I am looking for open-source tools which can generate 2d molecular structure from the MOL or SMILES file. Further, it SHOULD number the atoms in the order of occurrence of atoms in the connection table of MOL file or SMILE string. I used MarvinSketch 6.1.2 but the position of numbering is not very good, as it get cluttered with the bonds. Please refer some tools with which I can draw molecule similar to the one shown in figure but numbering is also clear. In the figure, all numbering except 1-7 are ok.
To answer the question, I assumed you would like to stick with Marvin if possible. Likely, the options described and found functional in version 5.2.4 met at this site are functional at later versions, too.
So I drew from scratch a similar representation of your molecule. And indeed, there is overlap by labels and the drawing.
Yet the software allows you to print the drawings. So, thanks to the installation of HP-1102P printer and printing into a file I got a postscript file. This vector format is of course beneficial, you may import it in inkscape, for example. Note two potential pitfalls: select "import" (instead of "open") and "import text as text". Twice you have to ungroup the drawing before being able to move the labels around as you prefer. Or to change their colour (vide infra), or substitute them. Eventually, you may either save it in numerous file formats or like in this case, export the resulting bitmap.