Remove uneeded code/attributes

choderalab · Jul 27, 2023 · 2e7aa04 · 2e7aa04
1 parent dd9d164
commit 2e7aa04
Showing 1 changed file with 0 additions and 13 deletions.
diff --git a/perses/app/relative_setup.py b/perses/app/relative_setup.py
@@ -613,8 +613,6 @@ def _setup_complex_phase(self):
             raise ValueError("You need to provide either a protein pdb or a receptor mol2 to run a complex simulation.")
 
         self._complex_md_topology_old = self._receptor_md_topology_old.join(self._ligand_md_topology_old)
-        # receptor is the same for "old" and "new" -- only for small molecule pipeline
-        self._complex_md_topology_new = self._receptor_md_topology_old.join(self._ligand_md_topology_new)
 
         n_atoms_spectators = 0
         if self._spectator_filenames:
@@ -623,22 +621,14 @@ def _setup_complex_phase(self):
                 self._complex_md_topology_old = self._complex_md_topology_old.join(spectator_topology)
                 n_atoms_spectators += spectator_topology.n_atoms
         self._complex_topology_old = self._complex_md_topology_old.to_openmm()
-        self._complex_topology_new = self._complex_md_topology_new.to_openmm()
 
         n_atoms_total_old = self._complex_topology_old.getNumAtoms()
-        n_atoms_total_new = self._complex_topology_new.getNumAtoms()
         n_atoms_protein_old = self._receptor_topology_old.getNumAtoms()
-        n_atoms_protein_new = n_atoms_protein_old  # Assumes it's the same target
         n_atoms_ligand_old = n_atoms_total_old - n_atoms_protein_old - n_atoms_spectators
-        n_atoms_ligand_new = n_atoms_total_new - n_atoms_protein_new - n_atoms_spectators
 
         self._complex_positions_old = unit.Quantity(np.zeros([n_atoms_total_old, 3]), unit=unit.nanometers)
         self._complex_positions_old[:n_atoms_protein_old, :] = self._receptor_positions_old
         self._complex_positions_old[n_atoms_protein_old:n_atoms_protein_old+n_atoms_ligand_old, :] = self._ligand_positions_old
-        self._complex_positions_new = unit.Quantity(np.zeros([n_atoms_total_new, 3]), unit=unit.nanometers)
-        self._complex_positions_new[:n_atoms_protein_new, :] = self._receptor_positions_old  # Assumes it's the same target
-        self._complex_positions_new[n_atoms_protein_new:n_atoms_protein_new + n_atoms_ligand_new,
-        :] = self._ligand_positions_new
 
         if self._spectator_filenames:
             start = n_atoms_protein_old+n_atoms_ligand_old
@@ -687,9 +677,6 @@ def _generate_solvent_topologies(self, topology_proposal, old_positions):
         old_solvated_topology, old_solvated_positions, old_solvated_system = self._solvate_system(
             old_ligand_topology.to_openmm(), old_ligand_positions, phase='solvent',
             box_dimensions=self._solvent_box_dimensions, model=self._solvent_model)
-        # Update attributes
-        self._ligand_topology_old_solvated = old_solvated_topology
-        self._ligand_positions_old_solvated = old_solvated_positions
 
         old_solvated_md_topology = md.Topology.from_openmm(old_solvated_topology)