[Rdkit-discuss] atom coordinates
Hello, In the Python API, is it possible to read the 3D coordinates of an atom (from a Mol object created from an SDF file with 3D coords)? Thanks, Michal -- November Webinars for C, C++, Fortran Developers Accelerate application performance with scalable programming models. Explore techniques for threading, error checking, porting, and tuning. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60136231iu=/4140/ostg.clktrk ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] atom coordinates
Yes, of course - try this: conf = mol.GetConformer() pt = conf.GetAtomPosition(0) Cheers JP On 8 November 2013 12:01, Michal Krompiec michal.kromp...@gmail.com wrote: Hello, In the Python API, is it possible to read the 3D coordinates of an atom (from a Mol object created from an SDF file with 3D coords)? Thanks, Michal -- November Webinars for C, C++, Fortran Developers Accelerate application performance with scalable programming models. Explore techniques for threading, error checking, porting, and tuning. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60136231iu=/4140/ostg.clktrk ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- November Webinars for C, C++, Fortran Developers Accelerate application performance with scalable programming models. Explore techniques for threading, error checking, porting, and tuning. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60136231iu=/4140/ostg.clktrk___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] atom coordinates
Thanks a lot!
Michal
On 8 November 2013 12:40, Paolo Tosco paolo.to...@unito.it wrote:
Hi Michal,
I think this Python snippet should do what you need:
from rdkit import Chem
from rdkit.Chem import AllChem
sdf = 'benzene.sdf'
supplier = Chem.SDMolSupplier(sdf, True, False)
mol = supplier[0]
for i in range(0, mol.GetNumAtoms()):
pos = mol.GetConformer().GetAtomPosition(i)
print '{0:12.4f}{1:12.4f}{2:12.4f}'.format(pos.x, pos.y, pos.z)
Cheers,
p.
On 11/08/2013 01:01 PM, Michal Krompiec wrote:
Hello,
In the Python API, is it possible to read the 3D coordinates of an
atom (from a Mol object created from an SDF file with 3D coords)?
Thanks,
Michal
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==
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[Rdkit-discuss] postgres FPs in python
Hi there, DB-related question again: When I retrieve fps from a postgres db, they look like this: \x020c00102204810001040001981408420180400040048088c020800423a192001814002021044200092400040208 Is there are way to convert them to RDKit bitvector fingerprint objects or at least bitvector strings in python? Thanks, George -- November Webinars for C, C++, Fortran Developers Accelerate application performance with scalable programming models. Explore techniques for threading, error checking, porting, and tuning. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60136231iu=/4140/ostg.clktrk___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] postgres FPs in python
Hi George,
On Fri, Nov 8, 2013 at 5:02 PM, George Papadatos gpapada...@gmail.comwrote:
Hi there,
DB-related question again:
When I retrieve fps from a postgres db, they look like this:
\x020c00102204810001040001981408420180400040048088c020800423a192001814002021044200092400040208
Is there are way to convert them to RDKit bitvector fingerprint objects or
at least bitvector strings in python?
There is an rdkit cartridge function called bfp_to_binary_text() that you
can use for the bit vector fingerprints:
In [61]: m = Chem.MolFromSmiles('COC')
In [62]: fp =
Chem.RDKFingerprint(m,minPath=1,maxPath=6,fpSize=1024,nBitsPerHash=2)
In [63]: curs.execute(select bfp_to_binary_text(rdkit_fp('COC')))
In [64]: row = curs.fetchone()
In [66]: nfp = DataStructs.CreateFromBinaryText(str(row[0]))
In [67]: nfp==fp
Out[67]: True
I don't think there's currently a way to do something equivalent for
count-based fingerprints (sfp's in the cartridge nomenclature), but it
could be added if there was demand.
-greg
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