Re: [Rdkit-discuss] postgresql cartridge and fingerprints
Hi Greg, Thanks. I haven't started tests yet, so we'll see. Best wishes, Michal On 17 Mar 2015 15:08, Greg Landrum greg.land...@gmail.com wrote: Hi Michal, On Tue, Mar 17, 2015 at 3:02 PM, Michal Krompiec michal.kromp...@gmail.com wrote: Hello, I understand that the index for substructure searching is created by, for example: create index molidx on mols using gist(m) where m is the molecule column in mols table. Is this correct? yes, that's correct. How do I select the type of fingerprint used for the index? I just suspect that my dataset may require tweaking the fingerprint type for best performance. That's not configurable at the moment. If you would like to change the fingerprint for substructure screening, you would need to edit the source for the cartridge itself. I'm curious about what you think might need to be changed -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
Re: [Rdkit-discuss] Wired dependencies.
Sorry, I mixed something up. I will try what you suggested, I think I actually did not do the installation in the environment. Please, add a corresponding comment here: https://github.com/rdkit/conda-rdkit It is not mentioned that you have to do conda install boost conda install rdkit in the environment. Thanks Soren -- Dr. Soren Wacker Centre For Molecular Simulations, BI # 547 The University of Calgary 2500 University Drive (NW) Calgary, Alberta Canada, T2N 1N4 Tel.: ++1 (403) 210 7860 Email: swac...@ucalgary.ca From: Soren Wacker [swac...@ucalgary.ca] Sent: Tuesday, March 17, 2015 11:33 AM To: Greg Landrum Cc: RDKit Discuss Subject: Re: [Rdkit-discuss] Wired dependencies. Yes, sorry, I did not mention that. But I did that, too. Soren -- Dr. Soren Wacker Centre For Molecular Simulations, BI # 547 The University of Calgary 2500 University Drive (NW) Calgary, Alberta Canada, T2N 1N4 Tel.: ++1 (403) 210 7860 Email: swac...@ucalgary.ca From: Greg Landrum [greg.land...@gmail.com] Sent: Monday, March 16, 2015 10:42 PM To: Soren Wacker Cc: RDKit Discuss Subject: Re: [Rdkit-discuss] Wired dependencies. Hi Soren, On Mon, Mar 16, 2015 at 11:58 PM, Soren Wacker swac...@ucalgary.camailto:swac...@ucalgary.ca wrote: Hi, I am using conda and rdkit, so installed https://github.com/rdkit/conda-rdkit with conda build boost conda build rdkit The installation seems to be successfull, at least in part, since I can import and use rdkit. Did you also do: conda install boost conda install rdkit in the environment you want to use? -greg However, I noticed some strange behaviour: When I activate a conda environment and import rdkit from ipython notebook, the kernel will crash. Apparently, I have to use the system python version at /usr/bin/python and import the packages installed with conda. Also upgrading the python packages with conda update --all will lead to a not working installation. Any ideas how to solve that? Or where it may come from? 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 -- 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
Re: [Rdkit-discuss] Wired dependencies.
Yes, sorry, I did not mention that. But I did that, too. Soren -- Dr. Soren Wacker Centre For Molecular Simulations, BI # 547 The University of Calgary 2500 University Drive (NW) Calgary, Alberta Canada, T2N 1N4 Tel.: ++1 (403) 210 7860 Email: swac...@ucalgary.ca From: Greg Landrum [greg.land...@gmail.com] Sent: Monday, March 16, 2015 10:42 PM To: Soren Wacker Cc: RDKit Discuss Subject: Re: [Rdkit-discuss] Wired dependencies. Hi Soren, On Mon, Mar 16, 2015 at 11:58 PM, Soren Wacker swac...@ucalgary.camailto:swac...@ucalgary.ca wrote: Hi, I am using conda and rdkit, so installed https://github.com/rdkit/conda-rdkit with conda build boost conda build rdkit The installation seems to be successfull, at least in part, since I can import and use rdkit. Did you also do: conda install boost conda install rdkit in the environment you want to use? -greg However, I noticed some strange behaviour: When I activate a conda environment and import rdkit from ipython notebook, the kernel will crash. Apparently, I have to use the system python version at /usr/bin/python and import the packages installed with conda. Also upgrading the python packages with conda update --all will lead to a not working installation. Any ideas how to solve that? Or where it may come from? 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 -- 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
Re: [Rdkit-discuss] tests failed on Cygwin
Hi Michal, regarding test 13, would you mind trying to change line 1400 in /home/m212767/RDKit/Code/ForceField/UFF/testUFFForceField.cpp from TEST_ASSERT((int)MolTransforms::getDihedralDeg(mol-getConformer(), 1, 3, 6, 8) == -10); to std::cout (int)MolTransforms::getDihedralDeg(mol-getConformer(), 1, 3, 6, 8) std::endl; and tell me what the return value of MolTransforms::getDihedralDeg(mol-getConformer(), 1, 3, 6, 8) actually is? It might just be a periodicity problem. Thanks for your collaboration, kind regards Paolo On 17/03/2015 14:48, Michal Krompiec wrote: Hello, I'm trying to build RDKit on Cygwin, on Windows 7 32-bit (current GitHub version). So far, everything looked fine, but some tests failed: The following tests FAILED: 13 - testUFFForceField (OTHER_FAULT) 66 - testFMCS (SEGFAULT) 79 - pythonTestDbCLI (Failed) - that's not a problem, as the db is not set up (yet) I repeated using --output-on-failure, and that's what I got: testUFFForceField: Test Assert Expression Failed: Violation occurred on line 1400 in file /home/m212767/RDKit/Code/ForceField/UFF/testUFFForceField.cpp Failed Expression: (int)MolTransforms::getDihedralDeg(mol-getConformer(), 1, 3, 6, 8) == -10 66/85 Test #66: testFMCS .***Exception: SegFault 0.28 sec [14:16:12] *** [14:16:12] FMCS Unit Test [14:16:12] - [14:16:12] FMCS test1Basics() System reboot and /bin/rebaseall did not help. Moreover, tests for the cartridge also failed: $ make make install make installcheck make: Nothing to be done for 'all'. /usr/bin/mkdir -p '/usr/lib/postgresql' /usr/bin/mkdir -p '/usr/share/postgresql/extension' /usr/bin/mkdir -p '/usr/share/postgresql/extension' /usr/bin/install -c -m 755 rdkit.dll '/usr/lib/postgresql/rdkit.dll' /usr/bin/install -c -m 644 rdkit.control '/usr/share/postgresql/extension/' /usr/bin/install -c -m 644 rdkit--3.4.sql '/usr/share/postgresql/extension/' /usr/lib/postgresql/pgxs/src/makefiles/../../src/test/regress/pg_regress --inputdir=./ --psqldir='/usr/bin'--dbname=contrib_regression rdkit-91 props btree molgist bfpgist-91 sfpgist slfpgist fps reaction (using postmaster on Unix socket, default port) == dropping database contrib_regression == NOTICE: database contrib_regression does not exist, skipping DROP DATABASE == creating database contrib_regression == CREATE DATABASE ALTER DATABASE == running regression test queries== test rdkit-91 ... LOG: server process (PID 9076) was terminated by signal 11: Segmentation fault DETAIL: Failed process was running: CREATE EXTENSION rdkit; Has anybody else encountered such problems? Any idea what to do? Thanks, Michal -- 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 -- 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
Re: [Rdkit-discuss] postgresql cartridge and fingerprints
Hi Michal, On Tue, Mar 17, 2015 at 3:02 PM, Michal Krompiec michal.kromp...@gmail.com wrote: Hello, I understand that the index for substructure searching is created by, for example: create index molidx on mols using gist(m) where m is the molecule column in mols table. Is this correct? yes, that's correct. How do I select the type of fingerprint used for the index? I just suspect that my dataset may require tweaking the fingerprint type for best performance. That's not configurable at the moment. If you would like to change the fingerprint for substructure screening, you would need to edit the source for the cartridge itself. I'm curious about what you think might need to be changed -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
[Rdkit-discuss] postgresql cartridge and fingerprints
Hello, I understand that the index for substructure searching is created by, for example: create index molidx on mols using gist(m) where m is the molecule column in mols table. Is this correct? How do I select the type of fingerprint used for the index? I just suspect that my dataset may require tweaking the fingerprint type for best performance. Thanks, Michal -- 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
[Rdkit-discuss] tests failed on Cygwin
Hello, I'm trying to build RDKit on Cygwin, on Windows 7 32-bit (current GitHub version). So far, everything looked fine, but some tests failed: The following tests FAILED: 13 - testUFFForceField (OTHER_FAULT) 66 - testFMCS (SEGFAULT) 79 - pythonTestDbCLI (Failed) - that's not a problem, as the db is not set up (yet) I repeated using --output-on-failure, and that's what I got: testUFFForceField: Test Assert Expression Failed: Violation occurred on line 1400 in file /home/m212767/RDKit/Code/ForceField/UFF/testUFFForceField.cpp Failed Expression: (int)MolTransforms::getDihedralDeg(mol-getConformer(), 1, 3, 6, 8) == -10 66/85 Test #66: testFMCS .***Exception: SegFault 0.28 sec [14:16:12] *** [14:16:12] FMCS Unit Test [14:16:12] - [14:16:12] FMCS test1Basics() System reboot and /bin/rebaseall did not help. Moreover, tests for the cartridge also failed: $ make make install make installcheck make: Nothing to be done for 'all'. /usr/bin/mkdir -p '/usr/lib/postgresql' /usr/bin/mkdir -p '/usr/share/postgresql/extension' /usr/bin/mkdir -p '/usr/share/postgresql/extension' /usr/bin/install -c -m 755 rdkit.dll '/usr/lib/postgresql/rdkit.dll' /usr/bin/install -c -m 644 rdkit.control '/usr/share/postgresql/extension/' /usr/bin/install -c -m 644 rdkit--3.4.sql '/usr/share/postgresql/extension/' /usr/lib/postgresql/pgxs/src/makefiles/../../src/test/regress/pg_regress --inputdir=./ --psqldir='/usr/bin'--dbname=contrib_regression rdkit-91 props btree molgist bfpgist-91 sfpgist slfpgist fps reaction (using postmaster on Unix socket, default port) == dropping database contrib_regression == NOTICE: database contrib_regression does not exist, skipping DROP DATABASE == creating database contrib_regression == CREATE DATABASE ALTER DATABASE == running regression test queries== test rdkit-91 ... LOG: server process (PID 9076) was terminated by signal 11: Segmentation fault DETAIL: Failed process was running: CREATE EXTENSION rdkit; Has anybody else encountered such problems? Any idea what to do? Thanks, Michal -- 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
