Data is input into
mBuild in a few different ways or from different file types.
Load a file or an existing topology into an mbuild Compound.
Files are read using the predefined backend, unless otherwise specified by the user (through the backend flag). Supported backends include “pybel”, “mdtraj”, “parmed”, “rdkit”, and “internal”. Please refer to http://mdtraj.org/1.8.0/load_functions.html for formats supported by MDTraj and https://parmed.github.io/ParmEd/html/readwrite.html for formats supported by ParmEd.
- filename_or_objectstr, mdtraj.Trajectory, parmed.Structure,
mbuild.Compound, pybel.Molecule, Name of the file or topology from which to load atom and bond information.
- relative_to_modulestr, optional, default=None
Instead of looking in the current working directory, look for the file where this module is defined. This is typically used in Compound classes that will be instantiated from a different directory (such as the Compounds located in mbuild.lib).
- compoundmb.Compound, optional, default=None
Existing compound to load atom and bond information into. New structure will be added to the existing compound as a sub compound.
- coords_onlybool, optional, default=False
Only load the coordinates into an existing compound.
- rigidbool, optional, default=False
Treat the compound as a rigid body
- backendstr, optional, default=None
Backend used to load structure from file or string. If not specified, a default backend (extension specific) will be used.
- smiles: bool, optional, default=False
Use RDKit or OpenBabel to parse filename as a SMILES string or file containing a SMILES string. If this is set to True, rdkit is the default backend.
- infer_hierarchybool, optional, default=True
If True, infer hierarchy from chains and residues
- ignore_box_warnbool, optional, default=False
If True, ignore warning if no box is present. Defaults to True when loading from SMILES
Key word arguments passed to mdTraj, GMSO, RDKit, or pybel for loading.
compound : mb.Compound
If smiles is True, either rdkit (default) or pybel can be used, but RDkit is the only option of these that allows the user to specify a random number seed to reproducibly generate the same starting structure. This is NOT possible with openbabel, use rdkit if you need control over starting structure’s position (recommended).
Load a CifFile object into an mbuild.Lattice.
- wrap_coordsbool, False
Wrap the lattice points back into the 0-1 acceptable coordinates.