Skip to content

Molenet dataset #48

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
aditya0by0 wants to merge 1 commit into
base: dev
Choose a base branch
from
+41 −1
Open

Molenet dataset #48

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
4 changes: 3 additions & 1 deletion chebai_graph/preprocessing/datasets/__init__.py
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,4 +1,5 @@
from .chebi import (
ChEBI25GraphProperties,
ChEBI50_Atom_WGNOnly_GraphProp,
ChEBI50_GN_WithAllNodes_FG_WithAtoms_FGE,
ChEBI50_GN_WithAllNodes_FG_WithAtoms_NoFGE,
Expand All @@ -9,6 +10,7 @@
ChEBI50_StaticGNI,
ChEBI50_WFGE_NGN_GraphProp,
ChEBI50_WFGE_WGN_AsPerNodeType,
ChEBI50_WFGE_WGN_ForAllPropsExceptNodeLevel,
ChEBI50_WFGE_WGN_ForAtomAndFGLevelOnly,
ChEBI50_WFGE_WGN_ForAtomLevelAndGraphNodeOnly,
ChEBI50_WFGE_WGN_ForAtomLevelOnly,
Expand All @@ -18,7 +20,6 @@
ChEBI50_WFGE_WGN_ForNodeLevelPropOnlyForAllNodes,
ChEBI50_WFGE_WGN_GraphProp,
ChEBI50GraphData,
ChEBI25GraphProperties,
ChEBI50GraphProperties,
ChEBI100GraphProperties,
)
Expand Down Expand Up @@ -60,6 +61,7 @@
"ChEBI50_WFGE_WGN_ForAtomLevelAndGraphNodeOnly",
"ChEBI50_WFGE_WGN_ForFGLevelAndGraphNodeOnly",
"ChEBI50_WFGE_WGN_ForNodeLevelPropOnlyForAllNodes",
"ChEBI50_WFGE_WGN_ForAllPropsExceptNodeLevel",
"BACE_WFGE_WGN_AsPerNodeType",
"BBBP_WFGE_WGN_AsPerNodeType",
"ClinTox_WFGE_WGN_AsPerNodeType",
Expand Down
7 changes: 7 additions & 0 deletions chebai_graph/preprocessing/datasets/augmentation_base.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -177,3 +177,10 @@ def _fill_node_tensor_with_molecule_type_property(
is_graph_node: torch.Tensor,
) -> torch.Tensor:
return node_tensor


class GraphPropAllPropsExceptNodeLevel(GraphPropAsPerNodeType):
def _fill_node_tensor_with_all_node_type_property(
self, node_tensor: torch.Tensor, property_values: torch.Tensor, offset: int
) -> torch.Tensor:
return node_tensor
7 changes: 7 additions & 0 deletions chebai_graph/preprocessing/datasets/chebi.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -25,6 +25,7 @@
from .augmentation_base import (
AugGraphPropMixIn_NoGraphNode,
AugGraphPropMixIn_WithGraphNode,
GraphPropAllPropsExceptNodeLevel,
GraphPropForAtomAndFGLevelOnly,
GraphPropForAtomLevelAndGraphNodeOnly,
GraphPropForAtomLevelOnly,
Expand Down Expand Up @@ -204,6 +205,12 @@ class ChEBI50_WFGE_WGN_ForNodeLevelPropOnlyForAllNodes(
READER = AtomFGReader_WithFGEdges_WithGraphNode


class ChEBI50_WFGE_WGN_ForAllPropsExceptNodeLevel(
GraphPropAllPropsExceptNodeLevel, ChEBIOver50
):
READER = AtomFGReader_WithFGEdges_WithGraphNode


# ---------- Final Augmentation: Different Thresholds ------------------------------
class ChEBI100_WFGE_WGN_AsPerNodeType(GraphPropAsPerNodeType, ChEBIOver100):
READER = AtomFGReader_WithFGEdges_WithGraphNode
Expand Down
24 changes: 24 additions & 0 deletions configs/data/augmented/properties/chebi50_all_props_except_node_lvl.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,24 @@
class_path: chebai_graph.preprocessing.datasets.ChEBI50_WFGE_WGN_ForAllPropsExceptNodeLevel
init_args:
properties:
# All Node type properties
- chebai_graph.preprocessing.properties.AtomNodeLevel
# Atom Node type properties
- chebai_graph.preprocessing.properties.AugAtomAromaticity
- chebai_graph.preprocessing.properties.AugAtomCharge
- chebai_graph.preprocessing.properties.AugAtomHybridization
- chebai_graph.preprocessing.properties.AugAtomNumHs
- chebai_graph.preprocessing.properties.AugAtomType
- chebai_graph.preprocessing.properties.AugNumAtomBonds
# FG Node type properties
- chebai_graph.preprocessing.properties.AtomFunctionalGroup
- chebai_graph.preprocessing.properties.IsHydrogenBondDonorFG
- chebai_graph.preprocessing.properties.IsHydrogenBondAcceptorFG
- chebai_graph.preprocessing.properties.IsFGAlkyl
# Graph Node type properties
- chebai_graph.preprocessing.properties.AugRDKit2DNormalized
# Bond properties
- chebai_graph.preprocessing.properties.BondLevel
- chebai_graph.preprocessing.properties.AugBondAromaticity
- chebai_graph.preprocessing.properties.AugBondInRing
- chebai_graph.preprocessing.properties.AugBondType
Loading