Ketcher hand over a mol file by c# application?

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gno...@web.de

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Jun 13, 2015, 4:12:54 PM6/13/15
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Hello,

I like to use Ketcher in my c# application by using a webbrowser control. Is there a way to hand over mol files by c#? Sorry, I have no java oder html skills, so this concern is not so clear for me :-|

An easy way could be reding the mol file from a local disc. So I write the mol file by c# to disc and refresh my webbrowser control und the html page with ketcher sould read and display this file?  Sorry I'm unable to change the demo pages to read from a local file:-| Or is ther a better way to handle this?

I look forward to any tips an informations!

Kind reguards
Marco

Nikolay_...@epam.com

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Jun 14, 2015, 3:35:13 PM6/14/15
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Hi, Marco,

I'm not sure that I got properly what you want to archive. How will c# part interact with the webbrowser? Do you intend to embed browser view in application or the .NET part will act as a server? Browser's JS cannot read files from disk due obvious security reasons but there is several ways to delegate this task to C#.

Mit besten Grüßen,
Kolya

Marco Gnotke

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Jun 15, 2015, 12:48:13 AM6/15/15
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Hello!

Tahank you for your reply! I have this html source:
Enter code here...<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">

<html xmlns="http://www.w3.org/1999/xhtml">
    <head>
        <meta http-equiv="Content-Type" content="text/html; charset=UTF-8"/>
        <script type="text/javascript" src="raphael.js"></script>
        <script type="text/javascript" src="util/common.js"></script>
        <script type="text/javascript" src="util/vec2.js"></script>
        <script type="text/javascript" src="util/set.js"></script>
        <script type="text/javascript" src="util/map.js"></script>
        <script type="text/javascript" src="util/pool.js"></script>
        <script type="text/javascript" src="chem/element.js"></script>
        <script type="text/javascript" src="chem/sgroup.js"></script>
        <script type="text/javascript" src="chem/struct.js"></script>
        <script type="text/javascript" src="chem/struct_valence.js"></script>
        <script type="text/javascript" src="chem/molfile.js"></script>
        <script type="text/javascript" src="prototype-min.js"></script>
        <script type="text/javascript" src="chem/dfs.js"></script>
        <script type="text/javascript" src="chem/smiles.js"></script>
        <script type="text/javascript" src="rnd/events.js"></script>
        <script type="text/javascript" src="rnd/visel.js"></script>
        <script type="text/javascript" src="rnd/restruct.js"></script>
        <script type="text/javascript" src="rnd/restruct_rendering.js"></script>
        <script type="text/javascript" src="rnd/render.js"></script>
        <script type="text/javascript" src="ketcher.js"></script>
        <title>Ketcher: Example</title>
    </head>
    <body onload="rrr=ketcher.showMolfileOpts('client_area', $('mf3').innerHTML, 100, {'autoScale':true, 'ignoreMouseEvents':true});">
        <div id="client_area" style="width:640px;height:480px"></div>
        <p id="mf3" style="display:none">
  Marvin  09211002102D

  0  0  0     0  0            999 V3000
M  V30 BEGIN CTAB
M  V30 COUNTS 32 34 0 0 0
M  V30 BEGIN ATOM
M  V30 1 C -0.1086 -2.4987 0 0
M  V30 2 N 1.2339 -4.8265 0 0 CHG=1
M  V30 3 C -0.1086 -4.0426 0 0
M  V30 4 C -1.4355 -1.7304 0 0
M  V30 5 N 5.261 -4.0118 0 0 RAD=3
M  V30 6 C -1.4355 -0.1941 0 0
M  V30 7 N 2.5762 -2.483 0 0
M  V30 8 C 1.2339 -1.7147 0 0
M  V30 9 O 1.2339 -6.3629 0 0 CHG=-1
M  V30 10 C 2.584 -4.0195 0 0
M  V30 11 A 5.2455 -2.4675 0 0 CFG=3
M  V30 12 C 3.9109 -4.7876 0 0
M  V30 13 C 6.5878 -4.78 0 0
M  V30 14 O -2.7701 0.5742 0 0 MASS=18
M  V30 15 C 3.903 -1.7073 0 0
M  V30 16 C -0.1086 0.5742 0 0 CFG=1
M  V30 17 C -1.4355 -4.811 0 0
M  V30 18 C -2.7701 -2.4987 0 0
M  V30 19 C -2.7701 -4.0426 0 0 RAD=2
M  V30 20 C 6.5878 -6.3241 0 0
M  V30 21 C 7.9149 -4.0118 0 0
M  V30 22 [C,N,O] 1.226 -0.1941 0 0
M  V30 23 C 9.2495 -4.78 0 0
M  V30 24 C 7.9149 -7.0922 0 0
M  V30 25 C 9.2495 -6.3241 0 0
M  V30 26 C 5.7594 -1.0158 0 0
M  V30 27 C 6.7646 -2.7207 0 0
M  V30 28 C -0.1107 2.1142 0 0 CHG=2
M  V30 29 C 1.224 1.3459 0 0
M  V30 30 C -4.1033 -1.7278 0 0 RAD=1
M  V30 31 Fe -1.4334 -6.351 0 0 MASS=56
M  V30 32 "NOT [Cl,Br,I]" 4.07 1.485 0 0
M  V30 END ATOM
M  V30 BEGIN BOND
M  V30 1 1 2 3
M  V30 2 2 3 1
M  V30 3 1 4 1
M  V30 4 1 5 12
M  V30 5 1 6 4
M  V30 6 1 7 8
M  V30 7 1 8 1
M  V30 8 1 9 2
M  V30 9 2 10 2
M  V30 10 1 11 15
M  V30 11 1 12 10
M  V30 12 1 13 5
M  V30 13 4 6 14
M  V30 14 1 10 7
M  V30 15 1 15 7
M  V30 16 1 16 6
M  V30 17 1 17 3
M  V30 18 2 18 4
M  V30 19 1 19 18
M  V30 20 4 20 13
M  V30 21 4 21 13
M  V30 22 1 22 16
M  V30 23 4 23 21
M  V30 24 4 24 20
M  V30 25 4 25 24
M  V30 26 2 17 19
M  V30 27 1 11 5 CFG=1
M  V30 28 4 25 23
M  V30 29 1 11 26 CFG=3
M  V30 30 1 11 27 CFG=2
M  V30 31 8 16 28
M  V30 32 1 16 29 CFG=1
M  V30 33 1 18 30
M  V30 34 1 17 31
M  V30 END BOND
M  V30 END CTAB
M  END
</p>
    </body>
</html>


That does exactly what i need.

My idear is to replace the <p></p> area to a java script function like  <p>funktion{ read \ketcherfolder\molfile.mol</p>

So my c# application could override the file and than call webbrowser refresh. Is it possible to do that? It would be very convenient for my application.

Nikolay Kuznetsov

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Jun 16, 2015, 2:55:13 PM6/16/15
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Hi Marco,

 

As was mentioned above Javascript cannot read files from disk by its own. However you could do it from your C# application and pass the contents to the webcontrol. For example you could generate the html source dynamically replacing the content of the <p></p> area and then put the string to the webcontrol or you could pass some code to invoke it from javascript. It depends of your needs.

 

Hope it helps,

Kolya

Marco Gnotke

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Jun 16, 2015, 5:32:25 PM6/16/15
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Hi Kolya,

thank you very much for this tip! More simply is often the best way :-)

Cheers!
Marco

Marco Gnotke

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Jun 17, 2015, 12:59:03 AM6/17/15
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Hello,

back again. The overwriting runs pretty good. But when I start the html File in a .Net WebControl I got an error in script molfile in Line 33.

chem.Molfile.partitionLine = function (/*string*/ str, /*array of int*/ parts, /*bool*/ withspace)
{
    var res = [];
    for (var i = 0, shift = 0; i < parts.length; ++i)
    {
        res.push(str.slice(shift, shift + parts[i]));
        if (withspace)
            shift++;
        shift += parts[i];
    }
    return res;
};


The html file ist basicly ok. When I start it with FireFox oder Internet Explorer ist runs as exspected. Have you got an idear what can be the problem?

Nikolay Kuznetsov

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Jun 18, 2015, 8:12:20 AM6/18/15
to indig...@googlegroups.com, Marco Gnotke

Hi,

 

The Molfiles are very whitespace sensitive. You know, every extra whitespace or trimmed linebreak can destroy the layout completely. In other hand, according to HTML spec, the whitespaces around the "raw text elements" are stripped except some special cases. I cannot say it for sure as I don't see your code, but I guess the root of evil lies there. You could try to replace `<p>` tag with something like `<pre>` or `<textarea>` (refer the spec and hope that IE guys do its job well) or encode the Molfile directly in a script.

 

Cheers,

Kolya.

> >> <http://stackoverflow.com/a/3694080/1206628>. It depends of your needs.

Marco Gnotke

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Jun 21, 2015, 3:48:59 AM6/21/15
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Hello Kolya,

the problem ist solved. I changed my standard Visual Studio WebBrowser to a third party component. Now I have what I need! Thank you very much for your hepl!

Kind regards
Marco
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