Java Molecular Energy

open-source library for powering innovation through molecular energy

fullerene
forcefield

A Java library that support various operations in force fields

JME is designed to help researchers and scientists explore and understand the behavior of molecules at the atomic level. You can analyze the interactions between atoms and molecules and optimize molecular structures.

Calculate potential energy

Potential energy surface can provide detailed information about the energy of the molecule as a function of atoms positions. This can provide information about the energy barriers and the most favorable pathways for the molecule to change its conformation.
energy surface

Energy Minimization

JME supports energy minimization for molecules using gradient descent and adam optimization algorithms. Minimization can be handful in many situations like:
  • Predicting 3D structure for molecules
  • Stabilizing protein conformation before simulation
  • Finding different conformations of molecules
  • Finding the most stable conformation of a molecule

Calculate Partial Charges

You can easily calculate partial charges for each atom in a molecule. This powerful feature allows you to gain a deeper understanding of the charge distribution in molecules, which can be crucial for predicting and analyzing their behavior.
energy surface

JME Features

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Clean Public API

Scientific libraries barely pay attention for providing clean public API. We believe that a well-designed public API is key to unlocking the full potential of force fields.

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Extendable

The most thing we appreciate here is the extendability. Many other projects are not open-source, overtuned to unextendable form or simply have no public low level API.

Lightweight

No complex dependency tree or heavy platform are required! We try to implement everything with the least requirements.

Use well established language

JME is built with Java, a versatile programming language that offers speed, reliability, and scalability

Integrated with CDK

JME is implemented on top of the most famous java library in chemoinformatics. You can directly use it along with CDK.

Supported Force Fields

JME now supports two highly regarded force fields, MMFF94 and MMFF94s. Development team has implemented and nearly fully validated these force fields, and we're continually working on adding more in the future. We're also hard at work on integrating molecular dynamics into JME. Stay tuned for more updates insha allah!

energy surface

Use JME through Maven

Adding JME to your Maven project is quick and easy. Simply include it as a dependency in your project's pom.xml file and you'll be up and running in no time.

<dependency>
    <groupId>io.github.ramimanaf</groupId>
    <artifactId>jme</artifactId>
    <version>1.0.0</version>
</dependency>