[Rdkit-discuss] Homebrew formula updated to 2013.09 release
Hi, This is a bit late, but I just updated the Homebrew formula for RDKit to the 2013.09 release, or more precisely, commit 3fec9346f5, which fixed the std::lib issue discussed in an earlier thread. (It will declare itself as "2014.03.1pre" as a result of this.) Note that if you recently upgraded your Mac with existing RDKit to Mavericks, you will need to rebrew boost before you install RDKit. It's always safe to just do brew uninstall boost rdkit brew install rdkit Regards, Eddie-- November Webinars for C, C++, Fortran Developers Accelerate application performance with scalable programming models. Explore techniques for threading, error checking, porting, and tuning. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] RDKit Carborane SMILES Support?
Hi,
Somewhat of a corner case I know but thought it might be worth just mentioning.
This class of compounds:
http://www.molport.com/buy-chemicals/molecular-formula/C2B10
I’m assuming that the SMILES are valid so:
Python 2.7.5 (default, Jul 30 2013, 12:06:31)
[GCC 4.2.1 Compatible Apple LLVM 4.2 (clang-425.0.28)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> from rdkit import Chem
>>> m =
>>> Chem.MolFromSmiles("[B]1234[B]567[B]118[B]229[B]33%10[B]454[B]656[B]711[B]822[C]933[B]%1045[C]6123")
[19:33:19] Explicit valence for atom # 0 B, 5, is greater than permitted
I have rdkit-2013.03.2 installed currently.
Kind regards--
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Re: [Rdkit-discuss] libc++ fix for RDKit_2013_06_1
FYI if you want to still use homebrew to install rdkit with the fixes applied: brew install --HEAD rdkit will pull from git head for the rdkit install and compiles on mavericks -David On Tue, Nov 5, 2013 at 11:26 AM, Hans De Winter wrote: > Hi all, > > all errors are gone with the given changes applied :-) > > Just for your information, my installation workflow was the following: > > 1) brew install boost > 2) brew install cmake > 3) export RDBASE="/usr/local/src/RDKit_2013_09_1" > 4) Modification of the $RDBASE/Code/RDGeneral/Dict.h file as indicated > 5) export > DYLD_LIBRARY_PATH="$DYLD_LIBRARY_PATH:$RDBASE/lib:/usr/local/lib" > 6) export PYTHONPATH="$PYTHONPATH:$RDBASE" > 7) mkdir build; cd build > 8) cmake -D > PYTHON_LIBRARY=/System/Library/Frameworks/Python.framework/Versions/2.7/lib/libpython2.7.dylib > -D > PYTHON_INCLUDE_DIR=/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7/ > -D PYTHON_EXECUTABLE=/usr/bin/python .. > 9) make > 10) sudo make install > > > > Still only a few warnings left, and just as a matter for being complete, > here are the snippets of these warnings: > > [ 15%] Building CXX object > Code/Numerics/Optimizer/CMakeFiles/Optimizer_static.dir/LinearSearch.cpp.o > Linking CXX static library libOptimizer_static.a > /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: > file: libOptimizer_static.a(BFGSOpt.cpp.o) has no symbols > /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: > file: libOptimizer_static.a(LinearSearch.cpp.o) has no symbols > /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: > file: libOptimizer_static.a(BFGSOpt.cpp.o) has no symbols > /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: > file: libOptimizer_static.a(LinearSearch.cpp.o) has no symbols > /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: > warning for library: libOptimizer_static.a the table of contents is empty > (no object file members in the library define global symbols) > > > [ 18%] Building CXX object > Code/ForceField/CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o > /usr/local/src/RDKit_2013_09_1/Code/ForceField/MMFF/Nonbonded.cpp:91:75: > warning: > adding 'unsigned int' to a string does not append to the string > [-Wstring-plus-int] > PRECONDITION(mmffVdWParamsIAtom, "bad MMFFVdW parameters for atom " > + idx1); > > ~~~^~ > /usr/local/src/RDKit_2013_09_1/Code/RDGeneral/Invariant.h:121:55: note: > expanded > from macro 'PRECONDITION' > Invar::Invariant inv( "Pre-condition Violation", mess, \ > ^ > /usr/local/src/RDKit_2013_09_1/Code/ForceField/MMFF/Nonbonded.cpp:91:75: note: > use array indexing to silence this warning > PRECONDITION(mmffVdWParamsIAtom, "bad MMFFVdW parameters for atom " > + idx1); > ^ >& [ > /usr/local/src/RDKit_2013_09_1/Code/RDGeneral/Invariant.h:121:55: note: > expanded > from macro 'PRECONDITION' > Invar::Invariant inv( "Pre-condition Violation", mess, \ > ^ > /usr/local/src/RDKit_2013_09_1/Code/ForceField/MMFF/Nonbonded.cpp:92:75: > warning: > adding 'unsigned int' to a string does not append to the string > [-Wstring-plus-int] > PRECONDITION(mmffVdWParamsJAtom, "bad MMFFVdW parameters for atom " > + idx2); > > ~~~^~ > /usr/local/src/RDKit_2013_09_1/Code/RDGeneral/Invariant.h:121:55: note: > expanded > from macro 'PRECONDITION' > Invar::Invariant inv( "Pre-condition Violation", mess, \ > ^ > /usr/local/src/RDKit_2013_09_1/Code/ForceField/MMFF/Nonbonded.cpp:92:75: note: > use array indexing to silence this warning > PRECONDITION(mmffVdWParamsJAtom, "bad MMFFVdW parameters for atom " > + idx2); > ^ >& [ > /usr/local/src/RDKit_2013_09_1/Code/RDGeneral/Invariant.h:121:55: note: > expanded > from macro 'PRECONDITION' > Invar::Invariant inv( "Pre-condition Violation", mess, \ > ^ > 2 warnings generated. > > > [ 21%] Building CXX object > Code/ForceField/CMakeFiles/ForceField_static.dir/MMFF/Nonbonded.cpp.o > /usr/local/src/RDKit_2013_09_1/Code/ForceField/MMFF/Nonbonded.cpp:91:75: > warning: > adding 'unsigned int' to a string does not append to the string > [-Wstring-plus-int] > PRECONDITION(mmffVdWParamsIAtom, "bad MMFFVdW parameters for atom " > + idx1); > > ~~~^~
Re: [Rdkit-discuss] libc++ fix for RDKit_2013_06_1
Hi all, all errors are gone with the given changes applied :-) Just for your information, my installation workflow was the following: 1) brew install boost 2) brew install cmake 3) export RDBASE="/usr/local/src/RDKit_2013_09_1" 4) Modification of the $RDBASE/Code/RDGeneral/Dict.h file as indicated 5) export DYLD_LIBRARY_PATH="$DYLD_LIBRARY_PATH:$RDBASE/lib:/usr/local/lib" 6) export PYTHONPATH="$PYTHONPATH:$RDBASE" 7) mkdir build; cd build 8) cmake -D PYTHON_LIBRARY=/System/Library/Frameworks/Python.framework/Versions/2.7/lib/libpython2.7.dylib -D PYTHON_INCLUDE_DIR=/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7/ -D PYTHON_EXECUTABLE=/usr/bin/python .. 9) make 10) sudo make install Still only a few warnings left, and just as a matter for being complete, here are the snippets of these warnings: [ 15%] Building CXX object Code/Numerics/Optimizer/CMakeFiles/Optimizer_static.dir/LinearSearch.cpp.o Linking CXX static library libOptimizer_static.a /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: libOptimizer_static.a(BFGSOpt.cpp.o) has no symbols /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: libOptimizer_static.a(LinearSearch.cpp.o) has no symbols /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: libOptimizer_static.a(BFGSOpt.cpp.o) has no symbols /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: libOptimizer_static.a(LinearSearch.cpp.o) has no symbols /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: warning for library: libOptimizer_static.a the table of contents is empty (no object file members in the library define global symbols) [ 18%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o /usr/local/src/RDKit_2013_09_1/Code/ForceField/MMFF/Nonbonded.cpp:91:75: warning: adding 'unsigned int' to a string does not append to the string [-Wstring-plus-int] PRECONDITION(mmffVdWParamsIAtom, "bad MMFFVdW parameters for atom " + idx1); ~~~^~ /usr/local/src/RDKit_2013_09_1/Code/RDGeneral/Invariant.h:121:55: note: expanded from macro 'PRECONDITION' Invar::Invariant inv( "Pre-condition Violation", mess, \ ^ /usr/local/src/RDKit_2013_09_1/Code/ForceField/MMFF/Nonbonded.cpp:91:75: note: use array indexing to silence this warning PRECONDITION(mmffVdWParamsIAtom, "bad MMFFVdW parameters for atom " + idx1); ^ & [ /usr/local/src/RDKit_2013_09_1/Code/RDGeneral/Invariant.h:121:55: note: expanded from macro 'PRECONDITION' Invar::Invariant inv( "Pre-condition Violation", mess, \ ^ /usr/local/src/RDKit_2013_09_1/Code/ForceField/MMFF/Nonbonded.cpp:92:75: warning: adding 'unsigned int' to a string does not append to the string [-Wstring-plus-int] PRECONDITION(mmffVdWParamsJAtom, "bad MMFFVdW parameters for atom " + idx2); ~~~^~ /usr/local/src/RDKit_2013_09_1/Code/RDGeneral/Invariant.h:121:55: note: expanded from macro 'PRECONDITION' Invar::Invariant inv( "Pre-condition Violation", mess, \ ^ /usr/local/src/RDKit_2013_09_1/Code/ForceField/MMFF/Nonbonded.cpp:92:75: note: use array indexing to silence this warning PRECONDITION(mmffVdWParamsJAtom, "bad MMFFVdW parameters for atom " + idx2); ^ & [ /usr/local/src/RDKit_2013_09_1/Code/RDGeneral/Invariant.h:121:55: note: expanded from macro 'PRECONDITION' Invar::Invariant inv( "Pre-condition Violation", mess, \ ^ 2 warnings generated. [ 21%] Building CXX object Code/ForceField/CMakeFiles/ForceField_static.dir/MMFF/Nonbonded.cpp.o /usr/local/src/RDKit_2013_09_1/Code/ForceField/MMFF/Nonbonded.cpp:91:75: warning: adding 'unsigned int' to a string does not append to the string [-Wstring-plus-int] PRECONDITION(mmffVdWParamsIAtom, "bad MMFFVdW parameters for atom " + idx1); ~~~^~ /usr/local/src/RDKit_2013_09_1/Code/RDGeneral/Invariant.h:121:55: note: expanded from macro 'PRECONDITION' Invar::Invariant inv( "Pre-condition Violation", mess, \ ^ /usr/local/src/RDKit_2013_09_1/Code/ForceField/MMFF/Nonbonded.cpp:91:75: note: u
[Rdkit-discuss] ReplaceSubstructs Output
Hello, I am building a tool with multiple calls of the ReplaceSustructs on the same structure. Is there any easy way to place the output of each call in a pickle or some temporary holder? At the moment I have to iterate through each output and the code looks a bit awkward. Thanks Basil -- November Webinars for C, C++, Fortran Developers Accelerate application performance with scalable programming models. Explore techniques for threading, error checking, porting, and tuning. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] UFF/MMFF atom types
Dear Greg and Paolo,
Thanks for your replies. Indeed, there is no quick fix - the perfect
solution would be to use a custom force field.
Best wishes,
Michal
On 5 November 2013 06:56, Paolo Tosco wrote:
> Hi both,
>
> now I realize that yesterday I replied to Michal and not to the list; sorry
> about that. Adding the option to force an atom type replacement wouldn't be
> too much work, but would not be ideal because in cause of selenium you would
> get, for instance, the same VdW radius and equilibrium bond distances as for
> sulfur, which would both be too short. That could also be handled upstream
> the atom typing by replacing Se with S and putting back Se downstream as I
> suggested yesterday to Michal, but again a bit of a hack. Probably a better
> solution would be to allow the user to provide some new parameters (as for
> UFF, adding Python support) and fall back to a related atom type (sulfur, in
> this case) for the missing ones. I'll look into that during the next days
> and let you know.
>
> Best,
> p.
>
>
> --
> ==
> Paolo Tosco, Ph.D.
> Department of Drug Science and Technology
> Via Pietro Giuria, 9 - 10125 Torino (Italy)
> Tel: +39 011 670 7680 | Mob: +39 348 5537206
> Fax: +39 011 670 7687 | E-mail: paolo.to...@unito.it
> http://open3dqsar.org | http://open3dalign.org
> ==
>
>
>
> On 5 Nov 2013, at 07:20, Greg Landrum wrote:
>
> Hi Michal,
>
>
> On Mon, Nov 4, 2013 at 11:45 AM, Michal Krompiec
> wrote:
>>
>> Hello,
>> Is Se defined in UFF and/or MMFF94? Apparently, molecules with
>> selenophene moieties don't optimize in RDKit, and a warning appears in
>> the log: UFFTYPER: Unrecognized atom type: Se2+2
>
>
> Right. UFF Parameters are there for sp3 Se ("Se3+2"), but not for the sp2
> version.
>
> There are no MMFF94 parameters for Se.
>
>> Is it possible to define/modify the force field by hand? (for example,
>> use the parametrs of S for Se)
>
>
> If you are working from C++, you can provide UFF parameters when you build
> the force field, but it's not currently possible to do so from Python. It's
> probably possible to add an option to the python UFF code to allow you to
> provide a new atom type (or to over-ride parameters for an existing atom
> type); I'd have to look into that.
> In the meantime, the quickest thing you could do would be to modify
> $RDBASE/Code/ForceField/UFF/Params.cpp to add the atom type you want and
> then to rebuild the RDKit.
>
> I guess that adding new atom types to MMFF94S is considerably more complex.
> Here one could imagine providing an interface to explicitly set the type of
> an atom to another existing atom type. Paolo would have to let us know how
> much work that is.
>
> -greg
>
> --
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> techniques for threading, error checking, porting, and tuning. Get the most
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Re: [Rdkit-discuss] MolFromXYZ?
Dear Sereina, No, I have just a table of 3D coordinates (generated by cclib). This is equivalent to having an xyz file. I know that this conversion is possible with OpenBabel, but I would like to avoid using it for this particular purpose. It seems that the simplest way is to hardcode generation of SDF myself. Thanks, Michal On 4 November 2013 13:52, sereina riniker wrote: > Hi Michal, > > Well, if you have your 3D coordinates as a PDB file, you can read them in > with the new PDB parser and assign the bond orders based on a template > (generated from the SMILES of your molecule): > tmp = Chem.MolFromPDBFile(yourfilename) > template = Chem.MolFromSmiles(yoursmiles) > mol = AllChem.AssignBondOrdersFromTemplate(template, tmp) > > I don't know if this is what you were looking for. > > Best, > Sereina > > > > 2013/11/4 Michal Krompiec >> >> Hello, >> Is it possible to construct a Mol (or EditableMol) object out of a >> list of 3D coordinates? I am trying to write a bridge between cclib >> and RDKit, and I need a function to convert 3D geometries to SDF. >> Thanks, >> Michal >> >> >> -- >> Android is increasing in popularity, but the open development platform >> that >> developers love is also attractive to malware creators. Download this >> white >> paper to learn more about secure code signing practices that can help keep >> Android apps secure. >> >> http://pubads.g.doubleclick.net/gampad/clk?id=65839951&iu=/4140/ostg.clktrk >> ___ >> Rdkit-discuss mailing list >> Rdkit-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > > -- November Webinars for C, C++, Fortran Developers Accelerate application performance with scalable programming models. Explore techniques for threading, error checking, porting, and tuning. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
