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Merged
lohedges merged 1 commit into from
Dec 5, 2025
Merged

Just set intrascale on the basis of the connectivity #490

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205 changes: 1 addition & 204 deletions python/BioSimSpace/Align/_merge.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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)
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