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

..

1mol.sdf

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

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

1mup.pdb

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

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

aid466.trunc.sdf

Fixes #351

2014-10-14 01:20:42 +02:00

auto2D.out

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

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

auto2D.out.new

[MRG] Fix PDB reader + add argument to toggle proximity bonding (#1629)

2017-11-15 06:53:31 +01:00

auto3D_dragon.out

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

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

auto3Dcustom.out

Add custom 3D Descriptors (#1867)

2018-05-14 15:07:55 +02:00

bace_200_bcut.sdf

Add BCUT 2D descriptors (#2957)

2020-02-23 16:09:36 +01:00

bobmol.sdf

Add CoulombMat calculator (#2993)

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

chlorobenzene2.sdf

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

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

chlorobenzene.sdf

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

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

CM1.out

Add CoulombMat calculator (#2993)

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

cyclohexane.mol

implementation of USRCAT descriptor added

2013-08-22 14:56:00 +02:00

doravirine.mol

add test for inertial shape factor

2018-09-17 08:47:11 +02:00

eem1.out

Add EEM partial charges (#1828)

2018-05-07 17:48:15 +02:00

eem2.out

Add EEM partial charges (#1828)

2018-05-07 17:48:15 +02:00

EGFR_first10_10confs.sdf

[MRG] Fix PDB reader + add argument to toggle proximity bonding (#1629)

2017-11-15 06:53:31 +01:00

ethane.sdf

DCLV updates (#8756)

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

GETAWAY2.out

[MRG] Fix PDB reader + add argument to toggle proximity bonding (#1629)

2017-11-15 06:53:31 +01:00

GETAWAY.new.out

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

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

GETAWAYcustom.out

Add custom 3D Descriptors (#1867)

2018-05-14 15:07:55 +02:00

github4167.sdf

Fixes #4167 (#4174)

2021-05-27 07:30:06 -04:00

linear_2atom.mol

Add some 3D molecular descriptors (#1084)

2016-10-10 08:34:08 -04:00

linear.mol

Add some 3D molecular descriptors (#1084)

2016-10-10 08:34:08 -04:00

MORSE.out

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

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

MORSEcustom.out

Add custom 3D Descriptors (#1867)

2018-05-14 15:07:55 +02:00

PBF_egfr.out

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

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

PBF_egfr.sdf

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

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

planar_3atom.mol

Add some 3D molecular descriptors (#1084)

2016-10-10 08:34:08 -04:00

planar.mol

Add some 3D molecular descriptors (#1084)

2016-10-10 08:34:08 -04:00

PMI_egfr.out

Fix/github1262 (#1265)

2017-01-22 05:49:52 +01:00

pmi.py

Reformat Python code for 2023.03 release (#6294)

2023-04-28 06:53:56 +02:00

pmi.sdf

Fix/github1262 (#1265)

2017-01-22 05:49:52 +01:00

RDF.out

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

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

RDFcustom.out

Add custom 3D Descriptors (#1867)

2018-05-14 15:07:55 +02:00

setEEM1.sdf

Add EEM partial charges (#1828)

2018-05-07 17:48:15 +02:00

setEEM2.sdf.gz

Add EEM partial charges (#1828)

2018-05-07 17:48:15 +02:00

TZL_model.sdf

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

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

Untitled.ipynb

[MRG] Fix PDB reader + add argument to toggle proximity bonding (#1629)

2017-11-15 06:53:31 +01:00

WHIM1custom.out

Add custom 3D Descriptors (#1867)

2018-05-14 15:07:55 +02:00

whim.new.out

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

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

whim.out

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

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

whim.out.txt

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

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

WHIMcustom.out

Add custom 3D Descriptors (#1867)

2018-05-14 15:07:55 +02:00

ZINC03815325.mol

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

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