Add other MLPs

.gitignore

@@ -1,3 +1,216 @@
+# FEGrow
 ignore_git
-.idea
-fegrow.egg-info/
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[codz]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py.cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# UV
+#   Similar to Pipfile.lock, it is generally recommended to include uv.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#uv.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+#poetry.toml
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#   pdm recommends including project-wide configuration in pdm.toml, but excluding .pdm-python.
+#   https://pdm-project.org/en/latest/usage/project/#working-with-version-control
+#pdm.lock
+#pdm.toml
+.pdm-python
+.pdm-build/
+
+# pixi
+#   Similar to Pipfile.lock, it is generally recommended to include pixi.lock in version control.
+#pixi.lock
+#   Pixi creates a virtual environment in the .pixi directory, just like venv module creates one
+#   in the .venv directory. It is recommended not to include this directory in version control.
+.pixi
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.envrc
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+.idea/
+
+# Abstra
+# Abstra is an AI-powered process automation framework.
+# Ignore directories containing user credentials, local state, and settings.
+# Learn more at https://abstra.io/docs
+.abstra/
+
+# Visual Studio Code
+#  Visual Studio Code specific template is maintained in a separate VisualStudioCode.gitignore 
+#  that can be found at https://github.com/github/gitignore/blob/main/Global/VisualStudioCode.gitignore
+#  and can be added to the global gitignore or merged into this file. However, if you prefer, 
+#  you could uncomment the following to ignore the entire vscode folder
+# .vscode/
+
+# Ruff stuff:
+.ruff_cache/
+
+# PyPI configuration file
+.pypirc
+
+# Cursor
+#  Cursor is an AI-powered code editor. `.cursorignore` specifies files/directories to
+#  exclude from AI features like autocomplete and code analysis. Recommended for sensitive data
+#  refer to https://docs.cursor.com/context/ignore-files
+.cursorignore
+.cursorindexingignore
+
+# Marimo
+marimo/_static/
+marimo/_lsp/
+__marimo__/
+
+# Streamlit
+.streamlit/secrets.toml
+
+# VSCode
+.vscode

CHANGELOG

@@ -1,6 +1,9 @@
 
 Authors: Mateusz K. Bieniek, Ben Cree, Rachael Pirie, Joshua T. Horton, Natalie J. Tatum, Daniel J. Cole
 
+**version 3.0.0**
+ - Compatibility with MACE MLPs for optimising the ligand.
+
 **version 2.0.1 **
  - The scaffold's R atom breaks the constrained embedding. The R atom is now omitted. (#74)
 

docs/notebooks/notebook1-basic-tutorial-full/1_basic_tutorial_full.md

@@ -554,7 +554,7 @@ The remaining conformers are optimised using hybrid machine learning / molecular
 energies = rmol.optimise_in_receptor(
     receptor_file="rec_final.pdb", 
     ligand_force_field="openff", 
-    use_ani=True,
+    ligand_intramolecular_force_field="ani2x",
     sigma_scale_factor=0.8,
     relative_permittivity=4,
     water_model = None,

docs/notebooks/notebook2.1-tutorial-single-molecule/2_tutorial_single_mol.md

@@ -4448,7 +4448,7 @@ The remaining conformers are optimised using hybrid machine learning / molecular
 energies = rmol.optimise_in_receptor(
     receptor_file="rec_final.pdb", 
     ligand_force_field="openff", 
-    use_ani=True,
+    ligand_intramolecular_force_field="ani2x",
     sigma_scale_factor=0.8,
     relative_permittivity=4,
     water_model = None,

docs/notebooks/notebook4-introduce-chemspace/4_tutorial_introduce_chemspace.md

@@ -4447,7 +4447,7 @@ The remaining conformers are optimised using hybrid machine learning / molecular
 energies = cs.optimise_in_receptor(
     receptor_file="rec_final.pdb", 
     ligand_force_field="openff", 
-    use_ani=True,
+    ligand_intramolecular_mlp="ani2x",
     sigma_scale_factor=0.8,
     relative_permittivity=4,
     water_model = None,

docs/tutorials/0_basic/0_basic_tutorial_full.md

@@ -328,8 +328,8 @@ fegrow.fix_receptor("rec.pdb", "rec_final.pdb")
 rec_final = prody.parsePDB("rec_final.pdb")
 ```
 
-    File ‘7L10.pdb’ already there; not retrieving.
-    
+    File ‘7L10.pdb’ already there; not retrieving.
+
 
 
     @> 2609 atoms and 1 coordinate set(s) were parsed in 0.05s.
@@ -544,7 +544,7 @@ The remaining conformers are optimised using hybrid machine learning / molecular
 energies = rmol.optimise_in_receptor(
     receptor_file="rec_final.pdb",
     ligand_force_field="openff",
-    use_ani=True,
+    ligand_intramolecular_mlp="ani2x",
     sigma_scale_factor=0.8,
     relative_permittivity=4,
     water_model=None,

docs/tutorials/1_chemspace/1_tutorial_introduce_chemspace.md

@@ -49,7 +49,7 @@ The provided core structure is adapted from a recent study by [Jorgensen and co-
 !obabel -ipdb sarscov2/lig.pdb -osdf -O sarscov2/coreh.sdf -p 7
 ```
 
-    1 molecule converted
+    1 molecule converted
 
 
 
@@ -4238,8 +4238,8 @@ fegrow.fix_receptor("rec.pdb", "rec_final.pdb")
 rec_final = prody.parsePDB("rec_final.pdb")
 ```
 
-    File ‘7L10.pdb’ already there; not retrieving.
-    
+    File ‘7L10.pdb’ already there; not retrieving.
+
 
 
     @> 2609 atoms and 1 coordinate set(s) were parsed in 0.05s.
@@ -4411,7 +4411,7 @@ The remaining conformers are optimised using hybrid machine learning / molecular
 energies = cs.optimise_in_receptor(
     receptor_file="rec_final.pdb",
     ligand_force_field="openff",
-    use_ani=True,
+    ligand_intramolecular_mlp="ani2x",
     sigma_scale_factor=0.8,
     relative_permittivity=4,
     water_model=None,

environment.yml

@@ -30,3 +30,5 @@ dependencies:
   - modal # modAL on pip
   - cachey
   - pyparsing<3.1.0 # temporary fix for prody
+  - nnpops
+  - pooch

fegrow/__init__.py

@@ -3,6 +3,7 @@
 # activate nanomolar units in Pandas
 import pint_pandas  # noqa: F401
 
+from . import mlp  # noqa: F401
 from .conformers import WrongCoreForMolecule, generate_conformers
 from .package import (
     ChemSpace,

fegrow/cli/utils.py

@@ -8,6 +8,7 @@
 
 from fegrow import RMol
 from fegrow.receptor import ForceField
+from fegrow.mlp import MLForceFieldName
 
 
 class Settings(BaseModel):
@@ -25,9 +26,14 @@ class Settings(BaseModel):
         "openff",
         description="The force field model to use for the small molecule during the restrained optimisation.",
     )
-    use_ani: bool = Field(
-        True,
-        description="If we should attempt to use ANI2x to model the internal energies of the ligand in an ML/MM optimisation.",
+    use_ani: Optional[bool] = Field(
+        None,
+        description="**DEPRECATED**: Use 'ligand_intramolecular_mlp' instead. This field is kept for backwards compatibility only.",
+    )
+    ligand_intramolecular_mlp: Optional[MLForceFieldName] = Field(
+        None,
+        description="The machine learning force field that should be used for the ligand intramolecular interactions. "
+        "If set to None, the molecular mechanics ligand_force_field is used for all ligand interactions. ",
     )
     sigma_scale_factor: float = Field(
         0.8,
@@ -54,6 +60,21 @@ class Settings(BaseModel):
         description="The relative energy cutoff in kcal/mol used to select the top conformers for scoring.",
     )
 
+    def model_post_init(self, __context) -> None:
+        """Validate and handle deprecated use_ani parameter."""
+        if self.use_ani is not None:
+            raise ValueError(
+                "The 'use_ani' parameter has been deprecated and removed. "
+                "Please use 'ligand_intramolecular_mlp' instead.\n\n"
+                "Migration guide:\n"
+                "  - Old: use_ani=true\n"
+                "  - New: ligand_intramolecular_mlp='ani2x'\n\n"
+                "  - Old: use_ani=false\n"
+                "  - New: ligand_intramolecular_mlp=None\n\n"
+                "Available MLPs: 'ani2x', 'mace-off23-small', 'mace-off23-medium', "
+                "'mace-off23-large', 'egret-1'"
+            )
+
 
 @dask.delayed
 def score_ligand(
@@ -86,7 +107,7 @@ def score_ligand(
     rmol.optimise_in_receptor(
         receptor_file=receptor,
         ligand_force_field=settings.ligand_force_field,
-        use_ani=settings.use_ani,
+        ligand_intramolecular_mlp=settings.ligand_intramolecular_mlp,
         sigma_scale_factor=settings.sigma_scale_factor,
         relative_permittivity=settings.relative_permittivity,
         water_model=settings.water_model,