Remove un-used Topology attributes #1213
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j-wags
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Mar 11, 2022
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Looks good. I spent a little while trying to figure out if we should also pull the aromaticity model and constraints info from topology objects, but I didn't end up coming to a conclusion there, so this PR should be fine to move ahead with its current scope.
Feel free to ignore tests failing due to the RDKit/cairo and OE stereochemistry issues.
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Thanks! |
mattwthompson
added a commit
that referenced
this pull request
Mar 24, 2022
commit d34fe857e7cf28c312141bca58ff3b81173eecb0
Author: Matthew W. Thompson <mattwthompson@protonmail.com>
Date: Thu Mar 24 13:27:43 2022 -0500
Fix bad merge
commit 7d309f2
Merge: 9273dbb b373e40
Author: Matthew W. Thompson <mattwthompson@protonmail.com>
Date: Thu Mar 24 11:42:15 2022 -0500
Merge remote-tracking branch 'upstream/add-topology' into add-topology
commit 9273dbb
Author: Matthew W. Thompson <mattwthompson@protonmail.com>
Date: Thu Mar 24 10:44:12 2022 -0500
Fix mypy
commit 4ec3ea7
Merge: b8a5793 45fb642
Author: Matthew W. Thompson <mattwthompson@protonmail.com>
Date: Thu Mar 24 10:41:13 2022 -0500
Merge remote-tracking branch 'upstream/topology-biopolymer-refactor' into add-topology
commit 45fb642
Author: Matt Thompson <mattwthompson@protonmail.com>
Date: Wed Mar 23 21:34:20 2022 -0500
Raise descriptive error when OpenEye stereochemistry assumptions fail (#1218)
commit fc3d637
Author: Matt Thompson <mattwthompson@protonmail.com>
Date: Wed Mar 23 21:33:52 2022 -0500
Performance improvements in from_openeye (#1217)
OpenMM quantities are generally as quick and lightweight as
corresponding NumPy arrays, but Pint units tend to be slower. Most of
these changes simply defer unit tagging until a final step, carrying
values with implicit units in some internal functions where the units
are known and can be expected not to vary.
commit b373e40
Merge: b8a5793 f297b64
Author: Jeff Wagner <jwagnerjpl@gmail.com>
Date: Wed Mar 23 16:04:17 2022 -0700
Merge branch 'topology-biopolymer-refactor' into add-topology
commit f297b64
Author: Matt Thompson <mattwthompson@protonmail.com>
Date: Wed Mar 23 17:21:16 2022 -0500
Fix incorrect assignment of TIP3P parameters in Sage (#1200) (#1220)
* Add test for TIP3P charges with Sage
* Do not uniquify SMARTS in LibraryChargeHandler
* Also test standalone TIP3P file
* Consolidate tip3p charge tests
* black
* Update release history
Co-authored-by: j-wags <jwagnerjpl@gmail.com>
Co-authored-by: j-wags <jwagnerjpl@gmail.com>
commit a8d8b09
Author: Jeff Wagner <jwagnerjpl@gmail.com>
Date: Mon Mar 21 14:44:21 2022 -0700
Resolve conflicts (#1224)
commit 8d4a0a8
Author: Matt Thompson <mattwthompson@protonmail.com>
Date: Fri Mar 11 18:27:50 2022 -0600
Remove un-used Topology attributes (#1213)
* Remove un-used Topology attributes
* Lint
* Update release history
commit ba879b2
Author: Matt Thompson <mattwthompson@protonmail.com>
Date: Fri Mar 11 18:26:50 2022 -0600
Remove some internal calls to deprecated API points (#1204)
* Remove some internal calls to deprecated API points
* Fixes
* Add test that deprecated Topology methods still exist
* Fix broken list population
commit 59f35b8
Author: Matt Thompson <mattwthompson@protonmail.com>
Date: Fri Mar 11 17:45:05 2022 -0600
Avoid silent/implicit units checks in Topology.to_file, update docstring (#1207)
commit 46893b0
Author: Matt Thompson <mattwthompson@protonmail.com>
Date: Fri Mar 11 16:15:22 2022 -0600
Add Electrostatics tag to `test_forcefields/tip3p.offxml` (#1188)
* Add Electrostatics section to data/test_forcefields/tip3p.offxml
* Update release history
commit 0c42148
Author: Jeff Wagner <jwagnerjpl@gmail.com>
Date: Fri Mar 11 13:43:59 2022 -0800
fix #837 (#1214)
commit 0cb3a72
Author: Matt Thompson <mattwthompson@protonmail.com>
Date: Thu Mar 10 14:34:37 2022 -0600
Fix formatting in a `.assign_partial_charges` docstring (#1212)
commit b8a5793
Author: Matthew W. Thompson <mattwthompson@protonmail.com>
Date: Wed Feb 9 11:58:02 2022 -0600
Remove old mendeleev import
commit 373262a
Merge: 31c7755 0beef75
Author: Matthew W. Thompson <mattwthompson@protonmail.com>
Date: Wed Feb 9 11:38:27 2022 -0600
Merge remote-tracking branch 'upstream/topology-biopolymer-refactor' into add-topology
commit 31c7755
Author: Matthew W. Thompson <mattwthompson@protonmail.com>
Date: Wed Feb 9 11:30:23 2022 -0600
Update Topology.__add__/__iadd__, add tests, fix annotations
commit fc12de1
Author: Matthew W. Thompson <mattwthompson@protonmail.com>
Date: Tue Feb 8 15:33:41 2022 -0600
Add first implementation of Topoogy.__add__
commit 0321d99
Author: Matthew W. Thompson <mattwthompson@protonmail.com>
Date: Thu Jan 27 12:30:12 2022 -0600
Remove Atom.element
commit a2e7bf9
Author: Matthew W. Thompson <mattwthompson@protonmail.com>
Date: Thu Jan 27 12:25:03 2022 -0600
Fix virtual site creation
commit a383a0a
Author: Matthew W. Thompson <mattwthompson@protonmail.com>
Date: Thu Jan 27 11:26:19 2022 -0600
Fix setting masses while adding OpenMM particles
commit 37e86db
Author: Matthew W. Thompson <mattwthompson@protonmail.com>
Date: Thu Jan 27 10:20:30 2022 -0600
Fix more typos
commit 6555475
Author: Matthew W. Thompson <mattwthompson@protonmail.com>
Date: Thu Jan 27 09:33:13 2022 -0600
Fix typos, tests
commit c529ee0
Author: Matthew W. Thompson <mattwthompson@protonmail.com>
Date: Wed Jan 26 18:49:04 2022 -0600
Draft a refactor to openff.units.elements
mattwthompson
added a commit
that referenced
this pull request
May 11, 2022
* Squashed commit of the following:
commit d34fe857e7cf28c312141bca58ff3b81173eecb0
Author: Matthew W. Thompson <mattwthompson@protonmail.com>
Date: Thu Mar 24 13:27:43 2022 -0500
Fix bad merge
commit 7d309f2
Merge: 9273dbb b373e40
Author: Matthew W. Thompson <mattwthompson@protonmail.com>
Date: Thu Mar 24 11:42:15 2022 -0500
Merge remote-tracking branch 'upstream/add-topology' into add-topology
commit 9273dbb
Author: Matthew W. Thompson <mattwthompson@protonmail.com>
Date: Thu Mar 24 10:44:12 2022 -0500
Fix mypy
commit 4ec3ea7
Merge: b8a5793 45fb642
Author: Matthew W. Thompson <mattwthompson@protonmail.com>
Date: Thu Mar 24 10:41:13 2022 -0500
Merge remote-tracking branch 'upstream/topology-biopolymer-refactor' into add-topology
commit 45fb642
Author: Matt Thompson <mattwthompson@protonmail.com>
Date: Wed Mar 23 21:34:20 2022 -0500
Raise descriptive error when OpenEye stereochemistry assumptions fail (#1218)
commit fc3d637
Author: Matt Thompson <mattwthompson@protonmail.com>
Date: Wed Mar 23 21:33:52 2022 -0500
Performance improvements in from_openeye (#1217)
OpenMM quantities are generally as quick and lightweight as
corresponding NumPy arrays, but Pint units tend to be slower. Most of
these changes simply defer unit tagging until a final step, carrying
values with implicit units in some internal functions where the units
are known and can be expected not to vary.
commit b373e40
Merge: b8a5793 f297b64
Author: Jeff Wagner <jwagnerjpl@gmail.com>
Date: Wed Mar 23 16:04:17 2022 -0700
Merge branch 'topology-biopolymer-refactor' into add-topology
commit f297b64
Author: Matt Thompson <mattwthompson@protonmail.com>
Date: Wed Mar 23 17:21:16 2022 -0500
Fix incorrect assignment of TIP3P parameters in Sage (#1200) (#1220)
* Add test for TIP3P charges with Sage
* Do not uniquify SMARTS in LibraryChargeHandler
* Also test standalone TIP3P file
* Consolidate tip3p charge tests
* black
* Update release history
Co-authored-by: j-wags <jwagnerjpl@gmail.com>
Co-authored-by: j-wags <jwagnerjpl@gmail.com>
commit a8d8b09
Author: Jeff Wagner <jwagnerjpl@gmail.com>
Date: Mon Mar 21 14:44:21 2022 -0700
Resolve conflicts (#1224)
commit 8d4a0a8
Author: Matt Thompson <mattwthompson@protonmail.com>
Date: Fri Mar 11 18:27:50 2022 -0600
Remove un-used Topology attributes (#1213)
* Remove un-used Topology attributes
* Lint
* Update release history
commit ba879b2
Author: Matt Thompson <mattwthompson@protonmail.com>
Date: Fri Mar 11 18:26:50 2022 -0600
Remove some internal calls to deprecated API points (#1204)
* Remove some internal calls to deprecated API points
* Fixes
* Add test that deprecated Topology methods still exist
* Fix broken list population
commit 59f35b8
Author: Matt Thompson <mattwthompson@protonmail.com>
Date: Fri Mar 11 17:45:05 2022 -0600
Avoid silent/implicit units checks in Topology.to_file, update docstring (#1207)
commit 46893b0
Author: Matt Thompson <mattwthompson@protonmail.com>
Date: Fri Mar 11 16:15:22 2022 -0600
Add Electrostatics tag to `test_forcefields/tip3p.offxml` (#1188)
* Add Electrostatics section to data/test_forcefields/tip3p.offxml
* Update release history
commit 0c42148
Author: Jeff Wagner <jwagnerjpl@gmail.com>
Date: Fri Mar 11 13:43:59 2022 -0800
fix #837 (#1214)
commit 0cb3a72
Author: Matt Thompson <mattwthompson@protonmail.com>
Date: Thu Mar 10 14:34:37 2022 -0600
Fix formatting in a `.assign_partial_charges` docstring (#1212)
commit b8a5793
Author: Matthew W. Thompson <mattwthompson@protonmail.com>
Date: Wed Feb 9 11:58:02 2022 -0600
Remove old mendeleev import
commit 373262a
Merge: 31c7755 0beef75
Author: Matthew W. Thompson <mattwthompson@protonmail.com>
Date: Wed Feb 9 11:38:27 2022 -0600
Merge remote-tracking branch 'upstream/topology-biopolymer-refactor' into add-topology
commit 31c7755
Author: Matthew W. Thompson <mattwthompson@protonmail.com>
Date: Wed Feb 9 11:30:23 2022 -0600
Update Topology.__add__/__iadd__, add tests, fix annotations
commit fc12de1
Author: Matthew W. Thompson <mattwthompson@protonmail.com>
Date: Tue Feb 8 15:33:41 2022 -0600
Add first implementation of Topoogy.__add__
commit 0321d99
Author: Matthew W. Thompson <mattwthompson@protonmail.com>
Date: Thu Jan 27 12:30:12 2022 -0600
Remove Atom.element
commit a2e7bf9
Author: Matthew W. Thompson <mattwthompson@protonmail.com>
Date: Thu Jan 27 12:25:03 2022 -0600
Fix virtual site creation
commit a383a0a
Author: Matthew W. Thompson <mattwthompson@protonmail.com>
Date: Thu Jan 27 11:26:19 2022 -0600
Fix setting masses while adding OpenMM particles
commit 37e86db
Author: Matthew W. Thompson <mattwthompson@protonmail.com>
Date: Thu Jan 27 10:20:30 2022 -0600
Fix more typos
commit 6555475
Author: Matthew W. Thompson <mattwthompson@protonmail.com>
Date: Thu Jan 27 09:33:13 2022 -0600
Fix typos, tests
commit c529ee0
Author: Matthew W. Thompson <mattwthompson@protonmail.com>
Date: Wed Jan 26 18:49:04 2022 -0600
Draft a refactor to openff.units.elements
* Preserve constraints in `Topology.__add__`
* Update release history
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Resolves #784