What is the official stance on this? On the one hand Babel can't be expected to fix files that other software has screwed up. On the other hand, is there really such a thing as "incorrect" bond lengths in a 2D SDF?
Quoting cadeddu <cade...@unistra.fr> on Mon, 06 Aug 2012 16:25:11 +0200:
To conclude:
this small workaround works - but great care must be taken into
checking the structures:
--------------------------------------------------
import pybel, openbabel
mol=pybel.readfile("cdx", "benzene_acs.cdx").next()
factor=1.39/1.89 # this is the error of the bond length: real
value/wrong one
for each in mol.atoms:
x=each.coords[0]*factor
y=each.coords[1]*factor
z=each.coords[2]*factor
each.OBAtom.SetVector(x,y,z)
mol.addh()
output = pybel.Outputfile("mol2", "benzene_acs.mol2","overwrite=True")
output.write(mol)
output.close()
--------------------------------------------------
hope this will help
thank you guys for this wonderful software and those lovely python
libraries! :)
andrea
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Description: Binary data
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