:
Pavel,
this is a bit hacky, but you can try the below:
```
def get_frag_smi(mol,frag_atoms):
if len(frag_atoms) > 1:
b2b = [] # bonds to break
fsmi = "" #fragment smiles
# get bonds outside of fragment
for b in mol.GetBonds():
b_idx = b.Ge
Kind regards,
Pavel
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solve real chemoinformatic tasks and
win prizes.
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Please feel free to share this information with those who can be
interested in participation in such event. Thank you!
Kind regards,
Pavel
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suitable for your needs.
Kind regards,
Pavel.
On 30/03/2022 18:16, Enrico Martinez wrote:
Dear RDKIT users!
I am dealing with the analysis of the results of the docking poses
calculated via VINA and saved into the multi-model pdb. I need to find
a possibility to compare each docking pose
Hi Chris,
Error reported a bin (0,2,0) which does not satisfy the triangle rule. I
cannot check it, but I suppose that the error may disappear if you set
trianglePruneBins=False in SigFactory, but this would be a workaround
not a proper solution I think.
Pavel.
On 12/08/2021 10:25, Chris
Hi Ling,
this can be a workaround if RDKit does not have a built-in function
to extract a submolecule by atom ids. You may assign atom property
labels to these atoms and then looping over atoms in EditableMol remove
those ones which do not have this property assigned.
Kind regards,
Pavel
0.057937898735270194
read template mol file, AddHs
Could not embed molecule. # <-- here rdkit spends a lot of time but
fails
embed template mol in rdkit, no AddHs
0.1012757033705761
Pavel.
On 07/07/2020 21:41, Sunhwan Jo wrote:
Makes sense :)
On Jul 7, 2020, at 12:35 PM, Sereina Ri
sue is caused by some implicit properties of a molecule? How to solve
this properly?
Kind regards,
Pavel.
1.mol
Description: MOL mdl chemical test
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leConfs(mol, 50, Chem.rdDistGeom.ETKDGv2())
mol.GetConformers()
Kind regards,
Pavel.
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Sorry for the mistake, the dates are 3-7 of *February* 2020.
Pavel.
On 20/11/2019 09:39, Pavel Polishchuk wrote:
Dear colleagues,
we would like to invite you on the 5th Drug Design workshop which
will be held 3-7 January 2020 in Olomouc (Czech Republic). It is
focused on practical
,
Pavel.
--
Dr. Pavel Polishchuk
senior researcher
Institute of Molecular and Translational Medicine
Faculty of Medicine and Dentistry
Palacky University
Hněvotínská 1333/5
779 00 Olomouc
Czech Republic
+420 585632298
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Thank you, Paolo!
That was not obvious for me how RDKit manage hydrogens in this case.
Pavel.
On 22/03/2019 12:15, Paolo Tosco wrote:
Hi Pavel,
After you have first called AddHs(), all hydrogens in your molecule
are now in the molecule graph as real atoms, and there are no more
implicit
][cH][cH][cH]1
add Hs
[H][O][c]1[c]([H])[c]([H])[c]([H])[c]([H])[c]1[H]
remove H
[H][O][c]1[c][c]([H])[c]([H])[c]([H])[c]1[H]
add Hs
[H][O][c]1[c][c]([H])[c]([H])[c]([H])[c]1[H]
update property cache
[H][O][c]1[c][c]([H])[c]([H])[c]([H])[c]1[H]
Pavel.
_
Hi Pawan,
I can suggest to use our developed module for 3D pharmacophore
representation: https://github.com/DrrDom/pmapper
I added an example to answer your particular question:
https://github.com/DrrDom/pmapper/blob/master/examples/screen_example.ipynb
Hope this will help,
Pavel
tasks and win prizes.
http://fch.upol.cz/en/research/conferences-workshops/4add/
Please feel free to share this information to those who can be
interested in participation in such event. Thank you.
Kind regards,
Pavel.
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senior researcher
Institute of Molecular and
Hi Michal,
I think if you can provide several examples of structures having
identical bitstrings this will help a lot to better understand the issue.
Pavel.
On 10/10/18 14:15, Michal Krompiec wrote:
Hi Thomas,
Radius 2, 2048 bits, 5200 data points.
On Wed, 10 Oct 2018 at 13:13, Thomas
Hello,
I'm curious, would it be possible to use regression models for
similarity maps drawing or only classification ones?
If someone has a piece of code, I would appreciate this. Because I
tried to modify the example given in the cookbook, but without success.
= Chem.MolFromSmiles('F[C@@H](Cl)Br')
m = Chem.AddHs(m)
AllChem.EmbedMolecule(m)
AllChem.MMFFOptimizeMolecule(m, confId=0)
Descriptors3D.PMI1(m, 0)
Pavel.
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participation in such event. Thank you.
Kind regards,
Pavel.
3rd Advanced in silico Drug Design workshop/hackathon 2018
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senior researcher
Institute of Molecular and Translational Medicine
Faculty of Medicine and Dentistry
Palacky University
Hněvotínská 1333/5
779 00 Olomouc
, 1, Chem.rdchem.BondType.SINGLE)
m.AddBond(1, 2, Chem.rdchem.BondType.SINGLE)
m.AddBond(1, 3, Chem.rdchem.BondType.SINGLE)
s = Chem.MolToSmiles(m, isomericSmiles=True)
re.sub('\[[0-9]+([a-z]+)H?[0-9]?\]', '\\1', s) # remove isotope in
output SMILES
OUTPUT: 'CC(c)[*
atom 2 as aromatic
m2.GetAtomWithIdx(3).SetAtomMapNum(1)
m2.AddBond(0, 1, Chem.rdchem.BondType.SINGLE)
m2.AddBond(1, 2, Chem.rdchem.BondType.SINGLE)
m2.AddBond(1, 3, Chem.rdchem.BondType.SINGLE)
Chem.MolToSmiles(m2)
OUTPUT: 'CC(c
I had some issues to run rdkit from Python console in PyCharm (4.5.5) on
Linux. After recent installation of PyCharm 2017.1.3 it started to work.
Maybe updating PyCharm will help on Win as well.
Pavel.
On 05/30/2017 10:10 PM, West, Richard wrote:
We're having trouble getting RDKit to
[H]c1c([H])c([H])c(C([H])([H])[*:1])c([H])c1[H] c1ccc(C[*:1])cc1
[H][*:1] [*:1]
If this is a bug I can create an issue on github
Pavel.
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unReactants((mol,))
print(Chem.MolToSmiles(ps[0][0]))
print(Chem.MolToSmiles(ps[0][1]))
for a in ps[0][0].GetAtoms():
if a.GetAtomicNum() == 16 and a.GetFormalCharge() == 1:
a.SetNoImplicit(True)
print(Chem.MolToSmiles(ps[0][0]))
print(Chem.MolToSmiles(ps[0][1]))
Pavel.
On 05/28/2017 08:2
smiles it would be easy to
relabel attachment points back.
Thank you again!
Pavel.
On 05/27/2017 03:03 PM, Brian Kelley wrote:
Pavel, this isn't exactly trivial so I went ahead and made an
example. The basics are that atomMaps are canonicalized, i.e. their
value is used in the generati
les(Chem.MolFromSmiles(s)))
output:
S=c1c([*:1])c(Cl)[nH]c([*:3])c1[*:2]
S=c1c([*:1])c(Cl)[nH]c([*:2])c1[*:3]
S=c1c([*:1])c([*:3])[nH]c(Cl)c1[*:2]
S=c1c([*:2])c(Cl)[nH]c([*:1])c1[*:3]
S=c1c([*:1])c([*:2])[nH]c(Cl)c1[*:3]
S=c1c([*:2])c([*:1])[nH]c(Cl)c1[*:3]
Kind regards,
Pavel.
-
indices speed up similarity search or what is a reason to add them?
Pavel.
On 04/26/2017 02:36 PM, Greg Landrum wrote:
Hi Pavel,
On Wed, Apr 26, 2017 at 8:41 AM, Pavel Polishchuk
mailto:pavel_polishc...@ukr.net>> wrote:
Hello,
is it possible to store custom fingerprints i
5)cc23)cs1')
fp = Generate.Gen2DFingerprint(mol, sigFactory)
Pavel.
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(0, 1, 2), (0, 2, 1), (0, 2, 2), (1, 0, 0), (1, 0, 1), (1, 0, 2), (1, 1,
0), (1, 1, 1), (1, 1, 2), (1, 2, 0), (1, 2, 1), (1, 2, 2), (2, 0, 1),
(2, 0, 2), (2, 1, 0), (2, 1, 1), (2, 1, 2), (2, 2, 0), (2, 2, 1), (2, 2,
2)], 0]
Kind regards,
Pavel.
Hi Maxim,
if you change your query to SMARTS it would be possible to delete
what you want
m=Chem.MolFromSmiles('C1(C2=NC=CC=C2)=CC=CC(C)=C1')
ss = Chem.MolFromSmarts('c1c1C')
frag = AllChem.DeleteSubstructs(m, ss)
print(Chem.MolToSmiles(frag))
Pavel.
On
2]
CC[*].CC[*].cn([*])c.CN([*])C
[0, 0, 3, 2]
Kind regards,
Pavel.
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Thank you!
That was a bug in my expectations. :)
BTW, as I see from test examples for the 0 atom in CC1CC1 an environment
with radius 3 exists. Thus, radius should be interpreted as a number of
bonds from the rooted atom, not a number of atoms. I did not expect this
as well.
Pavel.
On 03
ation?
Pavel.
On 03/27/2017 03:53 PM, Peter Gedeck wrote:
Hello,
The atom numbers start with 0. From the middle atom, there are no
environments with radius 2. You will get a result if you use the first
(=0) or the last (=2) atom. Try this:
m = Chem.MolFromSmiles(&qu
1)
Chem.MolToSmiles(Chem.PathToSubmol(m, i))
returns ""
In the latter case I expected the same output "NCO". Were my
expectations mistaken?
Kind regards,
Pavel.
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reasonable to revise SMARTS to avoid
such overlapping or create a list of rules (maybe hierarchical) which
will define valid and not valid overlappings.
Pavel.
On 03/08/2017 06:32 PM, Chenyang Shi wrote:
Dear Hongbin,
I tried your method on a molecule, 4-Methylsalicylic acid
(CC1=CC(=C(C=C1)C
Hi Jacob,
you need to call AssignStereochemistry with force=True parameter
Chem.AssignStereochemistry(mol, force=True)
Pavel.
On 01/28/2017 05:43 AM, Jacob Durrant wrote:
I'm trying to set the configuration of a molecule with a double bond,
but it doesn't seem to be working.
Thank you, that helped!
I noticed that I need to substantially increase the height of the image
to make the second line visible. If I'll want to draw more lined I
should increase the height further.
Pavel.
On 12/20/2016 03:14 PM, Peter Gedeck wrote:
Hello,
I thought we had removed a
it returns the picture with
labels, but with spaces instead of new line symbols.
What can I do in this situation? RDKit 2016.03.2
Kind regards,
Pavel.
---
AttributeError Traceback (most recen
r own risk :)
If you will find mistakes let me know.
Pavel.
On 12/10/2016 03:44 AM, Brian Cole wrote:
So I may need a little guidance on this one from someone with a little
more historical knowledge of RDKit.
I found the findPotentialStereoBonds function inside Chirality.cpp
that appears to do wh
ative ones.
Alternatively you may use more general SMARTS pattern to produce many
possible sets of fragments and then select that set which is optimal for
your task, e.g. fragment set having the longest alkyl chain(s) or the
lowest number of fragments, etc.
Kind regards,
Pavel
On 12/08/2016
.
Pavel.
On 12/02/2016 11:11 AM, Greg Landrum wrote:
An initial start on some regexps that match SMILES is here:
https://gist.github.com/lsauer/1312860/264ae813c2bd2c27a769d261c8c6b38da34e22fb
that may also be useful
On Fri, Dec 2, 2016 at 11:07 AM, Alexis Parenty
mailto:alexis.parenty.h
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