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18 Commits

Author SHA1 Message Date
David Cosgrove
5235f53910 Gaussian shape overlays (#9095) 2026-03-26 21:53:54 +01:00
jasondbiggs
5065340b20 a few doxygen comment fixes (#4368) 
* collection of doxygen fixes

* more files with fixed doxygen comments

* more doxygen fixes

* more doxygen fixes

* last set of doxygen comment fixes

Co-authored-by: Jason Biggs <jasonb@wolfram.com>
 2021-08-09 04:58:01 +02:00
Paolo Tosco
261fd7812e fixes #4302 (#4303) 
Co-authored-by: Paolo Tosco <paolo.tosco@novartis.com>
 2021-07-10 05:06:25 +02:00
Greg Landrum
9ab84f0884 Add rendering of SGroup brackets to MolDraw2D (#3586) 
* backup

* further progress

* backup

* refactor handling of atom/bond annotations

move to a single annotation list to make it easier to add new annotation
types

* backup, doesn't actually work

* not unhappy with how the bracket rendering now works
still need to do bracket annotations

* backup

* commit first pass at brackets annotations

* add a bit more flexibility to how we handle annotations
Stll needs to be elaborated a bit, but the tests currently pass

* cleanup

* support comic mode with brackets

moves the handdrawnLine code to MolDraw2D_detail, which is a better place for it

* updates in response to review
 2020-11-28 08:03:20 +01:00
Eisuke Kawashima
e86e2c1d5d Modernization: use nullptr (#3143) 2020-05-25 09:40:01 +02:00
Eisuke Kawashima
5cd27a242f Fix typo (#2862) 
* Fix typo

* Reflect the comments

* Fix more typos
 2019-12-31 06:43:27 +01:00
Eisuke Kawashima
dc7cc84a0c Fix typo [ci skip] 2019-10-17 17:45:50 +09:00
Greg Landrum
ec31bea97b clang-tidy-7 pass (#2408) 2019-04-16 12:05:47 -04:00
Greg Landrum
2738c35178 Fixes #1903 (#1971) 
* Fixes #1903

* update SWIG bindings too
 2018-07-25 09:14:17 +02:00
Paolo Tosco
c08ea49bda - enable building DLLs on Windows (#1861) 
* - enable building DLLs on Windows

* - export.h and test.h are now auto-generated by CMake
 2018-05-16 08:42:41 +02:00
Greg Landrum
fb2c546948 Fix/github1262 (#1265) 
* fix for calculation of prinicipal moments of inertia

* fix a typo
update expected values

* PMI and NPR tests working

* cleanup some of the other descriptors and tests

* Test against Moments.py descriptors

* add new tests from Brian

* remove some warnings
 2017-01-22 05:49:52 +01:00
Greg Landrum
4f2ec84e7b Add some 3D molecular descriptors (#1084) 
* update .gitignore

* foundation for 3D descriptors
move PBF into core

* cleanup work

* a bit more cleanup

* move the principal moments calc to MolTransforms

* cleanup

* cleanups

* add caching of the principal moments and values

* do not include the 3D descriptors in MolDescriptors.h

* the properties are computed

* add PMI descriptors and tests

* add tests for NPR descriptors

* return 0 when the largest PMI is zero

* PMI edge case tests

* NPR edge case tests

* PBF edge case tests

* PBF edge case tests

* more edge cases

* add a few more 3d descriptors

* add defns to docs

* tests for the new descriptors

* add versions to new descriptors

* add 3d descriptors to python wrapper

* add eigen support to the travis build

* try to get non-windows builds working

* remove computeCovarianceMatrix() from java wrapper

* make pmi property names "private"
 2016-10-10 08:34:08 -04:00
Paolo Tosco
dbaff21056 - fixed a few missing "const" declarations on "get" functions 2016-02-21 21:24:56 +00:00
Greg Landrum
e08e0d16d8 first pass, using google style 2015-11-14 14:58:11 +01:00
ptosco
865175104b - added getters/setters for bond lengths, angles, dihedrals 
in the MolTransforms namespace:

  * getBondLength(conf, iAtomId, jAtomId)
                 (only in this case, atoms need not be covalently bonded)
  * setBondLength(conf, iAtomId, jAtomId, value)
  * getAngleRad(conf, iAtomId, jAtomId, kAtomId)
  * setAngleRad(conf, iAtomId, jAtomId, kAtomId, value)
  * getAngleDeg(conf, iAtomId, jAtomId, kAtomId)
  * setAngleDeg(conf, iAtomId, jAtomId, kAtomId, value)
  * getDihedralRad(conf, iAtomId, jAtomId, kAtomId, lAtomId)
  * setDihedralRad(conf, iAtomId, jAtomId, kAtomId, lAtomId, value)
  * getDihedralDeg(conf, iAtomId, jAtomId, kAtomId, lAtomId)
  * setDihedralDeg(conf, iAtomId, jAtomId, kAtomId, lAtomId, value)

- added the corresponding Python wrappers in rdMolTransforms
  (same prototype as C++; as usual all Python methods
  have an uppercase initial)

- added relevant C++/Python tests
 2013-10-15 11:59:08 +02:00
Greg Landrum
f3fbef45c5 update copyright statements 2010-09-26 17:04:37 +00:00
Greg Landrum
052ec66542 cleanups: 
remove x bit from headers and sources;
remove a couple empty files from Code/GraphMol
 2010-09-08 04:25:57 +00:00
Greg Landrum
75a79b6327 initial import 2006-05-06 22:20:08 +00:00