vendor perses atom mapper

docs/installation.rst

@@ -673,10 +673,10 @@ Optional dependencies
 Certain functionalities are only available if you also install other,
 optional packages.
 
-* **perses tools**: To use perses, you need to install perses and OpenEye,
-  and you need a valid OpenEye license. To install both packages, use::
+* **perses tools**: To use the perses atom mapper and scorer, you need to install OpenEye, and you need a valid OpenEye license. 
+  To install OpenEye, use::
 
-    $ mamba install -c openeye perses openeye-toolkits
+    $ mamba install -c openeye openeye-toolkits
 
 Supported Hardware
 ------------------

environment.yml

@@ -23,7 +23,6 @@ dependencies:
   - openmmtools >=0.25.0
   - packaging
   - pandas
-  - perses>=0.10.3
   - plugcli
   - pint>=0.24.0
   - pip

news/perses-vendor.rst

@@ -0,0 +1,26 @@
+**Added:**
+
+* <news item>
+
+**Changed:**
+
+* We have vendored the perses atom mapper and scorer.
+  This means the ``perses`` package is no longer needed to use the ``perses`` atom mapper and scorer.
+  However, OpenEye is still needed to use the ``perses`` atom mapper and scorer.
+  This is an internal packaging change and does not affect user scripts.
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>

openfe/setup/atom_mapping/perses_mapper.py

@@ -6,18 +6,15 @@
 
 """
 
-from openfe.utils import requires_package
 from gufe.settings.typing import AngstromQuantity
 from openff.units import unit, Quantity
 from openff.units.openmm import to_openmm
 
+from openff.utilities.utilities import requires_oe_module
+
 from ...utils.silence_root_logging import silence_root_logging
 
-try:
-    with silence_root_logging():
-        from perses.rjmc.atom_mapping import AtomMapper, InvalidMappingException
-except ImportError:
-    pass  # Don't throw  error, will happen later
+from openfe.vendor.perses._atom_mapping import _AtomMapper, _InvalidMappingException
 
 from .ligandatommapper import LigandAtomMapper
 
@@ -49,7 +46,7 @@ def _from_dict(cls, dct: dict):
     def _defaults(cls):
         return {}
 
-    @requires_package("perses")
+    @requires_oe_module("oechem")
     def __init__(
         self,
         allow_ring_breaking: bool = True,
@@ -81,7 +78,7 @@ def __init__(
 
     def _mappings_generator(self, componentA, componentB):
         # Construct Perses Mapper
-        _atom_mapper = AtomMapper(
+        _atom_mapper = _AtomMapper(
             use_positions=self.use_positions,
             coordinate_tolerance=to_openmm(self.coordinate_tolerance),
             allow_ring_breaking=self.allow_ring_breaking,
@@ -92,7 +89,7 @@ def _mappings_generator(self, componentA, componentB):
             _atom_mappings = _atom_mapper.get_all_mappings(
                 old_mol=componentA.to_openff(), new_mol=componentB.to_openff()
             )
-        except InvalidMappingException:
+        except _InvalidMappingException:
             return
 
         # Catch empty mappings here

openfe/setup/atom_mapping/perses_scorers.py

@@ -3,15 +3,11 @@
 
 from typing import Callable
 
-from openfe.utils import requires_package
+from openff.utilities.utilities import requires_oe_module
 
 from ...utils.silence_root_logging import silence_root_logging
 
-try:
-    with silence_root_logging():
-        from perses.rjmc.atom_mapping import AtomMapper, AtomMapping
-except ImportError:
-    pass  # Don't throw  error, will happen later
+from openfe.vendor.perses._atom_mapping import _AtomMapper, _AtomMapping
 
 from . import LigandAtomMapping
 
@@ -34,7 +30,7 @@ def _get_all_mapped_atoms_with(
     return numMaxPossibleMappings
 
 
-@requires_package("perses")
+@requires_oe_module("oechem")
 def default_perses_scorer(
     mapping: LigandAtomMapping,
     use_positions: bool = False,
@@ -67,8 +63,8 @@ def default_perses_scorer(
     -------
         float
     """
-    score = AtomMapper(use_positions=use_positions).score_mapping(
-        AtomMapping(
+    score = _AtomMapper(use_positions=use_positions).score_mapping(
+        _AtomMapping(
             old_mol=mapping.componentA.to_openff(),
             new_mol=mapping.componentB.to_openff(),
             old_to_new_atom_map=mapping.componentA_to_componentB,

openfe/tests/setup/atom_mapping/test_perses_scorers.py

@@ -11,6 +11,7 @@
 
 from ....utils.silence_root_logging import silence_root_logging
 
+from openfe.vendor.perses._atom_mapping import _AtomMapper, _AtomMapping
 
 USING_OLD_OFF = False
 
@@ -67,13 +68,13 @@ def test_perses_regression(gufe_atom_mapping_matrix):
     for x in gufe_atom_mapping_matrix.items():
         (i, j), ligand_atom_mapping = x
         # Build Perses Mapping:
-        perses_atom_mapping = AtomMapping(
+        perses_atom_mapping = _AtomMapping(
             old_mol=ligand_atom_mapping.componentA.to_openff(),
             new_mol=ligand_atom_mapping.componentB.to_openff(),
             old_to_new_atom_map=ligand_atom_mapping.componentA_to_componentB,
         )
         # score Perses Mapping - Perses Style
-        matrix[i, j] = matrix[j, i] = AtomMapper().score_mapping(perses_atom_mapping)
+        matrix[i, j] = matrix[j, i] = _AtomMapper().score_mapping(perses_atom_mapping)
 
     assert matrix.shape == (8, 8)
 

openfe/vendor/perses/README.md

@@ -0,0 +1,25 @@
+The files in this folder are copied from [perses](https://github.com/choderalab/perses/blob/main/perses/rjmc/atom_mapping.py) commit: c716ba936fff992d596a342daebe4248597d287d
+They have been modified and are licensed under the MIT license.
+The orginal license is reproduced below:
+
+MIT License
+
+Copyright (c) 2015-2017 Chodera lab // Memorial Sloan Kettering Cancer Center
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.