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Molecule Model

A Python implementations of the MolSSI QCSchema Molecule object. A "Molecule" many definitions of Molecule depending on the domain; this particular Molecule is an immutable 3D Cartesian representation with support for quantum chemistry constructs.

Creation

A Molecule can be created using the normal kwargs fashion as shown below:

>>> mol = qcel.models.Molecule(**{"symbols":["He"], "geometry": [0, 0, 0]})

In addition, there is the from_data attribute to create a molecule from standard strings:

>>> mol = qcel.models.Molecule.from_data("He 0 0 0")
>>> mol
<    Geometry (in Angstrom), charge = 0.0, multiplicity = 1:

       Center              X                  Y                   Z
    ------------   -----------------  -----------------  -----------------
    He                0.000000000000     0.000000000000     0.000000000000
>

Identifiers

A number of unique identifiers are automatically created for each molecule. Additional implementation such as InChI and SMILES are actively being looked into.

Molecular Hash

A molecule hash is automatically created to allow each molecule to be uniquely identified. The following keys are used to generate the hash:

  • symbols
  • masses (1.e-6 tolerance)
  • molecular_charge (1.e-4 tolerance)
  • molecular_multiplicity
  • real
  • geometry (1.e-8 tolerance)
  • fragments
  • fragment_charges (1.e-4 tolerance)
  • fragment_multiplicities
  • connectivity

Hashes can be acquired from any molecule object and a FractalServer automatically generates canonical hashes when a molecule is added to the database.

>>> mol = qcel.models.Molecule(**{"symbols": ["He", "He"], "geometry": [0, 0, -3, 0, 0, 3]})
>>> mol.get_hash()
'84872f975d19aafa62b188b40fbadaf26a3b1f84'

Molecular Formula

The molecular formula is also available sorted in alphabetical order with title case symbol names. Any symbol with a count of one does not have a number associated with it.

>>> mol.get_molecular_formula()
    'He2'

Fragments

A Molecule with fragments can be created either using the -- separators in the from_data function or by passing explicit fragments in the Molecule constructor:

>>> mol = qcel.models.Molecule.from_data(
>>>       """
>>>       Ne 0.000000 0.000000 0.000000
>>>       --
>>>       Ne 3.100000 0.000000 0.000000
>>>       """)

>>> mol = qcel.models.Molecule(
>>>       geometry=[0, 0, 0, 3.1, 0, 0],
>>>       symbols=["Ne", "Ne"],
>>>       fragments=[[0], [1]]
>>>       )

Fragments from a molecule containing fragment information can be aquired by:

>>> mol.get_fragment(0)
<    Geometry (in Angstrom), charge = 0.0, multiplicity = 1:

       Center              X                  Y                   Z
    ------------   -----------------  -----------------  -----------------
    Ne                0.000000000000     0.000000000000     0.000000000000
>

Obtaining fragments with ghost atoms is also supported:

>>> mol.get_fragment(0, 1)
<    Geometry (in Angstrom), charge = 0.0, multiplicity = 1:

       Center              X                  Y                   Z
    ------------   -----------------  -----------------  -----------------
    Ne                0.000000000000     0.000000000000     0.000000000000
    Ne      (Gh)      3.100000000572     0.000000000000     0.000000000000
>

Molecule Attributes

Below are the documentations for all attributes and initialization keywords for a Molecule object

qcelemental.models.Molecule