Re: [Rdkit-discuss] Tests failing on Windows: more info
Hi Greg Thanks for the fix – I can confirm that rev4861 builds and passes all the tests under my environment now. 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.. __ -- 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] RDKit YYDEBUG Redefined error
Hi Dante, Looks like you are trying to build a fairly old version of the RDKit. Newer versions no longer require the flex/bison step, so if you could switch to one of those I think it would make your life easier. -greg On Wed, Feb 11, 2015 at 4:35 AM, Dante wrote: > Hello, > > I am trying to install rdkit on Ubuntu 14.04, and am building from source > so I can get the inchi functionality. When I run make, I get: > > [ 24%] Building CXX object > Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o > > smiles.yy:25:1: warning: "YYDEBUG" redefined > > In file included from smiles.yy:21: > > /sw64/src/fink.build/rdkit-2013.06.1-5/RDKit_2013_06_1/Code/GraphMol/SmilesParse/smiles.tab.hpp:37:1: > warning: this is the location of the previous definition > > smiles.yy: In function 'int yysmiles_parse(const char*, > std::vector >*, > std::list >*, void*)': > > smiles.yy:23: error: too few arguments to function 'int > yysmiles_lex(YYSTYPE*, void*)' > > /sw64/src/fink.build/rdkit-2013.06.1-5/RDKit_2013_06_1/Code/GraphMol/SmilesParse/smiles.tab.cpp:1245: > error: at this point in file > > make[2]: *** > [Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o] Error > 1 > > make[1]: *** [Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/all] Error > 2 > > make: *** [all] Error 2 > > I've seen on previous messages that one potential fix to this is to downgrade > to bison 2.7.1, which I've done, but this error persists. Any ideas? > > Thanks, > > DP > > > > > -- > 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] Tests failing on Windows: more info
This particular problem was my fault. It had been a while since I did a windows build, so I hadn't caught the problem you point out below. I just fixed it and checked in the changes. Apologies that you ended up wasting time on this. If anyone knows of an online continuous-integration providers (like Travis) that support Windows, I would be very, very happy to hear about it. -greg On Tue, Feb 10, 2015 at 7:14 PM, James Davidson wrote: > Hi Paolo, Greg, et al. > > > > I have also been having some problems recently building (64-bit Windows) > from recent github versions, but I don’t know if this is related to what > you see, Paolo… > > My environment is Win 7 64-bit, CMake 3.0.0, boost_1_55_0-msvc-11.0-64, MS > Visual Studio Express 2012. > > > > I have done a bit of version rolling-back and forwards to see if I can > pinpoint the last version that builds with no errors, and this is what I > have found so far (sorted by revision, not by sequence of attempts!): > > > > 4577 - compiles fine, - passes all tests > > *4618* - as above > > 4649 - some errors during compile, -passes all tests except the > molDraw2D bits (which are also involved in the errors) > > 4651 - as above > > 4743 - as above > > *4765* - as above > > 4780 - pyGraphMolWrap now fails test > > 4826 - this is where significant problems start (for me at least). > pyGraphMolWrap still fails, but now with a segfault > > 4859 - same segfault as above. Also pymolDraw2D test fails… > > > > > > The errors I start to see for molDraw2D are this sort of thing (is this > expected?): > > > > Error 49 error C2668: 'boost::tuples::tie' : ambiguous call > to overloaded function > C:\RDKit\Code\GraphMol\MolDraw2D\MolDraw2D.cpp 341 > 1 MolDraw2D > > Error 50 error C2668: 'boost::tuples::tie' : ambiguous call > to overloaded function > C:\RDKit\Code\GraphMol\MolDraw2D\MolDraw2D.cpp 353 > 1 MolDraw2D > > Error 51 error C2668: 'boost::tuples::tie' : ambiguous call > to overloaded function > C:\RDKit\Code\GraphMol\MolDraw2D\MolDraw2D.cpp 357 > 1 MolDraw2D > > Error 61 error C2668: 'boost::tuples::tie' : ambiguous call > to overloaded function > C:\RDKit\Code\GraphMol\MolDraw2D\MolDraw2D.cpp 544 > 1 MolDraw2D > > Error 63 error C2668: 'boost::tuples::tie' : ambiguous call > to overloaded function > C:\RDKit\Code\GraphMol\MolDraw2D\MolDraw2D.cpp 591 > 1 MolDraw2D > > Error 131 error LNK1181: cannot open input file > '..\..\..\lib\Release\MolDraw2D.lib' > C:\RDKit\build\Code\GraphMol\MolDraw2D\LINK moldraw2DTest1 > > Error 149 error LNK1181: cannot open input file > '..\..\..\lib\Release\MolDraw2D.lib' > C:\RDKit\build\Code\GraphMol\Wrap\LINK rdmolops > > > > > > If I see the above errors when building ‘ALL_BUILD’, I also see the > following error when building the ‘INSTALL’ section: > > > > Error 41 error MSB3073: The command "setlocal > > "C:\Program Files (x86)\CMake\bin\cmake.exe" -DBUILD_TYPE=Release -P > cmake_install.cmake > > if %errorlevel% neq 0 goto :cmEnd > > :cmEnd > > endlocal & call :cmErrorLevel %errorlevel% & goto :cmDone > > :cmErrorLevel > > exit /b %1 > > :cmDone > > if %errorlevel% neq 0 goto :VCEnd > > :VCEnd" exited with code 1.C:\Program Files > (x86)\MSBuild\Microsoft.Cpp\v4.0\V110\Microsoft.CppCommon.targets > 134 5 INSTALL > > > > > > > > Anyway, 4618 is the latest revision that I have tested where I see no > build errors, and 4765 is the latest revision I’ve found before I start to > see pyGraphMolWrap tests failing (or segfaults). For now, I have > rolled-back my installation to 4618 (but would be very happy if anyone can > figure-out what causes the problems with later revisions). > > > > 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. > >
[Rdkit-discuss] RDKit YYDEBUG Redefined error
Hello, I am trying to install rdkit on Ubuntu 14.04, and am building from source so I can get the inchi functionality. When I run make, I get: [ 24%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o smiles.yy:25:1: warning: "YYDEBUG" redefined In file included from smiles.yy:21: /sw64/src/fink.build/rdkit-2013.06.1-5/RDKit_2013_06_1/Code/GraphMol/SmilesParse/smiles.tab.hpp:37:1: warning: this is the location of the previous definition smiles.yy: In function 'int yysmiles_parse(const char*, std::vector >*, std::list >*, void*)': smiles.yy:23: error: too few arguments to function 'int yysmiles_lex(YYSTYPE*, void*)' /sw64/src/fink.build/rdkit-2013.06.1-5/RDKit_2013_06_1/Code/GraphMol/SmilesParse/smiles.tab.cpp:1245: error: at this point in file make[2]: *** [Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o] Error 1 make[1]: *** [Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/all] Error 2 make: *** [all] Error 2 I've seen on previous messages that one potential fix to this is to downgrade to bison 2.7.1, which I've done, but this error persists. Any ideas? Thanks, DP -- 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] Bad conformer ID?
On 02/10/2015 10:33 AM, Greg Landrum wrote: > You might want to take a look at this older thread for some additional > hints: > http://www.mail-archive.com/rdkit-discuss%40lists.sourceforge.net/msg00484.html That's why programmers hate "domain" scientists: why num = mol.GetNumAtoms() if num > 500 ... Why not 499 or 502? I guess I'll run def _to_mol( self ) : assert isinstance(self._mol,rdkit.Chem.rdchem.Mol) m = rdkit.Chem.AddHs(self._mol) rc = rdkit.Chem.AllChem.EmbedMolecule(m) if rc < 0 : rc = rdkit.Chem.AllChem.EmbedMolecule(m,useRandomCoords=True) if rc == 0 : try : if rdkit.Chem.AllChem.UFFOptimizeMolecule(m) != 0 : rdkit.Chem.AllChem.UFFOptimizeMolecule(m,maxIters=1000) except ValueError : pass return rdkit.Chem.MolToMolBlock( m ) until the next one crashes it. Thank you -- Dimitri Maziuk Programmer/sysadmin BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu signature.asc Description: OpenPGP digital signature -- 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 failing on Windows: more info
Hi Paolo, Greg, et al. I have also been having some problems recently building (64-bit Windows) from recent github versions, but I don't know if this is related to what you see, Paolo... My environment is Win 7 64-bit, CMake 3.0.0, boost_1_55_0-msvc-11.0-64, MS Visual Studio Express 2012. I have done a bit of version rolling-back and forwards to see if I can pinpoint the last version that builds with no errors, and this is what I have found so far (sorted by revision, not by sequence of attempts!): 4577 - compiles fine, - passes all tests 4618 - as above 4649 - some errors during compile, -passes all tests except the molDraw2D bits (which are also involved in the errors) 4651 - as above 4743 - as above 4765 - as above 4780 - pyGraphMolWrap now fails test 4826 - this is where significant problems start (for me at least). pyGraphMolWrap still fails, but now with a segfault 4859 - same segfault as above. Also pymolDraw2D test fails... The errors I start to see for molDraw2D are this sort of thing (is this expected?): Error 49 error C2668: 'boost::tuples::tie' : ambiguous call to overloaded function C:\RDKit\Code\GraphMol\MolDraw2D\MolDraw2D.cpp 341 1 MolDraw2D Error 50 error C2668: 'boost::tuples::tie' : ambiguous call to overloaded function C:\RDKit\Code\GraphMol\MolDraw2D\MolDraw2D.cpp 353 1 MolDraw2D Error 51 error C2668: 'boost::tuples::tie' : ambiguous call to overloaded function C:\RDKit\Code\GraphMol\MolDraw2D\MolDraw2D.cpp 357 1 MolDraw2D Error 61 error C2668: 'boost::tuples::tie' : ambiguous call to overloaded function C:\RDKit\Code\GraphMol\MolDraw2D\MolDraw2D.cpp 544 1 MolDraw2D Error 63 error C2668: 'boost::tuples::tie' : ambiguous call to overloaded function C:\RDKit\Code\GraphMol\MolDraw2D\MolDraw2D.cpp 591 1 MolDraw2D Error 131 error LNK1181: cannot open input file '..\..\..\lib\Release\MolDraw2D.lib' C:\RDKit\build\Code\GraphMol\MolDraw2D\LINK moldraw2DTest1 Error 149 error LNK1181: cannot open input file '..\..\..\lib\Release\MolDraw2D.lib' C:\RDKit\build\Code\GraphMol\Wrap\LINK rdmolops If I see the above errors when building 'ALL_BUILD', I also see the following error when building the 'INSTALL' section: Error 41 error MSB3073: The command "setlocal "C:\Program Files (x86)\CMake\bin\cmake.exe" -DBUILD_TYPE=Release -P cmake_install.cmake if %errorlevel% neq 0 goto :cmEnd :cmEnd endlocal & call :cmErrorLevel %errorlevel% & goto :cmDone :cmErrorLevel exit /b %1 :cmDone if %errorlevel% neq 0 goto :VCEnd :VCEnd" exited with code 1.C:\Program Files (x86)\MSBuild\Microsoft.Cpp\v4.0\V110\Microsoft.CppCommon.targets 134 5 INSTALL Anyway, 4618 is the latest revision that I have tested where I see no build errors, and 4765 is the latest revision I've found before I start to see pyGraphMolWrap tests failing (or segfaults). For now, I have rolled-back my installation to 4618 (but would be very happy if anyone can figure-out what causes the problems with later revisions). 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.. __-- Dive into the World of Paralle
Re: [Rdkit-discuss] Tests failing on Windows: more info
Hi James, investigating what is going wrong in the Windows build is on my to-do list for 21-22 Feb; I'll let you know if I manage to find something. Kind regards, Paolo On 02/10/2015 06:14 PM, James Davidson wrote: Hi Paolo, Greg, et al. I have also been having some problems recently building (64-bit Windows) from recent github versions, but I don’t know if this is related to what you see, Paolo… My environment is Win 7 64-bit, CMake 3.0.0, boost_1_55_0-msvc-11.0-64, MS Visual Studio Express 2012. I have done a bit of version rolling-back and forwards to see if I can pinpoint the last version that builds with no errors, and this is what I have found so far (sorted by revision, not by sequence of attempts!): 4577 - compiles fine, - passes all tests *4618* - as above 4649 - some errors during compile, -passes all tests except the molDraw2D bits (which are also involved in the errors) 4651 - as above 4743 - as above *4765* - as above 4780 - pyGraphMolWrap now fails test 4826 - this is where significant problems start (for me at least). pyGraphMolWrap still fails, but now with a segfault 4859 - same segfault as above. Also pymolDraw2D test fails… The errors I start to see for molDraw2D are this sort of thing (is this expected?): Error 49 error C2668: 'boost::tuples::tie' : ambiguous call to overloaded function C:\RDKit\Code\GraphMol\MolDraw2D\MolDraw2D.cpp 341 1 MolDraw2D Error 50 error C2668: 'boost::tuples::tie' : ambiguous call to overloaded function C:\RDKit\Code\GraphMol\MolDraw2D\MolDraw2D.cpp 353 1 MolDraw2D Error 51 error C2668: 'boost::tuples::tie' : ambiguous call to overloaded function C:\RDKit\Code\GraphMol\MolDraw2D\MolDraw2D.cpp 357 1 MolDraw2D Error 61 error C2668: 'boost::tuples::tie' : ambiguous call to overloaded function C:\RDKit\Code\GraphMol\MolDraw2D\MolDraw2D.cpp 544 1 MolDraw2D Error 63 error C2668: 'boost::tuples::tie' : ambiguous call to overloaded function C:\RDKit\Code\GraphMol\MolDraw2D\MolDraw2D.cpp 591 1 MolDraw2D Error 131 error LNK1181: cannot open input file '..\..\..\lib\Release\MolDraw2D.lib' C:\RDKit\build\Code\GraphMol\MolDraw2D\LINK moldraw2DTest1 Error 149 error LNK1181: cannot open input file '..\..\..\lib\Release\MolDraw2D.lib' C:\RDKit\build\Code\GraphMol\Wrap\LINK rdmolops If I see the above errors when building ‘ALL_BUILD’, I also see the following error when building the ‘INSTALL’ section: Error 41 error MSB3073: The command "setlocal "C:\Program Files (x86)\CMake\bin\cmake.exe" -DBUILD_TYPE=Release -P cmake_install.cmake if %errorlevel% neq 0 goto :cmEnd :cmEnd endlocal & call :cmErrorLevel %errorlevel% & goto :cmDone :cmErrorLevel exit /b %1 :cmDone if %errorlevel% neq 0 goto :VCEnd :VCEnd" exited with code 1. C:\Program Files (x86)\MSBuild\Microsoft.Cpp\v4.0\V110\Microsoft.CppCommon.targets 134 5 INSTALL Anyway, 4618 is the latest revision that I have tested where I see no build errors, and 4765 is the latest revision I’ve found before I start to see pyGraphMolWrap tests failing (or segfaults). For now, I have rolled-back my installation to 4618 (but would be very happy if anyone can figure-out what causes the problems with later revisions). 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.. __ ---
Re: [Rdkit-discuss] Bad conformer ID?
On 2/9/2015 11:12 PM, Greg Landrum wrote:
> Hi Dimitri,
>
> AllChem.EmbedMolecule returns the ID of the conformer that is generated,
> -1 on failure. In this case you get -1.
>
> In [13]: m = Chem.MolFromMolFile('./tetraoleylcardiolipin.sdf')
> In [15]: AllChem.EmbedMolecule(m)
> Out[15]: -1
>
> For large molecules like this one, it is often more effective to provide
> the useRandomCoords argument to EmbedMolecule:
Thanks, but I'm trying to run an unattended pipeline. Is there a
downside of calling useRandomCoords on molecules that don't have this
problem? Would this be the way to go:
x = AllChem.EmbedMolecule(m)
if x < 0 :
x = AllChem.EmbedMolecule(m,useRandomCoords=True)
# if x is still < 0 -- then what?
try :
AllChem.UFFOptimizeMolecule( m )
except :
pass
MolToMolBlock( m )
Thanks again,
Dima
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Re: [Rdkit-discuss] Bad conformer ID?
You might want to take a look at this older thread for some additional
hints:
http://www.mail-archive.com/rdkit-discuss%40lists.sourceforge.net/msg00484.html
-greg
On Tue, Feb 10, 2015 at 5:13 PM, Dmitri Maziuk
wrote:
> On 2/9/2015 11:12 PM, Greg Landrum wrote:
>
>> Hi Dimitri,
>>
>> AllChem.EmbedMolecule returns the ID of the conformer that is generated,
>> -1 on failure. In this case you get -1.
>>
>> In [13]: m = Chem.MolFromMolFile('./tetraoleylcardiolipin.sdf')
>> In [15]: AllChem.EmbedMolecule(m)
>> Out[15]: -1
>>
>> For large molecules like this one, it is often more effective to provide
>> the useRandomCoords argument to EmbedMolecule:
>>
>
> Thanks, but I'm trying to run an unattended pipeline. Is there a downside
> of calling useRandomCoords on molecules that don't have this problem? Would
> this be the way to go:
>
> x = AllChem.EmbedMolecule(m)
> if x < 0 :
> x = AllChem.EmbedMolecule(m,useRandomCoords=True)
>
> # if x is still < 0 -- then what?
>
> try :
> AllChem.UFFOptimizeMolecule( m )
> except :
> pass
> MolToMolBlock( m )
>
>
> Thanks again,
>
> Dima
>
>
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