moldesign.units package¶

Submodules¶

moldesign.units.constants module¶

moldesign.units.quantity module¶

Set up physical constants and unit systems

class moldesign.units.quantity.Array(*args)[source]¶

Bases: moldesign.units.quantity.MdtQuantity

A matrix quantity (i.e., a matrix of floats) with attached units, which behaves like a 2-dimensional numpy array

class moldesign.units.quantity.MdtQuantity[source]¶

Bases: pint.unit.Quantity

This is a ‘patched’ version of pint’s quantities that can be pickled (slightly hacky) and supports more numpy operations. Users should never need to instantiate this directly - instead, construct MDT quantities by multiplying numbers/arrays with the pre-defined units

Examples

>>> 5.0 * units.femtoseconds
>>> [1.0,2.0,3.0] * units.eV

compare(other, op)[source]¶

Augments the pint._Quantity method with the following features: - Comparisons to dimensionless 0 can proceed without unit checking

cross(other)[source]¶

defunits()[source]¶

Return this quantity in moldesign’s default unit system (as specified in moldesign.units.default)

defunits_inplace()[source]¶

Internally convert quantity to default units

defunits_value()[source]¶

dot(other)[source]¶

Dot product that correctly multiplies units

Returns:	MdtQuantity

get_units()[source]¶

Return the base unit system of an quantity

ldot(other)[source]¶

Left-multiplication version of dot. Use this to preserve units (built-in numpy versions don’t) getting hackier ...

norm()[source]¶

Compute norm but respect units

normalized()[source]¶

shape¶

to_json()[source]¶

to_simtk()[source]¶

value_in(units)¶

Quantity’s magnitude expressed in particular units.

Parameters:	units (Quantity, str or dict) – destination units

class moldesign.units.quantity.MdtUnit[source]¶

Bases: pint.unit.Unit

Pickleable version of pint’s Unit class.

class moldesign.units.quantity.Scalar(*args)[source]¶

Bases: moldesign.units.quantity.MdtQuantity

A scalar quantity (i.e., a single floating point number) with attached units

class moldesign.units.quantity.Tensor(*args)[source]¶

Bases: moldesign.units.quantity.MdtQuantity

A vector quantity (i.e., a list of floats) with attached units, which behaves like a multidimensional numpy array

class moldesign.units.quantity.Vector(*args)[source]¶

Bases: moldesign.units.quantity.MdtQuantity

A vector quantity (i.e., a list of floats) with attached units, which behaves like a 1-dimensional numpy array

moldesign.units.tools module¶

moldesign.units.tools.array(qlist, baseunit=None)[source]¶

Facilitates creating an array with units - like numpy.array, but it also checks

units for all components of the array

Args:

qlist (List[MdtQuantity]): List-like object of quantity objects baseunit (MdtUnit) unit to standardize with

Returns:	array with standardized units
Return type:	MdtQuantity

moldesign.units.tools.broadcast_to(arr, *args, **kwargs)[source]¶

moldesign.units.tools.get_units(q)[source]¶

Return the base unit system of an quantity

moldesign.units.tools.units_transfer(from_var, to_var, force=False)[source]¶

Give the “to_var” object the same units as “from_var”

Parameters:	from_var (MdtQuantity) – use this quantities units to_var (MdtQuantity) – apply units to this quantity force (bool) – Transfer the units even if from_var and to_var have incompatible units
Returns:	to_var with from_var’s units
Return type:	MdtQuantity

moldesign.units.unitsystem module¶

class moldesign.units.unitsystem.UnitSystem(length, mass, time, energy, temperature=<Unit('kelvin')>, force=None, momentum=None, angle=<Unit('radian')>, charge=<Unit('elementary_charge')>)[source]¶

Bases: object

Class for standardizing units - specifies preferred units for length, mass, energy etc.

In MDT, many methods will automatically convert output using the UnitSystem at moldesign.units.default

convert(quantity)[source]¶

Convert a quantity into this unit system

Parameters:	quantity (MdtQuantity) – quantity to convert

force¶

get_baseunit(quantity)[source]¶

momentum¶