Molecule program

The software automatically orients bonds in the correct directions, merges bond strokes together, places attributes in the best locations and automatically makes smart decisions that lead to the most beautiful and appealing images. Of course, you can always override the software to your preference.

Every component of the graphic is fully customizable. Whether you are looking to control bond widths, arrowhead sizes or shape transparency and color; you are in control. Represent chemical structures with the widest range of chemical bonds avialable in any software tool. From standard integer bonds, to specialty bonds like ionic and covalent, you can accurately depict any structure. All of the bonds orient themselves and merge together for the most aesthetic graphics.

In other programs, you will see disconnects where bonds meet, or a heavy reliance on rounded bond ends. In ChemDoodle, all of the bonds merge together for the most aestheic figures.

Formatted atom labels allow you to clearly represent chemical entities as text and create concise, professional graphics. Any characters supported by your fonts are available over the entire unicode range. Quick access to chemically relevant symbols is provided through the Symbols widget. ChemDoodle is the only chemical drawing tool to contain superscript and subscript merge formatting in text fields to easily create atomic notations and other chemical text.

Render charges, radicals and electrons, dipole moments, asterisks, tags and custom attributes on your structures, with full control over how they render. Atomic and molecular orbital graphics are easily added to figures. These are completely customizable just like the rest of ChemDoodle, so you can control color, stroke styling, fill type and more! ChemDoodle provides you with all the tools to build perfect figures of Lewis Dot Structures.

Easily create 3D effects in figures by using protruding and bold bonds. ChemDoodle will automatically merge their strokes for an optimal appearance.

Bonds in the foreground will buffer intersecting bonds in the background. Choose from 7 different stroke styles to add a bit of character to your figures Basic, Bristle, Brush, Charcoal, Scribble, Slant, Wobble. Perfect for use in group meetings and in presentations.

And of course, all of the shapes are fully stylable. Tables are very powerful shapes for creating organized groupings of content in grid patterns. You can control the table grid and its formatting as well as the content that appears within each table cell and cell formatting. Tables can be drawn in several styles and are defined and controlled by an intuitive anchor box set that provides instant feedback for edits you may want to perform.

Rowspans, colspans, padding and alignment are supported. Tables can be fit to contained content. This is a great way of creating really attractive and informative figures of data. Copious visual feedback is provided. There are also many options for customizing the drawing tools to your preference, including for accessibility concerns. ChemDoodle will help guide your drawing to create the most aesthetic figures using a feature we call the "Optimize Zone" for standard bond angles and lengths.

Just move your mouse out of the zone to override it. In addition to the standard elemental labels, you can input any custom label you desire. ChemDoodle will automatically chemically interpret and format labels. You can also directly control text formatting. Labels can be expanded to full atom models and full atom models can be automatically collapsed into concise labels based on your abbreviation library or to a custom label.

Abbreviations and compound labels like "COOH" and "Ph", as well as formulae can be expanded to quickly build and work with complex chemical structures. You can define your own custom abbreviations to be used in ChemDoodle. If you need to tag atoms or bonds by increments, ChemDoodle provides powerful tools to do this.

Simply click on the atom or bond to tag them and the next tag is automatically incremented. Tag by alphabet, number, roman numeral or greek letter. ChemDoodle will automatically place your charges, radicals, stereocenter labels and other attributes for you in an aesthetic manner. You can override these decisions at any time by holding down and dragging the mouse during placement. In addition to standard ring tools and templates, ChemDoodle provides special arbitrary ring and crown ether tools for quickly building advanced ring systems.

Quickly build structures using our built-in template libraries, or create your own templates. The Templates widget organizes the templates for you. Several tools are provided to help you quickly build complex 3D geometries, including carbon nanotube and prism builders. Armchair, zigzag and chiral nanotubes can be built.

Use the Rotate in 3D tool to change the 3D perspective of the drawn structure. Complex algorithms have been implemented to automatically lay out chemical structures aesthetically.

Select only part of a structure to clean only that part, leaving the remaining structure untouched. There are so many tools in ChemDoodle for working with chemical graphics, including alignment and distribution functions, bond adjustment features, action tracking, transforms and more. Our algorithms name molecules naturally and accurately, down to the character and formatting.

If you find any problems, simply contact us with the structure so we can correct it. The majority of the periodic table is handled. Implicit hydrogens will be added for you to your drawings. You have the ability to turn them off for single atoms, globally or override them as appropriate.

Detect the aromaticity and anti-aromaticity of your rings and display the number of pi electron contributors. You can also force aromatic ring recognition using all resonance bonds. This is useful when dealing with large, embedded, aromatic ring systems.

Perceive stereochemistry for drawn 2D structures. CIP stereochemistry is determined for chiral centers and double bonds using our advanced and accurate CIP algorithms.

When you draw a stereochemical configuration for a chiral center in ChemDoodle, it is recognized by the software exactly as drawn, being one of two enantiomers. In certain cases, you may wish to define a current chiral center as one configuration or the other, or as a mixture of both and.

This can be defined using the enhanced stereochemistry features in ChemDoodle. You may then output this information into several file formats for use by compatible registration and search engines, for instance.

Repeat units aka repeat groups or repeating brackets are used to define linearly repeating substructures in molecules. A repeat unit consists of a pair of square brackets denoting the substructure to be repeated and a repeat value defining how many times the substructure is repeated. Most conveniently, when properly defined in chemical structures in ChemDoodle, repeat units are automatically recognized, evaluated and expanded so you can quickly draw complex structures and perform cheminformatics tasks such as calculating molecular masses and formulas.

This is very convenient for oligomers and polymers. Calculate dozens of descriptors for structures, including masses, formulae, volumes, physical properties, topological indexes, counts, bioactivity filters and more.

Use the Elemental Analysis widget to calculate molecular masses, elemental analysis and isotopic distributions for structures as you draw them. Select entire complexes to calculate bulk properties. ChemDoodle will double check your work for you and notify you when it finds chemistry issues, such as overvalanced atoms, incorrectly drawn stereocenters, or partially intersecting repeat units.

ChemDoodle contains an entire elemental database. Most of the calculations performed by ChemDoodle use this data. The data is kept relevant and referenced and includes many elemental properties such as electronegativites, radii, thermodynamic properties, years of discovery and more.

Databases of ionization energies and isotopes are also provided. You may view this data at any time in the View menu. A fully interactive periodic table is provided for visualization and reference. You can even customize it and print it out! A SciFinder n account is required. Google Patents searching is integrated.

You may perform structure, substructure and similarity searching into the Google Patents and non-patent literature databases at Google using structures drawn in ChemDoodle. In it, you can browse various molecular files and view respective molecule structures in 3D. It provides a nice Bioclipse navigator to easily navigate through added files. Different molecule structures can be visualized due to its multi-tab interface.

An outline of the molecule file containing atoms is displayed in the right panel. You can also select an atom, bond, or molecule from the structure and view its respective properties like atomic number, mass number, symbol, bond order, etc.

A 2D structure of opened molecule file is also displayed on the interface. Now, talking about its display and navigation options, you get all standard viewing tools in it. These include r otate, zoom, move, spin , etc. Also, you can customize rendering style atoms, label, scheme, bond, etc. RasMol is a free open source molecule viewer for Windows. You can change the color of molecules to monochrome, structure, chain, group, model, user, temperature, etc.

You can rotate molecule bond too. After opening a file, you can also view related information which includes molecule name, classification, database name, and number of chains, groups, atoms, and bonds. QuteMol is the next free 3D molecule viewer for Windows. You can also customize display as per your preference. The molecules can be viewed by customizing geometry.

It also lets you setup various other preferences to visualize molecules. These include customizing base color, background, point light, depth cueing, halos, ambient light, borders, etc. Also, creating a GIF animation of molecules is also possible. PubChem is another one of simple molecule viewer software for Windows. It lets you browse molecule files and then visualize molecule structure in 3D.

As you open a file, it displays molecules in both tiled and overlay structures. So, you can view single molecule structure or multiple molecules in tiles. To view molecule, you can use options like rotate, scale, zoom, align, etc. Also, you can customize display options like atoms, bonds, molecules, box, symbol, etc. Using the Preference button, you can configure options like image quality, light model, background color, viewing angle, scale strategy, orthogonal projection, atom scale, atom coloring, atom info, bond coloring, bond info, bond width, etc.

VMD is yet another 3D molecule viewer for Windows. It provides separate windows in order to import and manage molecule files and for molecule visualization.

As you do that, it displays file information and 3D molecule view in dedicated windows. You can open multiple molecule files and toggle between each of them to view respective molecules.

Like other molecular visualization software, it also lets you customize molecular view by configuring representation, color, materials, and labels. For better molecule viewing experience, you can use options like automatic rotation, perspective or orthogonal view, FPS indicator, change background, stereo, stage, render mode, etc.

Furthermore, you can configure your mouse in rotation, translate or scale mode, add atom, bond, angle, or dihedral labels, add or remove bonds, etc. Compartmentalized biochemical reaction networks. Intrinsically universal tile assembly model. Capacity of string-replication systems. Self-assembly of DNA origami into 3D shapes. Delays in transcriptional signaling networks.

Active self-assembly of algorithmic shapes.