TouchMol 2.0.0 Release 

Tuesday, September 03, 2013 7:58:00 AM

TouchMol for Office is a set of add-ins to the Microsoft Office application programs.  Using the latest Microsoft Office add-in technology, TouchMol for Office extends Word, Excel, PowerPoint, and OneNote with structure editing, query entry, and chemical property search and display. With version 2.0, Scilligence has enhanced the structure sketching capabilities of TouchMol to include:


Customized Structure Templates - (http://www.elncloud.com/jsdrawapp/jsdraw/CustomTemplate.htm)
New Drawing Features - Curved Arrows, Freehand Shapes, Rectangles and Ellipses (http://www.elncloud.com/jsdrawapp/jsdraw/Shapes.htm)
TLC Plates - (http://www.elncloud.com/jsdrawapp/jsdraw/TLC.htm)
One-Click Conversion to ChemDraw - (TouchMol for Word) (http://www.scilligence.com/web/one-click-to-convert-touchmol-structures-into-chemdraw-style-in-word.aspx)
Expandable Atom Labels
Flip and Rotate Selected Atoms and Bonds
Adjust Text Size
Export SMILES and
Molfile for peptides/oligonucleotides
Customizable Display - Including Fonts, Bond Width, Bond Spacing, Color, Carbon Display, etc.


To download TouchMol for Office, follow the links below:

TouchMol for Office 2010 and 2013 (for both x86 and x64):
http://www.scilligence.com/web/download.aspx?prod=TouchMol4Office2010

 

TouchMol for Office2007:
http://www.scilligence.com/web/download.aspx?prod=TouchMol4Office2007

 

TouchMol Desktop:
http://www.scilligence.com/web/download.aspx?prod=TouchMolDesktop



 

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DevSuite 3.0.0 Release, Including JSDraw, JSDraw.NET, MolEngine and MolSql 

Friday, August 02, 2013 7:41:00 AM

Scilligence Cheminformatics Development Suite (DevSuite, http://devsuite.scilligence.com) is a complete toolkit for developers to build web applications and .NET applications.  DevSuite contains following modules:

  1. JSDraw.Draw - 100% Javascript Chemical/Biological Structure Editor
  2. JSDraw.NET - A .NET wrapper of JSDraw (New in DevSuite 3.0)
  3. JSDraw.WebServices - JSDraw server side web services to exend JSDraw capabilities
  4. MolEngine - .NET Cheminformatics Toolkit
  5. MolEngine.Plugins - Third-party modules to extend MolEngine capabilities
  6. MolSql - Chemistry Cartridge for Microsoft SQL Server

DevSuite release 3.0.0 includes (demo):

  1. JSDraw 3.0.0
    1. Draw TLC plates (http://www.elncloud.com/jsdrawapp/jsdraw/TLC.htm)
    2. Use custom templates (http://www.elncloud.com/jsdrawapp/jsdraw/CustomTemplate.htm)
    3. Draw curve arrows
    4. Draw shapes, rectangles and ellipses (http://www.elncloud.com/jsdrawapp/jsdraw/Shapes.htm)
    5. Be able to expand abbreciations
    6. Be able to flip and rotate partial molecule
    7. Be able to set text font sizes
    8. Export SMILES and Molfile from drawn peptides/oligonucleotides
    9. bugfix: hydrogen count and valuence attributes are not read correctly in molfiles
    10. bugfix: superatom definition lost if having text
    11. bugfix: isotope is not writen correctly in molfile
    12. bugfix: cannot set any isotope
    13. bugfix: fragment selection tool doesn't work correctly
    14. bugfix: Double Bonds not centered properly
    15. bugfix: be able show all carbon atoms, or termal carbon atoms
  2. JSDraw.NET 3.0.0
    1. All features in JSDraw 3.0.0
    2. Copy/paste ChemDraw and ISIS/Symyc/Accelrys Draw structures
    3. .NET APIs
  3. JSDraw.WebServices 3.0.0
    1. Upgraded MolEngine to version 3.0.0
  4. MolEngine 3.0.0
    1. Support JSDraw 3.0.0 new objects, including TLC plates, Shapes, curves
    2. Expose configuration to customize structure display, including font name, font size, line width, bond space, monocolor, carbon display etc.
    3. Atom labels are now all transparent
    4. Some arrows from old ChemDraw version not read correctly
    5. MemorySearch output SDF defaulted to kekulized mode
    6. bugfix: be able to handle multiple attach point on one atom
    7. bugfix: Cleanup doesn't generate coordinates at all for some structures
    8. bugfix: Oracle boolean column not read correctly
  5. MolEngine Plugins
    1. No changes for this release
  6. MolSql 3.0.0
    1. Upgrade MolEngine core to version 3.0.0

To download DevSuite or individual modules:

  1. JSDraw: http://www.scilligence.com/web/download.aspx?prod=JSDraw
  2. JSDraw.WebServices: http://www.scilligence.com/web/download.aspx?prod=JSDraw.WebServices
  3. MolEngine: http://www.scilligence.com/web/download.aspx?prod=MolEngine
  4. MolEngine.Plugins: http://www.scilligence.com/web/download.aspx?prod=MolEngine.Plugins
  5. MolSql: http://www.scilligence.com/web/download.aspx?prod=MolSql

Please contact us here http://www.scilligence.com/web/contact.aspx to schedule a demo, begin an evaluation, or request further information.

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JSDraw.NET - Draw Chemical/Biological Structures in .NET Application 

Wednesday, July 24, 2013 3:58:00 PM

Scilligence will release JSDraw.NET as a new module in DevSuite 3.0.  JSDraw.NET will allow cheminformatics developers to embed chemical structure editing, query entry, and results disply within their own .NET application.

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JSDraw 3.0 Feature: Change Font Sizes 

Monday, July 22, 2013 9:48:00 PM

It is able to change text font sizes in JSDraw 3.0:

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Draw Curves and Shapes in JSDraw 3.0 

Friday, July 05, 2013 3:17:00 PM

The development of another JSDraw 3.0 feature is finished: draw curves and shapes.

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How to load an SDF into a SQL Server Database Table? 

Friday, July 05, 2013 8:49:00 AM
// -----------------------------------------------------
// How to load an SDF into a SQL Server Database Table
// -----------------------------------------------------
// 
// Part I. Prepare database
// 1. Create SQL Server database
// 2. Install MolSql cartridge
// 3. Create the structure database
//    create table Structures (ID bigint not null primary key, Molfile nvarchar(max), Vender nvarchar(256));
// 4. Create structure index
//    molindex 'create', 'Structures', 'Molfile', 0
// 
// Part II. Load the sdf into the created database table with following C# code
// 1. Add Scilligence.MolEngine.dll and Scilligence.MolEngine.Companion.dll refrence
// 2. The following code does the importing

// create sdf reader
using (Scilligence.MolEngine.IO.SDFile sdf = 
    new Scilligence.MolEngine.IO.SDFile(@"c:\compounds.sdf", Scilligence.MolEngine.IO.MDLDBBase.OpenMode.Read))
{
    // connect to sql server database
    string connectionstring = "Data Source=(local);Initial Catalog=Database;Integrated Security=True";
    using (Scilligence.MolEngine.Companion.Database db = 
        Scilligence.MolEngine.Companion.Database.Create("sqlserver", connectionstring))
    {
        int id = 0;
        Scilligence.MolEngine.IO.SDFile.Record r;
        Scilligence.MolEngine.Companion.Database.Row row = new Scilligence.MolEngine.Companion.Database.Row();

        // read records
        while ((r = sdf.ReadNext()) != null)
        {
            ++id;
                        
            // create database record
            row.Clear();
            row.Add("ID", id);
            row.Add("Molfile", r.m.ToString(Scilligence.MolEngine.Molecule.MimetypeMol));
            row.Add("Vendor", r.items["Vendor"]);

            // write into sql server
            db.Insert("Structures", row);
        }
    }
}
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Working in Black & White Display Mode 

Tuesday, July 02, 2013 9:47:00 AM

You can now set TouchMol, MolEngine, and JSDraw to display structures in black and white mode.

For TouchMol and MolEngine, add the following in scilligence.config or to your application config:

<add key="molengine.draw.monocolor" value="1" />

scilligence.config location:

Windows XP: C:\Documents and Settings\All Users\Application Data\Scilligence\Common\

Window 7, 8: C:\ProgramData\Scilligence\Common\

For JSDraw:

JSDraw.defaultoptions = { monocolor: true };

or

new JSDraw("div1", { monocolor: true });

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Use Custom Templates in JSDraw 

Friday, June 28, 2013 3:21:00 PM

Custom Structure Templates have been implemented in JSDraw 3.0.

Try it live

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One-Click Converts TouchMol Structures to ChemDraw CDX 

Friday, June 21, 2013 7:53:00 AM

In TouchMol version 2.0.0, we can convert TouchMol structures into ChemDraw CDX with 1 click:

TouchMol 2.0.0 is scheduled for August release.

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Insert Symbols and Special Characters in JSDraw 

Wednesday, June 19, 2013 7:46:00 PM

It will be much easier to insert symbols and special characters in JSDraw:

It is able to show Symbol dialog using toolbar, but it is also be able to show it using Ctrl+Down-Arrow shortcut in textbox.  Using Ctrl+Up-Arrow to hide Symbol dialog.

Try it now

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RegMol 2.1.2 release 

Friday, June 07, 2013 8:00:00 AM

RegMol is compound registration and assay database system, enabling scientists to register and track small-molecule, biologics and biological conjugates, storing and retreiving biological assay data.

RegMol 2.1.2 includes following improvements and changes:

  1. New sequence editor, with sequence annotation features
  2. Support Oligonucleotides and their conjugates
  3. Batch register sequence and macro-molecules
  4. Revamped virtual compound registration
  5. Be able register new batch from an existing one, or from its parent structure
  6. Add more biological fields
  7. Users are able to change password and other information themselves
  8. Grouped registration fields
  9. Barcode printer now write log
  10. Add Amdin tool to correct Compound IDs

Please contact us from our website http://www.scilligence.com/web/contact.aspx to schedule a demo, begin an evaluation, or request further information.

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JSDraw to Support Non-English Languages 

Wednesday, June 05, 2013 11:51:00 PM

Chinese, Japanese, and many other languages

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Scilligence ELN 2.1.2 Release 

Tuesday, June 04, 2013 1:00:00 PM

Scilligence ELN is a completely web-based electronic lab notebook system for Chemistry and Biology.

Scilligence ELN 2.1.2 includes following changes and improvements:

  1. [Chem] Add Salt field single-step reaciton, which can be carried over to RegMol
  2. Improved security control by limiting IP Ranges
  3. Add a time expiration to greeting message
  4. DB changes: two new form; accounts and users changed
  5. Be able to set user's expiration date
  6. Show all annoations when loading a picture
  7. bugfix: cannot recover items from recycle bin
  8. Add biological sequence form with sequence annotation
  9. Navigating pages not working for search results
  10. Typing passwords when closing and witnessing experiments

Please contact us from our website http://www.scilligence.com/web/contact.aspx to schedule a demo, begin an evaluation, or request further information.

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Cheminformatics DevSuite 2.7.0 Release, Including JSDraw, MolEngine and MolSql 

Monday, June 03, 2013 8:00:00 AM

Scilligence Cheminformatics Development Suite (DevSuite, http://devsuite.scilligence.com) is a complete toolkits for developers to build web applications and .NET applications.  Dev Suite contains following key modules:

  1. JSDraw - 100% Javascript Chemical/Biological Structure Editor
  2. JSDraw.WebServices - JSDraw server side web services to exend JSDraw capabilities
  3. MolEngine - .NET Cheminformatics Toolkit
  4. MolEngine.Plugins - Third-party modules to extend MolEngine capabilities
  5. MolSql - Chemistry Cartridge for Microsoft SQL Server

DevSuite release 2.7.0 includes:

  1. JSDraw 2.7.0
    1. Fully support atom label and abbreviations, such as COOH, Ph, Fmoc.  All supported abbreviations: http://www.elncloud.com/jsdrawapp/jsdraw/JSDrawAbbreviation.htm
    2. Allow R group in R group
    3. Add number shortcuts to change R index
    4. Add atom type M for metal
    5. Open/Save/Copy/Paste ChemDraw structures and preserve atom labels
    6. bugfix: cannot add template bonds to R-group substructure
    7. bugfix: bracket not saved in Rxnfile
    8. bugfix: context menu off screen
  2. JSDraw.WebServices 2.7.0
    1. Upgraded MolEngine to version 2.7.0
  3. MolEngine 2.7.0
    1. Be able to preserve atom labels in ChemDraw file
    2. Support atom abbreviations.  All supported abbreviations: http://www.elncloud.com/jsdrawapp/jsdraw/JSDrawAbbreviation.htm
    3. Support custom atom abbreviations
    4. RemoveHydrogen() is able to keep Hs on metal
    5. Support DNA/RNA sequences
  4. MolEngine Plugins
    1. No changes for this release
  5. MolSql 2.7.0
    1. Upgrade MolEngine core to version 2.7.0
    2. Add functions: JSDraw() and JSDrawS()
    3. bugfix: Structure indices are not all created when creating indices on existing tables

To download DevSuite or individual modules:

  1. JSDraw: http://www.scilligence.com/web/download.aspx?prod=JSDraw
  2. JSDraw.WebServices: http://www.scilligence.com/web/download.aspx?prod=JSDraw.WebServices
  3. MolEngine: http://www.scilligence.com/web/download.aspx?prod=MolEngine
  4. MolEngine.Plugins: http://www.scilligence.com/web/download.aspx?prod=MolEngine.Plugins
  5. MolSql: http://www.scilligence.com/web/download.aspx?prod=MolSql

Please contact us from our website http://www.scilligence.com/web/contact.aspx to schedule a demo, begin an evaluation, or request further information.

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TouchMol 1.5.0 Release 

Friday, May 31, 2013 8:00:00 AM

TouchMol for Office is delivered as a set of add-ins to the Microsoft Office application programs.  Enabling the input and editing of molecular structures within Word, Excel, PowerPoint, and OneNote.

TouchMol 1.5.0 includes the following new features:

  1. Draw Markush structures
  2. Fully support atom labels and abbreviation
  3. Add Atom/Bond Properties to context menu
  4. Support Rgfile
  5. Be able to set settings to show structure in monocolor mode
  6. New Sequence Editor for protein and gene
  7. Combine table data by structures (TouchMol.Table)
  8. Support multiple Compound Profilers
  9. Be able to include a shared configuration
  10. Be able to combine attributes by structures
  11. bugfix: copy structure on compound profile doesn't work

To download our TouchMol, follow the links below:

TouchMol for Office 2010 and 2013 (for both x86 and x64):
http://www.scilligence.com/web/download.aspx?prod=TouchMol4Office2010

TouchMol for Office 2007:
http://www.scilligence.com/web/download.aspx?prod=TouchMol4Office2007

TouchMol Desktop:
http://www.scilligence.com/web/download.aspx?prod=TouchMolDesktop

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Oligonucleotides and their conjugates will be widely supported in Scilligence Products 

Friday, May 17, 2013 7:57:00 PM

Oligonucleotide and thier conjugates will be widely supported in Scilligence products, including JSDraw, MolEngine, Scilligence ELN and RegMol:

Antibody-Drug conjugates are supported already:

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JSDraw Atom Label Tool 

Monday, May 13, 2013 4:24:00 PM

JSDraw 2.7 will introduce Atom Label/Abbreviation features.  With the Text tool, it is able to click on an atom, and edit the atom label.  The atom label can be element symbol, such as C, N, Br, or abbreviations, such as CH3, Ph, COOH, generic group, such Cyclic, Alkyl etc.

All these features will be available in TouchMol of Office 1.5.0 as well.

Try it now.  List of supported Abbreviations.

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JSDraw Fully Supports Atom Labels/Abbreviations 

Tuesday, May 07, 2013 11:28:00 AM

Another big feature is implemented in JSDraw 2.7.0: fully supporting atom labels and abbreviations:

Try it now.  List of supported Abbreviations.

This feature will be available in version 2.7.0, which is scheduled for June release.

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DevSuite 2.6.0 Release, Including JSDraw, MolEngine and MolSql 

Thursday, May 02, 2013 11:32:00 AM

Scilligence Cheminformatics Development Suite (DevSuite, http://devsuite.scilligence.com) is a complete toolkits for developers to build web applications and .NET applications.  Dev Suite contains following key modules:

  1. JSDraw - 100% Javascript Chemical/Biological Structure Editor
  2. JSDraw.WebServices - JSDraw server side web services to exend JSDraw capabilities
  3. MolEngine - .NET Cheminformatics Toolkit
  4. MolEngine.Plugins - Third-party modules to extend MolEngine capabilities
  5. MolSql - Chemistry Cartridge for Microsoft SQL Server

DevSuite 2.6.0 synchronizes all modules to version 2.6.0.

DevSuite release 2.6.0 includes:

  1. JSDraw 2.6.0
    1. Draw Markush structures (demo)
    2. Add Sequence Editor (demo)
    3. Support RGfile
    4. Add Atom/Bond Properties to context menu
    5. Be able export plain texts from JSDraw.Table
    6. bugfix: Formulation getXml() failed on IE7/8
    7. bugfix: has no method 'pasteUseCdx'
    8. bugfix: DatePicker is broken
    9. bugfix: Problem on deleting batches on FormulationTable
  2. JSDraw.WebServices 2.6.0
    1. Upgraded MolEngine to version 2.6.0
    2. Add Encrypting Tool
  3. MolEngine 2.6.0
    1. Support RGfile and Markush structures
    2. Support JSDraw SeqEditor xml format
    3. Support atom aliases
    4. Be able to encrypt appSettings values
    5. Be able to refter to another appSettings key
    6. Be able to include other config file in the main config file
    7. Molengine I/O can read/writer Stream
    8. bugfix: category is not read from xml on Compound Profile
    9. bugfix: isotope is not read correctly from SKC files
    10. bugfix: extracted sequences from ADC are not correct
    11. bugfix: Some ISIS/Symx/Acclrys OLE object not read correctly
    12. bugfix: be able to read unknown atom types
    13. bugfix: cannot read license code out of Oracle database
  4. MolEngine Plugins
    1. No changes for this release
  5. MolSql 2.6.0
    1. Upgrade MolEngine core to version 2.6.0

To download DevSuite or individual modules:

  1. JSDraw: http://www.scilligence.com/web/download.aspx?prod=JSDraw
  2. JSDraw.WebServices: http://www.scilligence.com/web/download.aspx?prod=JSDraw.WebServices
  3. MolEngine: http://www.scilligence.com/web/download.aspx?prod=MolEngine
  4. MolEngine.Plugins: http://www.scilligence.com/web/download.aspx?prod=MolEngine.Plugins
  5. MolSql: http://www.scilligence.com/web/download.aspx?prod=MolSql

Please contact us from our website http://www.scilligence.com/web/contact.aspx to schedule a demo, begin an evaluation, or request further information.

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Drawing Markush Structures in JSDraw 

Wednesday, May 01, 2013 6:29:00 AM

Another new big feature is available in JSDraw: draw Markush structures:

To try it live: http://www.elncloud.com/jsdrawapp/jsdraw/RGroup.htm

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