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naming water and ion residues during solvate #90

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naming water and ion residues during solvate #90

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af50b65
naming water and ion residues during solvate
amburan Aug 7, 2025
47c0975
Merge branch 'main' into feature/assign_residue_names
mikemhenry Sep 26, 2025
c862cd1
Merge branch 'main' into feature/assign_residue_names
mikemhenry Nov 3, 2025
c1f260f
Merge branch 'main' into feature/assign_residue_names
mikemhenry Nov 21, 2025
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21 changes: 21 additions & 0 deletions openpharmmdflow/pipeline/sm/pipeline.py
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Original file line number Diff line number Diff line change
Expand Up @@ -143,18 +143,39 @@ def solvate(self):
if m.to_smiles() == "[H][O][H]"
]
)
# Assign residue name for atoms in water molecule
for molecule in self.solvated_topology.molecules:
if molecule.to_smiles() == "[H][O][H]":
for atom in molecule.atoms:
if not hasattr(atom, "metadata") or atom.metadata is None:
atom.metadata = {}
atom.metadata["residue_name"] = "HOH"
# create a Sodium ion
self.sodium_ion = Molecule.from_smiles("[Na+]")
# find out the number of sodium ions in the system
self.n_sodium_ion = len(
[m for m in self.solvated_topology.molecules if m.to_smiles() == "[Na+]"]
)
# Assign residue name for atoms in Na ion
for molecule in self.solvated_topology.molecules:
if molecule.to_smiles() == "[Na+]":
for atom in molecule.atoms:
if not hasattr(atom, "metadata") or atom.metadata is None:
atom.metadata = {}
atom.metadata["residue_name"] = "NAP"
# create a Chlorine ion
self.chlorine_ion = Molecule.from_smiles("[Cl-]")
# find out the number of sodium ions in the system
self.n_chlorine_ion = len(
[m for m in self.solvated_topology.molecules if m.to_smiles() == "[Cl-]"]
)
# Assign residue name for atoms in Cl ion
for molecule in self.solvated_topology.molecules:
if molecule.to_smiles() == "[Cl-]":
for atom in molecule.atoms:
if not hasattr(atom, "metadata") or atom.metadata is None:
atom.metadata = {}
atom.metadata["residue_name"] = "[Cl-]"

# Apply residue names to water and ions added during solvation
# The write_residue_names function will automatically detect and name:
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