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htmd.builder.ionize module#

htmd.builder.ionize.ionize(mol: Molecule, netcharge: float, nwater: int, neutralize: bool = True, saltconc: float | None = None, cation: str | None = None, anion: str | None = None, ff: str | None = None)#

Calculate the number of ions required to neutralize or salt a system.

Computes the anion and cation counts needed to neutralize the system’s net charge, and optionally adds extra ions to reach a target salt concentration. Ion stoichiometry is inferred from the ion charges (e.g. MgCl2 for Mg2+/Cl-).

Parameters:

  • mol (Molecule) – The molecular system (used to count existing ions when saltconc is set).

  • netcharge (float) – Net charge of the molecular system (e.g. from partial charges).

  • nwater (int) – Number of water molecules in the system (used to estimate box volume for salt concentration calculations).

  • neutralize (bool) – If True, return only the counts needed for neutralization. If saltconc is not None, this is automatically set to False.

  • saltconc (float, optional) – Target salt concentration in molar. If given, additional ions are added on top of the neutralizing ions to reach this concentration.

  • cation (str, optional) – Cation residue name. Accepts canonical keys ("NA", "K", "MG", "CA", "CS"), full names ("sodium"), AMBER names ("Na+"), or CHARMM names ("SOD"). If None, defaults to "NA".

  • anion (str, optional) – Anion residue name. Accepts canonical keys ("CL"), full names ("chloride"), AMBER names ("Cl-"), or CHARMM names ("CLA"). If None, defaults to "CL".

  • ff (str, optional) – Deprecated. No longer needed; pass standard ion names via cation / anion.

Returns:

When neutralize is True: (anion, cation, nanion, ncation). When saltconc is given: (anion, cation, anion, cation, nanion, ncation).

Return type:

tuple

Raises:

NameError – If the ion charges cannot neutralize the system, if no waters are found, or if the requested salt concentration is already exceeded.

htmd.builder.ionize.ionizePlace(solvent_mol: Molecule, solute_mol: Molecule | None, anion_resname: str, cation_resname: str, anion_name: str, cation_name: str, nanion: int, ncation: int, dfrom: float = 5, dbetween: float = 5, segname: str | None = None) → Molecule#

Place a given number of negative and positive ions in the solvent.

Uses farthest point sampling to produce well-spaced ion positions and randomly assigns ion types for uniform spatial mixing. Replaces water molecules as long as they respect the given distance criteria.

Parameters:

  • solvent_mol (Molecule) – The solvent (water) molecule.

  • solute_mol (Molecule or None) – The solute molecule used for minimum-distance filtering. If None or empty, no minimum distance from solute is enforced.

  • anion_resname (str) – Resname of the added anions.

  • cation_resname (str) – Resname of the added cations.

  • anion_name (str) – Name of the added anions.

  • cation_name (str) – Name of the added cations.

  • nanion (int) – Number of anions to add.

  • ncation (int) – Number of cations to add.

  • dfrom (float) – Minimum distance of ions from solute molecule in Angstroms.

  • dbetween (float) – Minimum distance between ions in Angstroms.

  • segname (str, optional) – Segment name to assign to the ions.

Returns:

mol – The solvent molecule with ions replacing some water molecules.

Return type:

Molecule

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