

2018-10-12 06:39:32 -04:00

testBCUT.cpp

Run clang-format across everything (#7849)

2024-09-26 13:39:02 +02:00

testCoulombMat.cpp

Run clang-format against cpp (#4358)

2021-10-20 04:25:27 +02:00

testEEM.cpp

Run clang-format against cpp (#4358)

2021-10-20 04:25:27 +02:00

testGETAWAY.cpp

Address compile warnings & trivial improvements (#2097)

2018-10-12 06:39:32 -04:00

testMORSE.cpp

Address compile warnings & trivial improvements (#2097)

2018-10-12 06:39:32 -04:00

testPBF.cpp

Update CI, remove some warnings (#6882)

2023-11-09 13:14:00 -05:00

testRDF.cpp

Address compile warnings & trivial improvements (#2097)

2018-10-12 06:39:32 -04:00

testRDFcustom.cpp

Cleanup warnings from clang-10 (#3238)

2020-06-19 17:16:22 -04:00

testSMWHIM.txt

Add a collection of new 3D descriptors (#1467)

2017-07-02 11:28:48 +02:00

testWHIM.cpp

Update CI, remove some warnings (#6882)

2023-11-09 13:14:00 -05:00

USRDescriptor.cpp

Run clang-format across everything (#7849)

2024-09-26 13:39:02 +02:00

USRDescriptor.h

clang-tidy-7 pass (#2408)

2019-04-16 12:05:47 -04:00

WHIM.cpp

Run clang-format across everything (#7849)

2024-09-26 13:39:02 +02:00

WHIM.h

clang-tidy-7 pass (#2408)

2019-04-16 12:05:47 -04:00