I want to use Marvin Viewer to Create a Table

working on linux system

after running setup jchem environment script

I can use chemaxon/jchem_releases/JChem_latest/bin/mview which is JChem_5_5_1_0 to view molecules. Which I have linked to command mview. Molecules are in SMILES representation and there is 10 of them.

Now I want to view molecules with my own generated properties; so I followed instructions on site and created a file with 10 SMILES in followed by their relevant properties in format:

c1ccccc1 10 20 394 39 19 28 1 1 2 1

c1ncccc1 30 27 49 12 38 29 3 2 1 2

etc this file was called fileof10molecules.smi

I wanted to view these molecules graphically with each of their properties in seperate fields.(molecules in same field, 10 and 30 in same field, 20 and 27 in same field...etc)

So I did command

mview -f "X:XY:XYZ:XYZA:A:AB:ABC:ABCD:ABCDE:ABCDEF" -c 11 fileof10molecules.smi

and the output is:

column # (a numbering column)       column structure (has the correct structures in)    column $Molname (A column which I do not want or need, but this column contains all the properties (30 27 49 ...) which I do need all space separated (these should be in there own relavant fields))    columnpropertyfield X (is all empty) columnpropertyfieldXY (is also empty) etc

I have also tried the same command on an SDF file format and the same mistakes happen. Is there some sought of delimiter I need in the file...I have tried tabs and commas both together and seperately and with and without spaces to no avail. I have looked at some pages on here which seem to suggest it should all work fine the way I am doing it.

Any help would be greatly appreciated. Hope you understand. Cheers Dan.

You can not pass field names from SMILES directly to MarvinView. It accepts fields names only from SD files.

Thus, you have to create an SD file from your SMILES file.

To get the desired output in MarvinView, do the followings:

• Replace every space character to Tab character (\t) in the SMILES file (\t is the delimiter character between SMILES sting and field values).


• Convert SMILES to SD file and specifies field names. You can do it with molconvert:

molconvert sdf "fileof10molecules.smi{fX,fXY,fXYZ,fXYZA,fA,fAB,fABC,fABCD,fABCDE,fABCDEF}" > fileof10molecules.sdf

• In the output SD file, the property part looks like this:

>  <X>


10


>  <XY>


20


>  <XYZ>


394


>  <XYZA>


39


>  <A>


19


>  <AB>


28


>  <ABC>


1


>  <ABCD>


1


>  <ABCDE>


2


>  <ABCDEF>


1

mview fileof10molecules.sdf

Hi,

Smiles is not able to store field names and the corresponding values, so the user have to assign field names to the values during import:

mview -f "X:XY:XYZ:XYZA:A:AB:ABC:ABCD:ABCDE:ABCDEF" -c 11 "test1.smi{fX,fXY,fXYZ,fXYZA,fA,fAB,fABC,fABCD,fABCDE,fABCDEF}"

I have attached a test file in which the field values are 'tab' separated. (Tab separation is necessary between the field data.)