uclchem.makerates.species
=========================

.. py:module:: uclchem.makerates.species


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

Classes
~~~~~~~

.. autoapisummary::

   uclchem.makerates.species.Species



Functions
~~~~~~~~~

.. autoapisummary::

   uclchem.makerates.species.is_number



Attributes
~~~~~~~~~~

.. autoapisummary::

   uclchem.makerates.species.elementList
   uclchem.makerates.species.elementMass
   uclchem.makerates.species.symbols


.. py:class:: Species(inputRow)

   Species is a class that holds all the information about an individual species in the
   network. It also has convenience functions to check whether the species is a gas or grain
   species and to help compare between species.

   A class representing chemical species, it reads in rows which are formatted as follows:
   NAME,MASS,BINDING ENERGY,SOLID FRACTION,MONO FRACTION,VOLCANO FRACTION,ENTHALPY
   :param inputRow:
   :type inputRow: list


   .. py:method:: add_default_freeze() -> None

      Adds a defalt freezeout, which is freezing out to the species itself, but with no ionization.



   .. py:method:: find_constituents(quiet=False)

      Loop through the species' name and work out what its consituent
      atoms are. Then calculate mass and alert user if it doesn't match
      input mass.



   .. py:method:: get_charge() -> int

      Get the charge of the chemical species in e. Positive integer indicates positive ion,
      negative indicates negative ion. Assumes species are at most charged +1 or -1.

      :returns: The charge of the species
      :rtype: int



   .. py:method:: get_desorb_products() -> list[str]

      Obtain the desorbtion products of ice species

      :returns: The desorption products
      :rtype: list[str]



   .. py:method:: get_freeze_alpha(product_list: list[str]) -> float

      Obtain the freeze out ratio of a species for a certain reaction

      :param product_list: For a specific reaction, get the freezeout ratio
      :type product_list: list[str]

      :returns: The freezeout ratio
      :rtype: float



   .. py:method:: get_freeze_products() -> dict[list[str], float]

      Obtain the product to which the species freeze out

      :returns: Reactions and their respective freeze out ratios.
      :rtype: dict[str, float]

      :Yields: *Iterator[dict[str, float]]* -- Iterator that returns all of the freeze out reactions with ratios



   .. py:method:: get_freeze_products_list() -> list[list[str]]

      Returns all the freeze products without their ratios

      :returns: List of freeze products
      :rtype: list[list[str]]



   .. py:method:: get_mass() -> int

      Get the molecular mass of the chemical species

      :returns: The molecular mass
      :rtype: int



   .. py:method:: get_n_atoms() -> int

      Obtain the number of atoms in the molecule

      :returns: The number of atoms
      :rtype: int



   .. py:method:: get_name() -> str

      Get the name of the chemical species.

      :returns: The name
      :rtype: str



   .. py:method:: is_bulk_species() -> bool

      Checks if the species is in the bulk

      :returns: True if a bulk species
      :rtype: bool



   .. py:method:: is_grain_species() -> bool

      Return whether the species is a species on the grain

      :returns: True if it is a grain species.
      :rtype: bool



   .. py:method:: is_ice_species() -> bool

      Return whether the species is a species on the grain

      :returns: True if it is an ice species.
      :rtype: bool



   .. py:method:: is_ion() -> bool

      Checks if the species is ionized, either postively or negatively.

      :returns: True if it is an ionized
      :rtype: bool



   .. py:method:: is_surface_species() -> bool

      Checks if the species is on the surface

      :returns: True if a surface species
      :rtype: bool



   .. py:method:: set_desorb_products(new_desorbs: list[str]) -> None

      Set the desorption products for species on the surface or in the bulk.
      It is assumed that there is only one desorption pathway.

      :param new_desorbs: The new desorption products
      :type new_desorbs: list[str]



   .. py:method:: set_freeze_products(product_list: list[str], freeze_alpha: float) -> None

      Add the freeze products of the species, one species can have several freeze products.

      :param product_list: The list of freeze out products
      :type product_list: list[str]
      :param freeze_alpha: The freeze out ratio.
      :type freeze_alpha: float

      It is called alpha, since it is derived from the alpha column in the UCLCHEM reaction format:
      https://github.com/uclchem/UCLCHEM/blob/08d37f8c3063f8ff8a9a7aa16d9eff0ed4f99538/Makerates/src/network.py#L160



   .. py:method:: set_n_atoms(new_n_atoms: int) -> None

      Set the number of atoms

      :param new_n_atoms: The new number of atoms
      :type new_n_atoms: int



   .. py:method:: to_UCL_format() -> str


   .. py:attribute:: enthalpy


   .. py:attribute:: is_refractory
      :value: False



   .. py:attribute:: mass


   .. py:attribute:: monoFraction


   .. py:attribute:: n_atoms
      :value: 0



   .. py:attribute:: name


   .. py:attribute:: solidFraction


   .. py:attribute:: volcFraction


.. py:function:: is_number(s) -> bool

   Try to convert input to a float, if it succeeds, return True.

   :param s: Input element to check for

   :returns: True if a number, False if not.
   :rtype: bool


.. py:data:: elementList
   :value: ['H', 'D', 'HE', 'C', 'N', 'O', 'F', 'P', 'S', 'CL', 'LI', 'NA', 'MG', 'SI', 'PAH', '15N',...


.. py:data:: elementMass
   :value: [1, 2, 4, 12, 14, 16, 19, 31, 32, 35, 3, 23, 24, 28, 420, 15, 13, 18, 0, 56]


.. py:data:: symbols
   :value: ['#', '@', '*', '+', '-', '(', ')']