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0 0 0 0 0 0 0 0 0 0 + 9.9220 -5.0423 -6.3371 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 + 1 37 1 0 + 1 38 1 0 + 1 39 1 0 + 2 3 2 0 + 2 6 1 0 + 3 4 1 0 + 3 26 1 0 + 4 5 1 0 + 4 14 1 0 + 5 6 2 0 + 5 11 1 0 + 6 7 1 0 + 7 8 2 0 + 7 9 1 0 + 9 10 1 0 + 9 40 1 0 + 9 41 1 0 + 10 11 1 0 + 10 12 1 0 + 10 13 1 0 + 11 42 1 0 + 11 43 1 0 + 12 44 1 0 + 12 45 1 0 + 12 46 1 0 + 13 47 1 0 + 13 48 1 0 + 13 49 1 0 + 14 15 2 0 + 14 19 1 0 + 15 16 1 0 + 15 50 1 0 + 16 17 2 0 + 16 51 1 0 + 17 18 1 0 + 17 34 1 0 + 18 19 2 0 + 18 20 1 0 + 19 52 1 0 + 20 21 1 0 + 20 53 1 0 + 21 22 1 0 + 21 33 1 0 + 21 54 1 1 + 22 23 1 0 + 22 32 1 0 + 22 55 1 1 + 23 24 1 0 + 23 56 1 0 + 23 57 1 0 + 24 25 1 0 + 24 27 1 0 + 25 26 1 0 + 25 58 1 0 + 25 59 1 0 + 26 60 1 0 + 26 61 1 0 + 27 28 2 0 + 27 29 1 0 + 29 30 1 0 + 29 31 1 0 + 29 62 1 6 + 30 63 1 0 + 30 64 1 0 + 30 65 1 0 + 31 66 1 0 + 31 67 1 0 + 31 76 1 0 + 32 68 1 0 + 32 69 1 0 + 32 70 1 0 + 33 71 1 0 + 33 72 1 0 + 33 73 1 0 + 34 35 2 0 + 34 36 1 0 + 36 74 1 0 + 36 75 1 0 +M CHG 1 31 1 +M END +> (7) +-12.74 + +> (7) 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 + +> (7) +kcal/mol + +> (7) +r_exp_dg + +> (7) +-53.30416 + +> (7) +-12.74 + +$$$$ diff --git a/tests/rest/test_single_topology_rest.py b/tests/rest/test_single_topology_rest.py index 14f48f20..5d6dac32 100644 --- a/tests/rest/test_single_topology_rest.py +++ b/tests/rest/test_single_topology_rest.py @@ -19,6 +19,7 @@ import jax import matplotlib.pyplot as plt +import networkx as nx import numpy as np import pytest from common import ligand_from_smiles @@ -40,8 +41,9 @@ from tmd.fe.rest.single_topology import REST_REGION_ATOM_FLAG, SingleTopologyREST from tmd.fe.single_topology import SingleTopology from tmd.fe.system import GuestSystem -from tmd.fe.utils import get_romol_conf, read_sdf_mols_by_name +from tmd.fe.utils import get_romol_conf, read_sdf, read_sdf_mols_by_name from tmd.ff import Forcefield +from tmd.graph_utils import convert_to_nx from tmd.md import builders from tmd.potentials import NonbondedInteractionGroup from tmd.utils import path_to_internal_file @@ -72,13 +74,55 @@ def get_single_topology(mol_a, mol_b, core) -> SingleTopology: @cache def get_single_topology_rest( - mol_a, mol_b, core, max_temperature_scale: float, temperature_scale_interpolation_fxn: InterpolationFxnName + mol_a, + mol_b, + core, + max_temperature_scale: float, + temperature_scale_interpolation_fxn: InterpolationFxnName, + **kwargs, ) -> SingleTopologyREST: return SingleTopologyREST( - mol_a, mol_b, np.asarray(core), forcefield, max_temperature_scale, temperature_scale_interpolation_fxn + mol_a, mol_b, np.asarray(core), forcefield, max_temperature_scale, temperature_scale_interpolation_fxn, **kwargs ) +@pytest.mark.nogpu +def test_single_topology_rest_macrocycle(): + mols = read_sdf("tests/data/3RKZ_macrocycles.sdf") + assert len(mols) >= 2 + + mol_a = mols[0] + mol_b = mols[1] + + max_ring_size = 7 + core = get_core(mol_a, mol_b) + st_rest = get_single_topology_rest(mol_a, mol_b, core, 2.0, "exponential", maximum_ring_size=max_ring_size) + + assert all(len(cycle) < max_ring_size for cycle in st_rest._cycles_a) + assert all(len(cycle) < max_ring_size for cycle in st_rest._cycles_b) + + alchemical_mol = st_rest.mol(0.0) + alchemical_nx = convert_to_nx(alchemical_mol) + + # Verify that there is a macrocyclic ring larger than max_ring_size + largest_ring = max(nx.cycle_basis(alchemical_nx), key=lambda x: len(x)) + assert len(largest_ring) > max_ring_size + + rest_region_atoms = st_rest.rest_region_atom_idxs + # There may be parts of the ring included, but shouldn't be all of it + assert len(set(largest_ring).intersection(rest_region_atoms)) < len(largest_ring) + + st_rest_include_largest_ring = get_single_topology_rest( + mol_a, mol_b, core, 2.0, "exponential", maximum_ring_size=None + ) + + assert len(st_rest_include_largest_ring.rest_region_atom_idxs) > len(st_rest.rest_region_atom_idxs) + + # If we allow it, all atoms will be selected + assert len(set(largest_ring).intersection(st_rest_include_largest_ring.rest_region_atom_idxs)) == len(largest_ring) + + +@pytest.mark.nogpu @pytest.mark.parametrize("lamb", [0.0, 0.4, 0.5, 1.0]) @pytest.mark.parametrize("temperature_scale_interpolation_fxn", ["linear", "quadratic", "exponential"]) @pytest.mark.parametrize("mol_pair", np.random.default_rng(2024).choice(hif2a_ligand_pairs, size=3)) @@ -252,6 +296,7 @@ def get_identity_transformation(mol): return SingleTopologyREST(mol, mol, core, forcefield, 2.0, "linear") +@pytest.mark.nogpu def test_single_topology_rest_propers(): """Example with some propers not in the REST region""" mol_a = hif2a_ligands["15"] @@ -261,6 +306,7 @@ def test_single_topology_rest_propers(): assert set(st.target_propers.items()) < set(st.candidate_propers.items()) +@pytest.mark.nogpu def test_single_topology_rest_propers_identity(): # benzene: no propers are scaled benzene = ligand_from_smiles("c1ccccc1") @@ -278,6 +324,7 @@ def test_single_topology_rest_propers_identity(): assert len(set(st.candidate_propers.values())) == 9 * 6 + 6 +@pytest.mark.nogpu @pytest.mark.parametrize("seed", [2026]) def test_single_topology_custom_rest_atoms(seed): """Test the ability to manually specify which atoms should be included in the REST region by setting @@ -329,6 +376,7 @@ def test_single_topology_custom_rest_atoms(seed): assert len(st.rest_region_atom_idxs) == st.get_num_atoms() +@pytest.mark.nogpu @pytest.mark.parametrize( "lamb", [0.0, 0.4, 0.51, 1.0] ) # NOTE: asymmetry at lambda = 0.5 due to discontinuity in combine_confs diff --git a/tmd/fe/rest/single_topology.py b/tmd/fe/rest/single_topology.py index 69439112..09818056 100644 --- a/tmd/fe/rest/single_topology.py +++ b/tmd/fe/rest/single_topology.py @@ -1,4 +1,5 @@ # Copyright 2019-2025, Relay Therapeutics +# Modifications Copyright 2026, Forrest York # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. @@ -83,6 +84,7 @@ def __init__( forcefield: Forcefield, max_temperature_scale: float, temperature_scale_interpolation: InterpolationFxnName = "exponential", + maximum_ring_size: int | None = 7, ): """ Parameters @@ -104,15 +106,27 @@ def __init__( temperature_scale_interpolation: str Interpolation function to use for temperature scaling. One of "linear", "quadratic", or "exponential" + + maximum_ring_size: integer | None + Maximum size of ring that will be considered for expansion. If none, all rings will be accepted """ super().__init__(mol_a, mol_b, core, forcefield) self._temperature_scale_interpolation_fxn: InterpolationFxn = get_temperature_scale_interpolation_fxn( max_temperature_scale, temperature_scale_interpolation ) + self._maximum_ring_size = maximum_ring_size self._nxg_a = convert_to_nx(mol_a) self._nxg_b = convert_to_nx(mol_b) - self._cycles_a = nx.cycle_basis(self._nxg_a) - self._cycles_b = nx.cycle_basis(self._nxg_b) + self._cycles_a = [ + cycle + for cycle in nx.cycle_basis(self._nxg_a) + if self._maximum_ring_size is None or len(cycle) < self._maximum_ring_size + ] + self._cycles_b = [ + cycle + for cycle in nx.cycle_basis(self._nxg_b) + if self._maximum_ring_size is None or len(cycle) < self._maximum_ring_size + ] # expand REST region to include complete ring groups @staticmethod