Brown Computer Graphics Group

ChemPad

3D Structure Interpreted from Diagram

ChemPad allows chemistry students to draw molecule diagrams on a Tablet PC or tablet-enabled Windows Vista PC and have the computer automatically generate the corresponding 3D models. As always, ChemPad is free to download and use.

Software Downloads

June 2, 2008: There has been a pretty serious bug reported by people who draw every 'C' in their carbon chains. The bug causes the 3D model building system to hang and report that it is trying to build a model with many more atoms than was intended. You can download a patched ChemPad 3.4.1 which has a workaround for this bug until we can make a 3.5 version.

May 22, 2008: ChemPad 3.4 (Graduation Edition) is available. This is a slight update from 3.3 with a few critical bugs that snuck into 3.3 fixed and the newly updated User Manual included in the documentation section. This will be my last ChemPad update as a Brown University graduate student due to my impending graduation. There is certainly a lot of interest in ChemPad, so I believe that it will continue on in some form. -Dana

May 15, 2008: ChemPad 3.3 is available. This version fixes some bugs with ink input and non-English versions of Windows as well as some speed improvements. The 3D generation system is now able to make a few molecules containing boron.

Apr. 14, 2008: We've had a bug reported that prevents ChemPad from being able to create 3D models on computers using versions of Windows other than the US English version. If this bug affects you, please use this foreign language version of ChemPad3.2 until we can release a 3.3 version with a full fix to the bug included.

Feb. 29, 2008: ChemPad 3.2 is now available. This update to 3.1 fixes various bugs and includes an option to enable the alpha version of Reactor, a tool for learning reaction pathways. To try Reactor, download these mixture files and load one within ChemPad. Enable Reactor from the Options menu.

Feb. 15, 2008: ChemPad 3.1 is now available. ChemPad3 is now our full standard version, even though we still have a lot to do with it yet. We don't have a full user manual nor tutorial ready yet, but you can download a cheat sheet of how to use ChemPad3. ChemPad3 will run under XP Tablet Edition or Vista and supports Wacom digitizer tablets, SmartBoards, and even mouse input ... although I wouldn't recommend the mouse.

Project Motivation & Overview

Organic chemistry is a hard course. Early in their college studies, students who wish to pursue a career in medicine must have a solid understanding of organic chemistry and, perhaps more importantly to the students, a good grade in organic chemistry. The difficulty of the material prevents many students from continuing with this career path. One of the major difficulties for students in organic chemistry is understanding the three-dimensional nature of molecules. Students usually have no background in three-dimensional visualization and have great difficulty converting between the two-dimensional drawings used in text books and on classroom blackboards to represent molecules and their three-dimensional structures. Without this understanding, to survive the course, students must memorize a large vocabulary of molecules and rules to fake an understanding of the three-dimensional structures. Although this is possible for some, good students and good chemists tend to learn to visualize the molecules in three dimensions and apply a much simpler set of rules to these visualizations.

To address students' need for three-dimensional visualization in chemistry at Brown, University President Ruth Simmons authorized $50,000 of Atlantic Philanthropies funding to develop a new piece of educational technology targeted at this goal. This resulted in Professor Matthew Zimmt's Chemistry 35 course this spring being equipped with ChemPad, a Tablet PC application shown above. ChemPad assists students learning to visualize molecules from standard two-dimensional drawings as a digital substitute for physical ball-and-stick modelling kits. Students can build the same structures they would with the modelling kit and see the same 3D features of the molecules. However, students using ChemPad can construct these models much quicker than with a physical model and receive interactive feedback about their 3D intuitions which would otherwise be unavailable without a TA or a professor available. By using the visualization assistance ChemPad offers to solve a 3D thinking task, students develop the skills to reach correct intuitions without assistance.

The rest of the Report On The Development of ChemPad for Teaching Organic Chemistry Students to Visualize Three-Dimensional Molecular Structures (pdf, 87k)

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On 02 Jun 2005, 11:21.

Publications & Resources

Dissertation

  Dissertation (pdf, 7.6M)
  Defense Talk (Link to flash movie with option to download video)
  Defense Talk Slide Deck (zip of ppt, 21.7M)
  Bibtex

WIPTE 2007 Paper

  Monograph (Amazon.com link, paper appears in this book)
  Talk (ppt, 21.5M)
  Bibtex

SIGGRAPH 2005 Poster

  Abstract (pdf, 18k)
  Video (mov, 10M)
  Poster (ppt, 1.54M)
  Bibtex

Master's Thesis (Department Research Comprehensive) 2005

  Paper (pdf, 155k)
  Talk (ppt, 565k)
  Bibtex

Narrated Videos

2006 Video (Pedagogical Value) (wmv, 12.4M)
2008 Video (3D Model Algorithm) (divx, 31.9M)

Tutorial

ChemPad v3 tutorial (pdf, 875k, as of May 21, '08)
ChemPad v2 tutorial (pdf, 633k, as of Mar. 8, '05)

Publication papers are included with software install.

Source Code

The ChemPad source is not publically available. However, a few components are.

MMCore

MMCore, the core molecular mechanics engine in ChemPad is available for download in source form. MMCore is written in C#.
MM Core (zipped VS 2005 sln, 451k)

IM3Engine

The Ink-Modified Molecular Mechanics (IM3) Engine, which is used to create 3D molecule models from diagrams, has its source now available. IM3Engine is written in C# and includes MMCore. A sample application is included which shows the basic input and output for giving IM3Engine a molecule diagram and getting out 3D model data.
IM3 Engine (zipped VS 2005 sln, 7.92M)

Conformation Generation Benchmark

The test data set and a distilled version of the code used to evaluate the IM3 Engine in "Interpretation of Molecule Conformations from Drawn Diagrams". Includes MMCore, IM3Engine, and the dissertation.
Benchmark (zipped VS 2005 sln, 13.7M)