Load files
mol2 files
Create an mbuild.Compound
(i.e., the “pentane” variable) by loading a molecule from a mol2 file.
Import the required mbuild packages.
import mbuild as mb
Load the “pentane.mol2” file from its directory.
pentane = mb.load("path_to_mol2_file/pentane.mol2")
CIF files
Build an mbuild.Compound
(i.e., the “ETV_triclinic” variable) by loading a Crystallographic Information File (CIF) file and selecting the number of cell units to populate in the x, y, and z-dimensions.
Import the required mbuild packages.
import mbuild as mb
from mbuild.lattice import load_cif
The CIF file is loaded using the load_cif
function. Next, three (3) cell units shall be built for all the x, y, and z-dimensions with the populate function. Finally, the CIF’s residues are named ‘ETV’.
lattice_cif_ETV_triclinic = load_cif("path_to_cif_file/ETV_triclinic.cif")
ETV_triclinic = lattice_cif_ETV_triclinic.populate(x=3, y=3, z=3)
ETV_triclinic.name = 'ETV'
Other file types
mBuild also supports Loading Data or files via hoomd_snapshot, GSD, SMILES strings, and ParmEd structures.