February 2017 at 07:35, Greg Landrum <greg.land...@gmail.com> wrote:
>
>
> On Mon, Feb 20, 2017 at 6:17 PM, Thomas Evangelidis <teva...@gmail.com>
> wrote:
>
>>
>> Thank you for your useful hints. All the compounds that I want to align
>> are supp
, refCid=0,
reflect=True)
AllChem.TransformMol(qmol, bestRMSDTrans[1], confId=bestconfID,
keepConfs=False)
and then I write the qmol in an sdf file. But when I visualize it the qmol
is far from the refmol!
On 20 February 2017 at 02:33, Thomas Evangelidis <teva...@gmail.com> wrote:
>
Greg and Brian,
Thank you for your useful hints. All the compounds that I want to align are
supposed to belong to the same analogue series so they should shave a
common substructure with substantial size.
What I want to emulate is the "core restrained docking" with glide, where
you specify the
st
>>
>> This might not be what you want, but we had good success with similar
>> methods and virtual screening, especially when using multiple co-crystal
>> active sites. I can send you a reference link if this interests you
>>
>> Cheers,
>> Brian
>>
automatic way to find it on the fly
while aligning the 2 molecules.
--
==
Thomas Evangelidis
Research Specialist
CEITEC - Central European Institute of Technology
Masaryk University
Kamenice 5/A35/1S081,
62500 Brno, Czech Republic
OK, I am almost there!
First, I tried the AllChem.ConstrainedEmbed(qmol, core) function to
generate conformers, where core was a mol object created from the MCS with
3D coordinates copied from template's MCS. But is seems that this functions
works only when core is an intact molecule, because I
Hi Greg,
Actually this question is relevant to my recent thread about aligning MCS
of 2 compounds. As also seen in the code I have posted in my last email, I
first generate N conformers of each query compound and then optimize them
using distance restraints in order to superimpose their MCS with
gt; A python implementation of this would be a good topic for Friday's UGM
> hackathon, we can see if anyone finds it interesting enough to work on.
>
> -greg
>
>
> On Tue, Oct 25, 2016 at 2:16 AM, Thomas Evangelidis <teva...@gmail.com>
> wrote:
>
>> H
Greetings everyone,
I use Ubuntu 14.04.4 LTS and first I tried to install RDkit through Conda.
After getting a strange segmentation fault when invoking USRCAT functions
that imported scipy, I managed to fix it by installing accelerate libraries:
conda install accelerate
However, in order to
Thomas
--
==
Thomas Evangelidis
Research Specialist
CEITEC - Central European Institute of Technology
Masaryk University
Kamenice 5/A35/1S081,
62500 Brno, Czech Republic
email: tev...@pharm.uoa.gr
teva...@gmail.com
version of Python and that you PYTHONPATH is not set.
>
> -greg
>
>
> _________
> From: Thomas Evangelidis <teva...@gmail.com>
> Sent: Wednesday, October 19, 2016 8:10 AM
> Subject: [Rdkit-discuss] installation issues
> To: <rdkit-discuss@lists.
--
==
Thomas Evangelidis
Research Specialist
CEITEC - Central European Institute of Technology
Masaryk University
Kamenice 5/A35/1S081,
62500 Brno, Czech Republic
email: tev...@pharm.uoa.gr
teva...@gmail.com
website: https://sites.google.com/site
--
==
Thomas Evangelidis
Research Specialist
CEITEC - Central European Institute of Technology
Masaryk University
Kamenice 5/A35/1S081,
62500 Brno, Czech Republic
email: tev...@pharm.uoa.gr
teva...@gmail.com
website: https
division*
>>
>> *mol1 = Chem.MolFromSmiles('CCO')*
>> *mol2 = Chem.MolFromSmiles('CCC')*
>>
>> *fp1 = np.array(AllChem.GetMorganFingerprintAsBitVect(mol1, 8),
>> dtype='bool')*
>> *fp2 = np.array(AllChem.GetMorganFingerprintAsBitVect(mol2, 8),
>>
gt;
>
> On Tue, Oct 25, 2016 at 2:16 AM, Thomas Evangelidis <teva...@gmail.com>
> wrote:
>
>> Hello everyone,
>>
>> I am a new user of RDkit and I was looking in the documentation for an
>> easy way to load multiple conformers from a structure file like .sdf.
!??)
molnames_list.append(molname)
if get_molnames:
return molname_SMILES_conformersMol_multidict, molnames_list
else:
> return molname_SMILES_conformersMol_multidict
--
==
Dr Thomas Evangelidis
Post-doctoral Research
--
==
Dr Thomas Evangelidis
Post-doctoral Researcher
CEITEC - Central European Institute of Technology
Masaryk University
Kamenice 5/A35/2S049,
62500 Brno, Czech Republic
email: tev...@pharm.uoa.gr
teva...@gmail.com
website: https://sites.google.com/site
ther poor since it was
>> adapted for screening millions of compounds in short time scales.
>>
>> I would appreciate any advice.
>>
>> best,
>> Thomas
>>
>>
>> --
>>
>>
u think that this is the
source of the problem? You can download the structures (also attached) from
this link:
https://www.dropbox.com/s/pp9srlkemweboaf/failed_compounds.sdf.gz?dl=0
thanks in advance
Thomas
--
==========
Dr Thoma
would.
thanks,
Thomas
--
==
Dr Thomas Evangelidis
Post-doctoral Researcher
CEITEC - Central European Institute of Technology
Masaryk University
Kamenice 5/A35/2S049,
62500 Brno, Czech Republic
email: tev...@pharm.uoa.gr
_
> Rdkit-discuss mailing list
> Rdkit-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
--
==
Dr Thomas Evangelidis
R
gt;
>
> On Thu, Oct 4, 2018 at 11:22 AM Thomas Evangelidis
> wrote:
>
>> Dear RDKit community,
>>
>> I need some advice regarding the usage of RDK5 fingerprints for machine
>> learning. I have a big training set (2200 molecules) and a small test set
>> (130
risk
> of bit collisions in folded fingerprints.
>
If you increase the fpSize to 8192, won't you reduce the risk of bit
collisions?
>
> Am 04.10.2018 um 19:56 schrieb Thomas Evangelidis:
> > Hi Nils,
> >
> > In general, yes, but there are still cases where RDK5 gives
samples to go up to bitvector length 8192 without overfitting the networks,
although that will make the training much slower.
On Wed, 10 Oct 2018 at 14:15, Michal Krompiec
wrote:
> Hi Thomas,
> Radius 2, 2048 bits, 5200 data points.
>
> On Wed, 10 Oct 2018 at 13:13, Thomas Evangeli
ar
99 46 96 1
100 47 48 ar
101 47 97 1
102 48 98 1
@SUBSTRUCTURE
1 UNK 1 GROUP 0 0 ROOT
--
==
Dr Thomas Evangelidis
Research Scientist
IOCB - Institute
.
Thanks in advance.
Thomas
--
==
Dr Thomas Evangelidis
Research Scientist
IOCB - Institute of Organic Chemistry and Biochemistry of the Czech Academy
of Sciences <https://www.uochb.cz/web/structure/31.html?lang=en>
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>
>
>
>
>
> ___
> Rdkit-discuss mailing list
> Rdkit-discuss@lists.sourceforge.net
> https:
d isn't the slowest thing I came up with):
>>> def np_to_bv(fv):
>>> bv = DataStructs.ExplicitBitVect(len(fv))
>>> for i,v in enumerate(fv):
>>> if v:
>>> bv.SetBit(i)
>>>return bv
>>>
>>> -greg
>>>
&
ow do I do it?
fv1 = numpy.array([1,1,0,0,1,0,1])
fv2 = numpy.array([0,1,1,0,1,0,0])
Thanks in advance.
Thomas
--
==
Dr. Thomas Evangelidis
Research Scientist
IOCB - Institute of Organic Chemistry and Biochemistry of
ffice to add this extra line in generateAtomInvariant() function?
descriptors.append(a.GetFormalCharge())
I thank you in advance.
Thomas
--
==========
Dr. Thomas Evangelidis
Research Scientist
IOCB - Institute of Organic Chemistry and
ts
>>
>>
>> And then generate the fingerprint like this:
>>
>>
>> fp = AllChem.GetMorganFingerprint(mol, radius=3,
>> invariants=generateAtomInvariant(mol))
>>
>>
>>
--
==
Dr. Thomas Eva
r-defined invariants are much less (795) and the performance of the ML
model is significantly different. Could someone point out what I am doing
wrong?
~Thomas
--
==========
Dr. Thomas Evangelidis
Research Scientist
IOC
Dne po 2. 12. 2019 4:45 PM uživatel Greg Landrum
napsal:
> [Adding the mailing list back on]
>
Oops, sorry about that.
> But if you add partial charges (a floating point number) then essentially
> every atom is going to end up with its own invariant. That's unlikely to
> end well.
>
>
I
acilitate linking or extension. What is wrong in this case and the results
do not agree? Am I not using SubstructLibrary correctly?
I thank you in advance.
Thomas
--
==========
Dr. Thomas Evangelidis
Research Scientist
IOCB -
ld, at the very
> least, generate an error when you try to do this), but it's easy enough to
> fix in your code: just stop specifying the length of the pattern
> fingerprints.
>
> Best,
> -greg
>
>
>
> On Mon, Aug 31, 2020 at 3:57 PM Thomas Evangelidis
> wrote:
>
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