Skip to content

Add support for merging CMAP terms #508

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
lohedges merged 1 commit into from
Mar 18, 2026
Merged

Add support for merging CMAP terms #508

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
93 changes: 93 additions & 0 deletions src/BioSimSpace/Align/_merge.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -332,6 +332,7 @@ def merge(
"angle",
"dihedral",
"improper",
"cmap",
"connectivity",
"intrascale",
]
Expand Down Expand Up @@ -683,6 +684,52 @@ def merge(
# Add the impropers to the merged molecule.
edit_mol.set_property("improper0", impropers)

# 5) cmap
if "cmap" in shared_props:
# Get the user defined property names.
prop0 = inv_property_map0.get("cmap", "cmap")
prop1 = inv_property_map1.get("cmap", "cmap")

# Get the "cmap" property from the two molecules.
cmaps0 = molecule0.property(prop0)
cmaps1 = molecule1.property(prop1)

# Get the molInfo object for each molecule.
info0 = molecule0.info()
info1 = molecule1.info()

# Create the new set of CMAP functions.
cmaps = _SireMM.CMAPFunctions(edit_mol.info())

# Add all of the CMAP functions from molecule0.
for func in cmaps0.parameters():
atom0 = mol0_merged_mapping[info0.atom_idx(func.atom0())]
atom1 = mol0_merged_mapping[info0.atom_idx(func.atom1())]
atom2 = mol0_merged_mapping[info0.atom_idx(func.atom2())]
atom3 = mol0_merged_mapping[info0.atom_idx(func.atom3())]
atom4 = mol0_merged_mapping[info0.atom_idx(func.atom4())]
cmaps.set(atom0, atom1, atom2, atom3, atom4, func.parameter())

# Loop over all CMAP functions in molecule1.
for func in cmaps1.parameters():
# This CMAP function contains an atom that is unique to molecule1.
if (
info1.atom_idx(func.atom0()) in atoms1_idx
or info1.atom_idx(func.atom1()) in atoms1_idx
or info1.atom_idx(func.atom2()) in atoms1_idx
or info1.atom_idx(func.atom3()) in atoms1_idx
or info1.atom_idx(func.atom4()) in atoms1_idx
):
atom0 = mol1_merged_mapping[info1.atom_idx(func.atom0())]
atom1 = mol1_merged_mapping[info1.atom_idx(func.atom1())]
atom2 = mol1_merged_mapping[info1.atom_idx(func.atom2())]
atom3 = mol1_merged_mapping[info1.atom_idx(func.atom3())]
atom4 = mol1_merged_mapping[info1.atom_idx(func.atom4())]
cmaps.set(atom0, atom1, atom2, atom3, atom4, func.parameter())

# Add the CMAP functions to the merged molecule.
edit_mol.set_property("cmap0", cmaps)

##############################
# SET PROPERTIES AT LAMBDA = 1
##############################
Expand Down Expand Up @@ -1016,6 +1063,52 @@ def merge(
# Add the impropers to the merged molecule.
edit_mol.set_property("improper1", impropers)

# 5) cmap
if "cmap" in shared_props:
# Get the user defined property names.
prop0 = inv_property_map0.get("cmap", "cmap")
prop1 = inv_property_map1.get("cmap", "cmap")

# Get the "cmap" property from the two molecules.
cmaps0 = molecule0.property(prop0)
cmaps1 = molecule1.property(prop1)

# Get the molInfo object for each molecule.
info0 = molecule0.info()
info1 = molecule1.info()

# Create the new set of CMAP functions.
cmaps = _SireMM.CMAPFunctions(edit_mol.info())

# Add all of the CMAP functions from molecule1.
for func in cmaps1.parameters():
atom0 = mol1_merged_mapping[info1.atom_idx(func.atom0())]
atom1 = mol1_merged_mapping[info1.atom_idx(func.atom1())]
atom2 = mol1_merged_mapping[info1.atom_idx(func.atom2())]
atom3 = mol1_merged_mapping[info1.atom_idx(func.atom3())]
atom4 = mol1_merged_mapping[info1.atom_idx(func.atom4())]
cmaps.set(atom0, atom1, atom2, atom3, atom4, func.parameter())

# Loop over all CMAP functions in molecule0.
for func in cmaps0.parameters():
# This CMAP function contains an atom that is unique to molecule0.
if (
info0.atom_idx(func.atom0()) in atoms0_idx
or info0.atom_idx(func.atom1()) in atoms0_idx
or info0.atom_idx(func.atom2()) in atoms0_idx
or info0.atom_idx(func.atom3()) in atoms0_idx
or info0.atom_idx(func.atom4()) in atoms0_idx
):
atom0 = mol0_merged_mapping[info0.atom_idx(func.atom0())]
atom1 = mol0_merged_mapping[info0.atom_idx(func.atom1())]
atom2 = mol0_merged_mapping[info0.atom_idx(func.atom2())]
atom3 = mol0_merged_mapping[info0.atom_idx(func.atom3())]
atom4 = mol0_merged_mapping[info0.atom_idx(func.atom4())]
cmaps.set(atom0, atom1, atom2, atom3, atom4, func.parameter())

# Add the CMAP functions to the merged molecule.
edit_mol.set_property("cmap1", cmaps)

# The number of potentials should be consistent for the "bond0"
# and "bond1" properties, unless a ring is broken or changes size.
if not (allow_ring_breaking or allow_ring_size_change):
Expand Down
93 changes: 93 additions & 0 deletions src/BioSimSpace/Sandpit/Exscientia/Align/_merge.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -317,6 +317,7 @@ def merge(
"angle",
"dihedral",
"improper",
"cmap",
"connectivity",
"intrascale",
]
Expand Down Expand Up @@ -668,6 +669,52 @@ def merge(
# Add the impropers to the merged molecule.
edit_mol.set_property("improper0", impropers)

# 5) cmap
if "cmap" in shared_props:
# Get the user defined property names.
prop0 = inv_property_map0.get("cmap", "cmap")
prop1 = inv_property_map1.get("cmap", "cmap")

# Get the "cmap" property from the two molecules.
cmaps0 = molecule0.property(prop0)
cmaps1 = molecule1.property(prop1)

# Get the molInfo object for each molecule.
info0 = molecule0.info()
info1 = molecule1.info()

# Create the new set of CMAP functions.
cmaps = _SireMM.CMAPFunctions(edit_mol.info())

# Add all of the CMAP functions from molecule0.
for func in cmaps0.parameters():
atom0 = mol0_merged_mapping[info0.atom_idx(func.atom0())]
atom1 = mol0_merged_mapping[info0.atom_idx(func.atom1())]
atom2 = mol0_merged_mapping[info0.atom_idx(func.atom2())]
atom3 = mol0_merged_mapping[info0.atom_idx(func.atom3())]
atom4 = mol0_merged_mapping[info0.atom_idx(func.atom4())]
cmaps.set(atom0, atom1, atom2, atom3, atom4, func.parameter())

# Loop over all CMAP functions in molecule1.
for func in cmaps1.parameters():
# This CMAP function contains an atom that is unique to molecule1.
if (
info1.atom_idx(func.atom0()) in atoms1_idx
or info1.atom_idx(func.atom1()) in atoms1_idx
or info1.atom_idx(func.atom2()) in atoms1_idx
or info1.atom_idx(func.atom3()) in atoms1_idx
or info1.atom_idx(func.atom4()) in atoms1_idx
):
atom0 = mol1_merged_mapping[info1.atom_idx(func.atom0())]
atom1 = mol1_merged_mapping[info1.atom_idx(func.atom1())]
atom2 = mol1_merged_mapping[info1.atom_idx(func.atom2())]
atom3 = mol1_merged_mapping[info1.atom_idx(func.atom3())]
atom4 = mol1_merged_mapping[info1.atom_idx(func.atom4())]
cmaps.set(atom0, atom1, atom2, atom3, atom4, func.parameter())

# Add the CMAP functions to the merged molecule.
edit_mol.set_property("cmap0", cmaps)

##############################
# SET PROPERTIES AT LAMBDA = 1
##############################
Expand Down Expand Up @@ -995,6 +1042,52 @@ def merge(
# Add the impropers to the merged molecule.
edit_mol.set_property("improper1", impropers)

# 5) cmap
if "cmap" in shared_props:
# Get the user defined property names.
prop0 = inv_property_map0.get("cmap", "cmap")
prop1 = inv_property_map1.get("cmap", "cmap")

# Get the "cmap" property from the two molecules.
cmaps0 = molecule0.property(prop0)
cmaps1 = molecule1.property(prop1)

# Get the molInfo object for each molecule.
info0 = molecule0.info()
info1 = molecule1.info()

# Create the new set of CMAP functions.
cmaps = _SireMM.CMAPFunctions(edit_mol.info())

# Add all of the CMAP functions from molecule1.
for func in cmaps1.parameters():
atom0 = mol1_merged_mapping[info1.atom_idx(func.atom0())]
atom1 = mol1_merged_mapping[info1.atom_idx(func.atom1())]
atom2 = mol1_merged_mapping[info1.atom_idx(func.atom2())]
atom3 = mol1_merged_mapping[info1.atom_idx(func.atom3())]
atom4 = mol1_merged_mapping[info1.atom_idx(func.atom4())]
cmaps.set(atom0, atom1, atom2, atom3, atom4, func.parameter())

# Loop over all CMAP functions in molecule0.
for func in cmaps0.parameters():
# This CMAP function contains an atom that is unique to molecule0.
if (
info0.atom_idx(func.atom0()) in atoms0_idx
or info0.atom_idx(func.atom1()) in atoms0_idx
or info0.atom_idx(func.atom2()) in atoms0_idx
or info0.atom_idx(func.atom3()) in atoms0_idx
or info0.atom_idx(func.atom4()) in atoms0_idx
):
atom0 = mol0_merged_mapping[info0.atom_idx(func.atom0())]
atom1 = mol0_merged_mapping[info0.atom_idx(func.atom1())]
atom2 = mol0_merged_mapping[info0.atom_idx(func.atom2())]
atom3 = mol0_merged_mapping[info0.atom_idx(func.atom3())]
atom4 = mol0_merged_mapping[info0.atom_idx(func.atom4())]
cmaps.set(atom0, atom1, atom2, atom3, atom4, func.parameter())

# Add the CMAP functions to the merged molecule.
edit_mol.set_property("cmap1", cmaps)

# The number of potentials should be consistent for the "bond0"
# and "bond1" properties, unless a ring is broken or changes size.
if not (allow_ring_breaking or allow_ring_size_change):
Expand Down
Loading