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

Linuxcomics linuxcomics at neuf.fr
Wed Apr 22 16:47:56 CEST 2009


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





--- 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.

-- 
Configure bugmail: https://bugs.kde.org/userprefs.cgi?tab=email
------- You are receiving this mail because: -------
You are the assignee for the bug.


More information about the Kalzium mailing list