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91
Working with Structures
3.
The structures are converted to SMARTS strings.
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92
Working with Structures
It is also possible to keep the original structures in the Structure
column and insert a new column for the SMARTS strings. In this case
the value of the  Convert From Structure - Placement option has to
be set to InsertRight (instead of Replace) in the appropriate part of
Options/Actions topic.
You can reach the "To SMILES" conversion in this context menu as
well.
3.18
Convert from IUPAC Name or CAS Number (to Structure)
Converts IUPAC names or CAS numbers to JChem for Excel specific
structures. Please, note that you need to have a Name to Structure
license to complete this conversion process. If you don't have this
license,  please  contact sales@chemaxon.com. 
1.
Select cells (or a whole column), which contain IUPAC names or
CAS numbers.
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93
Working with Structures
2.
Click on the Convert|Convert from Text|Name or CAS Number
context menu item.
3.
The IUPAC names and CAS numbers are converted to structures.
4. If you don't have a valid Name to Structure license, after step 2
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94
Working with Structures
you will receive the following error message:
You can reach this function with From any Text in Advanced ribbon
button as well.
3.19
Convert to IUPAC Name (from Structure)
Converts JChem for Excel specific structures to IUPAC names. Please,
note that you need to have a Name to Structure license to complete
this conversion process. If you don't have this license, please
contact sales@chemaxon.com.
1.
Select cells (or a whole column) which contains structures.
2.
Click on the Convert|Convert to Text|IUPAC Name context menu
item.
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95
Working with Structures
3.
The structures are converted to IUPAC names.
It is also possible to keep the original structures in the Structure
column and insert a new column for the IUPAC names. In this case
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96
Working with Structures
the value of the ConvertFromStructureAction - Placement option has
to be set to InsertRight (instead of Replace) in the appropriate part
of Options/Actions topic.
3.20
Structure  Transformation  Actions
There are some structure transformation actions, which are not
available in the JChem for Excel ribbon/context menu/menu/toolbar
by default, but it is possible to make them available by 
customization of the ribbon/context menu/menu/toolbar. The Images
folder contains images (AromatizeStructureAction.png,
DearomatizeStructureAction.png, ThreeDCleanStructureAction.png,
TwoDCleanStructureAction.png, HydrogenizeToStructureAction.png,
DehydrogenizeStructureAction) which can be used as icons for these
functions.
AromatizeStructureAction
Changes the type of alternating single-double bonds of aromatic rings
to aromatic bonds.
DeromatizeStructureAction
Converts aromatic bonds to alternating single-double bonds.
97
Working with Structures
ThreeDCleanStructureAction
Calculates new 3D coordinates for the molecule. Clean3D builds up
conformers of fragments from which the best, i.e. the lowest energy
conformer is given back. The quality of the structures is measured by
a simple energy function (Dreiding type molecular mechanics).
TwoDCleanStructureAction
Calculates new 2D coordinates for the molecule.
98
Working with Structures
HydrogenizeToStructureAction
Converts implicit hydrogens to explicit (adds hydrogen atoms to the
molecule graph).
DehydrogenizeStructureAction
Converts explicit hydrogens to implicit (removes hydrogen atoms from
the molecule graph). Charged, radical, mapped, isotope or wedged
hydrogens are not removed.
99
Working with Structures
3.21
Convert Accord, ChemDraw and ISIS for Excel files to JChem
for Excel files
It is possible to convert Accord, ChemDraw or ISIS for Excel files to
JChem for Excel compatible format three different ways:
·with JChem for Excel File Converter, a standalone tool.
·with a JChem for Excel ribbon action
·with right-click menu option
3.21.1
JChem for Excel File Converter Tool
About installation see more in the Admin Guide:
http://www.chemaxon.com/jchem4excel/adminguide/
1.
After installation (according to the selected option during
installation) the application can be started from Start menu or click
100
Working with Structures
on the icon on the desktop, JChem for Excel File Converter window
comes up.
2.
Clicking on Browse  file(s)  manually... you can select Accord,
ChemDraw or ISIS for Excel files to be converted.
3.
Conversion method selection (radio buttons): 
ISIS/Symyx method - converts ISIS/Symyx workbooks to JChem for
Excel workbooks,
ChemDraw method - converts ChemDraw workbooks to JChem for
Excel workbooks,
Accord method - converts Accord for excel workbooks to JChem for
Excel workbooks,
Recognize method - recognizes types of selected workbooks and
converts them to JChem for Excel workbooks. You can use this
method to convert multiple workbooks with different types. (This is
the default method.)
4.
Clicking on Select output directory the location of the result file
can be selected.
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