Loading Data¶
Data is input into mBuild in a few different ways or from different file types.
Load¶
Load a file or an existing topology into an mbuild Compound.
Files are read using the MDTraj package unless the use_parmed argument is specified as True. 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.
Parameters¶
- 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
**kwargskeyword argumentsKey word arguments passed to mdTraj, RDKit, or pybel for loading.
Returns¶
compound : mb.Compound
Notes¶
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).