htmd.builder.solvate module#
- htmd.builder.solvate.solvate(mol, pad=None, minmax=None, negx=0, posx=0, negy=0, posy=0, negz=0, posz=0, buffer=2.4, watsize=65.4195, prefix='W', rotate=False, spdb=None)#
Solvates the system in a water box
- Parameters:
mol (
Molecule
object) – The molecule object we want to solvatepad (float) – The padding to add to the minmax in all dimensions. You can specify different padding in each dimension using the negx, negy, negz, posx, posy, posz options. This option will override any values in the neg and pos options.
minmax (list) – Min and max dimensions. Should be a 2D matrix of the form [[minx, miny, minz], [maxx, maxy, maxz]]. If none is given, it is calculated from the minimum and maximum coordinates in the mol.
negx (float) – The padding in the -x dimension
posx (float) – The padding in the +x dimension
negy (float) – The padding in the -y dimension
posy (float) – The padding in the +y dimension
negz (float) – The padding in the -z dimension
posz (float) – The padding in the +z dimension
buffer (float) – How much buffer space to leave empty between waters and other molecules
watsize (float) – The size of the water box
prefix (str) – The prefix used for water segments
keysel (str) – The key selection for water atoms
rotate (bool) – Enable automated rotation of molecule to fit best in box
rotsel (str) – The selection of atoms to rotate
rotinc (float) – The increment in degrees to rotate
spdb (str) – The path to the water pdb file
- Returns:
mol – A solvated molecule
- Return type:
Molecule
object
Examples
>>> smol = solvate(mol, pad=10) >>> smol = solvate(mol, minmax=[[-20, -20, -20],[20, 20, 20]])