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Calculator Plugins in MarvinSketch

Known Issue

In some environments, Calculator Plugins that can display their results in MarvinSpace causes MarvinSketch to close unexpectedly when the user closes the separate MarvinSpace window.
To avoid this issue, simply uncheck the Display in MarvinSpace checkbox before displaying the calculation results.

In addition to the drawing capabilities, MarvinSketch offers predictions of several properties for your compounds.

Calculator Plugins are modules of ChemAxon's Marvin and JChem cheminformatics platforms which calculate physicochemical properties from chemical structures.

For more information, see Calculator Plugins.

Short Usage Guide

Calculator Plugins are available directly from Marvin, Instant JChem, and Reactor applications, and also from the command line, API, or through ChemAxon's Chemical Terms language.

  • The available calculator plugins are located in the Calculations menu in the graphical user interface of MarvinSketch, (and in the Tools menu in MarvinView.)
  • cxcalc is the command-line tool of the Calculator Plugin. Batch processing is available using cxcalc (see the list of calculations accessible from cxcalc).
  • Calculators are used in the Chemical Terms language to calculate combinations of properties (like Lipinski's rule of 5) easily. Learn more about it in the Chemical Terms section.
  • Some of the calculators (such as logP, pKa and Predictor) can be trained with the user's data through cxtrain.
  • Third-party calculations can be integrated easily into MarvinSketch through the Services module of the graphical user interface. For more information on integrating third-party calculations, see Setting Services.

Calculator Plugins

Menu item Description
Elemental Analysis Calculates the elemental composition of the molecule.
Protonation > pKa Calculates the pKa values of the molecule.
Protonation > Major Microspecies Draws molecular microspecies at a given pH.
Protonation > Isoelectric Point Calculates the gross charge distribution of a molecule as a function of pH.
Partitioning > logP Calculates the octanol/water partition coefficient.
Partitioning > logD Calculates the octanol/water partition coefficient at any pH.
Partitioning > HLB Calculates the hydrophilic-lipophilic balance number (HLB number).
Solubility > Aqueous Solubility Calculates the solubility of the molecule in aqueous solution.
Charge > Charge Calculates the partial charge value of each atom.
Charge > Polarizability Calculates the polarizability of each atom.
Charge > Orbital Electronegativity Calculates electronegativity of each atom.
Charge > Dipole Moment Calculation Calculates the electric dipole moment of the molecule
NMR > CNMR Prediction Predicts 13C NMR chemical shifts of the molecule.
NMR > HNMR Prediction Predicts 1H NMR chemical shifts of the molecule.
NMR > NMR Spectrum Viewer Opens and displays JCAMP-DX NMR spectral file.
Isomers > Tautomers Generates two-dimensional tautomers of the molecule.
Isomers > Stereoisomers Generates all possible stereoisomers of the molecule.
Isomers > Resonance Generates all resonance structures of a molecule of the molecule.
Conformation > Conformer Generates the selected number of conformers or the lowest energy conformer of a molecule.
Conformation > Molecular Dynamics Calculates the configurations of the system by integrating Newton's laws of motion.
Conformation > 3D Alignment Overlays drug sized molecules onto each other in the 3D space.
Geometry > Topology Analysis Provides characteristic values related to the topological structure of a molecule.
Geometry > Geometrical Descriptors Provides characteristic values related to the geometrical structure of a molecule. It can calculate steric hindrance and Dreiding-energy.
Geometry > Polar Surface Area (2D) Provides estimation of topological polar surface area (TPSA).
Geometry > Molecular Surface Area (3D) Calculates van der Waals or solvent-accessible molecular surface area.
Other > H Bond Donor/Acceptor Calculates atomic hydrogen bond donor and acceptor inclination.
Other > Huckel Analysis Calculates localization energies L(+) and L(-) for electrophilic and nucleophilic attack at an aromatic center.
Other > Refractivity Calculates the molar refractivity of the molecule.
Other > Structural Frameworks Calculates Bemis and Murcko frameworks and other structure-based reduced representations of the input structures.