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 --> allconfs
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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