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Fix edge ordering #34

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merged 9 commits into from
Mar 22, 2023
Merged

Fix edge ordering #34

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36bd870
rm noarch
lilyminium Feb 16, 2023
2ac3c14
Merge branch 'main' of github.com:openforcefield/openff-nagl into main
lilyminium Mar 1, 2023
3c211b5
update tests
lilyminium Mar 21, 2023
72580f3
fix edge ordering
lilyminium Mar 21, 2023
c7b1352
Merge branch 'main' into fix-edges
lilyminium Mar 21, 2023
e5d57c9
add newline
lilyminium Mar 21, 2023
a38ff83
add more examples
lilyminium Mar 22, 2023
e463c94
uncomment mac nodgl tests
lilyminium Mar 22, 2023
a8c30ac
update changelog
lilyminium Mar 22, 2023
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6 changes: 3 additions & 3 deletions .github/workflows/gh-ci.yaml
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Expand Up @@ -38,9 +38,9 @@ jobs:
# broken OpenMM build for Mac on 3.10
- os: "macOS-latest"
python-version: "3.10"
- os: "macOS-latest"
python-version: "3.9"
include-dgl: false
# - os: "macOS-latest"
# python-version: "3.9"
# include-dgl: false


steps:
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17 changes: 16 additions & 1 deletion CHANGELOG.md
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Expand Up @@ -22,10 +22,25 @@ The rules for this file:
- @lilyminium

### Reviewers
- @mattwthompson
-

### Added
- `GNNModel.save` function (PR #29)

### Fixed
<!-- Bug fixes -->
- Fix edge ordering in NXMol graph (Issue #28, PR #34)

## v0.2.1

### Authors
<!-- GitHub usernames of contributors to this release -->
- @lilyminium

### Reviewers
- @mattwthompson

### Added
- `GNNModel.load` function (PR #26)
- `convolution_dropout` and `readout_dropout` keywords to GNNModel (PR #26)

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9 changes: 8 additions & 1 deletion openff/nagl/molecule/_graph/_graph.py
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Expand Up @@ -134,7 +134,14 @@ def number_of_nodes(self):

def in_edges(self, nodes, form="uv"):
u, v, i = self._all_edges()
mask = [x in nodes for x in v]
# mask = [x in nodes for x in v]

mask = []
for node in nodes:
for i_, v_ in enumerate(v):
if v_ == node:
mask.append(i_)

U, V, I = u[mask], v[mask], i[mask]

if form == "uv":
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14 changes: 14 additions & 0 deletions openff/nagl/tests/conftest.py
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Expand Up @@ -81,3 +81,17 @@ def openff_carboxylate():
from openff.toolkit.topology.molecule import Molecule

return Molecule.from_mapped_smiles("[H:1][C:2](=[O:3])[O-:4]")


@pytest.fixture()
def openff_ccnco():
from openff.toolkit.topology.molecule import Molecule

return Molecule.from_mapped_smiles("[H:6][C:1]([H:7])([H:8])[C:2]([H:9])([H:10])[N:3]([H:11])[C:4]([H:12])([H:13])[O:5][H:14]")


@pytest.fixture()
def openff_cnc():
from openff.toolkit.topology.molecule import Molecule

return Molecule.from_mapped_smiles("[H:4][C:1]([H:5])([H:6])[N:2]([H:7])[C:3]([H:8])([H:9])[H:10]")
14 changes: 14 additions & 0 deletions openff/nagl/tests/data/example_am1bcc_sage_charges/C#N.sdf
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@@ -0,0 +1,14 @@

-OEChem-03222312172D

3 2 0 0 0 0 0 0 0999 V2000
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.0000 0.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
-0.7500 0.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 3 0 0 0 0
1 3 1 0 0 0 0
M END
> <atom.dprop.PartialCharge>
0.299528 -0.437890 0.138363

$$$$
27 changes: 27 additions & 0 deletions openff/nagl/tests/data/example_am1bcc_sage_charges/C1CC1.sdf
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@@ -0,0 +1,27 @@

-OEChem-03222312172D

9 9 0 0 0 0 0 0 0999 V2000
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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-0.0747 1.3501 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
1.0747 1.3501 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
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1 2 1 0 0 0 0
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1 5 1 0 0 0 0
2 6 1 0 0 0 0
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M END
> <atom.dprop.PartialCharge>
-0.136480 -0.136480 -0.136480 0.068240 0.068240 0.068240 0.068240 0.068240 0.068240

$$$$
33 changes: 33 additions & 0 deletions openff/nagl/tests/data/example_am1bcc_sage_charges/C1CCC1.sdf
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@@ -0,0 +1,33 @@

-OEChem-03222312172D

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M END
> <atom.dprop.PartialCharge>
-0.094868 -0.094868 -0.094868 -0.094868 0.047434 0.047434 0.047434 0.047434 0.047434 0.047434 0.047434 0.047434

$$$$
41 changes: 41 additions & 0 deletions openff/nagl/tests/data/example_am1bcc_sage_charges/C1CNC(=O)CC1.sdf
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@@ -0,0 +1,41 @@

-OEChem-03222312172D

16 16 0 0 0 0 0 0 0999 V2000
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-0.8674 1.5027 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.7349 2.0002 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
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2 11 1 0 0 0 0
3 12 1 0 0 0 0
6 13 1 0 0 0 0
6 14 1 0 0 0 0
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M END
> <atom.dprop.PartialCharge>
-0.096102 0.100700 -0.573760 0.694888 -0.654050 -0.146955 -0.077452 0.052578 0.052578 0.037306 0.037306 0.319356 0.075585 0.075585 0.051219 0.051219

$$$$
37 changes: 37 additions & 0 deletions openff/nagl/tests/data/example_am1bcc_sage_charges/C1CNCC1.sdf
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@@ -0,0 +1,37 @@

-OEChem-03222312172D

14 14 0 0 0 0 0 0 0999 V2000
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.3065 0.9519 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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0.9224 -0.7458 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
1 5 1 0 0 0 0
1 2 1 0 0 0 0
2 3 1 0 0 0 0
3 4 1 0 0 0 0
4 5 1 0 0 0 0
1 6 1 0 0 0 0
1 7 1 0 0 0 0
2 8 1 0 0 0 0
2 9 1 0 0 0 0
3 10 1 0 0 0 0
4 11 1 0 0 0 0
4 12 1 0 0 0 0
5 13 1 0 0 0 0
5 14 1 0 0 0 0
M END
> <atom.dprop.PartialCharge>
-0.094856 0.147007 -0.807302 0.147007 -0.094856 0.046052 0.046052 0.040568 0.040568 0.356520 0.040568 0.040568 0.046052 0.046052

$$$$
110 changes: 110 additions & 0 deletions ...cc_sage_charges/C=C(C[N+](=O)[O-])N[C@@H](CCCCNc1ccc([N+](=O)[O-])cc1[NH+](O)O)C(=O)O.sdf
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@@ -0,0 +1,110 @@

-OEChem-03222312172D

50 50 0 1 0 0 0 0 0999 V2000
-7.7927 0.4827 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-7.7898 -0.5173 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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18 22 2 0 0 0 0
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29 50 1 0 0 0 0
M CHG 5 4 1 6 -1 19 1 21 -1 24 1
M END
> <atom.dprop.PartialCharge>
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$$$$
23 changes: 23 additions & 0 deletions openff/nagl/tests/data/example_am1bcc_sage_charges/CC(=O)([O-]).sdf
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@@ -0,0 +1,23 @@

-OEChem-03222312172D

7 6 0 0 0 0 0 0 0999 V2000
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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M CHG 1 4 -1
M END
> <atom.dprop.PartialCharge>
-0.239300 0.899138 -0.851818 -0.851818 0.014599 0.014599 0.014599

$$$$
24 changes: 24 additions & 0 deletions openff/nagl/tests/data/example_am1bcc_sage_charges/CC(=O)O.sdf
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@@ -0,0 +1,24 @@

-OEChem-03222312172D

8 7 0 0 0 0 0 0 0999 V2000
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M END
> <atom.dprop.PartialCharge>
-0.155042 0.633318 -0.550004 -0.608805 0.078161 0.078161 0.078161 0.446051

$$$$
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