Re: [Rdkit-discuss] Rdkit-discuss Digest, Vol 88, Issue 13
Kindly look through this aspect of my script below.
I keep getting the error:
AttributeError: 'tuple' object has no attribute 'HasSubstructMatch'
#!/usr/bin/python
from rdkit import Chem
from rdkit.Chem import Draw
from rdkit.Chem import AllChem
pains = []# Contains my PAINS query molecules
#Loop through data with PAINS query
for p in pains:
match = [x for x in mols if x.HasSubstructMatch(p)]
a = len(match)
print a
Thank you
Samuel Ayodele Egieyeh
South African National Bioinformatics Institute
University of the Western Cape
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Today's Topics:
1. Re: Chem.Draw darker colors (Soren Wacker)
2. Re: Chem.Draw darker colors (David Hall)
3. Re: Inchi installation in postgresql database driving me mad
(Jan Holst Jensen)
4. Re: Docker images (Greg Landrum)
5. Re: Inchi installation in postgresql database driving me mad (JP)
--
Message: 1
Date: Thu, 12 Feb 2015 17:58:42 +
From: Soren Wacker swac...@ucalgary.ca
Subject: Re: [Rdkit-discuss] Chem.Draw darker colors
To: Greg Landrum greg.land...@gmail.com
Cc: RDKit Discuss rdkit-discuss@lists.sourceforge.net
Message-ID:
cf4e4cc78f22f44bb773c76c066a3dd109255...@itcimexch03.uc.ucalgary.ca
Content-Type: text/plain; charset=us-ascii
but how?
Soren
From: Greg Landrum [greg.land...@gmail.com]
Sent: Wednesday, February 11, 2015 10:27 PM
To: Soren Wacker
Cc: RDKit Discuss
Subject: Re: [Rdkit-discuss] Chem.Draw darker colors
My other answer about using the DrawingOptions object applies here too.
Instead of setting elemDict to be a defaultDict, you would just change the
colors for S and F to whatever you prefer.
-greg
On Thu, Feb 12, 2015 at 12:13 AM, Soren Wacker
swac...@ucalgary.camailto:swac...@ucalgary.ca wrote:
Hi,
I printed some moecules with the Draw module of rdkit and generated some
useful figures.
I noticed that for some elements the contrast to white is very low.
Therefore, I suggest to change the default colors to the darker versions.
E.g. darkyellow instead of yellow for sulfur
and darkcyan instead of cyan for fluorine
kind regards
Soren
--
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Message: 2
Date: Thu, 12 Feb 2015 13:14:35 -0500
From: David Hall li...@cowsandmilk.net
Subject: Re: [Rdkit-discuss] Chem.Draw darker colors
To: Soren Wacker swac...@ucalgary.ca
Cc: RDKit Discuss rdkit-discuss@lists.sourceforge.net, Greg Landrum
greg.land...@gmail.com
Message-ID: 1a6e481e-8a31-46cc-b719-6fd1a4e2c...@cowsandmilk.net
Content-Type: text/plain; charset=us-ascii
In [6]: opt.elemDict
Out[6]:
{0: (0.5, 0.5, 0.5),
1: (0.55, 0.55, 0.55),
7: (0, 0, 1),
8: (1, 0, 0),
9: (0.2, 0.8, 0.8),
15: (1, 0.5, 0),
16: (0.8, 0.8, 0),
17: (0, 0.8, 0),
35: (0.5, 0.3, 0.1)}
presumably, you set fluorine and sulfur by changing the values of 9 and
16.
-David
On Feb 12, 2015, at 12:58 PM, Soren Wacker swac...@ucalgary.ca wrote:
but how?
Soren
From: Greg Landrum [greg.land...@gmail.com]
Sent: Wednesday, February 11, 2015 10:27 PM
To: Soren Wacker
Cc: RDKit Discuss
Subject: Re: [Rdkit-discuss] Chem.Draw darker colors
My other answer about using the DrawingOptions object applies here too.
Instead of setting elemDict to be a defaultDict, you would just change
the colors for S and F to whatever you prefer.
-greg
On Thu, Feb 12, 2015 at 12:13 AM, Soren Wacker
swac...@ucalgary.camailto:swac...@ucalgary.ca wrote:
Hi,
I printed some moecules with the Draw module of rdkit and generated some
useful figures.
I noticed that for some elements the contrast to white is very low.
Therefore, I suggest to change the default
Re: [Rdkit-discuss] Rdkit-discuss Digest, Vol 88, Issue 13
Hi Samuel,
The problem is that x is a tuple in your case not an rdkit molecule object.
Check your code to see what mols list actually has inside. I'm guessing
that x is a tuple containing a molecule object plus some other info.
Best.
Christos
Christos Kannas
Researcher
Ph.D Student
Mob (UK): +44 (0) 7447700937
Mob (Cyprus): +357 99530608
[image: View Christos Kannas's profile on LinkedIn]
http://cy.linkedin.com/in/christoskannas
On 13 February 2015 at 12:14, segie...@sanbi.ac.za wrote:
Kindly look through this aspect of my script below.
I keep getting the error:
AttributeError: 'tuple' object has no attribute 'HasSubstructMatch'
#!/usr/bin/python
from rdkit import Chem
from rdkit.Chem import Draw
from rdkit.Chem import AllChem
pains = []# Contains my PAINS query molecules
#Loop through data with PAINS query
for p in pains:
match = [x for x in mols if x.HasSubstructMatch(p)]
a = len(match)
print a
Thank you
Samuel Ayodele Egieyeh
South African National Bioinformatics Institute
University of the Western Cape
Send Rdkit-discuss mailing list submissions to
rdkit-discuss@lists.sourceforge.net
To subscribe or unsubscribe via the World Wide Web, visit
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
or, via email, send a message with subject or body 'help' to
rdkit-discuss-requ...@lists.sourceforge.net
You can reach the person managing the list at
rdkit-discuss-ow...@lists.sourceforge.net
When replying, please edit your Subject line so it is more specific
than Re: Contents of Rdkit-discuss digest...
Today's Topics:
1. Re: Chem.Draw darker colors (Soren Wacker)
2. Re: Chem.Draw darker colors (David Hall)
3. Re: Inchi installation in postgresql database driving me mad
(Jan Holst Jensen)
4. Re: Docker images (Greg Landrum)
5. Re: Inchi installation in postgresql database driving me mad (JP)
--
Message: 1
Date: Thu, 12 Feb 2015 17:58:42 +
From: Soren Wacker swac...@ucalgary.ca
Subject: Re: [Rdkit-discuss] Chem.Draw darker colors
To: Greg Landrum greg.land...@gmail.com
Cc: RDKit Discuss rdkit-discuss@lists.sourceforge.net
Message-ID:
cf4e4cc78f22f44bb773c76c066a3dd109255...@itcimexch03.uc.ucalgary.ca
Content-Type: text/plain; charset=us-ascii
but how?
Soren
From: Greg Landrum [greg.land...@gmail.com]
Sent: Wednesday, February 11, 2015 10:27 PM
To: Soren Wacker
Cc: RDKit Discuss
Subject: Re: [Rdkit-discuss] Chem.Draw darker colors
My other answer about using the DrawingOptions object applies here too.
Instead of setting elemDict to be a defaultDict, you would just change
the
colors for S and F to whatever you prefer.
-greg
On Thu, Feb 12, 2015 at 12:13 AM, Soren Wacker
swac...@ucalgary.camailto:swac...@ucalgary.ca wrote:
Hi,
I printed some moecules with the Draw module of rdkit and generated some
useful figures.
I noticed that for some elements the contrast to white is very low.
Therefore, I suggest to change the default colors to the darker versions.
E.g. darkyellow instead of yellow for sulfur
and darkcyan instead of cyan for fluorine
kind regards
Soren
--
Dive into the World of Parallel Programming. The Go Parallel Website,
sponsored by Intel and developed in partnership with Slashdot Media, is
your
hub for all things parallel software development, from weekly thought
leadership blogs to news, videos, case studies, tutorials and more. Take
a
look and join the conversation now. http://goparallel.sourceforge.net/
___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.netmailto:
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
--
Message: 2
Date: Thu, 12 Feb 2015 13:14:35 -0500
From: David Hall li...@cowsandmilk.net
Subject: Re: [Rdkit-discuss] Chem.Draw darker colors
To: Soren Wacker swac...@ucalgary.ca
Cc: RDKit Discuss rdkit-discuss@lists.sourceforge.net, Greg
Landrum
greg.land...@gmail.com
Message-ID: 1a6e481e-8a31-46cc-b719-6fd1a4e2c...@cowsandmilk.net
Content-Type: text/plain; charset=us-ascii
In [6]: opt.elemDict
Out[6]:
{0: (0.5, 0.5, 0.5),
1: (0.55, 0.55, 0.55),
7: (0, 0, 1),
8: (1, 0, 0),
9: (0.2, 0.8, 0.8),
15: (1, 0.5, 0),
16: (0.8, 0.8, 0),
17: (0, 0.8, 0),
35: (0.5, 0.3, 0.1)}
presumably, you set fluorine and sulfur by changing the values of 9 and
16.
-David
On Feb 12, 2015, at 12:58 PM, Soren Wacker swac...@ucalgary.ca wrote:
but how?
Soren
From: Greg Landrum [greg.land...@gmail.com]
Sent:
[Rdkit-discuss] New RDKit drawing code
Dear all, Noel's great blog post on using the RDKit from emscripten ( http://baoilleach.blogspot.ch/2015/02/cheminformaticsjs-rdkit.html) made me realize that I should post something here about the new RDKit drawing code that's currently available in github. Rather than do a long email message, I did a quick blog post that demonstrates some of the functionality: http://rdkit.blogspot.com/2015/02/new-drawing-code.html I'm still actively working on this, but I think what's there is already worth showing off a bit. :-) Many thanks are due to Dave Cosgrove, who did the initial work that makes this all possible. -greg -- Dive into the World of Parallel Programming. The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
