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 optimizationWhen 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 (https://www.hdfgroup.org) 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.

• Fix some issues when read/write all molecules into H5Mols