add mol support #157
add mol support #157
Conversation
|
|
||
| import numpy as np | ||
|
|
||
| BASE_ATOMS: List[str] = [ |
There was a problem hiding this comment.
We may want to have some different sets of allowable atoms. I can check some previous projects for the sets we allowed there
There was a problem hiding this comment.
I also checked this, OGB basically used atomic numbers from 1-120 and leave others as others. Feel free to change!
graphein/molecule/edges/atomic.py
Outdated
| if G.has_edge(n1, n2): | ||
| G.edges[n1, n2]["kind"].add("bond") | ||
| else: | ||
| G.add_edge(n1, n2, kind={"bond"}) |
There was a problem hiding this comment.
I think we should have an option to distinguish bond order (single/double/triple etc)
There was a problem hiding this comment.
Uh you are right, do we make it as edge feature or mark here?
There was a problem hiding this comment.
I think we can do it as the kind. E.g kind={"single", "bond"} or kind={"single_bond"}. I think the first one may be easier to work with (and is what I did for atomic protein graphs)
|
|
||
| config = MoleculeGraphConfig() | ||
|
|
||
| def test_generate_graph_sdf(): |
There was a problem hiding this comment.
We need some more checks on the graphs. We can follow a similar model to the protein graph tests.
Codecov Report
@@ Coverage Diff @@
## master #157 +/- ##
==========================================
+ Coverage 40.27% 49.25% +8.98%
==========================================
Files 48 74 +26
Lines 2811 4172 +1361
==========================================
+ Hits 1132 2055 +923
- Misses 1679 2117 +438
Continue to review full report at Codecov.
|
|
Kudos, SonarCloud Quality Gate passed!
|
PRs
Fixes #155. Add support for small molecules.
Support reading molecules from SMILES strings, .mol2, .sdf, .pdb files
Support one-hot node features
Support fully-connected, knn, bond, distance threshold edges
Test
See tests/molecule/test_data and tests/molecule/test_graphs.py
test basic functions to read either long or short molecules in the aforementioned ways