351
Custom Excel Chemical Functions
not necessary.
Here is an example of an .xml file containing rules to aromatize the
structures, clear the isotopes and remove the water and benzene as
solvent from the structure cells:
<?xml version="1.0" encoding="UTF-8" ?>
<StandardizerConfiguration Version="0.1">
<Actions>
<Aromatize ID="Aromatize"/> 
<ClearIsotopes ID="ClearIsotopes"/>
<Transformation ID="water" Structure="O>>" Exact="true"/>
<Transformation ID="benzene" Structure="c1ccccc1>>"
Exact="true"/>
</Actions>
</StandardizerConfiguration>
14.2.2.10
JCStructure
JCStructure
Returns the structure of a molecule using not only the hash
(JCSYSstructure) as input but other structure formats as well, such as
CAS number, InChi, IUPAC name, SMILES, SMARTS, Extended SMILES
and SMARTS. Structures returned by this function are not editable.
14.2.2.11
JCIDSYSStructure
JCIDSYSstructure
This function can be handled in an aggregated column, which
refers to SYSstructure and a text type identifier of the molecule and
handles information originating from these two columns together. By
setting the visibility parameter to True of False allows the user to
switch between text identifier and drawn structure. 
Function arguments: 
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352
Custom Excel Chemical Functions
·Identifier or Molecule (basically SYSstructure)
·ID or Name: any text type identifier or parameter such as ID,
SMILES, biological activity.
·Visible: 1 or 0; true or false.
14.2.3
Image
Enter topic text here.
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353
Custom Excel Chemical Functions
14.2.3.1
Display Options - Rendering
JCBallStickImage
Displays the structure with Ball and Stink rendering.
JCSpaceFillImage
Displays the structure with Spacefill rendering.
14.2.3.2
Display Options - Misc
JCAtomNumberImage
Displays atom numbers with the structure.
JCBondLengthImage
Displays bond lengths with the structure.
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354
Custom Excel Chemical Functions
JCGraphInvariantImage
Displays graph invariants with the structure.
JCLonePairImage
Displays lone pairs (valence electron pairs without bonding or sharing
with other atoms) with the structure.
N
N
N
N
O
O
H
3
C
CH
3
CH
3
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355
Custom Excel Chemical Functions
14.2.3.3
Plug-Ins
JCChargeImage
Displays partial charge value of each atom.
JCHBDAImage
Displays atomic hydrogen bond donor and acceptor multiplicity.
JCHuckelAnalysisImage
Localization energies L(+) and L(-) for electrophilic and nucleophilic
attack at an aromatic center are calculated by the Huckel method.
The smaller L(+) or L(-) means more reactive atomic location. Order
of atoms in E(+) or in Nu(-) attack are adjusted according to their
localization energies. The total pi energy, the pi electron density and
the total electron density are also calculated by the Huckel method.
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356
Custom Excel Chemical Functions
JClogPImage
Atomic contribution to logP.
JCOrbitalElectroNegativityImage
Orbital electronegativity is the measure of the ability of atoms to
attract electrons in the context of chemical bonds and is calculated
from the partial charge distribution of atoms.
JCpKaImage
Displays  the pKa values of all proton gaining or loosing atoms on the
basis of the partial charge distribution.
357
Custom Excel Chemical Functions
JCPolarizabilityImage
Displays  atomic  polarizability  values.
JCRefractivityImage
Displays refractivity values with the structure.
4.00
N
2.50
3.50
N
2.50
3.68
N
2.80
3.06
N
4.21
2.78
O
1.44
O
1.44
H
3
C
3.02
CH
3
3.02
CH
3
3.02
JCStericHindranceImage
Returns steric hindrance values on each atom in the image of the
input  molecule.
358
Custom Excel Chemical Functions
JCStericEffectImage
Returns steric effect index values on each atom in the image of the
input  molecule.
15
Troubleshooting
15.1
Manually  enabling  JChemExcel.Functions
After  installing, JChem for Excel Add-In will be loaded automatically
when starting Microsoft Excel.
1.
Click the Microsoft Office button and then click Excel  Options. 
2.
Click the Add-Ins category.
3.
In the Manage box, click Excel Add-ins, and then click Go. 
4.
To load an automation add-in, click Automation, then click
359
Troubleshooting
JChemExcel.Functions in the Automation servers  available box and
then click OK.
5.
To unload an automation add-in, you must remove it from the
registry. Contact your system administrator for details.
360
Troubleshooting
15.2
Disable and re-enable JChem for Excel
1.
Click the Microsoft Office Button 
and then click Excel Options.
2.
Click the Add-Ins category.
3.
In the Manage box, click COM Add-ins, and then click Go.
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