I just started testing JChem for Excel and so far I have not been able to figure out how to specify options when using JChemExcel.Functions. For example, I have a structure in a cell within Excel and I want to calculate the polar surface area of the structure. I use JCPSA(), which allows me to specify the structure and the pH but not whether to exclude/include sulfur and phosphorus atoms from calculation. It appears that by default, the function excludes sulfur and phosphorus but I would like to calculate the value including the two atoms. Is there a way to do that within JChem for Excel?
I am afraid that this type of options is missing from the Polar Surface Area plugin. It is not possibe to decide if you want to include these atoms into the calculation or not. You can find more information about the calculator plugins by using this link: http://www.chemaxon.com/marvin/help/calculations/calculator-plugins.html
I have pasted the available information about the Polar Surface Area plugin:
Polar surface area (PSA) is formed by polar atoms of a molecule.
It is a descriptor that shows good correlation with passive molecular
transport through membranes, and so allows estimation of transport
properties of drugs. Estimation of topoligical polar surface area (TPSA)
is based on the method given in this paper. The
method provides results which are practically identical with the 3D PSA,
while calculation time of TPSA is approximately 100-times faster. This
method is more suitable for fast bioavailability screening of large
virtual libraries. The TPSA value can be calculated both for the neutral form and
the major microspecies.
The calculation and the display options can be set in the Polar Surface Area (2D)
- Decimal places:setting the number of decimal places with which
the result values are given.
- Take major microspecies at pH: calculates the polar surface area
for the major microspecies present at the given pH.
initially we started off by putting the calculations in JChem for Excel with the default options. If there is need we will add the necessary options.
We also have a "universal function" called JCChemicalTerms, where it is possible to calculate any chemical terms expression on an input molecule. However I checked and as far as I can see, it is not even possible to specify it in Chemical Terms.
We will add these options to the 5.4 release of JChem for Excel.