2. • File operations, data movement
• Beyond the basic file input and output
operations, the export and import facilities
to/from other applications are of high
importance. For example, if one has to import a
3D structure from a modelling program or embed
an illustration created by another drawing
program.
3. File operation ,data movement:
To summarize, ChemBioDraw and ChemSketch are the most respected
applications followed by ChemDoodle and MarvinSketch, these
applications contain the highest number of export/import filters (although
in spite of intensive beta-testing not all of them are bug-free)
There are two basic chemical file types: program-specific sketch files,
which include all objects of the drawing, and molecule files or molfiles,
used mainly by modelling and database programs, these contain only the
description of the molecules.
4.
5. Dynamic Object embedding:
• 4D Draw can accept sketches in MDL skc format from the clipboard, but
only chemical objects (molecules) are supported.
• Chemistry Unfortunately, embedded ChemWindow drawings in older
documents cannot be opened from the text editor and edited in DrawIt, in
other words, the "ChemWindow object" does not exist anymore.
Moreover, it is not possible to copy/past structures as chemical entities
from DrawIt to any other chemical applications, the structures appear only
as graphics. This is a serious drawback. You have to export them as mol
files.
• Accelrys Draw: Delocalized aromatic rings do not show, when they are
copy/pasted into another application using the default paste operation.
Use Paste as… orPaste special and select the Windows metafile (emf)
option.
• The latest versions of ChemDoodle already fully supports OLE procedures.
•
6. Drawing chemistry:
• The basic operations, as for example the
sprouting or free hand drawing of different
bonds, the drawing and joining of rings, the
resizing of elements or the whole sketch etc, are
handled well by all of the six programs. In
Chemistry 4-D Draw the moving of the different
objects cannot be constrained to the horizontal
or vertical direction. The next figure depicts the
available different bond types. Some of them
7.
8.
9.
10.
11. •
Chemistry 4-D Draw Pro, when using its intelligent
NamExpert feature, can create structures from chemical
names in three styles: the generally used shorthand
structure, the linear semistructural and the so-called Kekulé
structure are the three available options (unfortunately, a
later interconversion between the styles is not possible)
. Note also the very useful Lewis dot structures available in
ChemDoodle:
•
•
12. Line notation to conversation:
• Smiles, SLN or InChi strings (formulation of
chemical structures in a line of text used mainly
to facilitate the search in databases) are
supported by ChemSketch, ChemBioDraw,
Accelrys Draw, ChemDoodle and MarvinSketch.
When you open a file of this type with a text
editor you see something like this:
• CCN(CC)CC1OCCC(OCC)=C1
• 2D → 3D and 3D → 2D conversion of structures
13. Conclusion:
• Accelrys Draw: Convert 2D to 3D (add-in)
• ChemBioDraw: must have Chem3D sister
program installed
• ChemSketch: 2D to 3D conversion included
• Chemistry 4-D Draw: sister program ChemSite
• DrawIt: bundled program 3DViewIt
• ChemDoodle: NIH Cactus 3D builder (needs
internet connection)
• MarvinSketch: built-in 2D → 3D module or
bundled program MarvinSpace
