[Rdkit-discuss] RDKit nodes in KNIME stopped working suddenly
Hello, We've been using the RDKit nodes in KNIME for quite a while without any problems. But suddenly they ceased to work on some computers, while still working on other ones. Tried with a fresh KNIME installation with latest RDKit nodes - same problem. What could be wrong? I pasted the warning/error messages below: WARNRDKitTypesPluginActivator Library file GraphMolWrap.dll found: C:\Temp\knime_2.9.1\plugins\org.rdkit.knime.bin.win32.x86_2.4.0.201402061135\os\win32\x86\GraphMolWrap.dll ERROR RDKitTypesPluginActivator Loading of library GraphMolWrap.dll failed (possibly a subsequent error): C:\Temp\knime_2.9.1\configuration\org.eclipse.osgi\bundles\libtemp\224_0\GraphMolWrap.dll: Can't find dependent libraries ERROR RDKitTypesPluginActivator The library GraphMolWrap.dll has dependency issues. Please run a dependency walker on this file to find out what is missing. ERROR RDKitTypesPluginActivator Suggestion for fix: Please correct your system libraries based on the outcome of the dependency walker. WARNHistogram 2 columns without a valid domain will be ignored. In order to calculate the domain use the Nominal Values or Domain Calculator node. WARNRDKit From Molecule Could not load native RDKit library: C:\Temp\knime_2.9.1\plugins\org.rdkit.knime.bin.win32.x86_2.4.0.201402061135\os\win32\x86\boost_system-vc100-mt-1_51.dll: Can't find dependent libraries WARNRDKit From Molecule Could not load native RDKit library: C:\Temp\knime_2.9.1\plugins\org.rdkit.knime.bin.win32.x86_2.4.0.201402061135\os\win32\x86\boost_system-vc100-mt-1_51.dll: Can't find dependent libraries WARNRDKit From Molecule Could not load native RDKit library: C:\Temp\knime_2.9.1\plugins\org.rdkit.knime.bin.win32.x86_2.4.0.201402061135\os\win32\x86\boost_system-vc100-mt-1_51.dll: Can't find dependent libraries Thanks in advance, Michal -- Managing the Performance of Cloud-Based Applications Take advantage of what the Cloud has to offer - Avoid Common Pitfalls. Read the Whitepaper. http://pubads.g.doubleclick.net/gampad/clk?id=121054471iu=/4140/ostg.clktrk ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] flexmatch in RDKit cartridge?
Many thanks Jan, that's very helpful.
Cheers,
George
On 20 February 2014 21:32, Jan Holst Jensen j...@biochemfusion.com wrote:
Hi George et al,
flexmatch(... 'all') is the most strict exact match that the
Symyx/Accelrys cartridge has. You can relax the matching behavior to
varying degrees by passing it different options, e.g. using 'tau' instead
of 'all' will make the identity check tautomer-agnostic (to the extent that
the cartridge will perceive tautomers correctly - an interesting
discussion topic in itself).
The various options to flexmatch() are well documented in the Accelrys
documentation for the cartridge, but I don't know if that is publicly
available.
The short answer in my opinion: Yes, @= should be the equivalent of
flexmatch(m1, m2, 'all'). To emulate flexmatch(..., 'all') with rdkit, I
find a small gotcha with regards to chiral matching:
-- Clearly not identical.
postgres=# select mol('CCC') @= mol('CCF');
?column?
--
f
(1 row)
-- Clearly identical.
postgres=# select mol('CCC') @= mol('CCC');
?column?
--
t
(1 row)
-- Ala versus dAla - should *not* be identical ?
postgres=# select mol('C[C@H](N)C(=O)O') @= mol('C[C@@H](N)C(=O)O');
?column?
--
t
(1 row)
To get the expected behavior of @= you need to turn on chiral matching.
Even though the parameter says that is controls SSS behavior it apparently
also has an effect on exact matching:
postgres=# set rdkit.do_chiral_sss=true;
SET
-- Ala versus dAla - no longer identical.
postgres=# select mol('C[C@H](N)C(=O)O') @= mol('C[C@@H](N)C(=O)O');
?column?
--
f
(1 row)
-- Ala versus Ala - phew, identical.
postgres=# select mol('C[C@H](N)C(=O)O') @= mol('C[C@H](N)C(=O)O');
?column?
--
t
(1 row)
Cheers
-- Jan
On 2014-02-20 13:46, George Papadatos wrote:
Hi there,
Wouldn't that be (at least partly) possible with an exact structure search?
- @= : returns whether or not two molecules are the same.
Cheers,
George
On 20 February 2014 11:59, Greg Landrum greg.land...@gmail.com wrote:
Sounds interesting. Can anyone provide a pointer to a doc with more
specific info about what this actually does?
On Thursday, February 20, 2014, Michał Nowotka mmm...@gmail.com wrote:
Hi,
Symix cartridge defines something called flexmatch - Finds records
that are an exact match of the 2D or 3D structure that you specify in the
query.
Is there anything similar in RDKit cartridge? I looked into
documentation and couldn't find this feature.
Regards,
Michal Nowotka
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Re: [Rdkit-discuss] RDKit nodes in KNIME stopped working suddenly
On 2014-02-21 11:04, Michal Krompiec wrote: Hello, We've been using the RDKit nodes in KNIME for quite a while without any problems. But suddenly they ceased to work on some computers, while still working on other ones. Tried with a fresh KNIME installation with latest RDKit nodes - same problem. What could be wrong? I pasted the warning/error messages below: WARNRDKitTypesPluginActivator Library file GraphMolWrap.dll found: C:\Temp\knime_2.9.1\plugins\org.rdkit.knime.bin.win32.x86_2.4.0.201402061135\os\win32\x86\GraphMolWrap.dll ERROR RDKitTypesPluginActivator Loading of library GraphMolWrap.dll failed (possibly a subsequent error): C:\Temp\knime_2.9.1\configuration\org.eclipse.osgi\bundles\libtemp\224_0\GraphMolWrap.dll: Can't find dependent libraries ERROR RDKitTypesPluginActivator The library GraphMolWrap.dll has dependency issues. Please run a dependency walker on this file to find out what is missing. ERROR RDKitTypesPluginActivator Suggestion for fix: Please correct your system libraries based on the outcome of the dependency walker. WARNHistogram 2 columns without a valid domain will be ignored. In order to calculate the domain use the Nominal Values or Domain Calculator node. WARNRDKit From Molecule Could not load native RDKit library: C:\Temp\knime_2.9.1\plugins\org.rdkit.knime.bin.win32.x86_2.4.0.201402061135\os\win32\x86\boost_system-vc100-mt-1_51.dll: Can't find dependent libraries WARNRDKit From Molecule Could not load native RDKit library: C:\Temp\knime_2.9.1\plugins\org.rdkit.knime.bin.win32.x86_2.4.0.201402061135\os\win32\x86\boost_system-vc100-mt-1_51.dll: Can't find dependent libraries WARNRDKit From Molecule Could not load native RDKit library: C:\Temp\knime_2.9.1\plugins\org.rdkit.knime.bin.win32.x86_2.4.0.201402061135\os\win32\x86\boost_system-vc100-mt-1_51.dll: Can't find dependent libraries Thanks in advance, Michal Hello Michal, Could it be missing VC++ runtime DLLs on those machines ? Do you have MSVCP100.DLL and MSVCR100.DLL in your path ? Cheers -- Jan -- Managing the Performance of Cloud-Based Applications Take advantage of what the Cloud has to offer - Avoid Common Pitfalls. Read the Whitepaper. http://pubads.g.doubleclick.net/gampad/clk?id=121054471iu=/4140/ostg.clktrk ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] RDKit cartridge - opposite of mol_from_ctab() would be nice.
Hi Greg, Are there any plans for a mol_*to*_ctab() function in the PG cartridge ? Would make SD file export from the database a bit easier. If there are no immediate plans, I can take a stab at adding it myself. * Looks like rdkit_io.c is the place to add it ? * Should I manually define the new SQL function in rdkit.sql.in, or is there some higher-level place I should add it instead ? Cheers -- Jan -- Managing the Performance of Cloud-Based Applications Take advantage of what the Cloud has to offer - Avoid Common Pitfalls. Read the Whitepaper. http://pubads.g.doubleclick.net/gampad/clk?id=121054471iu=/4140/ostg.clktrk___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] RDKit cartridge - opposite of mol_from_ctab() would be nice.
Hi Jan, Great idea. I'd be happy to add it, but I can also talk you through it if you want to gain the experience. One important question: if structures don't have conformers (if they are loaded from SMILES, for example), should ctabs with all zero coordinates be generated or should depictions be generated? -greg On Fri, Feb 21, 2014 at 2:23 PM, Jan Holst Jensen j...@biochemfusion.comwrote: Hi Greg, Are there any plans for a mol_*to*_ctab() function in the PG cartridge ? Would make SD file export from the database a bit easier. If there are no immediate plans, I can take a stab at adding it myself. * Looks like rdkit_io.c is the place to add it ? * Should I manually define the new SQL function in rdkit.sql.in, or is there some higher-level place I should add it instead ? Cheers -- Jan -- Managing the Performance of Cloud-Based Applications Take advantage of what the Cloud has to offer - Avoid Common Pitfalls. Read the Whitepaper. http://pubads.g.doubleclick.net/gampad/clk?id=121054471iu=/4140/ostg.clktrk ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- Managing the Performance of Cloud-Based Applications Take advantage of what the Cloud has to offer - Avoid Common Pitfalls. Read the Whitepaper. http://pubads.g.doubleclick.net/gampad/clk?id=121054471iu=/4140/ostg.clktrk___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] RDKit cartridge - opposite of mol_from_ctab() would be nice.
Hi Greg, It would be great to gain the experience. I am working on a registration project where we will likely need to surface additional functions in the cartridge, just to try them out. So, knowing how to do that in a way where things that turn out useful can be contributed back cleanly would be great. if structures don't have conformers Ah, yes; good question. Decisions, decisions... I'll dodge the question :-) and say it sounds like a perfect fit for an optional parameter, e.g. mol_to_ctab(m mol, add_depiction_if_missing bool default true) I would go for default true because I believe that is the general preference. Cheers -- Jan On 2014-02-21 16:47, Greg Landrum wrote: Hi Jan, Great idea. I'd be happy to add it, but I can also talk you through it if you want to gain the experience. One important question: if structures don't have conformers (if they are loaded from SMILES, for example), should ctabs with all zero coordinates be generated or should depictions be generated? -greg On Fri, Feb 21, 2014 at 2:23 PM, Jan Holst Jensen j...@biochemfusion.com mailto:j...@biochemfusion.com wrote: Hi Greg, Are there any plans for a mol_*to*_ctab() function in the PG cartridge ? Would make SD file export from the database a bit easier. If there are no immediate plans, I can take a stab at adding it myself. * Looks like rdkit_io.c is the place to add it ? * Should I manually define the new SQL function in rdkit.sql.in http://rdkit.sql.in, or is there some higher-level place I should add it instead ? Cheers -- Jan -- Managing the Performance of Cloud-Based Applications Take advantage of what the Cloud has to offer - Avoid Common Pitfalls. Read the Whitepaper. http://pubads.g.doubleclick.net/gampad/clk?id=121054471iu=/4140/ostg.clktrk ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net mailto:Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- Managing the Performance of Cloud-Based Applications Take advantage of what the Cloud has to offer - Avoid Common Pitfalls. Read the Whitepaper. http://pubads.g.doubleclick.net/gampad/clk?id=121054471iu=/4140/ostg.clktrk___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
