Dear Aniko,
Here is a Jupyter notebook that does what you need:
https://gist.github.com/ptosco/28bc22acbb6d000812c12699b6711be6
Cheers,
p.
On 05/23/18 14:11, Udvarhelyi, Aniko wrote:
Dear Paolo,
thank you very much for your quick reply! So does this mean that
Conformer Objects cannot have properties themselves, i.e. specific to
the conformer itself and independent of the properties of the parent
Mol Object? So there is no way to directly handle conformer properties
by reading/writing to/from SDFs?
I implemented your suggested round-about solution as follows.
# reading in confs as written below, calling AlignMolConformers
àallconfs object stores aligned confs
def copy_coords(source, to):
for i in range(source.GetNumAtoms()):
to.SetAtomPosition(i, source.GetAtomPosition(i))
i = 0
for conf in confs: # looping again over original confs to update
their coordinates from aligned allconfs
suppl = Chem.SDMolSupplier(conf, removeHs = False)
copy_coords(allconfs.GetConformer(i), suppl[0].GetConformer())
wname = conf.split(“.sdf”,1)[0] + “_aligned.sdf”
w = Chem.SDWriter(wname)
w.write(suppl[0])
i += 1
w.close()
Unfortunately it did not work. The original coordinates were kept in
the _aligned.SDF files and were not updated with the coordinates after
alignment. What am I doing wrong here?
I would highly appreciate any hints and help on this!
Many thanks and best regards,
Anikó
*From:*Paolo Tosco [mailto:[email protected]]
*Sent:* Mittwoch, 23. Mai 2018 11:41
*To:* Udvarhelyi, Aniko; Greg Landrum
*Cc:* [email protected]
*Subject:* Re: [Rdkit-discuss] Does AddConformer function lose SDF
properties of conformers when adding them?
Dear Aniko,
properties are associated to the Mol object, not to the Conformer
object. If you wish to retain the original properties associated with
each Mol you may copy the aligned coordinates to the original Mol
object and write that instead. This will allow you to retain the
original properties. Please note that I haven't tried to run my own
sample code below, so please bear with me if it does not quite work as
is, but it was just to give you an idea how to achieve your goal:
def copy_coords(from, to):
for i in range(from.GetNumAtoms()):
to.SetAtomPosition(i, from.GetAtomPosition(i))
w = Chem.SDWriter(“aligned.sdf”)
nconfs = len(allconfs.GetConformers())
i = 0
for conf in confs: # loop over my sdf files
suppl = Chem.SDMolSupplier(conf, removeHs = False)
if “_c0.sdf” in conf:
copy_coords(allconfs.GetConformer(0), suppl[0].GetConformer())
w.write(suppl[0])
else:
for mol in suppl:
i += 1
if (i == nconfs):
raise RuntimeError('Something went wrong, i = nconfs =
{0:d}'.format(nconfs))
copy_coords(allconfs.GetConformer(i), mol.GetConformer())
w.write(mol)
w.close()
HTH, Cheers,
p.
On 05/23/18 09:11, Udvarhelyi, Aniko wrote:
Dear Greg,
I have separate SDF files of conformers of the same molecule (they
are called xxxx_c0.sdf, xxxx_c1.sdf, xxxx_c2.sdf and so on), with
a few properties for each conformer. I am using the following code
to read them into RDKit and align them:
*for conf in confs: # loop over my sdf files*
* suppl = Chem.SDMolSupplier(conf, removeHs = False)*
* if “_c0.sdf” in conf:*
* allconfs = suppl[0]*
* else:*
* for i,mol in enumerate(suppl):*
*allconfs.AddConformer(mol.GetConformer(), assignId = True)*
And then I am using *AllChem.AlignMolConformers(allconfs)*to align
the conformers. It all works fine BUT: when I save the aligned
conformers with the SDWriter, all the conformers have the
properties of the very first conformer. What should I do to keep
the original SDF properties of the conformers from before the
alignment? Does AddConformer lose the properties or is something
wrong with how I write them out? I am using the following to save
the aligned conformers into one sdf:
*w = Chem.SDWriter(“aligned.sdf”)*
*for conf_id in range(len(allconf.GetConformers)):*
*w.write(allconfs, confId=conf_id)*
*w.close()*
What should I do to have all the original SDF properties from the
initial conformers in the aligned.sdf file?
Many thanks and best regards,
Anikó
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