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htmd.builder.solvate module#

htmd.builder.solvate.solvate(mol: Molecule, pad: float | None = None, minmax: list | ndarray | None = None, centersel: str | ndarray | None = None, boxsize: float | list | ndarray | None = None, negx: float = 0, posx: float = 0, negy: float = 0, posy: float = 0, negz: float = 0, posz: float = 0, buffer: float = 2.4, watsize: float = 65.4195, prefix: str = 'W', rotate: bool = False, spdb: str | None = None) → Molecule#

Solvate a molecular system in a water box.

Places water molecules around the input molecule by tiling a pre-built water box and removing waters that clash with existing atoms or fall outside the specified box boundaries.

Parameters:

  • mol (Molecule) – The molecule to solvate.

  • pad (float, optional) – Uniform padding in Angstroms to add around the molecule in all six directions. Overrides negx, posx, negy, posy, negz, posz.

  • minmax (list or np.ndarray, optional) – Explicit box boundaries as a 2D array of the form [[minx, miny, minz], [maxx, maxy, maxz]]. If None, derived from the molecule’s own coordinates.

  • centersel (str or np.ndarray, optional) – An atom selection string, a boolean mask, or an integer index array (see Molecule.atomselect) defining the center of the solvation box. The geometric center of the selected atoms is used. Must be combined with boxsize.

  • boxsize (float or list or np.ndarray, optional) – Dimensions of the solvation box. A single float creates a cubic box; a 3-element list [sx, sy, sz] creates an axis-aligned box. Must be combined with centersel.

  • negx (float, optional) – Padding in Angstroms in the -x direction.

  • posx (float, optional) – Padding in Angstroms in the +x direction.

  • negy (float, optional) – Padding in Angstroms in the -y direction.

  • posy (float, optional) – Padding in Angstroms in the +y direction.

  • negz (float, optional) – Padding in Angstroms in the -z direction.

  • posz (float, optional) – Padding in Angstroms in the +z direction.

  • buffer (float, optional) – Minimum distance in Angstroms between water molecules and other atoms.

  • watsize (float, optional) – Edge length in Angstroms of the pre-built water box tile.

  • prefix (str, optional) – Prefix string used for water segment names.

  • rotate (bool, optional) – If True, rotate the molecule to minimize box volume (not yet implemented).

  • spdb (str, optional) – Path to a custom water PDB file. If None, uses the built-in water box.

Returns:

mol – A copy of the input molecule with water molecules added.

Return type:

Molecule

Examples

>>> smol = solvate(mol, pad=10)
>>> smol = solvate(mol, minmax=[[-20, -20, -20],[20, 20, 20]])
>>> smol = solvate(mol, centersel="protein", boxsize=100)
>>> smol = solvate(mol, centersel="protein", boxsize=[80, 80, 120])
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