Re: [Rdkit-discuss] Does AddConformer function lose SDF properties of conformers when adding them?
Dear Paolo,
thank you very much! Now it is working as I hoped it would.
My error was that I was using suppl[0] when writing out, instead of defining a
new variable mol=suppl[0] and doing the copy_coords with that mol variable, as
you did.
Many thanks for your help!
best regards,
Anikó
From: Paolo Tosco [mailto:paolo.tosco.m...@gmail.com]
Sent: Mittwoch, 23. Mai 2018 17:02
To: Udvarhelyi, Aniko; Greg Landrum
Cc: rdkit-discuss@lists.sourceforge.net
Subject: Re: [Rdkit-discuss] Does AddConformer function lose SDF properties of
conformers when adding them?
Dear Aniko,
Here is a Jupyter notebook that does what you need:
https://gist.github.com/ptosco/28bc22acbb6d000812c12699b6711be6<https://urldefense.proofpoint.com/v2/url?u=https-3A__gist.github.com_ptosco_28bc22acbb6d000812c12699b6711be6=DwMDaQ=ZbgFmJjg4pdtrnL2HUJUDw=ANfhdkzkLaTzqQrdJ1uJyFwAJDWEMRAEFydqudcLj6o=PhG51Rc_bwPvECLKpbXXAAxoebXonCKrECV8ji1HgXM=TK6CbooNsGVu47UfabACw_De2-gBATimkGqC_xdKeD0=>
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 --> 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:paolo.tosco.m...@gmail.com]
Sent: Mittwoch, 23. Mai 2018 11:41
To: Udvarhelyi, Aniko; Greg Landrum
Cc:
rdkit-discuss@lists.sourceforge.net<mailto:rdkit-discuss@lists.sourceforge.net>
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
_c0.sdf, _c1.sdf, _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
Re: [Rdkit-discuss] Does AddConformer function lose SDF properties of conformers when adding them?
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:paolo.tosco.m...@gmail.com]
*Sent:* Mittwoch, 23. Mai 2018 11:41
*To:* Udvarhelyi, Aniko; Greg Landrum
*Cc:* rdkit-discuss@lists.sourceforge.net
*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 _c0.sdf, _c1.sdf, _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
--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org!http://sdm.link/slashdot
<https://urldefense.proofpoint.com/v2/url?u=http-3A__sdm.link_slashdot=DwMDaQ=ZbgFmJjg4pdtrnL2HUJUDw=ANfhdkzkLaTzqQrdJ1uJyFwAJDWEMRAEFydqudcLj6o=CZ6lBy8QxadPv6cUeoQ6ww4N4oaJ_g7z52waY421iNc=1NSYUS7IRMb60DuSVz4HNeUeGacas8a4g-iByKmIpvM=>
___
Rdkit-discuss mailing list
Rdkit-d
Re: [Rdkit-discuss] Does AddConformer function lose SDF properties of conformers when adding them?
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:paolo.tosco.m...@gmail.com]
Sent: Mittwoch, 23. Mai 2018 11:41
To: Udvarhelyi, Aniko; Greg Landrum
Cc: rdkit-discuss@lists.sourceforge.net
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
_c0.sdf, _c1.sdf, _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
--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org!
http://sdm.link/slashdot<https://urldefense.proofpoint.com/v2/url?u=http-3A__sdm.link_slashdot=DwMDaQ=ZbgFmJjg4pdtrnL2HUJUDw=ANfhdkzkLaTzqQrdJ1uJyFwAJDWEMRAEFydqudcLj6o=CZ6lBy8QxadPv6cUeoQ6ww4N4oaJ_g7z52waY421iNc=1NSYUS7IRMb60DuSVz4HNeUeGacas8a4g-iByKmIpvM=>
___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net<mailto:Rdkit-discuss@lists.sourceforge.net>
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss<https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.sourceforge.net_lists_listinfo_rdkit-2Ddiscuss=DwMDaQ=ZbgFmJjg4pdtrnL2HUJUDw=ANfhdkzkLaTzqQrdJ1uJyFwAJDWEMRAEFydqudcLj6o=CZ6lBy8QxadPv6cUeoQ6ww4N4
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 _c0.sdf, _c1.sdf, _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
--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] Does AddConformer function lose SDF properties of conformers when adding them?
Dear Greg, I have separate SDF files of conformers of the same molecule (they are called _c0.sdf, _c1.sdf, _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 -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
