Re: [Open Babel] stereo config question
We neither have R/S perception nor E/Z. - Noel On 19 November 2013 00:17, Dimitri Maziuk wrote: > Someone familiar with OB's stereo perception (Geoff?) > > -- is there a way to get 'R' and 'S' labels from one of the *Stereo classes? > > Also, is there a way to find E and Z labels for a bond? -- I could use > those, too. > > TIA > -- > Dimitri Maziuk > Programmer/sysadmin > BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu > > > > > -- > Shape the Mobile Experience: Free Subscription > Software experts and developers: Be at the forefront of tech innovation. > Intel(R) Software Adrenaline delivers strategic insight and game-changing > conversations that shape the rapidly evolving mobile landscape. Sign up now. > http://pubads.g.doubleclick.net/gampad/clk?id=63431311&iu=/4140/ostg.clktrk > ___ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311&iu=/4140/ostg.clktrk ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Problem for compiling the example files
Hello, I want to give an update of my problem in case other people face it in the future. I solved it only partially. Here is what I did, after installing on Virtualbox a clean Ubuntu Gnome 13.10 64bits system, and downloading the openbabel source (I tried with 2.3.1 and 2.3.2 the same procedure): tar zxf openbabel-2.3.2.tar.gz sudo apt-get install g++ cmake wx-common wx2.8-headers libwxbase2.8-dev libxml2-dev zlib1g-dev libeigen2-dev libcairo2-dev python-dev libperl-dev mkdir Programs mkdir Programs/Openbabel_2.3.2 cd openbabel-2.3.2/ cmake -DCMAKE_INSTALL_PREFIX=/home/nicolas/Programs/Openbabel_2.3.2 -DBUILD_GUI=OFF make make install make test The "make test" output was: "100% tests passed, 0 tests failed out of 58". I tried "obabel Aspirin.smi -O Aspirin.png --gen2D" (where Aspirin.smi is a file with only "O=C(Oc1c1C(=O)O)C Aspirin") and I get the good png scheme. So the installation of openbabel was successfull and is not the problem. I copied the Quickstart example found here http://openbabel.org/docs/current/UseTheLibrary/CppExamples.html in an example.cpp file. 1) I then created a "Makefile" file with : CC = g++ CFLAGS = -c -I /home/nicolas/Programs/Openbabel_2.3.1/include/openbabel-2.0 LDFLAGS = -lopenbabel -L /home/nicolas/Programs/Openbabel_2.3.1/lib all: example example: example.o $(CC) $(LDFLAGS) example.o -o example example.o: example.cpp $(CC) $(CFLAGS) $(LDFLAGS) example.cpp clean: rm -rf example.o example After typing "make", the compilation fails with the error previously reported : /tmp/cc2kfqde.o: In function `main': example.cpp:(.text+0x120): undefined reference to `OpenBabel::OBConversion::OBConversion(std::istream*, std::ostream*)' example.cpp:(.text+0x139): undefined reference to `OpenBabel::OBConversion::SetInAndOutFormats(char const*, char const*)' example.cpp:(.text+0x165): undefined reference to `OpenBabel::OBConversion::Convert()' example.cpp:(.text+0x19e): undefined reference to `OpenBabel::OBConversion::~OBConversion()' example.cpp:(.text+0x1e1): undefined reference to `OpenBabel::OBConversion::~OBConversion()' collect2: error: ld returned 1 exit status 2) I created a "CMakeLists.txt" file with: cmake_minimum_required(VERSION 2.6) add_executable(example example.cpp) target_link_libraries(example /home/nicolas/Programs/Openbabel_2.3.1/lib/libopenbabel.so) include_directories(/home/nicolas/Programs/Openbabel_2.3.1/include/openbabel-2.0) After typing "cmake" then "make", the file compiles. So I can compile and use the openbabel library for my project. However, I don't understant why it doesn't work directly with Makefile (and I would prefer use Makefile instead of cmake). Does anyone have an idea of why, and how to modify the Makefile to make it work? Thank you Nicolas -- View this message in context: http://forums.openbabel.org/Problem-for-compiling-the-example-files-tp4656837p4656869.html Sent from the General discussion mailing list archive at Nabble.com. -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311&iu=/4140/ostg.clktrk ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Problem for compiling the example files
When running "make" with the CMakeLists.txt, use instead "VERBOSE=1 make" and you can see the commands to g++. This may help answer your questions. - Noel On 17 November 2013 22:56, Nicolas Cheron wrote: > Hello, > > I want to give an update of my problem in case other people face it in the > future. I solved it only partially. Here is what I did, after installing on > Virtualbox a clean Ubuntu Gnome 13.10 64bits system, and downloading the > openbabel source (I tried with 2.3.1 and 2.3.2 the same procedure): > > tar zxf openbabel-2.3.2.tar.gz > sudo apt-get install g++ cmake wx-common wx2.8-headers libwxbase2.8-dev > libxml2-dev zlib1g-dev libeigen2-dev libcairo2-dev python-dev libperl-dev > mkdir Programs > mkdir Programs/Openbabel_2.3.2 > cd openbabel-2.3.2/ > cmake -DCMAKE_INSTALL_PREFIX=/home/nicolas/Programs/Openbabel_2.3.2 > -DBUILD_GUI=OFF > make > make install > make test > > The "make test" output was: "100% tests passed, 0 tests failed out of 58". I > tried "obabel Aspirin.smi -O Aspirin.png --gen2D" (where Aspirin.smi is a > file with only "O=C(Oc1c1C(=O)O)C Aspirin") and I get the good png > scheme. So the installation of openbabel was successfull and is not the > problem. > > I copied the Quickstart example found here > http://openbabel.org/docs/current/UseTheLibrary/CppExamples.html in an > example.cpp file. > > 1) I then created a "Makefile" file with : > > CC = g++ > CFLAGS = -c -I /home/nicolas/Programs/Openbabel_2.3.1/include/openbabel-2.0 > LDFLAGS = -lopenbabel -L /home/nicolas/Programs/Openbabel_2.3.1/lib > > all: example > > example: example.o > $(CC) $(LDFLAGS) example.o -o example > > example.o: example.cpp > $(CC) $(CFLAGS) $(LDFLAGS) example.cpp > > clean: > rm -rf example.o example > > > After typing "make", the compilation fails with the error previously > reported : > > /tmp/cc2kfqde.o: In function `main': > example.cpp:(.text+0x120): undefined reference to > `OpenBabel::OBConversion::OBConversion(std::istream*, std::ostream*)' > example.cpp:(.text+0x139): undefined reference to > `OpenBabel::OBConversion::SetInAndOutFormats(char const*, char const*)' > example.cpp:(.text+0x165): undefined reference to > `OpenBabel::OBConversion::Convert()' > example.cpp:(.text+0x19e): undefined reference to > `OpenBabel::OBConversion::~OBConversion()' > example.cpp:(.text+0x1e1): undefined reference to > `OpenBabel::OBConversion::~OBConversion()' > collect2: error: ld returned 1 exit status > > 2) I created a "CMakeLists.txt" file with: > > cmake_minimum_required(VERSION 2.6) > add_executable(example example.cpp) > target_link_libraries(example > /home/nicolas/Programs/Openbabel_2.3.1/lib/libopenbabel.so) > include_directories(/home/nicolas/Programs/Openbabel_2.3.1/include/openbabel-2.0) > > > After typing "cmake" then "make", the file compiles. So I can compile and > use the openbabel library for my project. However, I don't understant why it > doesn't work directly with Makefile (and I would prefer use Makefile instead > of cmake). Does anyone have an idea of why, and how to modify the Makefile > to make it work? > > Thank you > > Nicolas > > > > > > -- > View this message in context: > http://forums.openbabel.org/Problem-for-compiling-the-example-files-tp4656837p4656869.html > Sent from the General discussion mailing list archive at Nabble.com. > > -- > Shape the Mobile Experience: Free Subscription > Software experts and developers: Be at the forefront of tech innovation. > Intel(R) Software Adrenaline delivers strategic insight and game-changing > conversations that shape the rapidly evolving mobile landscape. Sign up now. > http://pubads.g.doubleclick.net/gampad/clk?id=63431311&iu=/4140/ostg.clktrk > ___ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311&iu=/4140/ostg.clktrk ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Problem for compiling the example files
Hi Nicolas, in my case (also Ubuntu) the problem was that I had to move the -lopenbabel to the end of the line. Seems like your's might be the same problem ? Also I'd recommend to split your command in two, first a compile and then the linking command. That way it's easier to locate problems. The following should work ? g++ -I /home/nicolas/Programmes/OpenBabel-2.3.2/include/openbabel-2.0 -c example.cpp g++ -L /home/nicolas/Programmes/OpenBabel-2.3.2/lib example.cpp -o example -lopenbabel regards, Rafel -- View this message in context: http://forums.openbabel.org/Problem-for-compiling-the-example-files-tp4656837p4656884.html Sent from the General discussion mailing list archive at Nabble.com. -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311&iu=/4140/ostg.clktrk ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Problem for compiling the example files
I'll update the docs... On 19 November 2013 15:03, rafel israels wrote: > Hi Nicolas, > > in my case (also Ubuntu) the problem was that I had to move the > -lopenbabel to the end of the line. Seems like your's might be the same > problem ? > > Also I'd recommend to split your command in two, first a compile and then > the linking command. That way it's easier to locate problems. The following > should work ? > > g++ -I /home/nicolas/Programmes/OpenBabel-2.3.2/include/openbabel-2.0 -c > example.cpp > g++ -L /home/nicolas/Programmes/OpenBabel-2.3.2/lib example.cpp -o example > -lopenbabel > > regards, > > Rafel > > > > -- > View this message in context: > http://forums.openbabel.org/Problem-for-compiling-the-example-files-tp4656837p4656884.html > Sent from the General discussion mailing list archive at Nabble.com. > > -- > Shape the Mobile Experience: Free Subscription > Software experts and developers: Be at the forefront of tech innovation. > Intel(R) Software Adrenaline delivers strategic insight and game-changing > conversations that shape the rapidly evolving mobile landscape. Sign up now. > http://pubads.g.doubleclick.net/gampad/clk?id=63431311&iu=/4140/ostg.clktrk > ___ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311&iu=/4140/ostg.clktrk ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] stereo config question
On 2013-11-19 03:09, Noel O'Boyle wrote: > We neither have R/S perception nor E/Z. OK, thanks. Dima -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311&iu=/4140/ostg.clktrk ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
[Open Babel] Openbabel system library compiled for Centos
Dear All,
Currently we are developing a Java application in Cent OS, and facing
difficulty to integrate Openbabel API:
I have attached Sample Test Code, Errors received and System library file
details here by.
Appreciate if someone can guide us to overcome this issue. If possible, Could
someone provide me a working bundle of '.so' files, compiled for CentOS?
Sample Test Code
package test.openbabelimpl;
import org.openbabel.*;
public class Test {
public static void main(String[] args) {
System.loadLibrary("openbabel_java");
OBConversion conv = new OBConversion();
OBMol mol = new OBMol();
.
.
Error received while compiling the Sample Test code
Exception in thread "main" java.lang.UnsatisfiedLinkError:
/root/libope2/libopenbabel_java.so: /root/libope2/libopenbabel_java.so:
undefined symbol: _ZTVN9OpenBabel22OBEnergyConformerScoreE
at java.lang.ClassLoader$NativeLibrary.load(Native Method)
at java.lang.ClassLoader.loadLibrary0(ClassLoader.java:1750)
at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1675)
at java.lang.Runtime.loadLibrary0(Runtime.java:840)
at java.lang.System.loadLibrary(System.java:1047)
at org.orion.plancore.util.openbabelimpl.Test.main(Test.java:10)
System library Files available in folder /root/libope2/
-rwxr-xr-x. 1 root root 3.1M Sep 17 20:24 libinchi.so
-rwxr-xr-x. 1 root root 3.1M Sep 17 20:24 libinchi.so.0
-rwxr-xr-x. 1 root root 3.1M Sep 17 20:24 libinchi.so.0.4.1
-rwxr-xr-x. 1 root root 6.2M Sep 17 20:24 libopenbabel_java.so
-rwxr-xr-x. 1 root root 20M Sep 17 20:24 libopenbabel.so
-rwxr-xr-x. 1 root root 20M Sep 17 20:24 libopenbabel.so.4
-rwxr-xr-x. 1 root root 20M Sep 17 20:24 libopenbabel.so.4.0.2
Note
We have compiled these system files in CentOS from the openbabel source.
Thanks and regards
Rajesh Hariharan
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Re: [Open Babel] Openbabel system library compiled for Centos
On Tue, Nov 19, 2013 at 7:17 AM, H Rajesh wrote: > Dear All, > > > > Currently we are developing a Java application in Cent OS, and facing > difficulty to integrate Openbabel API: > > *.* > > *Error received while compiling the Sample Test code* > > Exception in thread "main" java.lang.UnsatisfiedLinkError: > /root/libope2/libopenbabel_java.so: /root/libope2/libopenbabel_java.so: > undefined symbol: _ZTVN9OpenBabel22OBEnergyConformerScoreE > > at java.lang.ClassLoader$NativeLibrary.load(Native Method) > > at > java.lang.ClassLoader.loadLibrary0(ClassLoader.java:1750) > > at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1675) > > at java.lang.Runtime.loadLibrary0(Runtime.java:840) > > at java.lang.System.loadLibrary(System.java:1047) > > at > org.orion.plancore.util.openbabelimpl.Test.main(Test.java:10) > The first thing to check is whether your CentOS system came with OpenBabel already installed. A common reason for this error is that there are two versions of OpenBabel, one that comes with Linux (OpenBabel is included with many Linux distributions), and one that you compiled yourself. Your Java program could be compiled against one version (probably the version you installed), but at run time, it's linking to the pre-installed version of OpenBabel. Craig -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311&iu=/4140/ostg.clktrk___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
[Open Babel] baPHPel
Hello, I'd like to share with you my work involving PHP OpenBabel bindings: baPHPel. Basically it's pybel for php, and was intended to be as close API-wise as possible. So now you can do in php: https://github.com/mwojcikowski/openbabel/commit/288011f9b0672fb53e83423235dfa87580be442b There are few things missing which I intend to fix asap (mainly involving forcefields and fingerprints) due to SWIG errors. Any thoughts/ideas? Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311&iu=/4140/ostg.clktrk___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Openbabel system library compiled for Centos
On 11/19/2013 10:05 AM, Craig James wrote: > On Tue, Nov 19, 2013 at 7:17 AM, H Rajesh wrote: >> Currently we are developing a Java application in Cent OS, and facing >> difficulty to integrate Openbabel API: ... > The first thing to check is whether your CentOS system came with OpenBabel > already installed. A common reason for this error is that there are two > versions of OpenBabel, one that comes with Linux (OpenBabel is included > with many Linux distributions), and one that you compiled yourself. Specifically, EPEL has OpenBabel 2.2.3. According to http://openbabel.org/dev-api/classOpenBabel_1_1OBEnergyConformerScore.shtml#_details OBEnergyConformerScore is "Since: 2.3", so if you compiled with 2.3.1 and are running with with 2.2.3, "undefined symbol: _ZTVN9OpenBabel22OBEnergyConformerScoreE" sounds about right. -- Dimitri Maziuk Programmer/sysadmin BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu signature.asc Description: OpenPGP digital signature -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311&iu=/4140/ostg.clktrk___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
[Open Babel] Announcement: ChemicalToolBox
ChemcialToolBox: A Galaxy of cheminformatic tools in a web browser I am very happy to finally announce the first release of ChemicalToolBox! ChemicalToolBox (CTB) is an open source project that aims for reproducible, transparent and easy accessible cheminformatic research. It is based on the Galaxy [1] framework and can be installed on all unix like platforms. CTB integrates several cheminformatic toolkits and tools, like Open Babel, RDKit, CDK, chemfp, osra, opsin, silicos-it ... in one easy to use workbench running in a web browser. ChemicalToolBox with installation instructions:https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox A few highlights of the CTB and its framework: - every step in your analysis is logged with tool version, input dataset and used parameters, enabling reproducibility of your analysis at any time - building entire cheminformatic protocols/workflows via drag & drop by chaining small tools together. Abstracting complexness, enabling creativity, like assembling lego bricks. - over 40 different tools: - conversion - filtering (with predefined filtering rules) - substructure and similarity search - > 10 different fingerprints - structure recognition - structure depiction - descriptor calculation - property prediction - CTB is accessible via any recent web browser, without any shell knowledge. You can run a CTB instance for you lab or a whole university, like we do here at the university of Freiburg - CTB enables easy access to High-Performance-Computing (HPC). Based on the Galaxy project, CTB can run on any Cluster/Grid setup, including Cloud computing, like EC2 - by the means of the Galaxy Tool Shed, CTB comes with installation routines of all dependencies, like Open Babel, RDKit, osra, opsin ... once Galaxy is running you can install CTB with a few clicks - CTB can be accessed via a REST API, for example for massively parallel execution of workflows - tools can be easily integrated, independently from its programming language (it needs to be command line accessible) - every workflow, dataset, history can be shared with a group of researchers or can be made public available, enabling transparent and peer-reviewed research. For example the ChemicalBox, a merged database of many freely available compounds:http://galaxy.uni-freiburg.de/u/bgruening/w/preparation-of-a-large-compound-library-by-merging-of-chemical-databases-1 - every tool and every tool-parameter can have (and hopefully has) an exhaustive description to guide the researcher - automatic build-in mutiprocessing: most of the CTB tools will split the input datasets into smaller chunks before execution and merging the result files after execution I would like to thank the cheminformatic community, for all the great tools and libraries, for accepting patches and enlightening discussions! I hope CTB will be a useful contribution and can open the cheminformatic universe to many more researchers. Thanks and happy research! Björn [1] http://galaxyproject.org -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311&iu=/4140/ostg.clktrk___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
