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Use ELF10 for system creation when OpenEyeToolkitWrapper is available #837

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j-wags opened this issue Feb 15, 2021 · 1 comment
Closed

Use ELF10 for system creation when OpenEyeToolkitWrapper is available #837

j-wags opened this issue Feb 15, 2021 · 1 comment
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effort:low priority:high

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@j-wags
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j-wags commented Feb 15, 2021

Describe the bug
Original message by @SimonBoothroyd:

Am I right in thinking that since the 0.7.0 release of the toolkit we don't actually use ELF10 to compute partial charges, even when OE is installed and licensed?
(i.e. in #471 the call to a toolkit compute_partial_charges_am1bcc function by a molecules compute_partial_charges_am1bcc function was replaced by a call to assign_partial_charges with am1bcc explicitly stated)

The above is a regression introduced in the 0.7.0 release. We should fix it by having ToolkitAM1BCCHandler.create_force do a try/except where it attempts to use partial_charge_method='am1bccelf10' first, and then, if there's a ChargeMethodUnavailableError, drops down to partial_charge_method='am1bcc'. This will cause ELF10 to be used (if available), and vanilla AM1-BCC otherwise.

Additional context
cc #447
j-wags added a commit that referenced this issue Mar 10, 2022
@j-wags
fix #837
142d2cd
@j-wags j-wags mentioned this issue Mar 10, 2022
Merged
4 tasks
j-wags added a commit that referenced this issue Mar 11, 2022
@j-wags
fix #837 (#1214)
0c42148
mattwthompson added a commit that referenced this issue Mar 24, 2022
@mattwthompson
Squashed commit of the following:
530d4b9 
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 mattwthompson mentioned this issue Apr 4, 2022
Merged
@mattwthompson
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Fixed in 0.10.4 (and 0.11.0+)

#990 appears to be a duplicate

mattwthompson added a commit that referenced this issue May 11, 2022
@mattwthompson
Add Topology.__add__ (#1194)
a5b6000 
* 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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