polymerist.mdtools.openfftools.physprops
========================================

.. py:module:: polymerist.mdtools.openfftools.physprops

.. autoapi-nested-parse::

   For converting macroscopic parameters (such as concentration, bulk density, etc) into microscopic parameters for simulations



Functions
---------

.. autoapisummary::

   polymerist.mdtools.openfftools.physprops.molecular_weight
   polymerist.mdtools.openfftools.physprops.offmol_mass
   polymerist.mdtools.openfftools.physprops.offtop_mass
   polymerist.mdtools.openfftools.physprops.effective_radius
   polymerist.mdtools.openfftools.physprops.number_density
   polymerist.mdtools.openfftools.physprops.num_mols_in_box


Module Contents
---------------

.. py:function:: molecular_weight(rdmol: rdkit.Chem.Mol, exact_isotopes: bool = False) -> openmm.unit.Quantity

   Compute the molecular weight of an RDKit Mol


.. py:function:: offmol_mass(offmol: openff.toolkit.Molecule, as_openmm: bool = False) -> Union[openmm.unit.Quantity, openff.units.Quantity]

   Compute the molecular mass of an OpenFF Molecule (in Daltons)
   Returns mass with OpenFF-style units, or with OpenMM-style units if as_openmm=True


.. py:function:: offtop_mass(offtop: openff.toolkit.Topology, as_openmm: bool = False) -> Union[openmm.unit.Quantity, openff.units.Quantity]

   Compute the molecular mass of an OpenFF Topology (in Daltons)
   Returns mass with OpenFF-style units, or with OpenMM-style units if as_openmm=True


.. py:function:: effective_radius(offmol: openff.toolkit.Molecule, conf_id: int = 0) -> openmm.unit.Quantity

   Determine an effective spherical radius for a Molecule

   Defined to be the radius of the smallest sphere which contains all atoms in the molecule
   if that sphere is placed concentric to the centroid of the chosen conformer


.. py:function:: number_density(density: openmm.unit.Quantity, MW: openmm.unit.Quantity) -> openmm.unit.Quantity

   Determine the number of solvent molecules per unit volume from known physical constants
   For best results, provide arguments as Quantities with associated units


.. py:function:: num_mols_in_box(mol: Union[rdkit.Chem.Mol, openff.toolkit.Molecule, openff.toolkit.Topology], box_vol: openmm.unit.Quantity, density: openmm.unit.Quantity) -> int

   Return the number of particles/molecules needed to fill a box of given volume to the specified density