alvaMolecule Old

alvaMolecule is a software tool to visualise, analyse, curate and standardize your molecular dataset. alvaMolecule is free for academic and non-commercial use.

Molecular worksheet

alvaMolecule is conceived as a molecular worksheet where molecular datasets can be visualised both as a molecule grid or as a spreadsheet; additional data provided within SMILES and MDL files is automatically imported and can be used to sort and filter the molecular dataset, as well as using the calculated descriptors and physicochemical properties.


Molecule structure curation

alvaMolecule checkers and filters
alvaMolecule provides 10 predefined checkers that can help the identification of erroneous structure or for filtering specific structural feature:

  • Multiple structures
  • Unusual valence
  • Covalent/Ionic bond
  • Total charge
  • Isotope
  • Charged atom
  • None carbon atoms
  • Non-standard atom set (H,C,N,O,P,S,F,Cl,Br,I)
  • Aromaticity
  • Radical atom

Additionally, alvaMolecule provides the molecule structure verification using PubChem services.

Molecule structure standardization

alvaMolecule provides 12 predefined standardizers that can be used to fix erroneous representation of molecules, to remove specific features from molecules or to standardize specific structural features:

  • Convert unusual covalent bonds to ionic bonds
  • Add charge to quaternary nitrogen
  • Remove exceeding hydrogens
  • Add missing hydrogens
  • Remove monoatomic fragments
  • Retain biggest fragment
  • Standardize nitro group
  • Standardize azide group
  • Standardize diazo group
  • Clear isotopes
  • Clear chirality
  • Clear bond direction

Molecular descriptors and physicochemical properties

alvaMolecule calculates 88 molecular descriptors and physicochemical properties. Specifically alvaMolecule calculates a wide set of structural descriptors belonging to the constitutional and ring descriptors as implemented in alvaDesc.

alvaMolecule charts

Additionally, alvaMolecule calculates many physicochemical properties, drug-like and lead-like scores, among them alvaMolecule provides the calculation of several model-based physicochemical properties such as molar refractivity, topological polar surface area (TPSA), molecular volume estimations and two LogP models (Moriguchi and Ghose-Chippen octanol-water partition coefficient).
There is a significative list of drug-like and lead-like scores including the well-known Lipinski alert index, that can be used to filter drug- and lead-like compounds.

Sort, filter and charting

You can sort and filter molecules using:

  • data loaded from molecule files
  • calculated molecular descriptors
  • calculated physicochemical properties

The same data can also be visualized and filtered using the charting tools provided within the software.


A short video introduction:


The software is 64bit and it’s available for Windows, Linux and macOS.

Related tools

  • alvaMolecule is the perfect tool to prepare your molecular dataset to be used by alvaDesc for the calculation of molecular descriptors and fingerprints and to check your molecules before applying QSAR models by alvaRunner.
  • A tutorial showing how to build a QSAR model using Alvascience tools


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