[WIP] Topology biopolymer interoperability and ToolkitWrapper backend creation #1195

j-wags · 2022-02-15T00:52:20Z

This is still in progress, and the diff will be too large to review. I'm just using this PR to run tests and keep track of the to-do list.

…kw._smarts_to_networkx and rdktkw and oetkw._assign_aro_and_stereo_from_3d

… behavior up to Openeye

…le_conversion and linked to docs.

…dkit

lgtm-com · 2022-02-15T01:00:44Z

This pull request introduces 1 alert when merging 02b4a83 into 1115d25 - view on LGTM.com

new alerts:

1 for Module is imported with 'import' and 'import from'

…dkit

lgtm-com · 2022-03-25T20:22:05Z

This pull request introduces 1 alert when merging f25a5ab into 7fdc181 - view on LGTM.com

new alerts:

1 for Module is imported with 'import' and 'import from'

for more information, see https://pre-commit.ci

lgtm-com · 2022-04-06T02:28:34Z

This pull request introduces 2 alerts when merging 9bb6a2e into 4510bdb - view on LGTM.com

new alerts:

1 for Unused local variable
1 for Module is imported with 'import' and 'import from'

… HIS and TRP sidechains aren't correctly perceived in the MDL model)

…marts_to_networkx_rdkit # Conflicts: # openff/toolkit/topology/molecule.py # openff/toolkit/utils/openeye_wrapper.py # openff/toolkit/utils/rdkit_wrapper.py

…dkit

for more information, see https://pre-commit.ci

lgtm-com · 2022-04-08T19:10:55Z

This pull request introduces 2 alerts when merging f91e7d2 into 46a0876 - view on LGTM.com

new alerts:

1 for Unused local variable
1 for Module is imported with 'import' and 'import from'

… model values)

…marts_to_networkx_rdkit

lgtm-com · 2022-04-11T19:23:05Z

This pull request introduces 2 alerts when merging 8e88b52 into 46a0876 - view on LGTM.com

new alerts:

1 for Unused local variable
1 for Module is imported with 'import' and 'import from'

lgtm-com · 2022-04-20T02:14:07Z

This pull request introduces 3 alerts when merging f67a9a8 into 3f13de1 - view on LGTM.com

new alerts:

1 for Unused local variable
1 for Except block handles 'BaseException'
1 for Module is imported with 'import' and 'import from'

codecov · 2022-04-20T02:22:49Z

Codecov Report

❗ No coverage uploaded for pull request base (topology-biopolymer-refactor@3f13de1). Click here to learn what that means.
The diff coverage is n/a.

for more information, see https://pre-commit.ci

…line

…marts_to_networkx_rdkit

…dkit

for more information, see https://pre-commit.ci

j-wags added 12 commits December 20, 2021 11:44

in-progress commit

14d4be9

remove the last toolkit-specific code from molecule.from_pdb, add oet…

1a19c3c

…kw._smarts_to_networkx and rdktkw and oetkw._assign_aro_and_stereo_from_3d

update todos

7a0e940

cleanups

f0249fa

initial OE metadata implementation

2196e57

initial molecule conversion doc

a005108

undo minidrugbank short circuit

4f29fd1

stop trying to tiptoe around edge cases, leave partially-set metadata…

5c81a4f

… behavior up to Openeye

Implement to/from rdkit metadata handling and tests

128fdeb

Progress toward to/from openmm

2b82890

First working draft of to/from openmm, tests. Updated table in molecu…

cded788

…le_conversion and linked to docs.

Merge branch 'topology-biopolymer-refactor' into smarts_to_networkx_r…

02b4a83

…dkit

Merge branch 'topology-biopolymer-refactor' into smarts_to_networkx_r…

f25a5ab

…dkit

mattwthompson added this to the 0.11.0 milestone Mar 31, 2022

j-wags and others added 3 commits April 5, 2022 19:17

update metadata conversion docs

58618ff

comment out print statements for test debugging

6563c20

[pre-commit.ci] auto fixes from pre-commit.com hooks

9bb6a2e

for more information, see https://pre-commit.ci

j-wags and others added 6 commits April 7, 2022 17:57

Fix issue related to symmetric bonds having their order assigned twice

54ac8e4

cast residue numbers to int when going to RDK/OE

29a7662

fix aromaticity preception logic (this will cause tests to fail since…

d623b8d

… HIS and TRP sidechains aren't correctly perceived in the MDL model)

Merge remote-tracking branch 'origin/smarts_to_networkx_rdkit' into s…

fce06cf

…marts_to_networkx_rdkit # Conflicts: # openff/toolkit/topology/molecule.py # openff/toolkit/utils/openeye_wrapper.py # openff/toolkit/utils/rdkit_wrapper.py

Merge branch 'topology-biopolymer-refactor' into smarts_to_networkx_r…

b19e696

…dkit

[pre-commit.ci] auto fixes from pre-commit.com hooks

f91e7d2

for more information, see https://pre-commit.ci

j-wags added 2 commits April 8, 2022 17:16

fix aromatic sidechain tests (expect counterintuitive MDL aromaticity…

e8777cd

… model values)

Merge remote-tracking branch 'origin/smarts_to_networkx_rdkit' into s…

8e88b52

…marts_to_networkx_rdkit

j-wags added 3 commits April 19, 2022 16:26

more predictable metadata handling for to_rdkit

69c7ecf

Fix OE metadata tests

1039f3b

Update OpenMM residue exporting and update conversion docs

f67a9a8

j-wags and others added 11 commits April 21, 2022 11:56

cleanups and small fixes

e2f4eb8

Clean up API and comments, disable t4 SMILES test

5293887

[pre-commit.ci] auto fixes from pre-commit.com hooks

40f1fc7

for more information, see https://pre-commit.ci

something is out of sync here... Add a second copy of PDBFile import …

094ab09

…line

Merge remote-tracking branch 'origin/smarts_to_networkx_rdkit' into s…

fa48304

…marts_to_networkx_rdkit

Merge branch 'topology-biopolymer-refactor' into smarts_to_networkx_r…

5be1f92

…dkit

cosmetic commit to kick CI

552f776

forcefully set undefined OE metadata

f173101

Update molecule_conversion with info about unset OE metadata

0f75bc8

final code cleanups

c6ed56e

[pre-commit.ci] auto fixes from pre-commit.com hooks

da91a59

for more information, see https://pre-commit.ci

j-wags merged commit 52542c6 into topology-biopolymer-refactor Apr 26, 2022

j-wags deleted the smarts_to_networkx_rdkit branch April 26, 2022 03:19

This was referenced Apr 26, 2022

[WIP] Feature branch: Topology Biopolymer Refactor #951

Closed

Improving SMARTS matching performance with OpenEye backend #992

Closed

j-wags mentioned this pull request May 6, 2022

Use flake8 #1286

Merged

mattwthompson added a commit that referenced this pull request May 6, 2022

Fix bad merge re: #1195

91533ac

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

[WIP] Topology biopolymer interoperability and ToolkitWrapper backend creation #1195

[WIP] Topology biopolymer interoperability and ToolkitWrapper backend creation #1195

j-wags commented Feb 15, 2022 •

edited

Loading

lgtm-com bot commented Feb 15, 2022

lgtm-com bot commented Mar 25, 2022

lgtm-com bot commented Apr 6, 2022

lgtm-com bot commented Apr 8, 2022

lgtm-com bot commented Apr 11, 2022

lgtm-com bot commented Apr 20, 2022

codecov bot commented Apr 20, 2022 •

edited

Loading

[WIP] Topology biopolymer interoperability and ToolkitWrapper backend creation #1195

[WIP] Topology biopolymer interoperability and ToolkitWrapper backend creation #1195

Conversation

j-wags commented Feb 15, 2022 • edited Loading

lgtm-com bot commented Feb 15, 2022

lgtm-com bot commented Mar 25, 2022

lgtm-com bot commented Apr 6, 2022

lgtm-com bot commented Apr 8, 2022

lgtm-com bot commented Apr 11, 2022

lgtm-com bot commented Apr 20, 2022

codecov bot commented Apr 20, 2022 • edited Loading

Codecov Report

j-wags commented Feb 15, 2022 •

edited

Loading

codecov bot commented Apr 20, 2022 •

edited

Loading