🧪 Monomer ⚗️

A pure Java package for cheminformatics.

Documentation | Report a Bug | Submit a Pull Request

Installation

The artifact can be found at Maven Central:

<dependency>
  <groupId>io.github.elonlit</groupId>
  <artifactId>monomer</artifactId>
  <version>1.7</version>
</dependency>

Features

• Properties of all Elements
• Compounds
  • Formula
  • Molar Mass
  • Percentage Composition by Mass
  • Stoichiometric Amounts
• Empirical Formulae
  • Empirical Formula by Percentage Composition
  • Combustion Analysis of Hydrocarbons
• Chemical Reactions
  • Balancing the Equation
  • Combustion Reactions
  • Stoichiometric Amounts
  • Limiting Reagent
• Aqueous Solutions
  • Solute
  • Molarity (mol/L)
  • Stoichiometric Amounts
  • Dilutions
• Electrochemistry
  • Galvanic (Voltaic) Cells
    • Anode, Cathode, Cell Potential
  • Electrolysis
• Quantum Mechanics
  • Electromagnetic Waves
    • Frequency, Wavelength, Energy per photon
  • Energy in nth Hydrogen Orbital
  • Rydberg Equation
  • Nuclear-nuclear Repulsions
  • Vector Fields in Cylindrical and Spherical Coordinates
  • Quaternions
  • Gaussian Functions
• Monomers
  • Base Monomer
  • DNA
  • RNA
  • Residues
• Polymers
  • Generic Seq

Elements

Element carbon = Element("C"); // Declare Element from its symbol
        
System.out.println(carbon); // Carbon{atomicNumber=6.0,elementName='Carbon',elementSymbol='C',atomicMass=12.011,neutrons=6.0,protons=6.0,electrons=6.0,period=2.0,group=14.0,phase='solid',radioactive=false,natural=true,metal=false,nonmetal=true,metalloid=false,type='Nonmetal',atomicRadius='0.91',electronegativity='2.55',firstIonization='11.2603',density=2.27,meltingPoint=3948.15,boilingPoint=4300.0,isotopes=7.0,discoverer='Prehistoric',specificHeat=0.709,shells=2.0,valence=4.0,config='[He] 2s2 2p2',massNumber=12.0}

System.out.println(carbon.atomicMass) // 12.011

Compounds

Compound moronicAcid = new Compound("C30H46O3"); // Moronic acid (3-oxoolean-18-en-28-oic acid) is a natural triterpene

System.out.println(moronicAcid.humanReadableOccurrences); // {Oxygen=3,Hydrogen=46,Carbon=30}

System.out.println(moronicAcid.getMolarMass()); // 454.695
        
System.out.println(moronicAcid.getPercentCompositionByMass(new Element("O"))); // 10.555866

Stoichiometric Conversions

var water = new Compound("H2O"); // Instantiate a water compound

System.out.println(water.formula); // H2O
        
// Accepted inputs: grams, moles, and molecules
System.out.println(water.getAmounts("Molecules", 2e+24)); // {Grams=59.8505,Molecules=2.0E24,Moles=3.3222592}

Empirical Formula Utilities

// Construct a HashMapping of Elements in a Compound to their constituent relative frequencies
HashMap<Element, Float> percentCompositionMap = new HashMap<Element, Float>() {{
    put(new Element("C"), 52.14f);
    put(new Element("O"), 34.73f);
    put(new Element("H"), 13.13f);
}};

// Instantiate a Compound from the resulting empirical formula of a Compound that is composed of 52.14% C, 34.73% O, and 13.13% H by mass
Compound adipicAcid = new Compound(EmpiricalFormulaUtil.getEmpiricalFormulaFromPercentComposition(percentCompositionMap));
System.out.println(adipicAcid); // C2H6O1: {Oxygen=1, Hydrogen=6, Carbon=2}

// A hydrocarbon fuel is fully combusted with 18.214 g of oxygen to yield 23.118 g of carbon dioxide and 4.729 g of water. 
// Find the empirical formula for the hydrocarbon
Compound compound = new Compound(EmpiricalFormulaUtil.getHydrocarbonFromCombustion(23.118f, 4.729f));
System.out.println(compound); // C1H1: {Hydrogen=1, Carbon=1}

Chemical Equations

var photosynthesis = new Reaction("CO2 + H2O --> C6H12O6 + O2"); // Reactions delimited by "-->"

// Automatic balancing
System.out.println(photosynthesis.equation); // 6CO2 + 6H2O --> C6H12O6 + 6O2

System.out.println(EquationBalancerUtil.isBalanced(photosynthesis)); // true

// Get the amounts of ALL compounds in the above reaction given 5 grams of C6H12O6
System.out.println(photosynthesis.getAmounts("C6H12O6", "Grams", 5f)); // [{Grams=7.328481, Molecules=1.0024645E23, Moles=0.16652234}, {Grams=2.9998999, Molecules=1.0024645E23, Moles=0.16652234}, {Grams=5.0, Molecules=1.6707742E22, Moles=0.027753724}, {Grams=5.3283815, Molecules=1.0024645E23, Moles=0.16652234}]

// Find the limiting reagent of the reaction when using 3 moles of the first reactant (CO2) and 1 mole of the second reactant (H2O)
Compound limitingReagent = photosynthesis.getLimitingReagent("Moles", 3, 1);

System.out.println(limitingReagent); // H2O: {Oxygen=1, Hydrogen=2}

Solutions

// Instantiate a Solution with the solute and molarity
Solution solution = new Solution("NaCl", 0.25f);

// Find the dilution of 2.5 L of 0.25M NaCl to a 0.125M NaCl solution:
System.out.println(solution.dilute(2.5f, 0.125f, 0)); // {Volume=5.0, Molarity=0.125, Solute=NaCl}

Electrochemistry

// Make a Galvanic Cell with Lead and Zinc electrodes
GalvanicCell galvanicCell = new GalvanicCell("Pb", "Zn");

System.out.println(galvanicCell); // GalvanicCell{Cell='Zn|Zn2+||Pb2+|Pb', Anode=Zn, Cathode=Pb, CellPotential=0.63}
        
// A HashMapping of arguments to values of either two of "amps", "seconds", or "grams."
HashMap<String, Float> kwargs = new HashMap<>() {{
    put("seconds", 24*60*60f);
    put("grams", 805f);
}};

// Moles of electrons transferred
int mol = 3;

// How much current was used to produce 805 grams of Aluminum metal from Al2O3 in 24 hours?
System.out.println(GalvanicCell.electrolysis("Al", mol, kwargs)); // {Amps=99.95144, Grams=805.0, Seconds=86400.0}

Quantum Mechanics

// Determine the wavelength, frequency, and energy of a wave with energy 2.84e-19 Joules per particle
Wave red = new Wave("Energy", 2.84e-19);
System.out.println(red); // Wave{wavelength=6.99462948008421E-7, frequency=4.286145536363085E14, energy=2.84E-19}

// Determine the energy of an electron in the 3rd orbital of a Hydrogen atom in Joules
System.out.println(Wave.energyOfHydrogenOrbital(3)); // -2.4221748553237596E-19

Monomers & Seq

// Instantiate a Seq of type DNA
Seq<DNA> myCodingStrand = new Seq<>();

// Populate myCodingStrand with random DNA nucleotides
Random random = new Random();
for(int i=0; i<15000; i++) {
    myCodingStrand.elongate(new DNA(String.valueOf(DNA.nucleotidesDNA.values()[new Random().nextInt(DNA.nucleotidesDNA.values().length)])));
}

Citing

If you use Monomer in your scientific work, please consider citing:

| E. Litman, Monomer - An object-oriented cheminformatics library, 2022-- . Available at: https://github.com/elonlit/monomer.

The reference in the BibLaTeX format:

@software{monomer2022,
   author = {Litman, Elon},
   title = {{Monomer} -- An object-oriented cheminformatics library},
   url = {https://github.com/elonlit/Monomer},
   version = {1.7},
   date = {2022--},
}