diff --git a/docs/environment.yaml b/docs/environment.yaml index 21d99bdf7..0933cca80 100644 --- 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 index 9e9435085..2839a2d82 100644 --- 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 index 024680822..2411bb300 100644 --- 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 index 0d19acf64..4f9ce5350 100644 --- 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 index 27716842a..c89ec9ec9 100644 --- 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: