On 02/10/2015 10:33 AM, Greg Landrum wrote: > You might want to take a look at this older thread for some additional > hints: > http://www.mail-archive.com/rdkit-discuss%40lists.sourceforge.net/msg00484.html
That's why programmers hate "domain" scientists: why
num = mol.GetNumAtoms()
if num > 500 ...
Why not 499 or 502? I guess I'll run
def _to_mol( self ) :
assert isinstance(self._mol,rdkit.Chem.rdchem.Mol)
m = rdkit.Chem.AddHs(self._mol)
rc = rdkit.Chem.AllChem.EmbedMolecule(m)
if rc < 0 :
rc = rdkit.Chem.AllChem.EmbedMolecule(m,useRandomCoords=True)
if rc == 0 :
try :
if rdkit.Chem.AllChem.UFFOptimizeMolecule(m) != 0 :
rdkit.Chem.AllChem.UFFOptimizeMolecule(m,maxIters=1000)
except ValueError :
pass
return rdkit.Chem.MolToMolBlock( m )
until the next one crashes it.
Thank you
--
Dimitri Maziuk
Programmer/sysadmin
BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu
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