Kartograf integration (#249)

* preparing openFE for wally integration * name n refactor * improving import managment. * fixing network changes.. * reverting network extraction * reverting network extraction * refactor * adding license * refactor name * removing the layer too much. * Update environment.yml * Update kartograf_mapper.py * Update openfe/setup/__init__.py Co-authored-by: Mike Henry <[email protected]> * Update environment.yaml * Update environment.yml * Update environment.yaml * pin kartograf to v1.0.0 and above * fixup merge mistake in generate_radial_network * Update environment.yaml * add kartograf integration to yaml cli --------- Co-authored-by: Mike Henry <[email protected]> Co-authored-by: Richard Gowers <[email protected]>
OpenFreeEnergy · Nov 17, 2023 · 7d40a63 · 7d40a63
1 parent c96cb57
commit 7d40a63
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Showing 5 changed files with 9 additions and 2 deletions.
diff --git a/docs/environment.yaml b/docs/environment.yaml
@@ -5,6 +5,7 @@ channels:
 dependencies:
 - autodoc-pydantic<2.0
 - lomap2>=3.0.0
+- kartograf>=1.0.0
 - openff-models>=0.0.5
 - openff-toolkit >=0.13.0
 - openff-units
@@ -27,7 +28,7 @@ dependencies:
   - git+https://github.com/OpenFreeEnergy/gufe@main
   - git+https://github.com/OpenFreeEnergy/ofe-sphinx-theme@main
 
-# These are added automatically by RTD, so we include them here
+# These are added automatically by RTD, so we include them here 
 # for a consistent environment.
 - mock
 - pillow

diff --git a/environment.yml b/environment.yml
@@ -4,6 +4,7 @@ channels:
   - conda-forge
 dependencies:
   - duecredit
+  - kartograf>=1.0.0
   - lomap2>=3.0.0
   - numpy<1.24
   - networkx

diff --git a/openfe/setup/__init__.py b/openfe/setup/__init__.py
@@ -5,7 +5,8 @@
 from .atom_mapping import (LigandAtomMapping,
                            LigandAtomMapper,
                            LomapAtomMapper, lomap_scorers,
-                           PersesAtomMapper, perses_scorers)
+                           PersesAtomMapper, perses_scorers,
+                           KartografAtomMapper,)
 
 from gufe import LigandNetwork
 from . import ligand_network_planning

diff --git a/openfe/setup/atom_mapping/__init__.py b/openfe/setup/atom_mapping/__init__.py
@@ -3,6 +3,7 @@
 
 from .lomap_mapper import LomapAtomMapper
 from .perses_mapper import PersesAtomMapper
+from kartograf import KartografAtomMapper
 
 from . import perses_scorers
 from . import lomap_scorers
diff --git a/openfecli/parameters/plan_network_options.py b/openfecli/parameters/plan_network_options.py
@@ -107,6 +107,7 @@ def load_yaml_planner_options(path: Optional[str], context) -> PlanNetworkOption
     )
     from openfe.setup import (
         LomapAtomMapper,
+        KartografAtomMapper,
     )
     from openfe.setup.atom_mapping.lomap_scorers import (
         default_lomap_score,
@@ -127,6 +128,8 @@ def load_yaml_planner_options(path: Optional[str], context) -> PlanNetworkOption
         mapper_choices = {
             'lomap': LomapAtomMapper,
             'lomapatommapper': LomapAtomMapper,
+            'kartograf': KartografAtomMapper,
+            'kartografatommapper': KartografAtomMapper,
         }
 
         try: