Re: [Rdkit-discuss] Chopping and recombining molecules
HI Greg,
Ideally I’d like the output to be one ring cleaved from the molecule, which
then can be attached to another similar molecule. Nicks code yesterday allowed
me to cleave a ring pretty easily, just have to reattach it now.
Example output would be like this: n1ccc2nc3cc4cc5ccncc5cc4nc3nc2c1 =
c1ccncc1 + rest of molecule.
Josh
From: Greg Landrum [mailto:greg.land...@gmail.com]
Sent: 10 December 2014 02:41
To: Campbell J.E.
Cc: rdkit-discuss@lists.sourceforge.net
Subject: Re: [Rdkit-discuss] Chopping and recombining molecules
Hi Josh,
This looks like it might be doable, but before I start guessing: can you please
give examples(s) of what you would like to have as output for the molecule
below?
-greg
On Tue, Dec 9, 2014 at 3:23 PM, Campbell J.E.
mailto:jec1...@soton.ac.uk>> wrote:
Hi rdkit users,
I have some linear ring molecules (such as pentacene, anthracene etc) with
various substitutions that I want to fragment into individual rings and
recombine as a new molecule. What’s the best way to do this in rdkit? I’ve been
trying to use EditableMol but I can’t access all the fragments, or remove more
bond at once. Here’s my code so far:
#n1ccc2nc3cc4cc5ccncc5cc4nc3nc2c1
break_atoms = [list(x) for x in
m3.GetSubstructMatches(Chem.MolFromSmarts('[R2]'))]
break_bonds = ((3,20), (5,18), (7,16), (9,14))
em = Chem.EditableMol(m3)
em.RemoveBond(3,20)
nm = em.GetMol()
frags = Chem.GetMolFrags(nm,asMols=True)
[Chem.MolToSmiles(x,True) for x in frags]
I’ve had a look at the substructure replace function as well but I guess I’d
need to identify the ring substructures first? Thanks for any help.
Josh Campbell
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[Rdkit-discuss] Avalon test failing(?)
Hi Greg, I wondered if you (or anyone else) have been seeing any issues with win64 build of the RDKit - with Avalon toolkit support - recently? Yesterday I updated my local SVN copy of RDKit (to rev4274) and rebuilt. Everything seemed to go ok, but the testAvalonLib1 test is now failing (the pyAvalonTools test passes) - see below. I can see that test1.cpp has changed recently, but my AvalonTools source hasn't... Has a problem been introduced into the test? Kind regards James C:\RDKit\build>ctest -R testAvalon -V UpdateCTestConfiguration from :C:/RDKit/build/DartConfiguration.tcl UpdateCTestConfiguration from :C:/RDKit/build/DartConfiguration.tcl Test project C:/RDKit/build Constructing a list of tests Done constructing a list of tests Checking test dependency graph... Checking test dependency graph end test 2 Start 2: testAvalonLib1 2: Test command: C:\RDKit\build\External\AvalonTools\Release\testAvalonLib1.exe 2: Test timeout computed to be: 9.99988e+006 2: [12:31:18] testing canonical smiles generation 2: [12:31:18] done 2: [12:31:18] testing coordinate generation 2: [12:31:18] done 2: [12:31:18] testing fingerprint generation 2: [12:31:18] c1n1 18 2: returning 2: [12:31:18] c1n1 6 2: [12:31:18] c1nnccc1 28 2: [12:31:18] c1ncncc1 25 2: [12:31:18] c1cccnc1 18 2: [12:31:18] c1c1 6 2: [12:31:18] c1cccnc1 19 2: [12:31:18] c1cocc1 48 2: [12:31:18] 2: 2: 2: Test Assert 2: Expression Failed: 2: Violation occurred on line 146 in file ..\..\..\External\AvalonTools\test1.cpp 2: Failed Expression: bv.getNumOnBits()==53 2: 2: 1/1 Test #2: testAvalonLib1 ...***Failed2.87 sec 0% tests passed, 1 tests failed out of 1 Total Test time (real) = 2.98 sec The following tests FAILED: 2 - testAvalonLib1 (Failed) Errors while running CTest __ PLEASE READ: This email is confidential and may be privileged. It is intended for the named addressee(s) only and access to it by anyone else is unauthorised. If you are not an addressee, any disclosure or copying of the contents of this email or any action taken (or not taken) in reliance on it is unauthorised and may be unlawful. If you have received this email in error, please notify the sender or postmas...@vernalis.com. Email is not a secure method of communication and the Company cannot accept responsibility for the accuracy or completeness of this message or any attachment(s). Please check this email for virus infection for which the Company accepts no responsibility. If verification of this email is sought then please request a hard copy. Unless otherwise stated, any views or opinions presented are solely those of the author and do not represent those of the Company. The Vernalis Group of Companies 100 Berkshire Place Wharfedale Road Winnersh, Berkshire RG41 5RD, England Tel: +44 (0)118 938 To access trading company registration and address details, please go to the Vernalis website at www.vernalis.com and click on the "Company address and registration details" link at the bottom of the page.. __-- Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server from Actuate! Instantly Supercharge Your Business Reports and Dashboards with Interactivity, Sharing, Native Excel Exports, App Integration & more Get technology previously reserved for billion-dollar corporations, FREE http://pubads.g.doubleclick.net/gampad/clk?id=164703151&iu=/4140/ostg.clktrk___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Avalon test failing(?)
Hi James, The new version of the test code is targeting the 1.2 avalon toolkit version. Here's the commit that did that. https://github.com/rdkit/rdkit/commit/42dab414ee6fbe5489078e5e52046608bbf785cb As an FYI, to make these tests pass on windows, you need to edit the code to fix a bug: you need to comment out line 1446 of reaccsio.c: //MyFree((char *)tempdir); -greg On Wed, Dec 10, 2014 at 1:44 PM, James Davidson wrote: > Hi Greg, > > > > I wondered if you (or anyone else) have been seeing any issues with win64 > build of the RDKit – with Avalon toolkit support – recently? > > Yesterday I updated my local SVN copy of RDKit (to rev4274) and rebuilt. > Everything seemed to go ok, but the testAvalonLib1 test is now failing (the > pyAvalonTools test passes) – see below. > > I can see that test1.cpp has changed recently, but my AvalonTools source > hasn’t… Has a problem been introduced into the test? > > > > Kind regards > > > > James > > > > > > C:\RDKit\build>ctest -R testAvalon -V > > UpdateCTestConfiguration from :C:/RDKit/build/DartConfiguration.tcl > > UpdateCTestConfiguration from :C:/RDKit/build/DartConfiguration.tcl > > Test project C:/RDKit/build > > Constructing a list of tests > > Done constructing a list of tests > > Checking test dependency graph... > > Checking test dependency graph end > > test 2 > > Start 2: testAvalonLib1 > > > > 2: Test command: > C:\RDKit\build\External\AvalonTools\Release\testAvalonLib1.exe > > 2: Test timeout computed to be: 9.99988e+006 > > 2: [12:31:18] testing canonical smiles generation > > 2: [12:31:18] done > > 2: [12:31:18] testing coordinate generation > > 2: [12:31:18] done > > 2: [12:31:18] testing fingerprint generation > > 2: [12:31:18] c1n1 18 > > 2: returning > > 2: [12:31:18] c1n1 6 > > 2: [12:31:18] c1nnccc1 28 > > 2: [12:31:18] c1ncncc1 25 > > 2: [12:31:18] c1cccnc1 18 > > 2: [12:31:18] c1c1 6 > > 2: [12:31:18] c1cccnc1 19 > > 2: [12:31:18] c1cocc1 48 > > 2: [12:31:18] > > 2: > > 2: > > 2: Test Assert > > 2: Expression Failed: > > 2: Violation occurred on line 146 in file > ..\..\..\External\AvalonTools\test1.cpp > > 2: Failed Expression: bv.getNumOnBits()==53 > > 2: > > 2: > > 1/1 Test #2: testAvalonLib1 ...***Failed2.87 sec > > > > 0% tests passed, 1 tests failed out of 1 > > > > Total Test time (real) = 2.98 sec > > > > The following tests FAILED: > > 2 - testAvalonLib1 (Failed) > > Errors while running CTest > > > > __ > PLEASE READ: This email is confidential and may be privileged. It is > intended for the named addressee(s) only and access to it by anyone else is > unauthorised. If you are not an addressee, any disclosure or copying of the > contents of this email or any action taken (or not taken) in reliance on it > is unauthorised and may be unlawful. If you have received this email in > error, please notify the sender or postmas...@vernalis.com. Email is not > a secure method of communication and the Company cannot accept > responsibility for the accuracy or completeness of this message or any > attachment(s). Please check this email for virus infection for which the > Company accepts no responsibility. If verification of this email is sought > then please request a hard copy. Unless otherwise stated, any views or > opinions presented are solely those of the author and do not represent > those of the Company. > > The Vernalis Group of Companies > 100 Berkshire Place > Wharfedale Road > Winnersh, Berkshire > RG41 5RD, England > Tel: +44 (0)118 938 > > To access trading company registration and address details, please go to > the Vernalis website at www.vernalis.com and click on the "Company > address and registration details" link at the bottom of the page.. > __ > -- Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server from Actuate! Instantly Supercharge Your Business Reports and Dashboards with Interactivity, Sharing, Native Excel Exports, App Integration & more Get technology previously reserved for billion-dollar corporations, FREE http://pubads.g.doubleclick.net/gampad/clk?id=164703151&iu=/4140/ostg.clktrk___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Avalon test failing(?)
Hi Greg, > The new version of the test code is targeting the 1.2 avalon toolkit > version. > Here's the commit that did that. > https://github.com/rdkit/rdkit/commit/42dab414ee6fbe5489078e5e52046608bbf785cb > > As an FYI, to make these tests pass on windows, you need to edit the code > to fix a bug: > > you need to comment out line 1446 of reaccsio.c: >//MyFree((char *)tempdir); Following your advice, I downloaded the 1.2 source from Sourceforge (http://sourceforge.net/projects/avalontoolkit/files/AvalonToolkit_1.2/); commented-out the line in reaccsio.c; and then reconfigured in cmake and rebuilt in VS. The tests pass now - thanks! Kind regards James __ PLEASE READ: This email is confidential and may be privileged. It is intended for the named addressee(s) only and access to it by anyone else is unauthorised. If you are not an addressee, any disclosure or copying of the contents of this email or any action taken (or not taken) in reliance on it is unauthorised and may be unlawful. If you have received this email in error, please notify the sender or postmas...@vernalis.com. Email is not a secure method of communication and the Company cannot accept responsibility for the accuracy or completeness of this message or any attachment(s). Please check this email for virus infection for which the Company accepts no responsibility. If verification of this email is sought then please request a hard copy. Unless otherwise stated, any views or opinions presented are solely those of the author and do not represent those of the Company. The Vernalis Group of Companies 100 Berkshire Place Wharfedale Road Winnersh, Berkshire RG41 5RD, England Tel: +44 (0)118 938 To access trading company registration and address details, please go to the Vernalis website at www.vernalis.com and click on the "Company address and registration details" link at the bottom of the page.. __-- Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server from Actuate! Instantly Supercharge Your Business Reports and Dashboards with Interactivity, Sharing, Native Excel Exports, App Integration & more Get technology previously reserved for billion-dollar corporations, FREE http://pubads.g.doubleclick.net/gampad/clk?id=164703151&iu=/4140/ostg.clktrk___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
