Re: [Rdkit-discuss] Inconsistent sanitization of fragments

2020-02-19 Thread Puck van Gerwen 
Dear Paolo

That clears things up. Thanks very much!

Kind regards
Puck

On Tue, 18 Feb 2020 at 14:05, Paolo Tosco 
wrote:

> Dear Puck,
>
> Here there is some confusion between the concept of implicit/explicit
> hydrogens vs real hydrogen atoms.
>
> In your previous example you were fragmenting an acetone molecule with
> real hydrogen atoms explicitly present in the molecule graph. Therefore,
> after calling FragmentOnBonds() it was appropriate to convert the dummy
> atoms into real hydrogens and leave them as such.
>
> In your latest example you are fragmenting a molecule with no real
> hydrogen atoms, only implicit hydrogens, so after converting the dummy
> atoms into real hydrogens you have a mixture of real and implicit hydrogens.
>
> Please refer to this gist for a (hopefully) cleare explanation:
>
> https://gist.github.com/ptosco/162b52b018dc95709bd43757c0078a28
>
> You may also refer to the following threads on the mailing list:
>
> https://sourceforge.net/p/rdkit/mailman/message/29679834/
> https://sourceforge.net/p/rdkit/mailman/message/36696340/
>
> and to this blog post by Roger Sayle:
>
>
> https://nextmovesoftware.com/blog/2013/02/27/explicit-and-implicit-hydrogens-taking-liberties-with-valence/
>
> for further clarifications on the various kinds of hydrogen in the RDKit.
> Cheers,
> p.
>
> On 18/02/2020 12:18, Puck van Gerwen wrote:
>
> Dear Paolo
>
> Thank you for this illustrative example. I tried the same method on a few
> other molecules and didn't find consistent results. In the notebook
> attached, the first molecule is left with a bivalent carbon, and the second
> molecule is only sanitized after explicitly calling the SanitizeFrags
> option when getting individual fragments. Am I missing something?
>
> Kind regards
> Puck
>
> On Tue, 18 Feb 2020 at 11:17, Paolo Tosco 
> wrote:
>
>> Hi Puck,
>>
>> I modified your previous example to use FragmentOnBonds():
>>
>> from rdkit import Chemfrom rdkit.Chem.Draw import IPythonConsole, 
>> MolsToGridImage
>>
>> smiles = "COC"mol = Chem.MolFromSmiles("COC")mol
>>
>> Here there are no hydrogens (as expected from the SMILES)
>>
>> mol = Chem.AddHs(mol)mol
>>
>> mol_f = Chem.FragmentOnBonds(mol, (2,))
>>
>> mol_f
>>
>> for a in mol_f.GetAtoms():
>> if (a.GetAtomicNum() == 0):
>> # convert the dummy into hydrogen
>> a.SetAtomicNum(1)
>> # if you do not need the labels, you may clear them
>> a.SetIsotope(0)
>>
>> mol_f
>>
>> Cheers,
>> p.
>>
>> On 18/02/2020 09:45, Puck van Gerwen wrote:
>>
>> Dear Paolo
>>
>> Thanks very much for your continuous help. I'm not sure I like the idea
>> of explicitly defining the valence, so I'll consider switching to
>> FragmentOnBonds(). From the example you gave previously though, it quenched
>> the fragments with dummy atoms rather than hydrogen. Is it possible to
>> quench with hydrogen using FragmentOnBonds()?
>>
>> Kind regards
>> Puck
>>
>> On Mon, 17 Feb 2020 at 13:42, Paolo Tosco 
>> wrote:
>>
>>> Hi Puck,
>>>
>>> sorry dor the delay in replying.
>>>
>>> After removing the bond you will need to adjust the number of explicit
>>> Hs on both ends with SetNumExplicitHs(), and then add those Hs in the
>>> molecule graph as real atoms with Chem.AddHs():
>>>
>>> rwmol = Chem.RWMol(mol)
>>> bonds = rwmol.GetBonds()
>>> b = rwmol.GetBondWithIdx(2)
>>> a1 = b.GetBeginAtom()
>>> a2 = b.GetEndAtom()
>>> rwmol.RemoveBond(a1.GetIdx(), a2.GetIdx())
>>> a1.SetNumExplicitHs(a1.GetNumExplicitHs() + 1)
>>> a2.SetNumExplicitHs(a2.GetNumExplicitHs() + 1)
>>> rwmol = Chem.AddHs(rwmol, explicitOnly=True)
>>>
>>> The rdmolops.FragmentOnBonds() functions adjusts the valences for you,
>>> but you will need to adjust them manually if you do the fragmentation at a
>>> lower level with RemoveBond().
>>>
>>> I have attached the modified notebook.
>>>
>>> Cheers,
>>> p.
>>> On 12/02/2020 10:03, Puck van Gerwen wrote:
>>>
>>> Dear all,
>>>
>>> I am trying to read in SMILES to generate mol objects which I then break
>>> into fragments using rwmol.RemoveBond(). Thereafter I want to sanitize the
>>> fragments by saturating with hydrogen. However, I am finding that rdkit
>>> often doesn't sanitize the fragments consistently, leaving trivalent carbon
>>> atoms. I've attached a jupyter notebook of an example. Could anyone help me
>>> consistently generate sanitized fragments?
>>>
>>> Best regards
>>> --
>>> *Puck van Gerwen*
>>> Doktorandin / PhD candidate
>>> Departement Chemie
>>> Klingelbergstrasse 80
>>> CH-4056 Basel
>>> https://chemspacelab.org/
>>>
>>>
>>> ___
>>> Rdkit-discuss mailing 
>>> listRdkit-discuss@lists.sourceforge.nethttps://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>>
>>>
>>
>> --
>> *Puck van Gerwen*
>> Doktorandin / PhD candidate
>> Departement Chemie
>> Klingelbergstrasse 80
>> CH-4056 Basel
>> https://chemspacelab.org/
>>
>>
>
> --
> *Puck van Gerwen*
> Doktorandin / PhD candidate
> Departement Chemie
> Klingelbergstrasse 80
> CH-4056

Re: [Rdkit-discuss] Inconsistent sanitization of fragments

2020-02-18 Thread Paolo Tosco 

Dear Puck,

Here there is some confusion between the concept of implicit/explicit 
hydrogens vs real hydrogen atoms.


In your previous example you were fragmenting an acetone molecule with 
real hydrogen atoms explicitly present in the molecule graph. Therefore, 
after calling FragmentOnBonds() it was appropriate to convert the dummy 
atoms into real hydrogens and leave them as such.


In your latest example you are fragmenting a molecule with no real 
hydrogen atoms, only implicit hydrogens, so after converting the dummy 
atoms into real hydrogens you have a mixture of real and implicit hydrogens.


Please refer to this gist for a (hopefully) cleare explanation:

https://gist.github.com/ptosco/162b52b018dc95709bd43757c0078a28

You may also refer to the following threads on the mailing list:

https://sourceforge.net/p/rdkit/mailman/message/29679834/
https://sourceforge.net/p/rdkit/mailman/message/36696340/

and to this blog post by Roger Sayle:

https://nextmovesoftware.com/blog/2013/02/27/explicit-and-implicit-hydrogens-taking-liberties-with-valence/

for further clarifications on the various kinds of hydrogen in the RDKit.

Cheers,
p.

On 18/02/2020 12:18, Puck van Gerwen wrote:

Dear Paolo

Thank you for this illustrative example. I tried the same method on a 
few other molecules and didn't find consistent results. In the 
notebook attached, the first molecule is left with a bivalent carbon, 
and the second molecule is only sanitized after explicitly calling the 
SanitizeFrags option when getting individual fragments. Am I missing 
something?


Kind regards
Puck

On Tue, 18 Feb 2020 at 11:17, Paolo Tosco > wrote:


Hi Puck,

I modified your previous example to use FragmentOnBonds():

from  rdkit  import  Chem
from  rdkit.Chem.Draw  import  IPythonConsole,  MolsToGridImage

smiles  =  "COC"
mol  =  Chem.MolFromSmiles("COC")
mol

Here there are no hydrogens (as expected from the SMILES)

mol  =  Chem.AddHs(mol)
mol

mol_f  =  Chem.FragmentOnBonds(mol,  (2,))

mol_f

for  a  in  mol_f.GetAtoms():
 if  (a.GetAtomicNum()  ==  0):
 # convert the dummy into hydrogen a.SetAtomicNum(1)
 # if you do not need the labels, you may clear them
 a.SetIsotope(0)

mol_f

Cheers,
p.

On 18/02/2020 09:45, Puck van Gerwen wrote:

Dear Paolo

Thanks very much for your continuous help. I'm not sure I like
the idea of explicitly defining the valence, so I'll consider
switching to FragmentOnBonds(). From the example you gave
previously though, it quenched the fragments with dummy atoms
rather than hydrogen. Is it possible to quench with hydrogen
using FragmentOnBonds()?

Kind regards
Puck

On Mon, 17 Feb 2020 at 13:42, Paolo Tosco
mailto:paolo.tosco.m...@gmail.com>>
wrote:

Hi Puck,

sorry dor the delay in replying.

After removing the bond you will need to adjust the number of
explicit Hs on both ends with SetNumExplicitHs(), and then
add those Hs in the molecule graph as real atoms with
Chem.AddHs():

rwmol = Chem.RWMol(mol)
bonds = rwmol.GetBonds()
b = rwmol.GetBondWithIdx(2)
a1 = b.GetBeginAtom()
a2 = b.GetEndAtom()
rwmol.RemoveBond(a1.GetIdx(), a2.GetIdx())
a1.SetNumExplicitHs(a1.GetNumExplicitHs() + 1)
a2.SetNumExplicitHs(a2.GetNumExplicitHs() + 1)
rwmol = Chem.AddHs(rwmol, explicitOnly=True)

The rdmolops.FragmentOnBonds() functions adjusts the valences
for you, but you will need to adjust them manually if you do
the fragmentation at a lower level with RemoveBond().

I have attached the modified notebook.

Cheers,
p.

On 12/02/2020 10:03, Puck van Gerwen wrote:

Dear all,

I am trying to read in SMILES to generate mol objects which
I then break into fragments using rwmol.RemoveBond().
Thereafter I want to sanitize the fragments by saturating
with hydrogen. However, I am finding that rdkit often
doesn't sanitize the fragments consistently, leaving
trivalent carbon atoms. I've attached a jupyter notebook of
an example. Could anyone help me consistently generate
sanitized fragments?

Best regards
-- 
*Puck van Gerwen*

Doktorandin / PhD candidate
Departement Chemie
Klingelbergstrasse 80
CH-4056 Basel
https://chemspacelab.org/


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-- 
*Puck van Gerwen*

Doktorandin / PhD candidate
Departement Chemie
Klingelbergstrasse 80
CH-4056 Basel
https://chemspace

Re: [Rdkit-discuss] Inconsistent sanitization of fragments

2020-02-18 Thread Puck van Gerwen 
Dear Paolo

Thank you for this illustrative example. I tried the same method on a few
other molecules and didn't find consistent results. In the notebook
attached, the first molecule is left with a bivalent carbon, and the second
molecule is only sanitized after explicitly calling the SanitizeFrags
option when getting individual fragments. Am I missing something?

Kind regards
Puck

On Tue, 18 Feb 2020 at 11:17, Paolo Tosco 
wrote:

> Hi Puck,
>
> I modified your previous example to use FragmentOnBonds():
>
> from rdkit import Chemfrom rdkit.Chem.Draw import IPythonConsole, 
> MolsToGridImage
>
> smiles = "COC"mol = Chem.MolFromSmiles("COC")mol
>
> Here there are no hydrogens (as expected from the SMILES)
>
> mol = Chem.AddHs(mol)mol
>
> mol_f = Chem.FragmentOnBonds(mol, (2,))
>
> mol_f
>
> for a in mol_f.GetAtoms():
> if (a.GetAtomicNum() == 0):
> # convert the dummy into hydrogen
> a.SetAtomicNum(1)
> # if you do not need the labels, you may clear them
> a.SetIsotope(0)
>
> mol_f
>
> Cheers,
> p.
>
> On 18/02/2020 09:45, Puck van Gerwen wrote:
>
> Dear Paolo
>
> Thanks very much for your continuous help. I'm not sure I like the idea of
> explicitly defining the valence, so I'll consider switching to
> FragmentOnBonds(). From the example you gave previously though, it quenched
> the fragments with dummy atoms rather than hydrogen. Is it possible to
> quench with hydrogen using FragmentOnBonds()?
>
> Kind regards
> Puck
>
> On Mon, 17 Feb 2020 at 13:42, Paolo Tosco 
> wrote:
>
>> Hi Puck,
>>
>> sorry dor the delay in replying.
>>
>> After removing the bond you will need to adjust the number of explicit Hs
>> on both ends with SetNumExplicitHs(), and then add those Hs in the
>> molecule graph as real atoms with Chem.AddHs():
>>
>> rwmol = Chem.RWMol(mol)
>> bonds = rwmol.GetBonds()
>> b = rwmol.GetBondWithIdx(2)
>> a1 = b.GetBeginAtom()
>> a2 = b.GetEndAtom()
>> rwmol.RemoveBond(a1.GetIdx(), a2.GetIdx())
>> a1.SetNumExplicitHs(a1.GetNumExplicitHs() + 1)
>> a2.SetNumExplicitHs(a2.GetNumExplicitHs() + 1)
>> rwmol = Chem.AddHs(rwmol, explicitOnly=True)
>>
>> The rdmolops.FragmentOnBonds() functions adjusts the valences for you,
>> but you will need to adjust them manually if you do the fragmentation at a
>> lower level with RemoveBond().
>>
>> I have attached the modified notebook.
>>
>> Cheers,
>> p.
>> On 12/02/2020 10:03, Puck van Gerwen wrote:
>>
>> Dear all,
>>
>> I am trying to read in SMILES to generate mol objects which I then break
>> into fragments using rwmol.RemoveBond(). Thereafter I want to sanitize the
>> fragments by saturating with hydrogen. However, I am finding that rdkit
>> often doesn't sanitize the fragments consistently, leaving trivalent carbon
>> atoms. I've attached a jupyter notebook of an example. Could anyone help me
>> consistently generate sanitized fragments?
>>
>> Best regards
>> --
>> *Puck van Gerwen*
>> Doktorandin / PhD candidate
>> Departement Chemie
>> Klingelbergstrasse 80
>> CH-4056 Basel
>> https://chemspacelab.org/
>>
>>
>> ___
>> Rdkit-discuss mailing 
>> listRdkit-discuss@lists.sourceforge.nethttps://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>
>>
>
> --
> *Puck van Gerwen*
> Doktorandin / PhD candidate
> Departement Chemie
> Klingelbergstrasse 80
> CH-4056 Basel
> https://chemspacelab.org/
>
>

-- 
*Puck van Gerwen*
Doktorandin / PhD candidate
Departement Chemie
Klingelbergstrasse 80
CH-4056 Basel
https://chemspacelab.org/


TestFragmentation.ipynb
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Re: [Rdkit-discuss] Inconsistent sanitization of fragments

2020-02-18 Thread Paolo Tosco 

Hi Puck,

I modified your previous example to use FragmentOnBonds():

from  rdkit  import  Chem
from  rdkit.Chem.Draw  import  IPythonConsole,  MolsToGridImage

smiles  =  "COC"
mol  =  Chem.MolFromSmiles("COC")
mol

Here there are no hydrogens (as expected from the SMILES)

mol  =  Chem.AddHs(mol)
mol

mol_f  =  Chem.FragmentOnBonds(mol,  (2,))

mol_f

for  a  in  mol_f.GetAtoms():
if  (a.GetAtomicNum()  ==  0):
# convert the dummy into hydrogen a.SetAtomicNum(1)
# if you do not need the labels, you may clear them
a.SetIsotope(0)

mol_f

Cheers,
p.

On 18/02/2020 09:45, Puck van Gerwen wrote:

Dear Paolo

Thanks very much for your continuous help. I'm not sure I like the 
idea of explicitly defining the valence, so I'll consider switching to 
FragmentOnBonds(). From the example you gave previously though, it 
quenched the fragments with dummy atoms rather than hydrogen. Is it 
possible to quench with hydrogen using FragmentOnBonds()?


Kind regards
Puck

On Mon, 17 Feb 2020 at 13:42, Paolo Tosco > wrote:


Hi Puck,

sorry dor the delay in replying.

After removing the bond you will need to adjust the number of
explicit Hs on both ends with SetNumExplicitHs(), and then add
those Hs in the molecule graph as real atoms with Chem.AddHs():

rwmol = Chem.RWMol(mol)
bonds = rwmol.GetBonds()
b = rwmol.GetBondWithIdx(2)
a1 = b.GetBeginAtom()
a2 = b.GetEndAtom()
rwmol.RemoveBond(a1.GetIdx(), a2.GetIdx())
a1.SetNumExplicitHs(a1.GetNumExplicitHs() + 1)
a2.SetNumExplicitHs(a2.GetNumExplicitHs() + 1)
rwmol = Chem.AddHs(rwmol, explicitOnly=True)

The rdmolops.FragmentOnBonds() functions adjusts the valences for
you, but you will need to adjust them manually if you do the
fragmentation at a lower level with RemoveBond().

I have attached the modified notebook.

Cheers,
p.

On 12/02/2020 10:03, Puck van Gerwen wrote:

Dear all,

I am trying to read in SMILES to generate mol objects which I
then break into fragments using rwmol.RemoveBond(). Thereafter I
want to sanitize the fragments by saturating with hydrogen.
However, I am finding that rdkit often doesn't sanitize the
fragments consistently, leaving trivalent carbon atoms. I've
attached a jupyter notebook of an example. Could anyone help me
consistently generate sanitized fragments?

Best regards
-- 
*Puck van Gerwen*

Doktorandin / PhD candidate
Departement Chemie
Klingelbergstrasse 80
CH-4056 Basel
https://chemspacelab.org/


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--
*Puck van Gerwen*
Doktorandin / PhD candidate
Departement Chemie
Klingelbergstrasse 80
CH-4056 Basel
https://chemspacelab.org/
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Re: [Rdkit-discuss] Inconsistent sanitization of fragments

2020-02-18 Thread Puck van Gerwen 
Dear Paolo

Thanks very much for your continuous help. I'm not sure I like the idea of
explicitly defining the valence, so I'll consider switching to
FragmentOnBonds(). From the example you gave previously though, it quenched
the fragments with dummy atoms rather than hydrogen. Is it possible to
quench with hydrogen using FragmentOnBonds()?

Kind regards
Puck

On Mon, 17 Feb 2020 at 13:42, Paolo Tosco 
wrote:

> Hi Puck,
>
> sorry dor the delay in replying.
>
> After removing the bond you will need to adjust the number of explicit Hs
> on both ends with SetNumExplicitHs(), and then add those Hs in the
> molecule graph as real atoms with Chem.AddHs():
>
> rwmol = Chem.RWMol(mol)
> bonds = rwmol.GetBonds()
> b = rwmol.GetBondWithIdx(2)
> a1 = b.GetBeginAtom()
> a2 = b.GetEndAtom()
> rwmol.RemoveBond(a1.GetIdx(), a2.GetIdx())
> a1.SetNumExplicitHs(a1.GetNumExplicitHs() + 1)
> a2.SetNumExplicitHs(a2.GetNumExplicitHs() + 1)
> rwmol = Chem.AddHs(rwmol, explicitOnly=True)
>
> The rdmolops.FragmentOnBonds() functions adjusts the valences for you,
> but you will need to adjust them manually if you do the fragmentation at a
> lower level with RemoveBond().
>
> I have attached the modified notebook.
>
> Cheers,
> p.
> On 12/02/2020 10:03, Puck van Gerwen wrote:
>
> Dear all,
>
> I am trying to read in SMILES to generate mol objects which I then break
> into fragments using rwmol.RemoveBond(). Thereafter I want to sanitize the
> fragments by saturating with hydrogen. However, I am finding that rdkit
> often doesn't sanitize the fragments consistently, leaving trivalent carbon
> atoms. I've attached a jupyter notebook of an example. Could anyone help me
> consistently generate sanitized fragments?
>
> Best regards
> --
> *Puck van Gerwen*
> Doktorandin / PhD candidate
> Departement Chemie
> Klingelbergstrasse 80
> CH-4056 Basel
> https://chemspacelab.org/
>
>
> ___
> Rdkit-discuss mailing 
> listRdkit-discuss@lists.sourceforge.nethttps://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
>

-- 
*Puck van Gerwen*
Doktorandin / PhD candidate
Departement Chemie
Klingelbergstrasse 80
CH-4056 Basel
https://chemspacelab.org/
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Re: [Rdkit-discuss] Inconsistent sanitization of fragments

2020-02-17 Thread Paolo Tosco 

Hi Puck,

sorry dor the delay in replying.

After removing the bond you will need to adjust the number of explicit 
Hs on both ends with SetNumExplicitHs(), and then add those Hs in the 
molecule graph as real atoms with Chem.AddHs():


rwmol = Chem.RWMol(mol)
bonds = rwmol.GetBonds()
b = rwmol.GetBondWithIdx(2)
a1 = b.GetBeginAtom()
a2 = b.GetEndAtom()
rwmol.RemoveBond(a1.GetIdx(), a2.GetIdx())
a1.SetNumExplicitHs(a1.GetNumExplicitHs() + 1)
a2.SetNumExplicitHs(a2.GetNumExplicitHs() + 1)
rwmol = Chem.AddHs(rwmol, explicitOnly=True)

The rdmolops.FragmentOnBonds() functions adjusts the valences for you, 
but you will need to adjust them manually if you do the fragmentation at 
a lower level with RemoveBond().


I have attached the modified notebook.

Cheers,
p.

On 12/02/2020 10:03, Puck van Gerwen wrote:

Dear all,

I am trying to read in SMILES to generate mol objects which I then 
break into fragments using rwmol.RemoveBond(). Thereafter I want to 
sanitize the fragments by saturating with hydrogen. However, I am 
finding that rdkit often doesn't sanitize the fragments consistently, 
leaving trivalent carbon atoms. I've attached a jupyter notebook of an 
example. Could anyone help me consistently generate sanitized fragments?


Best regards
--
*Puck van Gerwen*
Doktorandin / PhD candidate
Departement Chemie
Klingelbergstrasse 80
CH-4056 Basel
https://chemspacelab.org/


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Re: [Rdkit-discuss] Inconsistent sanitization of fragments

2020-02-12 Thread Paolo Tosco 

Dear Puck,

Sure; I'll get back to you later today.

Cheers,
p.

On 12/02/2020 10:03, Puck van Gerwen wrote:

Dear all,

I am trying to read in SMILES to generate mol objects which I then 
break into fragments using rwmol.RemoveBond(). Thereafter I want to 
sanitize the fragments by saturating with hydrogen. However, I am 
finding that rdkit often doesn't sanitize the fragments consistently, 
leaving trivalent carbon atoms. I've attached a jupyter notebook of an 
example. Could anyone help me consistently generate sanitized fragments?


Best regards
--
*Puck van Gerwen*
Doktorandin / PhD candidate
Departement Chemie
Klingelbergstrasse 80
CH-4056 Basel
https://chemspacelab.org/


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[Rdkit-discuss] Inconsistent sanitization of fragments

2020-02-12 Thread Puck van Gerwen 
Dear all,

I am trying to read in SMILES to generate mol objects which I then break
into fragments using rwmol.RemoveBond(). Thereafter I want to sanitize the
fragments by saturating with hydrogen. However, I am finding that rdkit
often doesn't sanitize the fragments consistently, leaving trivalent carbon
atoms. I've attached a jupyter notebook of an example. Could anyone help me
consistently generate sanitized fragments?

Best regards
-- 
*Puck van Gerwen*
Doktorandin / PhD candidate
Departement Chemie
Klingelbergstrasse 80
CH-4056 Basel
https://chemspacelab.org/


NotSanitizing.ipynb
Description: Binary data
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