MolConverter scales incorrectly on non-Marvin MOL string

I have the following MOL string generated by our home-grown software:

Code:

Lewis   061306154538                                             11 10  0     0  0             99 V2000   182.0000  129.0000    0.0000 N   0  0  0  0  0  0   232.0000  129.0000    0.0000 N   0  0  0  0  0  0   132.0000  129.0000    0.0000 C   0  0  0  0  0  0   283.0000  129.0000    0.0000 C   0  0  0  0  0  0   232.0000  177.0000    0.0000 O   0  0  0  0  0  0   132.0000  176.0000    0.0000 H   0  0  0  0  0  0    85.0000  129.0000    0.0000 H   0  0  0  0  0  0   132.0000   83.0000    0.0000 H   0  0  0  0  0  0   283.0000   88.0000    0.0000 H   0  0  0  0  0  0   325.0000  129.0000    0.0000 H   0  0  0  0  0  0   283.0000  176.0000    0.0000 H   0  0  0  0  0  0   1  2  1  0     0   1  3  1  0     0   2  4  1  0     0   2  5  1  0     0   3  6  1  0     0   3  7  1  0     0   3  8  1  0     0   4  9  1  0     0   4 10  1  0     0   4 11  1  0     0 A    3 C A    4 C M  END

The result of

Code:

MolImporter.importMol(mol).getImageSize(jpeg:scale100...)

has width 547. I then ask MolConverter() to generate a jpeg with scale 40. The resulting image file has width 319 instead of 219.

I have tested the latest Marvin release with your molecule:

Code:

System.err.println(mol.getImageSize("jpeg:scale100")); System.err.println(mol.getImageSize("jpeg:scale40"));

I have got the following result:

Code:

w547,h283,scale100.0 w219,h113,scale40.0

It seems to me that image size calculation is correct in the latest release.


Have you tried the latest Marvin?

Tamas,





It could well be that getImageSize() is reporting 219 correctly However, the jpeg that MolConverter is producing when I request scale40 has width 319. (It could be that I have a bug in my code, but I am using similar code for other MOL strings without difficulty.)





Refoyl

Tamas,





It turns out that my input molecule is in MRV, not MOL format:

Code:

<?xml version="1.0" ?>   <MDocument>     <MChemicalStruct>       <molecule molID="m1">         <atomArray          atomID="a1 a2 a3 a4 a5 a6 a7 a8 a9 a10 a11"          elementType="N N C C O H H H H H H"          mrvAlias="0 0 C C 0 0 0 0 0 0 0"          x2="8.878049 11.317073              6.439024 13.804877              11.317073 6.439024              4.1463413 6.439024              13.804877 15.853658              13.804877"          y2="4.243902 4.243902              4.243902 4.243902              6.5853653 6.536585              4.243902 2.0              2.2439022 4.243902              6.536585"         />         <bondArray>           <bond atomRefs2="a1 a2" order="1" />           <bond atomRefs2="a1 a3" order="1" />           <bond atomRefs2="a2 a4" order="1" />           <bond atomRefs2="a2 a5" order="1" />           <bond atomRefs2="a3 a6" order="1" />           <bond atomRefs2="a3 a7" order="1" />           <bond atomRefs2="a3 a8" order="1" />           <bond atomRefs2="a4 a9" order="1" />           <bond atomRefs2="a4 a10" order="1" />           <bond atomRefs2="a4 a11" order="1" />         </bondArray>       </molecule>     </MChemicalStruct>   </MDocument>

I am using jchem3.1.6. I see the same behavior when I invoke the command-line version of molconvert: I get a figure scaled to width 319.

Code:

molconvert jpeg:mono,H_off,wireframe,#ffffff,scale40 -o /tmp/foo.jpeg /tmp/foo.mrv

Refoyl

Tamas,





Sorry. It turns out to be my mistake. As we convert from MOL to MRV, we change the scaling. I was measuring the size of the MOL but converting the MRV to a JPEG, hence the discrepancy.





Refoyl