User 677b9c22ff
20-11-2008 03:14:52
Hi,
if I try this is Marvin 5.1.2 and 5.1.0 under WINXP 32 bit
JAVA version 1.6 and 1.5 I get the following error.
Molecule File Converter, version 5.1.2, (C) 1999-2008 ChemAxon Ltd.
with smiles and SDF it works (not sure about PDB and others)
I reported that a while ago and Tamas said maybe its a class file error,
because of Marvin beans or different versions?
I actually found out that it is a problem related to the windows batch file.
So calling the molconvert.bat under windows with option XYZ does
not work (all other options work) but calling it directly with
classpath information works. This was confirmed on two different systems
with 3 different settings. I also don't have any DOS ENV variables XYZ or
xyz. Actually the solution is to put "" around xyz "xyz". Talk about DOS ...
Cheers
Tobias
if I try this is Marvin 5.1.2 and 5.1.0 under WINXP 32 bit
JAVA version 1.6 and 1.5 I get the following error.
Molecule File Converter, version 5.1.2, (C) 1999-2008 ChemAxon Ltd.
| Code: |
Z:\>molconvert xyz MOL1.mol Exception in thread "main" java.lang.NoClassDefFoundError: xyz Caused by: java.lang.ClassNotFoundException: xyz at java.net.URLClassLoader$1.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.net.URLClassLoader.findClass(Unknown Source) at java.lang.ClassLoader.loadClass(Unknown Source) at sun.misc.Launcher$AppClassLoader.loadClass(Unknown Source) at java.lang.ClassLoader.loadClass(Unknown Source) at java.lang.ClassLoader.loadClassInternal(Unknown Source) Z:\> Z:\>molconvert smiles MOL1.mol OC[C@@H]1O[C@@H](O[C@]2(CO)O[C@@H](CO)[C@H](O)[C@@H]2O)[C@@H](O)[C@@H](O)[C@H]1O Z:\> |
with smiles and SDF it works (not sure about PDB and others)
I reported that a while ago and Tamas said maybe its a class file error,
because of Marvin beans or different versions?
I actually found out that it is a problem related to the windows batch file.
| Code: |
Z:\>java -classpath %JCHEMHOME%\lib\jchem.jar chemaxon.formats.MolConverter xyz MOL1.mol 23 O 1.55380 0.23450 0.67770 C 0.23660 0.34830 0.14820 C 0.16750 1.36580 -1.01670 O 1.10930 0.95100 -2.03350 C 1.09920 1.73340 -3.24840 O -0.12850 1.60220 -4.00470 C -0.58630 0.28820 -4.43140 C -2.03370 0.52910 -4.94800 O -2.86050 1.08360 -3.92920 O -0.68840 -0.62370 -3.32150 C 0.12930 -1.78270 -3.53530 C -0.77810 -3.02240 -3.72660 O -1.62030 -3.21040 -2.59450 C 1.05250 -1.49790 -4.74420 O 2.34530 -1.07730 -4.31180 C 0.29400 -0.40200 -5.51330 O 1.14430 0.50070 -6.21730 C 1.39570 3.22510 -2.92750 O 1.29560 4.02490 -4.10520 C 0.47070 3.77570 -1.80610 O -0.85940 3.96370 -2.29420 C 0.47800 2.82710 -0.57540 O -0.45990 3.27710 0.40020 Z:\>molconvert smiles MOL1.mol OC[C@@H]1O[C@@H](O[C@]2(CO)O[C@@H](CO)[C@H](O)[C@@H]2O)[C@@H](O)[C@@H](O)[C@H]1O Z:\> |
So calling the molconvert.bat under windows with option XYZ does
not work (all other options work) but calling it directly with
classpath information works. This was confirmed on two different systems
with 3 different settings. I also don't have any DOS ENV variables XYZ or
xyz. Actually the solution is to put "" around xyz "xyz". Talk about DOS ...
| Code: |
Z:\>molconvert "xyz" MOL1.mol 23 O 1.55380 0.23450 0.67770 C 0.23660 0.34830 0.14820 C 0.16750 1.36580 -1.01670 O 1.10930 0.95100 -2.03350 C 1.09920 1.73340 -3.24840 O -0.12850 1.60220 -4.00470 C -0.58630 0.28820 -4.43140 C -2.03370 0.52910 -4.94800 O -2.86050 1.08360 -3.92920 O -0.68840 -0.62370 -3.32150 C 0.12930 -1.78270 -3.53530 C -0.77810 -3.02240 -3.72660 O -1.62030 -3.21040 -2.59450 C 1.05250 -1.49790 -4.74420 O 2.34530 -1.07730 -4.31180 C 0.29400 -0.40200 -5.51330 O 1.14430 0.50070 -6.21730 C 1.39570 3.22510 -2.92750 O 1.29560 4.02490 -4.10520 C 0.47070 3.77570 -1.80610 O -0.85940 3.96370 -2.29420 C 0.47800 2.82710 -0.57540 O -0.45990 3.27710 0.40020 Z:\> |
Cheers
Tobias