Periodic Table (chemicals.elements)¶
This module contains a complete periodic table, routines for working with chemical formulas, computing molecular weight, computing mass fractions and atom fractions, and assorted other tasks.
For reporting bugs, adding feature requests, or submitting pull requests, please use the GitHub issue tracker.
Periodic Table and Elements¶
- chemicals.elements.periodic_table = <chemicals.elements.PeriodicTable object>¶
Single instance of the PeriodicTable class. Use this, not the PeriodicTable class directly.
A brief overview of using the periodic table and its elements:
>>> periodic_table.Na <Element Sodium (Na), number 11, MW=22.98977> >>> periodic_table.U.MW 238.02891 >>> periodic_table['Th'].CAS '7440-29-1' >>> periodic_table.lead.protons 82 >>> periodic_table['7440-57-5'].symbol 'Au' >>> len(periodic_table) 118 >>> 'gold' in periodic_table True >>> periodic_table.He.protons, periodic_table.He.neutrons, periodic_table.He.electrons # Standard number of protons, neutrons, electrons (2, 2, 2) >>> periodic_table.He.phase # Phase of the element in the standard state 'g' >>> periodic_table.He.Hf # Heat of formation in standard state in J/mol - by definition 0 0.0 >>> periodic_table.He.S0 # Absolute entropy (J/(mol*K) in standard state - non-zero) 126.2 >>> periodic_table.Kr.block, periodic_table.Kr.period, periodic_table.Kr.group ('p', 4, 18) >>> periodic_table.Rn.InChI 'Rn' >>> periodic_table.Rn.smiles '[Rn]' >>> periodic_table.Pu.number 94 >>> periodic_table.Pu.PubChem 23940 >>> periodic_table.Bi.InChI_key 'JCXGWMGPZLAOME-UHFFFAOYSA-N'
- class chemicals.elements.Element(number, symbol, name, MW, CAS, AReneg, rcov, rvdw, maxbonds, elneg, ionization, elaffinity, period, group, PubChem, phase, Hf, S0, InChI_key=None)[source]¶
Class for storing data on chemical elements. Supports most common properties. If a property is not available, it is set to None.
The elements are created automatically and should be accessed via the periodic_table interface.
- Attributes
- number
int
Atomic number, [-]
- name
str
name, [-]
- symbol
str
Elemental symbol, [-]
- MW
float
Molecular weight, [g/mol]
- CAS
str
CAS number, [-]
- period
str
Period in the periodic table, [-]
- group
str
Group in the periodic table, [-]
block
str
Which block of the periodic table the element is in.
- AReneg
float
Allred and Rochow electronegativity, [-]
- rcov
float
Covalent radius, [Angstrom]
- rvdw
float
Van der Waals radius, [Angstrom]
- maxbonds
float
Maximum valence of a bond with this element, [-]
- elneg
float
Pauling electronegativity, [-]
- ionization
float
Ionization potential, [eV]
- elaffinity
float
Electron affinity, [eV]
protons
int
The number of protons of the element.
electrons
int
The number of electrons of the element.
InChI
str
The InChI identifier of the element.
- InChI_key
str
25-character hash of the compound’s InChI, [-]
smiles
str
The SMILES identification string of the element.
- PubChem
int
PubChem Compound identifier (CID) of the chemical, [-]
- phase
str
Standard state at 1 atm and 298.15 K, [-]
- Hf
float
Enthalpy of formation of the element in its standard state (0 by definition), [J/mol]
- S0
float
Standard absolute entropy of the element in its standard state (1 bar, 298.15 K), [J/mol/K]
- number
- class chemicals.elements.PeriodicTable(elements)[source]¶
Periodic Table object for use in dealing with elements.
As there is only one periodic table of elements, this is automatically initialized into the object periodic_table; there is no need to construct a new instance of this class.
See also
Notes
Can be checked to sese if an element in in this, can be iterated over, and as a current length of 118 elements.
References
- 1
N M O’Boyle, M Banck, C A James, C Morley, T Vandermeersch, and G R Hutchison. “Open Babel: An open chemical toolbox.” J. Cheminf. (2011), 3, 33. DOI:10.1186/1758-2946-3-33
Working with Formulas¶
- chemicals.elements.simple_formula_parser(formula)[source]¶
Basic formula parser, primarily for obtaining element counts from formulas as formated in PubChem. Handles formulas with integer or decimal counts (with period separator), but no brackets, no hydrates, no charges, no isotopes, and no group multipliers.
Strips charges from the end of a formula first. Accepts repeated chemical units. Performs no sanity checking that elements are actually elements. As it uses regular expressions for matching, errors are mostly just ignored.
- Parameters
- formula
str
Formula string, very simply formats only.
- formula
- Returns
- atoms
dict
dictionary of counts of individual atoms, indexed by symbol with proper capitalization, [-]
- atoms
Notes
Inspiration taken from the thermopyl project, at https://github.com/choderalab/thermopyl.
Examples
>>> simple_formula_parser('CO2') {'C': 1, 'O': 2}
- chemicals.elements.nested_formula_parser(formula, check=True)[source]¶
Improved formula parser which handles braces and their multipliers, as well as rational element counts.
Strips charges from the end of a formula first. Accepts repeated chemical units. Performs no sanity checking that elements are actually elements. As it uses regular expressions for matching, errors are mostly just ignored.
- Parameters
- Returns
- atoms
dict
dictionary of counts of individual atoms, indexed by symbol with proper capitalization, [-]
- atoms
Notes
Inspired by the approach taken by CrazyMerlyn on a reddit DailyProgrammer challenge, at https://www.reddit.com/r/dailyprogrammer/comments/6eerfk/20170531_challenge_317_intermediate_counting/
Examples
>>> nested_formula_parser('Pd(NH3)4.0001+2') {'Pd': 1, 'N': 4.0001, 'H': 12.0003}
- chemicals.elements.charge_from_formula(formula)[source]¶
Basic formula parser to determine the charge from a formula - given that the charge is already specified as one element of the formula.
Performs no sanity checking that elements are actually elements.
- Parameters
- formula
str
Formula string, very simply formats only, ending in one of ‘+x’, ‘-x’, n*’+’, or n*’-’ or any of them surrounded by brackets but always at the end of a formula.
- formula
- Returns
- charge
int
Charge of the molecule, [faraday]
- charge
Examples
>>> charge_from_formula('Br3-') -1 >>> charge_from_formula('Br3(-)') -1
- chemicals.elements.serialize_formula(formula)[source]¶
Basic formula serializer to construct a consistently-formatted formula. This is necessary for handling user-supplied formulas, which are not always well formatted.
Performs no sanity checking that elements are actually elements.
- Parameters
- formula
str
Formula string as parseable by the method nested_formula_parser, [-]
- formula
- Returns
- formula
str
A consistently formatted formula to describe a molecular formula, [-]
- formula
Examples
>>> serialize_formula('Pd(NH3)4+3') 'H12N4Pd+3'
- chemicals.elements.atoms_to_Hill(atoms)[source]¶
Determine the Hill formula of a compound, given a dictionary of its atoms and their counts, in the format {symbol: count}.
- Parameters
- atoms
dict
dictionary of counts of individual atoms, indexed by symbol with proper capitalization, [-]
- atoms
- Returns
- Hill_formula
str
Hill formula, [-]
- Hill_formula
Notes
The Hill system is as follows:
If the chemical has ‘C’ in it, this is listed first, and then if it has ‘H’ in it as well as ‘C’, then that goes next. All elements are sorted alphabetically afterwards, including ‘H’ if ‘C’ is not present. All elements are followed by their count, unless it is 1.
References
- 1
Hill, Edwin A.”“ON A SYSTEM OF INDEXING CHEMICAL LITERATURE; ADOPTED BY THE CLASSIFICATION DIVISION OF THE U. S. PATENT OFFICE.1.” Journal of the American Chemical Society 22, no. 8 (August 1, 1900): 478-94. doi:10.1021/ja02046a005.
Examples
>>> atoms_to_Hill({'H': 5, 'C': 2, 'Br': 1}) 'C2H5Br'
Working with Parsed Formulas¶
- chemicals.elements.molecular_weight(atoms)[source]¶
Calculates molecular weight of a molecule given a dictionary of its atoms and their counts, in the format {symbol: count}.
$MW = \sum_i n_i MW_i$- Parameters
- atoms
dict
Dictionary of counts of individual atoms, indexed by symbol with proper capitalization, [-]
- atoms
- Returns
- MW
float
Calculated molecular weight [g/mol]
- MW
Notes
Elemental data is from rdkit, with CAS numbers added. An exception is raised if an incorrect element symbol is given. Elements up to 118 are supported, as are deutreium and tritium.
References
- 1
RDKit: Open-source cheminformatics; http://www.rdkit.org
Examples
>>> molecular_weight({'H': 12, 'C': 20, 'O': 5}) # DNA 332.30628
- chemicals.elements.similarity_variable(atoms, MW=None)[source]¶
Calculates the similarity variable of an compound, as defined in [1]. Currently only applied for certain heat capacity estimation routines.
$\alpha = \frac{N}{MW} = \frac{\sum_i n_i}{\sum_i n_i MW_i}$- Parameters
- Returns
Notes
Molecular weight is optional, but speeds up the calculation slightly. It is calculated using the function molecular_weight if not specified.
References
- 1(1,2)
Laštovka, Václav, Nasser Sallamie, and John M. Shaw. “A Similarity Variable for Estimating the Heat Capacity of Solid Organic Compounds: Part I. Fundamentals.” Fluid Phase Equilibria 268, no. 1-2 (June 25, 2008): 51-60. doi:10.1016/j.fluid.2008.03.019.
Examples
>>> similarity_variable({'H': 32, 'C': 15}) 0.2212654140784498
- chemicals.elements.index_hydrogen_deficiency(atoms)[source]¶
Calculate the index of hydrogen deficiency of a compound, given a dictionary of its atoms and their counts, in the format {symbol: count}.
- Parameters
- atoms
dict
dictionary of counts of individual atoms, indexed by symbol with proper capitalization, [-]
- atoms
- Returns
- HDI
float
Hydrogen deficiency index, [-]
- HDI
Notes
The calculation is according to:
$\text{IDH} = 0.5\left(2C + 2 + N - H -X + 0O \right)$where X is the number of halogen atoms. The number of oxygen atoms does not impact this calculation.
References
- 1
Brown, William H., and Thomas Poon. Introduction to Organic Chemistry. 4th edition. Hoboken, NJ: Wiley, 2010.
Examples
Agelastatin A:
>>> index_hydrogen_deficiency({'C': 12, 'H': 13, 'Br': 1, 'N': 4, 'O': 3}) 8.0
- chemicals.elements.atom_fractions(atoms)[source]¶
Calculates the atomic fractions of each element in a compound, given a dictionary of its atoms and their counts, in the format {symbol: count}.
$a_i = \frac{n_i}{\sum_i n_i}$- Parameters
- atoms
dict
dictionary of counts of individual atoms, indexed by symbol with proper capitalization, [-]
- atoms
- Returns
- afracs
dict
dictionary of atomic fractions of individual atoms, indexed by symbol with proper capitalization, [-]
- afracs
Notes
No actual data on the elements is used, so incorrect or custom compounds would not raise an error.
References
- 1
RDKit: Open-source cheminformatics; http://www.rdkit.org
Examples
>>> atom_fractions({'H': 12, 'C': 20, 'O': 5}) {'H': 0.32432432432432434, 'C': 0.5405405405405406, 'O': 0.13513513513513514}
- chemicals.elements.mass_fractions(atoms, MW=None)[source]¶
Calculates the mass fractions of each element in a compound, given a dictionary of its atoms and their counts, in the format {symbol: count}.
$w_i = \frac{n_i MW_i}{\sum_i n_i MW_i}$- Parameters
- Returns
- mfracs
dict
Dictionary of mass fractions of individual atoms, indexed by symbol with proper capitalization, [-]
- mfracs
Notes
Molecular weight is optional, but speeds up the calculation slightly. It is calculated using the function molecular_weight if not specified.
Elemental data is from rdkit, with CAS numbers added. An exception is raised if an incorrect element symbol is given. Elements up to 118 are supported.
References
- 1
RDKit: Open-source cheminformatics; http://www.rdkit.org
Examples
>>> mass_fractions({'H': 12, 'C': 20, 'O': 5}) {'H': 0.03639798802478244, 'C': 0.7228692758981262, 'O': 0.24073273607709128}
- chemicals.elements.mixture_atomic_composition(atomss, zs)[source]¶
Simple function to calculate the atomic average composition of a mixture, using the mole fractions of each species and their own atomic compositions.
- Parameters
- Returns
Examples
>>> mixture_atomic_composition([{'O': 2}, {'N': 1, 'O': 2}, {'C': 1, 'H': 4}], [0.95, 0.025, .025]) {'O': 1.95, 'N': 0.025, 'C': 0.025, 'H': 0.1}
- chemicals.elements.mixture_atomic_composition_ordered(atomss, zs)[source]¶
Simple function to calculate the atomic average composition of a mixture, using the mole fractions of each species and their own atomic compositions. Returns the result as a sorted list with atomic numbers from low to high.
- Parameters
- Returns
Notes
Useful to ensure a matrix order is consistent in multiple steps.
Examples
>>> mixture_atomic_composition_ordered([{'O': 2}, {'N': 1, 'O': 2}, {'C': 1, 'H': 4}], [0.95, 0.025, .025]) ([0.1, 0.025, 0.025, 1.95], ['H', 'C', 'N', 'O'])
- chemicals.elements.atom_matrix(atomss, atom_IDs=None)[source]¶
Simple function to create a matrix of elements in each compound, where each row has the same elements.
- Parameters
- Returns
Examples
>>> atom_matrix([{'C': 1, 'H': 4}, {'C': 2, 'H': 6}, {'N': 2}, {'O': 2}, {'H': 2, 'O': 1}, {'C': 1, 'O': 2}]) [[4, 1, 0.0, 0.0], [6, 2, 0.0, 0.0], [0.0, 0.0, 2, 0.0], [0.0, 0.0, 0.0, 2], [2, 0.0, 0.0, 1], [0.0, 1, 0.0, 2]]