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Amit Kumar Mishra
11/14/23
Is there an example or thorough demonstration of oddt usage?
I am particularly interested in PLECscore. Documentations mention methods but don't consist of
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Is there an example or thorough demonstration of oddt usage?
I am particularly interested in PLECscore. Documentations mention methods but don't consist of
11/14/23
Priyanshu Sharma
,
Maciek Wójcikowski
2
3/10/23
oddt regarding problem
Hi Priuanshu, Could you please provide more details on the error? A full Tracestack would be ideal. -
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oddt regarding problem
Hi Priuanshu, Could you please provide more details on the error? A full Tracestack would be ideal. -
3/10/23
iwonaa.go...@gmail.com
, …
Bruna Katiele de Paula Sousa
7
11/30/20
Constant openbabel/pybel problem during installation
Many thanks Maciek! I tried at ubuntu and worked hehe Thanks in advance! Em segunda-feira, 30 de
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Constant openbabel/pybel problem during installation
Many thanks Maciek! I tried at ubuntu and worked hehe Thanks in advance! Em segunda-feira, 30 de
11/30/20
Scott Bembenek
,
Maciek Wójcikowski
2
11/12/20
electroshape is not printing the similarity score
Hi Scott, Unfortunately printing of the similarities was never a feature, since the CLI was intended
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electroshape is not printing the similarity score
Hi Scott, Unfortunately printing of the similarities was never a feature, since the CLI was intended
11/12/20
Tim Dudgeon
,
Maciek Wójcikowski
9
10/22/20
H-bond interaction questions
We already have the Molecule.protein property so that proteins get residues parsed, so what you
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H-bond interaction questions
We already have the Molecule.protein property so that proteins get residues parsed, so what you
10/22/20
Tim Dudgeon
,
Maciek Wójcikowski
5
9/25/20
Scoring ligands
PLEC Score alias is "plec" plus its variant, so pleclinear, plecrf and plecnn. All of the
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Scoring ligands
PLEC Score alias is "plec" plus its variant, so pleclinear, plecrf and plecnn. All of the
9/25/20
Tim Dudgeon
,
Maciek Wójcikowski
3
9/22/20
Adding hydrogens to protein changes the value of the strict property for h-bond interactions
Hi Maciek, Yes, using the latest doesn't show that problem Thanks! Tim On Mon, 21 Sep 2020 at 19:
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Adding hydrogens to protein changes the value of the strict property for h-bond interactions
Hi Maciek, Yes, using the latest doesn't show that problem Thanks! Tim On Mon, 21 Sep 2020 at 19:
9/22/20
Daviti Kharchilava
, …
Daviti Kharchilava
3
8/13/20
Trying to run oddt on win 10
Hello, Thank you so much for your attention ! I could actually resolve all the issues in Linux
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Trying to run oddt on win 10
Hello, Thank you so much for your attention ! I could actually resolve all the issues in Linux
8/13/20
Justine Camilla Williams
,
Maciek Wójcikowski
2
4/1/20
similarity_SPLIF Question
Dear Justine, SPLIF is non-standard fingerprint, as FP usually are invariant to 3d orientation. In
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similarity_SPLIF Question
Dear Justine, SPLIF is non-standard fingerprint, as FP usually are invariant to 3d orientation. In
4/1/20
Justine Camilla Williams
,
Maciek Wójcikowski
3
3/16/20
Fingerprint SPLIF Issue
I've googled a bit and it might be Windows/python/numpy issue. Could you try replacing in
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Fingerprint SPLIF Issue
I've googled a bit and it might be Windows/python/numpy issue. Could you try replacing in
3/16/20
Shirin Jamshidi
,
Maciek Wójcikowski
2
2/7/20
Run an oddt job in anaconda
Hi Shirin, What you want to do is to score the ligands not just train the scoring function, as
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Run an oddt job in anaconda
Hi Shirin, What you want to do is to score the ligands not just train the scoring function, as
2/7/20
hell...@gmail.com
9/5/19
Visualize/Compare PLECs
Hi, I'd like to compare PLECs for a given molecule docked into different proteins, in order to
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Visualize/Compare PLECs
Hi, I'd like to compare PLECs for a given molecule docked into different proteins, in order to
9/5/19
mate...@gmail.com
,
Maciek Wójcikowski
2
8/16/19
Treatment of Affinity Measurements in Original PLEC Paper
Hi, No additional processing was done on the target values in the PLEC paper. I also have not
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Treatment of Affinity Measurements in Original PLEC Paper
Hi, No additional processing was done on the target values in the PLEC paper. I also have not
8/16/19
Maciek Wójcikowski
7/6/19
Re: Explicit Valence Error when Calculating PLEC
Hi, In general it is really bad idea to skip the sanitization, as RDKit PDB parser is picky. Which
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Re: Explicit Valence Error when Calculating PLEC
Hi, In general it is really bad idea to skip the sanitization, as RDKit PDB parser is picky. Which
7/6/19
mate...@gmail.com
,
Maciek Wójcikowski
3
7/4/19
Possibility of bias with PLECs in DUD-E
Thank you. I will go ahead with rotating the ligands to non-ideal poses and seeing how this affects
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Possibility of bias with PLECs in DUD-E
Thank you. I will go ahead with rotating the ligands to non-ideal poses and seeing how this affects
7/4/19
mate...@gmail.com
,
Maciek Wójcikowski
2
6/17/19
Using SPLIF with sklearn Algorithms
Hi Mateo, As you noticed the `SimpleInteractionFingerprint` are complex fingerprint, because they
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Using SPLIF with sklearn Algorithms
Hi Mateo, As you noticed the `SimpleInteractionFingerprint` are complex fingerprint, because they
6/17/19
Oscar Arrúa
,
Maciek Wójcikowski
2
5/8/19
RMSD calculate
Hi Oscar, Running oddt_cli will ultimately run autodock_vina, so this is a bit redundant. If you want
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RMSD calculate
Hi Oscar, Running oddt_cli will ultimately run autodock_vina, so this is a bit redundant. If you want
5/8/19
gabm...@gmail.com
,
Maciek Wójcikowski
3
5/2/19
mol type conversion
Hello, Thank you for the help, it worked! Il giorno martedì 30 aprile 2019 22:49:29 UTC+2, Maciek
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mol type conversion
Hello, Thank you for the help, it worked! Il giorno martedì 30 aprile 2019 22:49:29 UTC+2, Maciek
5/2/19
Bakary N'tji Diallo
,
Maciek Wójcikowski
2
4/26/19
available on windows
Hi, Most certainly you can install oddt with conda or pip (see the README on Github - https://github.
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available on windows
Hi, Most certainly you can install oddt with conda or pip (see the README on Github - https://github.
4/26/19
Oscar Arrúa
4/23/19
Help ODDT Installation
Good Night! I have problems with my ODDT`s installation: I try to use in Python 3.6 and 2.7, but it
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Help ODDT Installation
Good Night! I have problems with my ODDT`s installation: I try to use in Python 3.6 and 2.7, but it
4/23/19
ryconn...@gmail.com
,
Maciek Wójcikowski
2
3/10/19
Help Running oddt_cli
Hi Ryan, Can you confirm that ODDT is in fact installed in that environment by "conda list"
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Help Running oddt_cli
Hi Ryan, Can you confirm that ODDT is in fact installed in that environment by "conda list"
3/10/19
Marawan Ahmed
,
Maciek Wójcikowski
2
4/23/18
New empirical scoring functions
Hi Marwan, Thanks for the interest in ODDT, I hope you found it useful. As for now the only stable
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New empirical scoring functions
Hi Marwan, Thanks for the interest in ODDT, I hope you found it useful. As for now the only stable
4/23/18
marcosv...@gmail.com
,
Maciek Wójcikowski
2
3/29/18
Error using SimpleInteractionFingerprint
Just for future reference, this issue was answered on Github Issue tracker: https://github.com/oddt/
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Error using SimpleInteractionFingerprint
Just for future reference, this issue was answered on Github Issue tracker: https://github.com/oddt/
3/29/18
rav...@protonmail.com
,
Maciek Wójcikowski
2
3/9/18
Question about NNScore implementation
Hi Ricardo, The main two components are the descriptor generator (Binana, https://github.com/oddt/
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Question about NNScore implementation
Hi Ricardo, The main two components are the descriptor generator (Binana, https://github.com/oddt/
3/9/18
Muela, Gerardo D
,
Maciek Wójcikowski
5
8/9/17
Issue with oddt.toolkit
Hi Maciek, Thank you for updating the snippets. I'll go ahead and update ODDT to the newest
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Issue with oddt.toolkit
Hi Maciek, Thank you for updating the snippets. I'll go ahead and update ODDT to the newest
8/9/17
rppn...@gmail.com
,
Maciek Wójcikowski
3
5/8/17
OpenBabel for centOS
Hello again, I followed on your problem and found a solution to manually install OB (although I
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OpenBabel for centOS
Hello again, I followed on your problem and found a solution to manually install OB (although I
5/8/17
Suhad Jihad
,
Maciek Wójcikowski
2
2/2/16
Re: [oddt] Fix building custom scoring functions
Hi, No, recent changes have no influence on NNscore. ---- Pozdrawiam, | Best regards, Maciek
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Re: [oddt] Fix building custom scoring functions
Hi, No, recent changes have no influence on NNscore. ---- Pozdrawiam, | Best regards, Maciek
2/2/16
Suhad Jihad
,
Maciek Wójcikowski
2
1/5/16
Analysis Of The Results
Hi, That's a flaw of NNScore itself. The determination between docking poses is not grate. You
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Analysis Of The Results
Hi, That's a flaw of NNScore itself. The determination between docking poses is not grate. You
1/5/16
Suhad Jihad
12/25/15
Merry Christmas
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Merry Christmas
12/25/15
Suhad Jihad
,
Maciek Wójcikowski
3
12/7/15
Reinstallation
Hello again, I think I found a bug in ODDT connected with old OpenBabel. You need to update ODDT: pip
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Reinstallation
Hello again, I think I found a bug in ODDT connected with old OpenBabel. You need to update ODDT: pip
12/7/15