XML format of Periodic table

User fec9e52845

28-06-2013 10:29:53

Hi,


We have using the Jchem and Marvin API in our project. We need to configure the Periodic table data into XML type. Can you please provide the XML format of Perodic table with example and confirm Jchem will support for configure the Periodic table data into XML type.


Please provide the response ASAP.


Regards


Siva

ChemAxon 5433b8e56b

29-06-2013 09:58:47

Hi Siva,


the periodic system data is not stored as an xml in our side, and I think it never will be, for specific reasons.


You can find information about how to override the values our periodic table implementation works with in the API documentation of PeriodicSystem class.


I hope the aproach we have to override periodic table settings is suitable for your needs.


Regards,
Istvan 

User fec9e52845

01-07-2013 06:36:52

Hi,


We have using the  .Net API Application.Can  you please provide the periodic table data settings format with Example. We can able to make a Xml format for that way.


 


Regards


Siva

ChemAxon bd13b5bd77

01-07-2013 06:47:23

 

Hi,


what Istvan sent you is a Java example, in the dotnet you can use the same code.


Low level JChem .NET API uses a clear Java -.NET compilation, so Java code will be working under dotnet.
Please add all the JChem.NET dlls from C:\Program Files\ChemAxon\JChem .NET API 6.x.x.


Viktor


User fec9e52845

01-07-2013 07:10:25

Hi,


 


Thanks for reply. We need  periodic table data settings format. So i can able to make a Xml for  same format.


Regards


Siva 

User fec9e52845

01-07-2013 09:58:31

 


Hi,

 As per Jchem API, You have own periodic table (Don't know the format) and calling the Jchem and Marvin API (PeriodicSystem) and calculating the Molecule Weight and Molecule Formula.



As per Our Client Requirement, Our application have own periodic table (not using for Chexaxon periodic table) , How we will configure and call the Jchem and Marvin API (PeriodicSystem) and calculate the Molecule Weight and Molecule Formula.



 We have the following doubts:



 1. How to configure (which format) our own periodic table  with Jchem and Marvin API classes.


 2. Your periodic table data details (periodic system) whichformat is save in the chemaxon directory or user_home/chemaxon directory.




 3. The periodic system is editable or replace with our own periodic data element?



 Can you please provide or suggest the best possible way of approach.




 



Regards



Siva



 









ChemAxon 2c555f5717

04-07-2013 14:19:22

Dear Siva!


   I hav attached two files:



   I hope it helps you to define your own periodic table.


Regards:
Balázs 

User fec9e52845

26-07-2013 07:50:17

Hi,


We have using Window 7 OS. Testing purpose We have changed the H and C mass value in element.ZIP and placed in C:\Program Files\ChemAxon\elements.ZIP.


We try to calculate this  "C6H7NO2.HCl"  compound. Still calculate the same Value from Your own periodic system. It is not showing the our own calculate value..


We have using the following code for calculate mass value for our own periodic tables :


Option 1 :  based on the structre


var molecule = MoleculeHandler.CreateMolecule(StructreData, MoleculeFormat.Unknown);


JChemMoleculeBase objMoleBase = (JChemMoleculeBase)molecule;


txtFormula.Text = objMoleBase.Formula;


txtMW.Text = objMoleBase.Mass.ToString();


Option 2 :  based on the formula


ElementalAnalyser ws = new ElementalAnalyser();


ws.setMolecule("C6H5NO2.HCl");


string Formula1 = ws.formula();


double Mass1 = ws.mass();


double EXMass = ws.exactMass();


int Prec = ws.exactMassPrecision();


int mapre = ws.massPrecision();


 


Both the above results provide the result based on your Periodic Table


PFA for Testing purpose changed element. ZIP file.  pls help regarding this and provide the solution


Regards


Siva

ChemAxon eb65a25631

26-07-2013 08:36:17

Hi,


You should put the elements.zip into <user_home_directory>\chemaxon


Regards,


Andras

User fec9e52845

26-07-2013 09:46:36

Hi,


We have using window 7 OS.  Then Chemaxon dll is installed in  C:\Program Files\ChemAxon\ChemAxon .NET 6.0.2.10, C:\Program Files\ChemAxon\JChem .NET API 6.0.2.215,C:\Program Files\ChemAxon\Marvin .NET 6.0.2.215;


 


I dont find <user_home_directory>. Please help regarding this..


Regards


Siva

ChemAxon eb65a25631

26-07-2013 09:57:56

That's just a placeholder for the user's home directory, for example:


C:\Users\UserName\chemaxon


The UserName is your actual user's name you logged in with.


A.

User fec9e52845

26-07-2013 11:49:13

Thanks for Quick response. it is working fine.


 


I need a another help. As per  ourrequirement . We need to show the compund structure for  MarvinApplet API and makes MarvinApplet readonly . Nothing to make changes for MarvinApplet. i can able to show the sturcture. but unable to find the option Readonly ( like nothing user can able to do ) in MarvinApplet.


Can  please provide the code for this.


 


Regards


Siva

ChemAxon eb65a25631

26-07-2013 12:30:13

Hi,


I suggest you should you MarvinView applet for such purposes:


http://www.chemaxon.com/marvin/examples/applets/view/index.html


 


Regards,


Andras

User fec9e52845

29-07-2013 13:37:14

Hi,


 


For using MarvinView need to save the file in mols-2d folder. as per requirement retrieve from database and showing the structure. but user can view only. unable to edit the structure.


 


Please help regarding this.


 


Regards


Siva

ChemAxon eb65a25631

30-07-2013 08:21:24

Hi,


Well, I'm not a HTML/MarvinApplet expert.


Why don't you just put a link of the molecule file beside the applet, in order the user to be able to download/save?


Regards,


Andras

User fec9e52845

30-07-2013 12:21:44

Hi, 


As per requirement retrieve from database and showing the structure. User wont allow to edit the structure.


If your not an MarvinApplet Expert then Can you assign to MarvinApplet Expert in ur team. We need a solution for this.


 


Regards


Siva


 

ChemAxon 2c555f5717

02-08-2013 06:27:48

Dear Siva!


   If you want to have a view-only molecule display, than you sould use Marvin View like this. You do not have to place the file under the mols-2D folder, you can set any URL's that is available for the applet.  I hope, it helps you!


Regards:
Balázs 

User 4997bac55f

09-09-2013 22:25:44

I had same problem long time ago, thx to you guys i fixed it 

User fec9e52845

26-11-2013 13:35:06










akovacs wrote:

Hi,


You should put the elements.zip into <user_home_directory>\chemaxon


Regards,


Andras




Hi ,


In my local machine, chemaxon override periodic table is under in C:\Users\UserName\chemaxon  and able to read the data and override dynamically. but in the server it is located to \adminusername \ chemaxon folder. so unable to read the able to showing as dont have access to the file and dynamically unable to override the elements and isotopics.


Can please help regarding this. Where need to locate the elements.zip and isotopics.dat file can change and read the data?


Regards


Siva


 

User fec9e52845

28-11-2013 11:31:59

Hi,


Still now didnt get the any response please help to us.


Regards


Siva

ChemAxon eb65a25631

28-11-2013 12:39:47

Hi Siva,


I don't really understand your problem:


you should put these files under the user (which you were authenticated with) home directory as mentioned.


If you cannot read the file in 'adminusername', that means you are not authenticated with the user whose home directory is this.


That leads to two options:


1. authenticate with the apropriate user


2. put the files into the user's home directory you are authenticated with.


Regards,


Andras

User fec9e52845

20-12-2013 09:18:27

Hi ,


In my local machine, chemaxon override our periodic table element.zip and isotopic.data is under in C:\Users\UserName\chemaxon  and Value is appearing correctly.


When installed the chemaxon in server and  Moved the  our updated periodic table element.zip and isotopic.data is under in C:\Users\UserName\chemaxon.


The Our Updated value is not reflecting . It is always taking your system periodic table values.


Can please help regarding this.  where need any installation or missing for retrive the value.


Regards


Siva


 

User fec9e52845

30-12-2013 10:57:00

Hi,


Awaiting for Response.


 


Regards


Siva

ChemAxon eb65a25631

30-12-2013 15:57:43

Hi,


What is the exact scenario:


- Cartridge search,


- JChemBase search,


- IIS,


- Applet,


- Windows service,


- simple application,


- etc..?


 

User fec9e52845

02-01-2014 09:45:07

 

Hi ,It is a web application and hosted in IIS. I am using following method.

 


 


ElementalAnalyser ws = new ElementalAnalyser();

 



 JchemServiceData JchemData = new JchemServiceData();
            try
            {
                    ws.setMolecule(MolecularFormula);
                    JchemData.CandidateMolecularWeight = ws.mass()


                    return JchemData;
            }
            catch (Exception ex)
            {
                throw ex;
            }



 


 


I have installed in server and  Moved the our updated periodic table element.zip(changed value of weight alone) and isotopic.data(changed value of weight alone)  is under in C:\Users\UserName\chemaxon.

 


The Our Updated value is not reflecting . It is always taking your system periodic table values.

 



 



Same code and same path in my local machine is working fine.The chemaxon override our periodic table element.zip and isotopic.data is under in C:\Users\UserName\chemaxon and getting the updated weight value correctly.

 


 


Can please help regarding this.  where need any install any thing or missing toretrive the value.

 


 






 




Regards

 




Siva

 




 


 


 


 


 


 


 


 


















ChemAxon eb65a25631

02-01-2014 12:33:24

If you add this to the code:


string homePath = Environment.ExpandEnvironmentVariables("%HOMEDRIVE%%HOMEPATH%");


 


What is the value of the homePath variable, when it is hosted on the IIS?


 


A.

User fec9e52845

06-01-2014 10:25:33

Hi,


My homepth  variable value is  C:\Users\Unamit(C:\Users\UserName\). our updated periodic table element.zip(changed value of weight alone) and isotopic.data(changed value of weight alone)  is under in C:\Users\Unamit(C:\Users\UserName\). 


Still My own periodic table value is not reflecting.



 It is hosted IIS on 2 weeks back.


Regards


Siva

ChemAxon eb65a25631

06-01-2014 18:16:48

Hi,

I made a WebApplication and hosted on IIS 7.5 .
I managed to reproduce the issue.

Here is how I was able to resolve it:
- Create a SYSTEM environment variable, name: CHEMAXON_HOME
    value: path where the elements.zip resides (in my case: d:\Projects\).
- Copy the elements.zip to that folder.
- Restart the system.
- Now, JChem API should be able to automatically read elements.zip on that location.

(You may have to give read permission to this file for the user used for authentication by the IIS.
In my case it wasn't neccesary, because I put the file to a generic location.)

A.