Just set intrascale on the basis of the connectivity.

Author: lohedges

python/BioSimSpace/Align/_merge.py

@@ -1180,216 +1180,13 @@ def merge(
     # Create the CLJNBPairs matrices.
     ff = molecule0.property(ff0)
 
+    # Create the new intrascale matrices.
     scale_factor_14 = _SireMM.CLJScaleFactor(
         ff.electrostatic14_scale_factor(), ff.vdw14_scale_factor()
     )
     clj_nb_pairs0 = _SireMM.CLJNBPairs(conn0, scale_factor_14)
     clj_nb_pairs1 = _SireMM.CLJNBPairs(conn1, scale_factor_14)
 
-    # Loop over all atoms unique to molecule0.
-    for idx0 in atoms0_idx:
-        # Map the index to its position in the merged molecule.
-        idx0 = mol0_merged_mapping[idx0]
-
-        # Loop over all atoms unique to molecule1.
-        for idx1 in atoms1_idx:
-            # Map the index to its position in the merged molecule.
-            idx1 = mol1_merged_mapping[idx1]
-
-            # Work out the connection type between the atoms, in molecule 0.
-            conn_type0 = conn0.connection_type(idx0, idx1)
-
-            # The atoms aren't bonded.
-            if conn_type0 == 0:
-                clj_scale_factor = _SireMM.CLJScaleFactor(1, 1)
-                clj_nb_pairs0.set(idx0, idx1, clj_scale_factor)
-
-            # The atoms are part of a dihedral.
-            elif conn_type0 == 4:
-                clj_scale_factor = _SireMM.CLJScaleFactor(
-                    ff.electrostatic14_scale_factor(), ff.vdw14_scale_factor()
-                )
-                clj_nb_pairs0.set(idx0, idx1, clj_scale_factor)
-
-            # The atoms are bonded
-            else:
-                clj_scale_factor = _SireMM.CLJScaleFactor(0, 0)
-                clj_nb_pairs0.set(idx0, idx1, clj_scale_factor)
-
-            # Work out the connection type between the atoms, in molecule 1.
-            conn_type1 = conn1.connection_type(idx0, idx1)
-
-            # The atoms aren't bonded.
-            if conn_type1 == 0:
-                clj_scale_factor = _SireMM.CLJScaleFactor(1, 1)
-                clj_nb_pairs1.set(idx0, idx1, clj_scale_factor)
-
-            # The atoms are part of a dihedral.
-            elif conn_type1 == 4:
-                clj_scale_factor = _SireMM.CLJScaleFactor(
-                    ff.electrostatic14_scale_factor(), ff.vdw14_scale_factor()
-                )
-                clj_nb_pairs1.set(idx0, idx1, clj_scale_factor)
-
-            # The atoms are bonded
-            else:
-                clj_scale_factor = _SireMM.CLJScaleFactor(0, 0)
-                clj_nb_pairs1.set(idx0, idx1, clj_scale_factor)
-
-    # Copy the intrascale from molecule1 into clj_nb_pairs0.
-
-    # Perform a triangular loop over atoms from molecule1.
-    if roi is None:
-        iterlen = molecule1.num_atoms()
-        iterrange = list(range(molecule1.num_atoms()))
-    # When region of interest is defined, perfrom loop from these indices
-    else:
-        for roi_res in roi:
-            # Get atom indices of ROI residue in molecule1
-            molecule1_roi = molecule1.residues()[roi_res]
-            molecule1_roi_idx = [a.index() for a in molecule1_roi]
-            iterlen = len(molecule1_roi_idx)
-            iterrange = molecule1_roi_idx
-
-    for x in range(0, iterlen):
-        # Convert to an AtomIdx.
-        idx = iterrange[x]
-        idx = _SireMol.AtomIdx(idx)
-
-        # Map the index to its position in the merged molecule.
-        idx_map = mol1_merged_mapping[idx]
-
-        for y in range(x + 1, iterlen):
-            idy = iterrange[y]
-            # Convert to an AtomIdx.
-            idy = _SireMol.AtomIdx(idy)
-
-            # Map the index to its position in the merged molecule.
-            idy_map = mol1_merged_mapping[idy]
-
-            # Get the connection type between the atoms.
-            conn_type = conn0.connection_type(idx_map, idy_map)
-
-            # The atoms aren't bonded.
-            if conn_type == 0:
-                clj_scale_factor = _SireMM.CLJScaleFactor(1, 1)
-                clj_nb_pairs0.set(idx_map, idy_map, clj_scale_factor)
-
-            # The atoms are part of a dihedral.
-            elif conn_type == 4:
-                clj_scale_factor = _SireMM.CLJScaleFactor(
-                    ff.electrostatic14_scale_factor(), ff.vdw14_scale_factor()
-                )
-                clj_nb_pairs0.set(idx_map, idy_map, clj_scale_factor)
-
-            # The atoms are bonded
-            else:
-                clj_scale_factor = _SireMM.CLJScaleFactor(0, 0)
-                clj_nb_pairs0.set(idx_map, idy_map, clj_scale_factor)
-
-    # Now copy in all intrascale values from molecule0 into clj_nb_pairs0.
-
-    # Work out the iteration length and range.
-    if roi is None:
-        iterlen = molecule0.num_atoms()
-        iterrange = list(range(molecule0.num_atoms()))
-    else:
-        for roi_res in roi:
-            # Get atom indices of ROI residue in molecule0.
-            molecule0_roi = molecule0.residues()[roi_res]
-            molecule0_roi_idx = [a.index() for a in molecule0_roi]
-            iterlen = len(molecule0_roi_idx)
-            iterrange = molecule0_roi_idx
-
-    # Perform a triangular loop over atoms from molecule0.
-    for x in range(0, iterlen):
-        # Convert to an AtomIdx.
-        idx = iterrange[x]
-        idx = _SireMol.AtomIdx(idx)
-
-        # Map the index to its position in the merged molecule.
-        idx_map = mol0_merged_mapping[idx]
-
-        for y in range(x + 1, iterlen):
-            idy = iterrange[y]
-            # Convert to an AtomIdx.
-            idy = _SireMol.AtomIdx(idy)
-
-            # Map the index to its position in the merged molecule.
-            idy_map = mol0_merged_mapping[idy]
-
-            # Get the connection type between the atoms.
-            conn_type = conn0.connection_type(idx_map, idy_map)
-
-            # The atoms aren't bonded.
-            if conn_type == 0:
-                clj_scale_factor = _SireMM.CLJScaleFactor(1, 1)
-                clj_nb_pairs0.set(idx_map, idy_map, clj_scale_factor)
-
-            # The atoms are part of a dihedral.
-            elif conn_type == 4:
-                clj_scale_factor = _SireMM.CLJScaleFactor(
-                    ff.electrostatic14_scale_factor(),
-                    ff.vdw14_scale_factor(),
-                )
-                clj_nb_pairs0.set(idx_map, idy_map, clj_scale_factor)
-
-            # The atoms are bonded
-            else:
-                clj_scale_factor = _SireMM.CLJScaleFactor(0, 0)
-                clj_nb_pairs0.set(idx_map, idy_map, clj_scale_factor)
-
-    # Finally, copy the intrascale from molecule1 into clj_nb_pairs1.
-
-    # Work out the iteration length and range.
-    if roi is None:
-        iterlen = molecule1.num_atoms()
-        iterrange = list(range(molecule1.num_atoms()))
-
-    else:
-        for roi_res in roi:
-            molecule1_roi = molecule1.residues()[roi_res]
-            molecule1_roi_idx = [a.index() for a in molecule1_roi]
-            iterlen = len(molecule1_roi_idx)
-            iterrange = molecule1_roi_idx
-
-    # Perform a triangular loop over atoms from molecule1.
-    for x in range(0, iterlen):
-        # Convert to an AtomIdx.
-        idx = iterrange[x]
-        idx = _SireMol.AtomIdx(idx)
-
-        # Map the index to its position in the merged molecule.
-        idx = mol1_merged_mapping[idx]
-
-        for y in range(x + 1, iterlen):
-            idy = iterrange[y]
-            # Convert to an AtomIdx.
-            idy = _SireMol.AtomIdx(idy)
-
-            # Map the index to its position in the merged molecule.
-            idy = mol1_merged_mapping[idy]
-
-            # Get the connection type between the atoms.
-            conn_type = conn1.connection_type(idx, idy)
-
-            if conn_type == 0:
-                clj_scale_factor = _SireMM.CLJScaleFactor(1, 1)
-                clj_nb_pairs1.set(idx, idy, clj_scale_factor)
-
-            # The atoms are part of a dihedral.
-            elif conn_type == 4:
-                clj_scale_factor = _SireMM.CLJScaleFactor(
-                    ff.electrostatic14_scale_factor(),
-                    ff.vdw14_scale_factor(),
-                )
-                clj_nb_pairs1.set(idx, idy, clj_scale_factor)
-
-            # The atoms are bonded
-            else:
-                clj_scale_factor = _SireMM.CLJScaleFactor(0, 0)
-                clj_nb_pairs1.set(idx, idy, clj_scale_factor)
-
     # Store the two molecular components.
     edit_mol.set_property("molecule0", molecule0)
     edit_mol.set_property("molecule1", molecule1)