import sys,gzip,os
from rdkit import Chem
from rdkit.Chem import Descriptors
from rdkit.ML.Descriptors import MoleculeDescriptors
inF = sys.argv[1]
if inF.endswith(".sdf.gz") or inF.endswith(".sd.gz"):
cpds = [x for x in Chem.ForwardSDMolSupplier(gzip.open(sys.argv[1]))
if x is not None]
else:
cpds = [x for x in Chem.SDMolSupplier(inF) if x is not None]
outF = inF+".descr.sdf"
cpds_out = Chem.SDWriter(outF)
nms=[x[0] for x in Descriptors._descList]
for dedede in nms:
print dedede
#nms.remove('MolecularFormula')
calc = MoleculeDescriptors.MolecularDescriptorCalculator(nms)
for i in range(len(cpds)):
print i
descrs = calc.CalcDescriptors(cpds[i])
for x in range(len(descrs)):
cpds[i].SetProp(str(nms[x]),str(descrs[x]))
cpds_out.write(cpds[i])
cpds_out.close()
f_in = open(outF, 'rb')
file_name_gz = outF+".sdf.gz"
f_out = gzip.open(file_name_gz, 'wb')
f_out.writelines(f_in)
os.remove(outF)
From: Greg Landrum <[email protected]>
To: "[email protected]" <[email protected]>
Cc: "[email protected]"
<[email protected]>
Date: 24.04.2013 17:46
Subject: Re: [Rdkit-discuss] any experience "boost::bad_any_cast"
Hrm, that's odd. Are you calling SetProp at any point on molecules that
are being written to that file?
Any chance you can send a script that shows the problem? It would be
great to get this fixed before the release later this week.
On Wednesday, April 24, 2013, wrote:
Dear Greg,
thanks a lot for the build!
Unfortunately, the same error appears.
Strangely enough, the SD export works fine with our Linux installation.
Cheers & Thanks,
Paul
> https://rdkit.googlecode.com/files/RDKit_2013_03_1beta2.win32.py27.zip
>
> On Tue, Apr 23, 2013 at 10:44 AM, Greg Landrum <[email protected]>
wrote:
> > ok, I'll do a build either this evening or tomorrow a.m.
> >
> > On Tue, Apr 23, 2013 at 6:58 AM, <[email protected]>
wrote:
> >> Yes, I would love to try out the windows build.
> >>
> >> Thank you so much!
> >>
> >>
> >> paul
> >>
> >>
> >>> >
> >>> > For the new beta, there is currently no compiled win32bit version
> >>> > available, or am I wrong?
> >>> >
> >>>
> >>> You're correct. I didn't do a windows binary. If you'd like to test
it
> >>> let me know; I can do a build and upload it.
> >>>
> >>> -greg
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