DrawMol

DrawMol is a powerful graphical interface to visualize and build molecular structures.

Features

• Build a molecular structure from scratch
  • Build a structure by clicking and dragging to add atoms and bonds.
  • You can then refine your structure in one click using UFF force field optimization. When building a structure, DrawMol can guess for you the type of bonds (single, double, triple or aromatic bonds) or you can force it by clicking on a bond.
  • Moreover, hydrogen atoms can be added automatically
  • Save your structure in xyz format or build a gaussian or gamess input file directly.
  • For Gamess, if the program is installed locally, you can even launch the job from DrawMol (in the background) and follow the progression of the job.
  • Paste directly a structure into the Cartesian Editor of DrawMolIt can recognize XYZ, Gaussian, Gamess, Turbomole and Z-matrix formats.
  • The Cartesian Editor can also be used to output the structure in any of these formats as well as to modify a given structure by adding/removing some atoms or by changing a given atom element.
  • Import a structure from ChemSpider database
• Visualize molecular structure as well as molecular properties
  • Open XYZ, MDL molfile, Gaussian log, Gaussian fchk, Gamess log, Dalton out, Molpro out file formats.
  • In addition to the molecular structure, DrawMol can read various molecular properties (for now only available for Gaussian fchk file format):
    • Mulliken charges
    • Dipole moment
    • Polarizability and first-hyperpolarizability
    • Vibrational normal modes
    • Magnetic shieldings (NMR)
    • Molecular Orbitals from the basis set and LCAO coefficients
    • Visualize molecular properties:
    • Atom labels
    • Mulliken Charges
    • NMR chemical shifts
    • Dipole moment vector
    • Beta vector
    • Unit sphere representation of the polarizability and hyperpolarizability
    • Atomic displacements of a vibrational normal modes via vectors, spheres or even animation
    • Molecular Orbital isosurfaces
    • Open gaussian cube files and visualize isosurfaces of the stored date.
• In addition, DrawMol provide some tools to:
  • Make two molecules or fragments to coincide with each other using a matching procedure (least-square approach)
  • Orient the Z axis of a molecule to be either perpendicular to a plane made by three or more atoms or going through two or more atoms using a least-square approach.
• Save any structure
  • As a picture either in png, tiff, jpeg or dae (Collada)
  • As a movie for the animation of the normal modes
  • As a XYZ, CIF, PDB files
  • As a limol fileThis format is basically a HDF5 container that store all the molecular properties as well as the visualization preferences.
  • This file can be read by DrawMol but can also be parsed easily using the C, Fortran, Python, … and even dump (with lidump utility) into a ASCII file.