Peter Eastman
8eeee16de9
Templates can match whole molecules ( #5181 )
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* Templates can match whole molecules
* addExtraParticles() supports molecule templates
* Documentation on molecule templates
* Bug fix
2026-01-30 11:16:39 -08:00
Evan Pretti
16efb71b6e
Add Lipid21 and update documentation ( #5066 )
2025-09-16 09:47:27 -07:00
Peter Eastman
0ae7458ecc
Fixed error adding vsites that depend on other vsites ( #4898 )
2025-04-17 09:51:32 -07:00
Peter Eastman
9e4b6ba594
addHydrogens() allows specifying exactly what hydrogens to add ( #4585 )
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* addHydrogens() allows specifying exactly what hydrogens to add
* Prevent CI from using numpy 2.0
2024-07-09 07:51:24 -07:00
Peter Eastman
5d407c944a
Fixed errors with residueTemplates arguments to Modeller methods ( #4528 )
2024-04-29 11:32:35 -07:00
Nicola De Mitri 2
127a373381
Preserve bond type and order in all Modeller operations ( #4323 )
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* Py wrapper: preserve bond data in Modeller operations
* regression tests for add(), delete(), deleteWater(), addSolvent()
* Tests for addHydrogens and addExtraParticles
* Cosmetic
* A single regression test spanning a whole workflow
* Remove now-redundant tests
* Test also deleteWater and addHydrogens. Remove excessive assertions.
2023-11-27 18:43:35 -08:00
Brian Andrews
87a70daf17
Add SWM4-NDP water to modeller.addSolvent() ( #3760 )
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* add swm4-ndp water to addSolvent
* add equilibrated box
* typo of water radius
* fixed addSolvent description
* add swm4 to tests
2022-09-06 09:34:49 -07:00
Peter Eastman
b1edd92261
Improvements to choosing box size ( #3537 )
2022-03-30 09:41:26 -07:00
Peter Eastman
b33a7a5a10
Added option for box shape when building solvent boxes ( #3480 )
2022-02-27 12:36:35 -08:00
Peter Eastman
d83c2724a4
Added GLYCAM ( #3303 )
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* Added GLYCAM
* Improved tests and documentation
* Fixed incorrect external bonds
2021-10-29 15:56:44 -07:00
Peter Eastman
e53bdc5eab
Top level Python module is now "openmm" ( #3000 )
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* Top level Python module is now "openmm"
* Updated module names in examples
* Updated module names in documentation
* Updated module in CI scripts
* Added deprecation warning
2021-02-01 09:40:37 -08:00
peastman
41d061dd24
Merge pull request #2440 from JoaoRodrigues/bugfix_ion_concentration
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Fixes _addIons behavior for membrane systems.
2019-10-28 14:09:58 -07:00
João Rodrigues
46b334cecd
Added test for addHydrogens to check for atom positions
2019-10-25 14:42:01 -07:00
João Rodrigues
1695878ac0
Adds test to check ion addition in addMembrane test. Was untested before
2019-10-22 21:44:05 -07:00
joaorodrigues
94d6275bf0
Forgot to undo my test optimization...
2019-10-12 12:15:04 -07:00
joaorodrigues
3a09cfe6c9
Modified test_addMembrane to be more thorough and use a realistic system.
2019-10-12 12:08:49 -07:00
peastman
4e37c418aa
Created test case for addMembrane()
2017-11-29 13:41:54 -08:00
jchodera
4b2ef27cb9
Fixed tests
2016-01-19 15:19:01 -05:00
Peter Eastman
4e794b3835
Improvements to addHydrogens()
2016-01-14 14:18:20 -08:00
Peter Eastman
3e4f386615
Added missing support for LocalCoordinatesSite
2015-11-06 16:07:19 -08:00
peastman
58f5168e7f
Merge pull request #1240 from peastman/extraparticles
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addExtraParticles() can use bonds to select positions
2015-11-06 15:00:47 -08:00
Peter Eastman
eb1c585820
Bug fix
2015-11-06 11:17:03 -08:00
Peter Eastman
bc41b7a000
addExtraParticles() can use bonds to select positions
2015-11-03 14:39:48 -08:00
Peter Eastman
85b0ef020e
Added neutralize option to addSolvent()
2015-11-02 16:15:35 -08:00
peastman
ffc96cc637
Removed spaces that got added by the editor
2015-05-04 11:02:00 -07:00
peastman
92dfd1ff4b
Added option to add a fixed number of solvent molecules
2015-05-04 10:42:33 -07:00
peastman
36cdbc8d34
Fixed exception in addExtraParticles()
2015-03-03 11:01:33 -08:00
Peter Eastman
21a39eaf11
Modeller supports triclinic boxes
2015-02-09 17:23:03 -08:00
Robert McGibbon
4ad1af2a6d
minor changes
2014-03-12 01:41:37 -07:00
peastman
d1d7400807
Moved Python app layer tests into the main source tree
2013-08-01 16:48:25 -07:00
