Mdanalysis
digesters.mdanalysis.HAS_MDANALYSIS = True
module-attribute
¶
digesters.mdanalysis.MDAnalysisDigester(*args, **kwargs)
¶
Bases: Digester
atom_symbols(atoms)
staticmethod
¶
Return the atomic coordinates in Angstroms.
Schema UUID: 81c21a83-4b72-48c6-a576-4541b468eb90
| PARAMETER | DESCRIPTION |
|---|---|
atoms |
The MDAnalysis atoms object associated with the frame.
TYPE:
|
| RETURNS | DESCRIPTION |
|---|---|
NDArray[str_]
|
A 1D array containing the atomic symbols. |
checks()
staticmethod
¶
Perform checks to ensure MDAnalysis is installed.
| RAISES | DESCRIPTION |
|---|---|
ImportError
|
If MDAnalysis is not installed. |
coordinates(atoms)
staticmethod
¶
Return the atomic coordinates in Angstroms.
Schema UUID: 81c7cec9-beec-4126-b6d8-91bee28951d6
| PARAMETER | DESCRIPTION |
|---|---|
atoms |
The MDAnalysis atoms object associated with the frame.
TYPE:
|
| RETURNS | DESCRIPTION |
|---|---|
NDArray[float64]
|
A 2D array containing the Cartesian coordinates of all atoms in. |
| RAISES | DESCRIPTION |
|---|---|
ValueError
|
If the coordinates are not a 2D NumPy array. |
ff_atom_type(atoms)
staticmethod
¶
Return the force field atom types of the atoms.
Schema UUID: e34c0e1b-0eaa-4679-b060-3fcfe737aa15
| PARAMETER | DESCRIPTION |
|---|---|
atoms |
The MDAnalysis atoms object associated with the frame.
TYPE:
|
| RETURNS | DESCRIPTION |
|---|---|
list[str]
|
Force field atom types. |
get_inputs_frame(inputs_digester)
classmethod
¶
next_frame(inputs_digester)
classmethod
¶
Move the MDAnalysis Universe to the next trajectory frame.
| PARAMETER | DESCRIPTION |
|---|---|
inputs |
A dictionary of inputs for the digestion process.
|
| RETURNS | DESCRIPTION |
|---|---|
dict[str, Any]
|
A dictionary of inputs for the digestion process. |
prepare_inputs_digester(*args, **kwargs)
classmethod
¶
Prepare and return the inputs necessary for the MDAnalysis digestion process.
This method loads the MDAnalysis Universe using the provided arguments and keyword arguments and prepares the inputs for digestion.
| PARAMETER | DESCRIPTION |
|---|---|
*args |
Variable length argument list.
TYPE:
|
**kwargs |
Arbitrary keyword arguments.
TYPE:
|
| RETURNS | DESCRIPTION |
|---|---|
dict[str, Universe]
|
A dictionary containing the MDAnalysis Universe. |
digesters.mdanalysis.accumulate_things(*args, **kwargs)
¶
Helper function for accumulating data over multiple structures in a MDAnalysis Universe.