Use interchange in some code paths

[mattwthompson]

No description provided.

[pep8speaks]

Hello @mattwthompson! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

• In the file devscripts/compare.py:

Line 15:80: E501 line too long (88 > 79 characters)
Line 33:80: E501 line too long (88 > 79 characters)
Line 36:80: E501 line too long (88 > 79 characters)
Line 123:80: E501 line too long (82 > 79 characters)
Line 149:80: E501 line too long (81 > 79 characters)
Line 152:80: E501 line too long (81 > 79 characters)
Line 224:80: E501 line too long (80 > 79 characters)
Line 226:80: E501 line too long (80 > 79 characters)
Line 290:80: E501 line too long (86 > 79 characters)
Line 294:80: E501 line too long (80 > 79 characters)
Line 355:80: E501 line too long (92 > 79 characters)
Line 387:80: E501 line too long (80 > 79 characters)
Line 413:80: E501 line too long (82 > 79 characters)
Line 421:80: E501 line too long (80 > 79 characters)
Line 423:80: E501 line too long (83 > 79 characters)
Line 432:80: E501 line too long (82 > 79 characters)
Line 436:57: E203 whitespace before ':'
Line 436:80: E501 line too long (85 > 79 characters)
Line 439:57: E203 whitespace before ':'
Line 439:80: E501 line too long (85 > 79 characters)
Line 444:80: E501 line too long (80 > 79 characters)
Line 480:80: E501 line too long (80 > 79 characters)
Line 481:80: E501 line too long (80 > 79 characters)
Line 484:80: E501 line too long (80 > 79 characters)
Line 485:80: E501 line too long (84 > 79 characters)

• In the file src/openfe_skunkworks/protocols/openmm_afe/base.py:

Line 483:17: E225 missing whitespace around operator
Line 484:21: E251 unexpected spaces around keyword / parameter equals
Line 484:23: E251 unexpected spaces around keyword / parameter equals
Line 508:80: E501 line too long (94 > 79 characters)
Line 510:80: E501 line too long (82 > 79 characters)
Line 516:80: E501 line too long (85 > 79 characters)
Line 518:80: E501 line too long (81 > 79 characters)
Line 521:80: E501 line too long (114 > 79 characters)
Line 522:80: E501 line too long (107 > 79 characters)
Line 524:80: E501 line too long (116 > 79 characters)
Line 526:80: E501 line too long (137 > 79 characters)
Line 529:80: E501 line too long (84 > 79 characters)
Line 530:80: E501 line too long (95 > 79 characters)
Line 535:80: E501 line too long (90 > 79 characters)
Line 536:1: W293 blank line contains whitespace
Line 537:80: E501 line too long (90 > 79 characters)
Line 539:80: E501 line too long (86 > 79 characters)
Line 540:80: E501 line too long (88 > 79 characters)
Line 555:26: E251 unexpected spaces around keyword / parameter equals
Line 555:28: E251 unexpected spaces around keyword / parameter equals
Line 556:24: E251 unexpected spaces around keyword / parameter equals
Line 556:26: E251 unexpected spaces around keyword / parameter equals
Line 571:80: E501 line too long (90 > 79 characters)
Line 583:80: E501 line too long (85 > 79 characters)
Line 585:80: E501 line too long (84 > 79 characters)
Line 588:9: E303 too many blank lines (2)
Line 637:80: E501 line too long (94 > 79 characters)

• In the file src/openfe_skunkworks/protocols/openmm_afe/equil_afe_settings.py:

Line 146:80: E501 line too long (80 > 79 characters)

• In the file src/openfe_skunkworks/protocols/openmm_utils/omm_settings.py:

Line 66:1: E302 expected 2 blank lines, found 1
Line 69:80: E501 line too long (119 > 79 characters)

• In the file tests/conftest.py:

Line 72:5: E129 visually indented line with same indent as next logical line
Line 72:80: E501 line too long (83 > 79 characters)
Line 175:9: E129 visually indented line with same indent as next logical line

• In the file tests/protocols/conftest.py:

Line 27:9: E124 closing bracket does not match visual indentation
Line 38:41: E231 missing whitespace after ','
Line 56:9: E124 closing bracket does not match visual indentation
Line 67:41: E231 missing whitespace after ','
Line 88:80: E501 line too long (80 > 79 characters)
Line 205:80: E501 line too long (94 > 79 characters)
Line 218:1: W293 blank line contains whitespace
Line 226:80: E501 line too long (81 > 79 characters)
Line 241:80: E501 line too long (92 > 79 characters)
Line 242:80: E501 line too long (86 > 79 characters)
Line 243:80: E501 line too long (96 > 79 characters)
Line 244:80: E501 line too long (92 > 79 characters)
Line 245:80: E501 line too long (113 > 79 characters)

• In the file tests/protocols/test_openmm_afe_solvation_protocol.py:

Line 55:80: E501 line too long (85 > 79 characters)
Line 323:1: W293 blank line contains whitespace
Line 369:80: E501 line too long (81 > 79 characters)
Line 689:80: E501 line too long (109 > 79 characters)
Line 690:80: E501 line too long (81 > 79 characters)
Line 691:80: E501 line too long (108 > 79 characters)
Line 692:80: E501 line too long (81 > 79 characters)
Line 715:80: E501 line too long (109 > 79 characters)
Line 716:80: E501 line too long (81 > 79 characters)
Line 717:80: E501 line too long (108 > 79 characters)
Line 718:80: E501 line too long (81 > 79 characters)
Line 748:80: E501 line too long (87 > 79 characters)

Comment last updated at 2024-04-18 18:09:50 UTC

[mattwthompson]

This is mostly working - re-running it with the slightly non-trivial molecule COC(=O)c1ccccc1

$ python devscripts/compare.py
Volumes differ by more than 10%, but densities are close (92.38 and 100.07 particles/nm^3)
Ewald error tolerances differ:
	force1.getEwaldErrorTolerance()=0.0005
	force2.getEwaldErrorTolerance()=0.0001
Ewald error tolerances differ:
	force1.getEwaldErrorTolerance()=0.0005
	force2.getEwaldErrorTolerance()=0.0001

The following were identified as needing strict equality:

• barostat
• thermostat
• small molecule forces
• FF applied to water (as close as I can get it)
• constraint distances
• masses

The following are noted as "fuzziness allowed (all due to solvation)":

• sigma on hydrogens (these are 0)
• system volume dimensions
  • See padding note below
• number of waters
  • Just comparing density within 10% (fairly arbitrary)
• position of waters
  • Not possible with just openmm.System XMLs

We've identified a handful of details that require a little bit more looking into

• Disagreements between Packmol/OpenMM on what padding distance means (will raise issue)
• Non-bonded cutoffs not being set correctly (will raise issue)
• Subtly different implementations of TIP3 (Add water models openforcefield/openff-forcefields#57 (comment))

[mattwthompson]

This is the function that is meant be used to solvate non-water; it's a bit different than the water one since "water" really means "water and Na+/Cl-"

https://github.com/openforcefield/openff-interchange/blob/v0.3.26/openff/interchange/components/_packmol.py#L893