XML format of Periodic table

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

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 

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

 

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

Hi,

 

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

Regards

Siva 

 

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

 

Dear Siva!

   I hav attached two files:

• elements.zip can be a good example to write your own Periodic Table. Finally you have to place it under your chemaxon home as István has told you.


• isotopes.txt should be compressed with our tool after editing. You can find the tool in <Marvin_i nstall_dir>/MarvinBeans/build/ It is called isotopescomp.jar

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

Regards:
Balázs 

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

Hi,

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

Regards,

Andras

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

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.

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

Hi,

I suggest you should you MarvinView applet for such purposes:

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

 

Regards,

Andras

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

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

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

 

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 

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

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

 

Hi,

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

Regards

Siva

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

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

 

Hi,

Awaiting for Response.

 

Regards

Siva

Hi,

What is the exact scenario:

- Cartridge search,

- JChemBase search,

- IIS,

- Applet,

- Windows service,

- simple application,

- etc..?

 

 

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

 

 

 

 

 

 

 

 

 

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.

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

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.