[Bug 189618] New: Unable to load a molecule in molecular editor

https://bugs.kde.org/show_bug.cgi?id=189618

           Summary: Unable to load a molecule in molecular editor
           Product: kalzium
           Version: unspecified
          Platform: unspecified
        OS/Version: Linux
            Status: UNCONFIRMED
          Severity: normal
          Priority: NOR
         Component: general
        AssignedTo: kalzium@...
        ReportedBy: linuxcomics@...


Version:           2.2.1 (using KDE 4.2.2)
OS:                Linux
Installed from:    Unlisted Binary Package

I am currently working on Pardus 2008.2 with KDE 4.2.2 installed from
pardus-2008-test repository.

The pisi package of kdeedu4 (version 4.2.2) is installed along with pisi
package of OpenBabel (version 2.2.0).

When I use Kalzium molecular editor and try to load a molecule from kalzium >
data > molecules, I obtain the following message :

Impossible to read the file format. Check your OpenBabel installation.

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Marcus D. Hanwell <marcus@...> changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
                 CC|                            |marcus@...




--- Comment #1 from Marcus D. Hanwell <marcus cryos org>  2009-04-15 19:32:07 ---
It sounds like openbabel is broken and not able to find its format plugins.
Have you tried testing the babel program too? Kalzium uses the Avogadro
library, which uses OpenBabel to load and save molecules.

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--- Comment #2 from Linuxcomics <linuxcomics neuf fr>  2009-04-16 15:39:21 ---
Excuse me but what do you mean by "testing the babel program too" ? Update
installed version of OpenBabel by compiling the last stable release ?

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--- Comment #3 from Marcus D. Hanwell <marcus cryos org>  2009-04-16 16:58:13 ---
Open Babel comes with some command line programs that also use the library. The
babel program is one such program - translate from one file format to another.
You could try `babel -H` and see what file formats are listed. Also taking one
chemical file and translating it to another. So the Avogadro tarball has
several test files - try `babel methanol.cml methanol.xyz` for example and
confirm the file is successfully translated.

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Anne-Marie Mahfouf <annma@...> changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|UNCONFIRMED                 |NEEDSINFO
                 CC|                            |annma@...
         Resolution|                            |WAITINGFORINFO




--- Comment #4 from Anne-Marie Mahfouf <annma kde org>  2009-04-21 17:20:43 ---
LinuxComic, can you do what Marcus explained please? Thanks in advance.

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--- Comment #5 from Linuxcomics <linuxcomics neuf fr>  2009-04-21 21:38:10 ---
(In reply to comment #4)
> LinuxComic, can you do what Marcus explained please? Thanks in advance.

Sorry, I was very busy last days. I will try to do the tests tomorrow.

Best regards,

Linuxcomics.

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--- Comment #6 from Linuxcomics <linuxcomics neuf fr>  2009-04-22 16:47:54 ---
When I use the command 'babel -H', there is a message which says :

"The following file formats are recognized:
acr -- ACR format [Read-only]            
adf -- ADF cartesian input format [Write-only]
adfout -- ADF output format [Read-only]      
alc -- Alchemy format                        
arc -- Accelrys/MSI Biosym/Insight II CAR format [Read-only]
bgf -- MSI BGF format                                      
box -- Dock 3.5 Box format                                  
bs -- Ball and Stick format                                
c3d1 -- Chem3D Cartesian 1 format                          
c3d2 -- Chem3D Cartesian 2 format                          
cac -- CAChe MolStruct format [Write-only]                  
caccrt -- Cacao Cartesian format                            
cache -- CAChe MolStruct format [Write-only]                
cacint -- Cacao Internal format [Write-only]                
can -- Canonical SMILES format.                            
car -- Accelrys/MSI Biosym/Insight II CAR format [Read-only]
ccc -- CCC format [Read-only]                              
cdx -- ChemDraw binary format [Read-only]                  
cdxml --  ChemDraw CDXML format                            
cht -- Chemtool format [Write-only]                        
cif -- Crystallographic Information File                    
ck -- ChemKin format                                        
cml -- Chemical Markup Language                            
cmlr -- CML Reaction format                                
com -- Gaussian 98/03 Input [Write-only]                    
copy -- Copies raw text [Write-only]                        
crk2d -- Chemical Resource Kit diagram(2D)                  
crk3d -- Chemical Resource Kit 3D format                    
csr -- Accelrys/MSI Quanta CSR format [Write-only]          
cssr -- CSD CSSR format [Write-only]                        
ct -- ChemDraw Connection Table format                      
cub -- Gaussian cube format                                
cube -- Gaussian cube format                                
dat -- Generic Output file format [Read-only]              
dmol -- DMol3 coordinates format                            
dx -- OpenDX cube format for APBS                          
ent -- Protein Data Bank format                            
fa -- FASTA format [Write-only]                            
fasta -- FASTA format [Write-only]                          
fch -- Gaussian formatted checkpoint file format [Read-only]
fchk -- Gaussian formatted checkpoint file format [Read-only]
fck -- Gaussian formatted checkpoint file format [Read-only]
feat -- Feature format                                      
fh -- Fenske-Hall Z-Matrix format [Write-only]              
fix -- SMILES FIX format [Write-only]                        
fpt -- Fingerprint format [Write-only]                      
fract -- Free Form Fractional format                        
fs -- FastSearching                                          
fsa -- FASTA format [Write-only]                            
g03 -- Gaussian98/03 Output [Read-only]                      
g92 -- Gaussian98/03 Output [Read-only]                      
g94 -- Gaussian98/03 Output [Read-only]                      
g98 -- Gaussian98/03 Output [Read-only]                      
gal -- Gaussian98/03 Output [Read-only]                      
gam -- GAMESS Output [Read-only]                            
gamess -- GAMESS Output [Read-only]                          
gamin -- GAMESS Input                                        
gamout -- GAMESS Output [Read-only]                          
gau -- Gaussian 98/03 Input [Write-only]                    
gjc -- Gaussian 98/03 Input [Write-only]                    
gjf -- Gaussian 98/03 Input [Write-only]                    
gpr -- Ghemical format                                      
gr96 -- GROMOS96 format [Write-only]                        
gukin -- GAMESS-UK Input                                    
gukout -- GAMESS-UK Output                                  
gzmat -- Gaussian Z-Matrix Input                            
hin -- HyperChem HIN format                                  
inchi -- InChI format                                        
inp -- GAMESS Input                                          
ins -- ShelX format [Read-only]                              
jin -- Jaguar input format [Write-only]                      
jout -- Jaguar output format [Read-only]                    
k -- Compare molecules using InChI [Write-only]              
log -- Generic Output file format [Read-only]                
mcdl -- MCDL format                                          
mcif -- Macromolecular Crystallographic Information          
mdl -- MDL MOL format                                        
ml2 -- Sybyl Mol2 format                                    
mmcif -- Macromolecular Crystallographic Information        
mmd -- MacroModel format                                    
mmod -- MacroModel format                                    
mol -- MDL MOL format                                        
mol2 -- Sybyl Mol2 format                                    
molden -- Molden input format [Read-only]                    
molreport -- Open Babel molecule report [Write-only]        
moo -- MOPAC Output format [Read-only]                      
mop -- MOPAC Cartesian format                                
mopcrt -- MOPAC Cartesian format                            
mopin -- MOPAC Internal                                      
mopout -- MOPAC Output format [Read-only]                    
mpc -- MOPAC Cartesian format                                
mpd -- Sybyl descriptor format [Write-only]
mpqc -- MPQC output format [Read-only]
mpqcin -- MPQC simplified input format [Write-only]
msi -- Accelrys/MSI Cerius II MSI format [Read-only]
msms -- M.F. Sanner's MSMS input format [Write-only]
nw -- NWChem input format [Write-only]
nwo -- NWChem output format [Read-only]
out -- Generic Output file format [Read-only]
outmol -- DMol3 coordinates format
pc --  PubChem format  [Read-only]
pcm -- PCModel Format
pdb -- Protein Data Bank format
png -- PNG files with embedded data
pov -- POV-Ray input format [Write-only]
pqr -- PQR format
pqs -- Parallel Quantum Solutions format
prep -- Amber Prep format [Read-only]
qcin -- Q-Chem input format [Write-only]
qcout -- Q-Chem output format [Read-only]
report -- Open Babel report format [Write-only]
res -- ShelX format [Read-only]
rsmi -- Reaction SMILES format
rxn -- MDL RXN format
sd -- MDL MOL format
sdf -- MDL MOL format
smi -- SMILES format
smiles -- SMILES format
sy2 -- Sybyl Mol2 format
t41 -- ADF TAPE41 format [Read-only]
tdd -- Thermo format
test -- Test format [Write-only]
therm -- Thermo format
tmol -- TurboMole Coordinate format
txt -- Title format
txyz -- Tinker MM2 format [Write-only]
unixyz -- UniChem XYZ format
vmol -- ViewMol format
xed -- XED format [Write-only]
xml --  General XML format [Read-only]
xtc -- XTC format [Read-only]
xyz -- XYZ cartesian coordinates format
yob -- YASARA.org YOB format
zin -- ZINDO input format [Write-only]"

When I try `babel methanol.cml methanol.xyz`, the translation fails.

"babel methanol.cml methanol.xyz
==============================
*** Open Babel Error  in OpenAndSetFormat
  Cannot open methanol.cml
0 molecules converted
1 errors"

Bests regards,

Linuxcomics.

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