Jchem bases: the problem of standardier molecular structure

If I input ( .cdx) file, for example ethanol's .cdx file, How can I operate at the second step in Standardizer software to get the .sdf output file.

Hi Xiaoya,

Your questions are answered here.

Best regards

Krisztina

Dear professor Krisztina,

   Thank you for your guidance. That's very nice of you.

   I have studied the website that you give , however still don't know which configure action is need to standaradizer molecular structure as the following format:

   Could you help me?

   Best wishes to you.

                                                                                                           Sincerely, Xiaoya Song.

I guess you want to add explicit hydrogens to the molecule (with the Add Explicit Hydrogens action), and use SDF output format.

Dear professor Zsolt,

     When I chose the Add Explicit Hydrogens action, the SDF output format see figure1. 

    When I chose the "Add Explicit Hydrogens "action +"Alias to Atom" action+ "Alias to Group" action+"Dearomatize" action +"Map"action+"Clean 2D"action , the SDF output format see figure 2. It is the same result with [ "Add Explicit Hydrogens "action +"Alias to Atom" action+ "Alias to Group" action+"Dearomatize" action+"Clean 2D"action ]

    However, these (figure1/figure2) aren't the result that I want to get.

   So, I want to know how to change my configuration to get the result of the "structural information" figure.

Please explain in plain English what do you want to do with your chemical structure (in this case it is ethanol, so the possibilities are quite limited).

Dear Professer,

   I want to calculate fragments simplex descriptors values with my chemical structure, as shown in Figure1.

So your workflow is:

input molecule  --(Standardizer)-->  standardized molecule  --(descriptor calculator)-->  descriptors

Your descriptor calculator expects the molecules to be in a certain state (e.g. 2D/3D coordinates, explicit hydrogens, aromatized) and format (e.g. SDF). Let us know the expected state and format and we can help.

Dear professor,

   Thank you for your help. It is my honor to get your guidance.

   My workflow is just as you say, input molecule --(Standardizer)--> standardized molecule --(descriptor calculator)-->  descriptors. And I indeed need the molecules to be in a certain state. 

  In terms of the molecule structure, my expected state and format is like the examples as shown in figures.That is, I want to get ethanol/n-butanol/i-propanol/acetone/butanone-2/cyclopentanone's style as shown in Figure 1/2/3/4/5/6 respectively at the same time.

Figure1

Figure2

Figure3

Figure4

Figure5

Figure6

Your help is highly appreciated, and I look forward to hearing from you.

Dear professor,

     How can I solve the above problems?

    Hope your solutions and help.

The information you provided is not enough to suggest a proper solution. I can see on SDfile screenshots (these are text files, why don't you attach them?) that the molecules contain explicit hydrogens, and they have 2D coordinates. Based on that I can recommend this standardizer configuration:

- Add Explicit Hydrogens
- Clean 2D

Dear engineers,

        I am very interested in molecular structure standardizer. I think it is important and  meaningful. Recently, I reinstall my work computer (win7 32bit) at the same time to reinstall this calculation software. 

       However, when I use ethanol's .cdx file as input file (C2H6O.cdx) and select “- Add Explicit Hydrogens、- Clean 2D” as this standardizer configuration, both the standardizer structures and the SDF output file are 0 as shown in Figure 1.

      No matter how can I adjust the configuration [for example, chose the "Add Explicit Hydrogens "action +"Alias to Atom" action+ "Alias to Group" action+"Dearomatize" action +"Map"action+"Clean 2D"action], the output file is always empty. What's going wrong?

      Your help is highly appreciated, and I look forward to hearing from you!

      Best regards.

Please attach the input file (C2H6O.cdx).

We discovered a bug: standardizer generated 3D coordinates for the molecule in C2H6O.cdx file with configuration "Add Explicit Hydrogens"+"Clean 2D". We have fixed the bug, the fixed version will be available next week.

Output with the fixed version:

  Mrv0541 10291417012D          



  9  8  0  0  0  0            999 V2000

    1.7495   -1.9335    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0

    1.3370   -1.2190    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0

    0.5120   -1.2190    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0

    1.0350   -2.3460    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0

    2.1620   -2.6480    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0

    2.4640   -1.5210    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0

    2.0263   -0.7657    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0

    1.3850   -0.3954    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0

    0.0995   -0.5046    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0

  1  2  1  0  0  0  0

  2  3  1  0  0  0  0

  1  4  1  0  0  0  0

  1  5  1  0  0  0  0

  1  6  1  0  0  0  0

  2  7  1  0  0  0  0

  2  8  1  0  0  0  0

  3  9  1  0  0  0  0

M  END

$$$$

Is this what you expect?

Dear engineer,

         Thank you for your help. It can correctly calculate now.

         Best wish to you !

                                                               (*^__^*)