[Rdkit-discuss] 2011.09 (Q3 2011) RDKit release
I'm very happy to announce that the next version of the RDKit -- 2011.09 (a.k.a Q3 2011) -- is released. The release notes are below. The source release is on the sourceforge downloads page: http://sourceforge.net/projects/rdkit/files/rdkit/Q3_2011/ The files can also be downloaded from the google project page: http://code.google.com/p/rdkit/downloads/list The binaries for Windows, Python 2.6 and Python 2.7 are uploaded already. Thanks to the everyone who submitted bug reports and suggestions for this release! Please let me know if you find any problems with the release or have suggestions for the next one. -greg ** Release_2011.09.1 *** (Changes relative to Release_2011.06.1) !! IMPORTANT !! - A bug in the definition of the Lipinski HBD descriptor was fixed in this release. The descriptor Lipinski.NHOHCount will return different values for molecules containing Ns or Os with more than one attached H. Acknowledgements: Eddie Cao, Richard Cooper, Paul Czodrowski, James Davidson, George Papadatos, Riccardo Vianello Bug Fixes: - A problem with interpretation of stereochemistry from mol files was fixed (Issue 3374639) - Sterochemistry information for exocyclic double bonds in mol blocks is no longer lost. (Issue 3375647) - linear double bonds from mol files now have their stereochemistry set correctly(Issue 3375684) - Chirality for phosphates and sulfates is not longer automatically removed. (Issue 3376319) - A bug with the reading of query information from mol files was fixed. (Issue 3392107) - Sterochemistry is now cleaned up after processing mol2 files. (Issue 3399798) - mergeQueryHs now correctly handles atoms with multiple Hs (Issue 3415204) - mergeQueryHs now correctly handles atoms without initial query information (Issue 3415206) - the calcLipinskiHBD() (equivalent to Lipinski.NHOHCount) descriptor now correctly handles Ns or Os with multiple Hs. (Issue 3415534) - Morgan fingerprints generated using the fromAtoms argument now have all bits from those atoms set.(Issue 3415636) - A problem with the way MolSuppliers handle the EOF condition when built with the most recent versions of g++ was fixed. - Translation of RDKit stereochemistry information into InChI stereochemistry information is improved. New Features: New Database Cartridge Features: - molecules can now be built from mol blocks using the function mol_from_ctab(). The corresponding is_valid_ctab() function was also added. - the radius argument is now optional for the functions morganbv_fp, morgan_fp, featmorganbv_fp, and featmorgan_fp. The default radius for all four functions is 2. Deprecated modules (to be removed in next release): Removed modules: Other: - The documentation in $RDBASE/Docs/Book has been migrated to use Sphinx instead of OpenOffice. - The optional InChI support can now be built using a system installation of the InChI library. -- All of the data generated in your IT infrastructure is seriously valuable. Why? It contains a definitive record of application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-d2dcopy2 ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] 2011.09 (Q3 2011) RDKit release
Hi Greg, I probably should have picked this up in the beta (but didn't...) When I try to import AllChem, I see the following: >>> from rdkit import Chem >>> from rdkit.Chem import AllChem Traceback (most recent call last): File "", line 1, in from rdkit.Chem import AllChem File "C:\Python27\RDKit_2011_09_1\rdkit\Chem\AllChem.py", line 28, in from rdkit.Chem.rdSLNParse import * ImportError: DLL load failed: The specified module could not be found. Any advice? 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 Oakdene Court 613 Reading Road Winnersh, Berkshire RG41 5UA. Tel: +44 118 977 3133 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.. __-- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity and more. Splunk takes this data and makes sense of it. Business sense. IT sense. Common sense. http://p.sf.net/sfu/splunk-d2d-oct___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] 2011.09 (Q3 2011) RDKit release
Hi James, This looks like there are missing dlls from the lib folder. The easiest solution would to be copy all the files from the lib folder of the previous (working) RDKit version and paste them in the lib folder of the current one (without overwriting them). Regards, George On 16 October 2011 15:56, James Davidson wrote: > ** > Hi Greg, > > I probably should have picked this up in the beta (but didn't...) When I > try to import AllChem, I see the following: > > >>> from rdkit import Chem > >>> from rdkit.Chem import AllChem > > Traceback (most recent call last): > File "", line 1, in > from rdkit.Chem import AllChem > File "C:\Python27\RDKit_2011_09_1\rdkit\Chem\AllChem.py", line 28, in > > from rdkit.Chem.rdSLNParse import * > ImportError: DLL load failed: The specified module could not be found. > > Any advice? > > 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 > Oakdene Court > 613 Reading Road > Winnersh, Berkshire > RG41 5UA. > Tel: +44 118 977 3133 > > 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.. > __ > > > -- > All the data continuously generated in your IT infrastructure contains a > definitive record of customers, application performance, security > threats, fraudulent activity and more. Splunk takes this data and makes > sense of it. Business sense. IT sense. Common sense. > http://p.sf.net/sfu/splunk-d2d-oct > ___ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > > -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity and more. Splunk takes this data and makes sense of it. Business sense. IT sense. Common sense. http://p.sf.net/sfu/splunk-d2d-oct___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] 2011.09 (Q3 2011) RDKit release
James, On Sun, Oct 16, 2011 at 7:56 AM, James Davidson wrote: > > I probably should have picked this up in the beta (but didn't...) When I > try to import AllChem, I see the following: > from rdkit import Chem from rdkit.Chem import AllChem > > Traceback (most recent call last): > File "", line 1, in > from rdkit.Chem import AllChem > File "C:\Python27\RDKit_2011_09_1\rdkit\Chem\AllChem.py", line 28, in > > from rdkit.Chem.rdSLNParse import * > ImportError: DLL load failed: The specified module could not be found. If it's being caused by the SLN parser import, then the problem has to do with the boost regex library. I just checked the binary and it looks like I included the wrong dlls in the distribution. The short-term solution is quite simple: comment out the offending line in AllChem.py. This will only cause problems if you are using the SLN parser in your code. -greg -greg -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity and more. Splunk takes this data and makes sense of it. Business sense. IT sense. Common sense. http://p.sf.net/sfu/splunk-d2d-oct ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] 2011.09 (Q3 2011) RDKit release
I'm traveling and don't have access to the machine where I normally do windows builds, but I tried to create an alternate binary using dlls from an older RDKit distribution. Please give this a try: http://code.google.com/p/rdkit/downloads/detail?name=RDKit_2011_09_1.win32.py27.pkg2.zip and let me know if it works. If so I will go ahead and replace the current binaries with this one. Sorry for the hassle and thanks for the help, -greg -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity and more. Splunk takes this data and makes sense of it. Business sense. IT sense. Common sense. http://p.sf.net/sfu/splunk-d2d-oct ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] 2011.09 (Q3 2011) RDKit release
Hi Greg, This should work - this is how I solved a similar problem with the latest RDKit version for Windows. Cheers, George On 16 October 2011 16:32, Greg Landrum wrote: > I'm traveling and don't have access to the machine where I normally do > windows builds, but I tried to create an alternate binary using dlls > from an older RDKit distribution. > > Please give this a try: > > http://code.google.com/p/rdkit/downloads/detail?name=RDKit_2011_09_1.win32.py27.pkg2.zip > and let me know if it works. If so I will go ahead and replace the > current binaries with this one. > > Sorry for the hassle and thanks for the help, > -greg > > > -- > All the data continuously generated in your IT infrastructure contains a > definitive record of customers, application performance, security > threats, fraudulent activity and more. Splunk takes this data and makes > sense of it. Business sense. IT sense. Common sense. > http://p.sf.net/sfu/splunk-d2d-oct > ___ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity and more. Splunk takes this data and makes sense of it. Business sense. IT sense. Common sense. http://p.sf.net/sfu/splunk-d2d-oct___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] 2011.09 (Q3 2011) RDKit release
Thanks Greg, and George. I have not tested the new win-py27 binary fully - but it does at least behave itself when importing AllChem! 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 Oakdene Court 613 Reading Road Winnersh, Berkshire RG41 5UA. Tel: +44 118 977 3133 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.. __-- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity and more. Splunk takes this data and makes sense of it. Business sense. IT sense. Common sense. http://p.sf.net/sfu/splunk-d2d-oct___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] 2011.09 (Q3 2011) RDKit release
Hi there, Has anyone tried installing the new release on Mac OS X Lion? I installed an earlier version on Leopard, had a few difficulties, but got there in the end. Would be great to know if any one had any advice on installing on Lion before I give it a go! Thanks Sarah Langdon On 8 Oct 2011, at 17:40, Greg Landrum wrote: > I'm very happy to announce that the next version of the RDKit -- > 2011.09 (a.k.a Q3 2011) -- is released. > > The release notes are below. > > The source release is on the sourceforge downloads page: > http://sourceforge.net/projects/rdkit/files/rdkit/Q3_2011/ > The files can also be downloaded from the google project page: > http://code.google.com/p/rdkit/downloads/list > The binaries for Windows, Python 2.6 and Python 2.7 are uploaded > already. > > Thanks to the everyone who submitted bug reports and suggestions for > this release! > > Please let me know if you find any problems with the release or have > suggestions for the next one. > > -greg > > > ** Release_2011.09.1 *** > (Changes relative to Release_2011.06.1) > > !! IMPORTANT !! > - A bug in the definition of the Lipinski HBD descriptor was fixed in > this release. The descriptor Lipinski.NHOHCount will return > different values for molecules containing Ns or Os with more than > one attached H. > > Acknowledgements: > Eddie Cao, Richard Cooper, Paul Czodrowski, James Davidson, George > Papadatos, Riccardo Vianello > > Bug Fixes: > - A problem with interpretation of stereochemistry from mol files was > fixed (Issue 3374639) > - Sterochemistry information for exocyclic double bonds in mol blocks > is no longer lost. (Issue 3375647) > - linear double bonds from mol files now have their stereochemistry > set correctly(Issue 3375684) > - Chirality for phosphates and sulfates is not longer automatically > removed. (Issue 3376319) > - A bug with the reading of query information from mol files was > fixed. (Issue 3392107) > - Sterochemistry is now cleaned up after processing mol2 > files. (Issue 3399798) > - mergeQueryHs now correctly handles atoms with multiple Hs (Issue > 3415204) > - mergeQueryHs now correctly handles atoms without initial query > information (Issue 3415206) > - the calcLipinskiHBD() (equivalent to Lipinski.NHOHCount) descriptor > now correctly handles Ns or Os with multiple Hs. (Issue 3415534) > - Morgan fingerprints generated using the fromAtoms argument now have > all bits from those atoms set.(Issue 3415636) > - A problem with the way MolSuppliers handle the EOF condition when > built with the most recent versions of g++ was fixed. > - Translation of RDKit stereochemistry information into InChI > stereochemistry information is improved. > > New Features: > > New Database Cartridge Features: > - molecules can now be built from mol blocks using the function > mol_from_ctab(). The corresponding is_valid_ctab() function was > also added. > - the radius argument is now optional for the functions morganbv_fp, > morgan_fp, featmorganbv_fp, and featmorgan_fp. The default radius > for all four functions is 2. > > Deprecated modules (to be removed in next release): > > Removed modules: > > Other: > - The documentation in $RDBASE/Docs/Book has been migrated to use > Sphinx instead of OpenOffice. > - The optional InChI support can now be built using a system > installation of the InChI library. > > -- > All of the data generated in your IT infrastructure is seriously > valuable. > Why? It contains a definitive record of application performance, > security > threats, fraudulent activity, and more. Splunk takes this data and > makes > sense of it. IT sense. And common sense. > http://p.sf.net/sfu/splunk-d2dcopy2 > ___ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network. -- The demand for IT networking professionals continues to grow, and the demand for specialized networking skills is growing even more rapidly. Take a complimentary Learning@Ciosco Self-Assessment and learn about Cisco certifications, training, and career opportunities. http://p.sf.net/sfu/cisco-dev2dev ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/
Re: [Rdkit-discuss] 2011.09 (Q3 2011) RDKit release
Hi Sarah, On Thu, Oct 20, 2011 at 5:07 AM, Sarah Langdon wrote: > > Has anyone tried installing the new release on Mac OS X Lion? I installed an > earlier version on Leopard, had a few difficulties, but got there in the > end. Would be great to know if any one had any advice on installing on Lion > before I give it a go! Unfortunately not. I'm still running Leopard. If you try the install using the system python (not something from macports or one of the related services) it really ought to work. If not, please post the error messages and I will try to help. -greg -- The demand for IT networking professionals continues to grow, and the demand for specialized networking skills is growing even more rapidly. Take a complimentary Learning@Cisco Self-Assessment and learn about Cisco certifications, training, and career opportunities. http://p.sf.net/sfu/cisco-dev2dev ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] 2011.09 (Q3 2011) RDKit release
Hi Greg, Managed to install RDkit fine. I had to specify where the Python libraries were at the cmake stage as it didn't work the first time round without specifying. Other than that it was fairly straight forward :) Sarah On 21 Oct 2011, at 02:21, Greg Landrum wrote: > Hi Sarah, > > On Thu, Oct 20, 2011 at 5:07 AM, Sarah Langdon > wrote: >> >> Has anyone tried installing the new release on Mac OS X Lion? I installed an >> earlier version on Leopard, had a few difficulties, but got there in the >> end. Would be great to know if any one had any advice on installing on Lion >> before I give it a go! > > Unfortunately not. I'm still running Leopard. If you try the install > using the system python (not something from macports or one of the > related services) it really ought to work. If not, please post the > error messages and I will try to help. > > -greg The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network. -- The demand for IT networking professionals continues to grow, and the demand for specialized networking skills is growing even more rapidly. Take a complimentary Learning@Cisco Self-Assessment and learn about Cisco certifications, training, and career opportunities. http://p.sf.net/sfu/cisco-dev2dev ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] 2011.09 (Q3 2011) RDKit release
On Sun, Oct 23, 2011 at 3:05 PM, Sarah Langdon wrote: > Hi Greg, > > Managed to install RDkit fine. I had to specify where the Python libraries > were at the cmake stage as it didn't work the first time round without > specifying. Other than that it was fairly straight forward :) Excellent. I'm glad to hear it. I would like to add the info to the list of working builds (http://code.google.com/p/rdkit/wiki/WorkingBuilds) Would you mind letting me know which versions of g++, boost, and python you used? Thanks, -greg -- The demand for IT networking professionals continues to grow, and the demand for specialized networking skills is growing even more rapidly. Take a complimentary Learning@Cisco Self-Assessment and learn about Cisco certifications, training, and career opportunities. http://p.sf.net/sfu/cisco-dev2dev ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] 2011.09 (Q3 2011) RDKit release
Hi Greg, Sure, I used g++ 4.2.1, boost 1.46.1 and python 2.7. Thanks, Sarah On 23 Oct 2011, at 15:04, Greg Landrum wrote: > On Sun, Oct 23, 2011 at 3:05 PM, Sarah Langdon > wrote: >> Hi Greg, >> >> Managed to install RDkit fine. I had to specify where the Python >> libraries were at the cmake stage as it didn't work the first time >> round without specifying. Other than that it was fairly straight >> forward :) > > Excellent. I'm glad to hear it. > > I would like to add the info to the list of working builds > (http://code.google.com/p/rdkit/wiki/WorkingBuilds) Would you mind > letting me know which versions of g++, boost, and python you used? > > Thanks, > -greg The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network. -- The demand for IT networking professionals continues to grow, and the demand for specialized networking skills is growing even more rapidly. Take a complimentary Learning@Cisco Self-Assessment and learn about Cisco certifications, training, and career opportunities. http://p.sf.net/sfu/cisco-dev2dev ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
