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JChem for Excel
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Actions Reference
2
Table of Contents
Foreword
0
Part I
JChem for Excel
8
................................................................................................................................... 
8
1
Before Using 
................................................................................................................................... 
10
2
Supported Versions 
Part II
JChem for Excel Ribbon
10
................................................................................................................................... 
12
1
Standard Menu 
................................................................................................................................... 
13
2
Advanced Menu 
................................................................................................................................... 
14
3
Switch From Standard to Advanced Menu 
Part III
Working with Structures
15
................................................................................................................................... 
15
1
Add a structure to a cell 
................................................................................................................................... 
21
2
Edit a structure in a cell 
................................................................................................................................... 
24
3
Insert single structures 
................................................................................................................................... 
27
4
Save single structure to file 
................................................................................................................................... 
28
5
Structure editing in task pane 
................................................................................................................................... 
33
6
Copy and Paste 
......................................................................................................................................................... 36
Inside Excel 
.................................................................................................................................................. 36
Copying Structures With or Without Data
.................................................................................................................................................. 40
Exclude Hidden Rows
.................................................................................................................................................. 44
Between Excel Instances
......................................................................................................................................................... 48
To External Applications 
.................................................................................................................................................. 49
Copy and Paste with IDs
.................................................................................................................................................. 53
Copy and Paste Single Structures with Ctrl+C-V
.................................................................................................................................................. 55
To External Structure Editors
......................................................................................................................................................... 57
From External Applications 
.................................................................................................................................................. 57
From Instant JChem (IJC)
.................................................................................................................................................. 59
From External Structure Editors
................................................................................................................................... 
64
7
Show and Hide Structures 
................................................................................................................................... 
65
8
Show structures and Show structure IDs 
................................................................................................................................... 
67
9
Delete structures from selected range 
................................................................................................................................... 
70
10
Resizing Structures 
................................................................................................................................... 
73
11
Printing Structures 
................................................................................................................................... 
77
12
Structures in merged cells 
................................................................................................................................... 
78
13
Convert to SMILES (from Structure) 
................................................................................................................................... 
80
14
Convert from SMILES (to Structure) 
................................................................................................................................... 
84
15
Convert to Image (from Structure) 
................................................................................................................................... 
87
16
Convert from Image (to Structure) 
................................................................................................................................... 
90
17
Convert to SMARTS (from Structure) 
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3
Contents
................................................................................................................................... 
92
18
Convert from IUPAC Name or CAS Number (to Structure) 
................................................................................................................................... 
94
19
Convert to IUPAC Name (from Structure) 
................................................................................................................................... 
96
20
Structure Transformation Actions 
................................................................................................................................... 
99
21
Convert Accord, ChemDraw and ISIS for Excel files to JChem for Excel files 
......................................................................................................................................................... 99
JChem for Excel File Converter Tool 
......................................................................................................................................................... 103
JChem for Excel File Converter Action 
......................................................................................................................................................... 103
JChem for Excel File Converter Right-Click Menu Item 
................................................................................................................................... 
105
22
Calculations with Third-Party Services 
Part IV
Open Structure Files
108
................................................................................................................................... 
108
1
Open Multiple Structure Files with and without Data 
................................................................................................................................... 
110
2
Open All Files in a Folder 
................................................................................................................................... 
113
3
Merge Files to a Single Worksheet 
Part V
Import From Database
115
................................................................................................................................... 
116
1
Import from Database 
......................................................................................................................................................... 116
Managing Connections 
.................................................................................................................................................. 117
Connecting to an Oracle Database
.................................................................................................................................................. 121
Connecting to a MySQL Database
.................................................................................................................................................. 122
Connecting to an MSSQL database
.................................................................................................................................................. 123
Connecting to PostgreSQL database
.................................................................................................................................................. 124
Connecting with JChem Webservices
.................................................................................................................................................. 126
Working with Connections
.................................................................................................................................................. 128
Favourite Tables
......................................................................................................................................................... 131
Exploring Database Tables, Views and Columns 
......................................................................................................................................................... 133
Mapping Results to a Worksheet 
......................................................................................................................................................... 136
Search Options 
......................................................................................................................................................... 143
Specify Query Criteria 
......................................................................................................................................................... 144
Selecting Columns for Import 
......................................................................................................................................................... 149
Selecting Rows for Import 
......................................................................................................................................................... 154
Running the Search 
................................................................................................................................... 
155
2
Import From Database By IDs 
................................................................................................................................... 
159
3
Associate IDs 
Part VI
Import From IJC Database
161
................................................................................................................................... 
162
1
Before Import 
................................................................................................................................... 
163
2
Selecting Source For Import 
................................................................................................................................... 
168
3
Selecting Columns For Import 
Part VII
Import from File
173
................................................................................................................................... 
174
1
Import from File 
......................................................................................................................................................... 178
Selecting Fields to Import 
......................................................................................................................................................... 181
Running the Import Process 
................................................................................................................................... 
183
2
Import From File By IDs 
................................................................................................................................... 
187
3
Import with Document to Structure 
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Export to File
4
Part VIII
Export to File
189
Part IX
Save to Share
198
Part X
R-group Decomposition
200
................................................................................................................................... 
200
1
Selecting Query and Target Structures 
................................................................................................................................... 
207
2
Specification of Different Options 
................................................................................................................................... 
213
3
Running the Decomposition Process 
Part XI
SAR Table Generation
216
................................................................................................................................... 
216
1
Running SAR Table Generation 
Part XII
Structure Filter
221
................................................................................................................................... 
223
1
Filter (Search) Options 
................................................................................................................................... 
225
2
Working with Filter Results 
................................................................................................................................... 
234
3
Clone Results to a New Sheet 
Part XIII
Options
238
................................................................................................................................... 
240
1
General 
......................................................................................................................................................... 245
Database Connection 
................................................................................................................................... 
248
2
Formatting 
................................................................................................................................... 
251
3
Licensing 
................................................................................................................................... 
253
4
File Import 
................................................................................................................................... 
254
5
IJC Import 
................................................................................................................................... 
255
6
File Export 
................................................................................................................................... 
256
7
Printing 
................................................................................................................................... 
260
8
Structure Sheet 
................................................................................................................................... 
262
9
Image Conversion 
................................................................................................................................... 
263
10
Structure Display 
................................................................................................................................... 
279
11
Structure Editor 
................................................................................................................................... 
281
12
Actions 
................................................................................................................................... 
284
13
Event Handling 
................................................................................................................................... 
284
14
Functions 
Part XIV
Custom Excel Chemical
Functions
285
................................................................................................................................... 
288
1
Using JChem Excel Functions 
................................................................................................................................... 
291
2
Reference 
......................................................................................................................................................... 292
Normal 
.................................................................................................................................................. 292
Charge
........................................................................................................................................... 292
Electronegativity
........................................................................................................................................... 292
Polarizability
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5
Contents
.................................................................................................................................................. 293
Chemical Terms
.................................................................................................................................................. 309
Dissimilarity
.................................................................................................................................................. 311
Drug Discovery Filtering
.................................................................................................................................................. 313
Elemental Analysis
.................................................................................................................................................. 314
Geometry
.................................................................................................................................................. 316
Hydrogen Bond Donor-Acceptor
.................................................................................................................................................. 317
Isomers
........................................................................................................................................... 318
Conformer
........................................................................................................................................... 318
Stereoisomer
........................................................................................................................................... 319
Resonance
.................................................................................................................................................. 319
Naming
.................................................................................................................................................. 319
Protonation and Partitioning
........................................................................................................................................... 320
Major microspecies
........................................................................................................................................... 320
Isoelectric Point
........................................................................................................................................... 320
Partitioning
........................................................................................................................................... 321
pKa
.................................................................................................................................................. 322
Solubility
.................................................................................................................................................. 323
Tautomers
.................................................................................................................................................. 323
Topology Analysis
........................................................................................................................................... 324
Ring
........................................................................................................................................... 327
Path based
........................................................................................................................................... 327
Distance based
........................................................................................................................................... 328
Refractivity
......................................................................................................................................................... 329
Structure 
.................................................................................................................................................. 329
R-group Decomposition Functions
.................................................................................................................................................. 332
Reactor
.................................................................................................................................................. 342
Markush Enumeration
.................................................................................................................................................. 342
Reactions
.................................................................................................................................................. 343
2D/3D Clean
.................................................................................................................................................. 344
MCS Structure
.................................................................................................................................................. 345
Structural Framework
.................................................................................................................................................. 345
Structure Checker
.................................................................................................................................................. 347
Standardizer
.................................................................................................................................................. 351
JCStructure
.................................................................................................................................................. 351
JCIDSYSStructure
......................................................................................................................................................... 352
Image 
.................................................................................................................................................. 353
Display Options - Rendering
.................................................................................................................................................. 353
Display Options - Misc
.................................................................................................................................................. 355
Plug-Ins
Part XV
Troubleshooting
358
................................................................................................................................... 
358
1
Manually enabling JChemExcel.Functions 
................................................................................................................................... 
360
2
Disable and re-enable JChem for Excel 
................................................................................................................................... 
361
3
Upgrade to Latest Version 
................................................................................................................................... 
362
4
No help available for JChem for Excel functions 
Part XVI
User Interface Customization
365
Part XVII
Actions Reference
365
................................................................................................................................... 
365
1
AboutAction 
................................................................................................................................... 
365
2
AddEditStructureSingleCellAction 
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Actions Reference
6
................................................................................................................................... 
365
3
AddEditStructureTaskPaneAction 
................................................................................................................................... 
365
4
ClearFilterAction 
................................................................................................................................... 
366
5
ConvertAccordToJC4XLAction 
................................................................................................................................... 
367
6
ConvertChemDrawToJC4XLAction 
................................................................................................................................... 
368
7
ConvertISISToJC4XLAction 
................................................................................................................................... 
369
8
DecreaseStructureSizeAction 
................................................................................................................................... 
370
9
EmbedInJCSMILESAction 
................................................................................................................................... 
371
10
ExportFileAction 
................................................................................................................................... 
372
11
HelpAction 
................................................................................................................................... 
372
12
ImportFileAction 
................................................................................................................................... 
372
13
ImportFileByKeyAction 
................................................................................................................................... 
374
14
ImportFromDatabaseAction 
................................................................................................................................... 
375
15
ImportFromDatabaseByKeyAction 
................................................................................................................................... 
377
16
IncreaseStructureSizeAction 
................................................................................................................................... 
377
17
LicenseAction 
................................................................................................................................... 
377
18
MoleculeWorksheetFilterAction 
................................................................................................................................... 
377
19
OpenStructureSingleCellAction 
................................................................................................................................... 
378
20
OptionsAction 
................................................................................................................................... 
378
21
RedrawStructuresAction 
................................................................................................................................... 
378
22
RemoveHitColoringAction 
................................................................................................................................... 
378
23
ResizeStructuresToDefaultInSelectionAction 
................................................................................................................................... 
378
24
RGroupDecompositionAction 
................................................................................................................................... 
379
25
SaveAsStructureSingleCellAction 
................................................................................................................................... 
379
26
ShowHideStructuresAction 
................................................................................................................................... 
379
27
ShowHideStructuresActionforIDs 
................................................................................................................................... 
379
28
UnembedFromJCSMILESAction 
................................................................................................................................... 
381
29
Conversions 
......................................................................................................................................................... 381
ConvertFromInChiToStructureAction 
......................................................................................................................................................... 381
ConvertFromIUPACNameToStructureAction 
......................................................................................................................................................... 381
ConvertFromMOLToStructureAction 
......................................................................................................................................................... 382
ConvertFromShapeAction 
......................................................................................................................................................... 382
ConvertFromSMILESToStructureAction 
......................................................................................................................................................... 383
ConvertFromTextToStructureAction 
......................................................................................................................................................... 384
ConvertToChemDrawOLEAction 
......................................................................................................................................................... 384
ConvertToCXSMARTSAction 
......................................................................................................................................................... 384
ConvertToCXSMILESAction 
......................................................................................................................................................... 384
ConvertToInChiAction 
......................................................................................................................................................... 384
ConvertToIUPACNameAction 
......................................................................................................................................................... 384
ConvertToOLEAction 
......................................................................................................................................................... 384
ConvertToSMARTSAction 
......................................................................................................................................................... 384
ConvertToSMILESAction 
......................................................................................................................................................... 385
ConvertToStructureCommentAction 
......................................................................................................................................................... 385
ConvertToStructureImageAction 
......................................................................................................................................................... 385
ConvertToJCSYSStructureAction 
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7
Contents
................................................................................................................................... 
385
30
Copy - Paste 
......................................................................................................................................................... 385
CopyToChemDrawOLEAction 
......................................................................................................................................................... 386
CopyToChemDrawOLEAndValuesAction 
......................................................................................................................................................... 386
CopyToClipboardAsMarvinOLESingleCellAction 
......................................................................................................................................................... 386
CopyToClipboardSingleCellAction 
......................................................................................................................................................... 386
CopyToOLEAction 
......................................................................................................................................................... 386
CopyToOLEAndValuesAction 
......................................................................................................................................................... 387
CopyToStructureImageAction 
......................................................................................................................................................... 387
CopyToStructureImageAndValuesAction 
......................................................................................................................................................... 387
PasteFromClipboardSingleCellAction 
................................................................................................................................... 
387
31
Structure Transformation 
......................................................................................................................................................... 387
AromatizeStructureAction 
......................................................................................................................................................... 388
DearomatizeStructureAction 
......................................................................................................................................................... 388
DehydrogenizeStructureAction 
......................................................................................................................................................... 388
HydrogenizeToStructureAction 
......................................................................................................................................................... 388
ThreeDCleanStructureAction 
......................................................................................................................................................... 389
TwoDCleanStructureAction 
Index
0
8
JChem for Excel
1
JChem for Excel
JChem for Excel is part of the JChem for Office package, ChemAxon's
chemoinformatics solution in Microsoft Office products enabling
scientists to manage and analyse chemical structures and their data
in Microsoft Excel, PowerPoint, Word and Outlook. Since JChem for
Excel is rather a data analysis tool, while JChem for Office is rather a
reporting tool, the documentation of these products is separated. You
can find the User's Guide for JChem for Office on our webpage:
http://www.chemaxon.com/jchem4office/userguide/
The main features of JChem for Excel are:
·Import structures and data from databases, and files.
·Export data to files.
·Add, edit structures. 
·Sort, filter structures and the associated data.
·R-Group decomposition.
·Custom chemical Excel functions for calculating structure
properties.
1.1
Before Using
JChem for Excel works with the standard ChemAxon licensing
infrastructure, and also allows several points of extension. If
additional license files are specified, JChem for Excel takes into
consideration all of the licenses. Since JChem for Excel (JCXL) is
part of the JChem for Office (JCO) package, the JCO license is valid
for JCXL as well, but JCXL license is not appropriate for JCO. When
installing JCO you can decide if you want to install it together with
JCXL (see in related topic in JCO User's Guide).
The default location of the license file (license.cxl) is: 
o
Windows Vista: C:\Users\current user\chemaxon
9
JChem for Excel
o
Windows XP: C:\Documents and Settings\current user\chemaxon
You can find information about licensing in JChem for Excel's Admin
Guide as well.
You can read the details about ChemAxon licensing here:
http://www.chemaxon.com/marvin/help/licensedoc/installToDesktop.
html
You can use a few JChem for Excel features without having a valid
license:
-visualize structures in JChem for Excel spreadsheets
-convert structures to images/shapes
-print out JChem for Excel worksheets
-run the license form/settings.
It is always advised to install the latest released versions, which can
be downloaded from ChemAxon's website:
JChem for Office (JCO):
http://www.chemaxon.com/download/jchem-for-office/#jc4o
JChem for Excel (JCXL):
http://www.chemaxon.com/download/jchem-for-office/#jc4xl
If you have only JCXL (without JCO) it is advised to uninstall first
your current version from your computer in Control Panel/Programs/
Programs and Features and then install the new version. 
If you previously had JChem for Excel but currently purchased a
10
JChem for Excel
JChem for Office license, please uninstall first your current version
from your computer in Control Panel/Programs/Programs and Features
and then install the new version of JChem for Office. If your JCO
license has already been installed in one of the four products (Word,
PowerPoint, Outlook, Excel), it will be valid in all other three
products. So, license installation has to be done only once.
1.2
Supported Versions
Supported versions of JChem for Office (and JChem for Excel)
Office 2007
Office 2010 Office 2013 Office 2016
Windows
Vista, 7
Windo
ws 8.1
Windo
ws 10
Windo
ws 7,
8.1
Wind
ows
10
Windo
ws 7,
8.1
Wind
ows
10
Window
s 7, 8.1
Windo
ws 10
Offic
e 32-
bit
Yes
Please
check*
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Offic
e 64-
bit
Not
available
Not
availab
le
Not
availa
ble
Yes
No
Yes
No
Yes
No
*: According to Microsoft's Official Compatibility Chart "Some folks
had problems with 8.1, so do research first."
Please, note that Office 2013 is supported when installed with O365,
but O365 itself is not
supported.
You can find the details how to check your current Office, here.
2
JChem for Excel Ribbon
JChem for Excel is a chemistry Add-In for Microsoft Excel and
available in the menu on the JChem tab.
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