Calculate MW based on the Molecule Formula throw the error

Hi,

We have using the .NET API Application. Using the ElementalAnalyser  to calculate the MW based on MF as input  then it is throwing the Invalid formula: C39H49ClN4O2.2(HCl) or C38[C14]H49ClN4O2.

Please find sample code below.

ElementalAnalyser ws = new ElementalAnalyser();

ws.setMolecule("C39H49ClN4O2.2(HCl)"); or ws.setMolecule("C38[C14]H49ClN4O2");

double Mass1 = ws.mass();

As per our requirement need to calculate the MW based on formula , formula like isotopes (contains either () or [ ] or non isotopes.

Please provide the solution for this or any other approach is available

Regards
Siva

Hi,

you can get the Molecule from an MSketchPane with the help of the getMol() method and you will get back a Molecule object which you can set to the ElementalAnalyzer via the setMolecule(MoleculeGraph) method instead of generating the formula and then parsing that again.

I suggest to use this approach, which is much more cheaper in calculation time, and much more safer, and avoids import and export issues.

Regards,
Istvan 

Hi,

Thanks for quick response, As per our Requirement , we have directly passing the Molecule formula not getting Molecule from an MSketchPane. So we have using the element analyser and throwing the  error when using the formula like isotopes (contains either () or [ ] or non isotopes.

Please provide the solution or any other approach for this Requirement with example.

Regards

Siva

Hi,

I am moving this topic to the Calculator Plugin related support topic, my colleagues will be able to give you a more specific answer.

For the first sight, I see a problem with the formulas, the Elemental Analysis plugin accepts the isotope in thi folloing form: C38[14C]H49ClN4O2 instead of C38[C14]H49ClN4O2. And from the code I am seeing that it does not accept the () brackets at all in the formula.

This seems a bug for me, since when Marvin generates the formula for a Repeating Unit SGroup it puts () type brackets to mark the repetition.

My colleagues will track this issue down, and will provide you a solution, if there is any.

Thank you for your patience in the mean time!

Regards,
Istvan 

Dear Siva,

The Istvan's answer is correct. The Elemental Analysis plugin accepts the isotope only in the [14C] form.
The another example (C39H49ClN4O2.2(HCl)) throws an exception because the plugin doesn't support formulas, which contains () brackets.

We will investigate it, but we have a workaround for this problem. Use the following form: C39H49ClN4O2.HCl.HCl

Best regards,
Laszlo

Hi,

We have using the dynamic data , So we dont know the which Formula is passing as a input and it is contain isotopes (either () or [ ] or non isotopes).

Please provide the solution for this problem as soon as possible. it is great helpful for us.

Regards

Siva

 

 

Hi,

We have fixed this issue. The new setMolecule() method also supports formulas like C39H49ClN4O2.2(HCl). It will be available in version 6.1.

Best regards,
Laszlo

Hi,

Thanks for quick response. please provide the link and steps to download the version 6.1.

Currently we have using 6.0 version.

Regards

Siva

Dear Siva,

You can download version 6.1.0 from the following link :

http://www.chemaxon.com/download/marvin/for-end-users/

Best regards,

                       Daniel

danielszisz wrote:

Dear Siva, You can download version 6.1.0 from the following link : http://www.chemaxon.com/download/marvin/for-end-users/ Best regards,                        Daniel

Hi,

As per our requirement the MW always will show 4 digit precision value. when calcualte the data using Jchem.dll.

Could please help us any option or method to show 4 (198.2345) digit precision value.

 

Regards

Siva

Dear Siva, 

The number of decimal digits computed by the Elemental Analysis Plugin depends on the atomic masses stored in the elements.zip. You have to modifiy those values (give them as e.g. 123.4567) to get the MW in 4 decimal digits.

That customized file should be placed under user_home/.chemaxon on your machine.

See the following forum topic that is about the same issue: https://www.chemaxon.com/forum/ftopic10781.html

I hope it helps.

Daniel 

Hi,

We have own periodic table in the customized file should be placed under user_home/.chemaxon on mymachine.

But in the server placed in the user_home/.chemaxon  place then when try to updated dynamically or read and show the page. the folde provide to us for not authorized folder.

Please provide me help on this.. it should a common place and accessable to all. we have using only for chemaxon dll alone for calculation. Any other option or location placed this file and access to all.

 

Regards

Siva

Dear Siva, 

We understand your problem, but as not being an issue of the Calculator Plugins, our team can't give you further help. Your problem is related to either IT or server configuration. We sent your message to the Marvin and the Core team also; they may have other ideas how to solve this problem.

Daniel 

Hi,

We have using the ElementalAnalyser to calculate the weight based on the formula. We get the molecule weight  “524.448” for “C27H27[2H]3Cl2O6" this formula Using your Periodic table. We need to get the Entire Value of M.W without any round off like 524.4479853

Find the Example 1 of using our code.

ElementalAnalyser ws = new ElementalAnalyser();

ws.setMolecule("C27H27[2H]3Cl2O6");

string Formula2 = ws.formula();

double Mass4 = ws.mass();

When we manually calculate based on the your Periodic table value the M.W is 524.4479853. But Element analyzer provide the M.W is 524.448

 

C27      -->    324.2889

H27     -->       27.21438

[2H]3  -->       6.042305334

Cl2     -->       70.906

O6      -->       95.9964

 

Total  -->  524.4479853

 

Example 2 :

 

We get the molecule weight  538.576 for “C27H29F3O6S "” this formula. When we manually calculate based on the your Periodic table value the M.W is 524.4479853 . But Element analyzer provide the M.W is 538.576

 

C27      -->     324.2889

H29     -->     29.23026

F3  -->         56.9952096

O6     -->         95.9964

S      -->           32.065 

Total  -->  538.5757696

 

Example 3:

We get the molecule weight for 528.4664 for “C26[13C]H27[2H]3[37Cl]2O6” this formula and weight for 652.8346 for “C31H30[3H]9N4O8. K”. For those example element analyzer provide the 4 digit precision.

 

We need to get the entire calculation value without any round off. Because some of the formula will showing 3 digit round-off and some of the formula 4 digit formula precision.

 

Please help to get the entire Molecule weight without any round off based on the formula. This is high priority issue for us. Please help asap.

 

Regards

Siva

Dear Siva, 

Unfortunately the number of decimal digits can't be set via the Elemental Analysis Plugin API. The number of digits of the MW is determined by the smallest number of decimal digits of the element weights in the molecule. So e.g. if you have a molecule with a Cl atom with an element weight of 2 decimal digits, the molecular weight will also have two decimal digits.

I also recalculated the second example you gave first with the plugin and then manually using the atomic values in the Periodic Table, and I got  538.5757696 in both cases. 

I hope this helps, 

Daniel