[Open Babel] Reg: Conformer Search Write Conformers as SDF File
Dear OpenBabelers
I am using OpenBabel in my Java application.I would like to generate set of
conformers for my molecule using Openbabel and write the generated
conformers to an output file (SDF format).
I am able to generate the conformers using GetConformers method in
OBConformerSearch class, Since, the return type of the method is void, I am
not able to get hold of the generated conformers and write them to the
output file. It would be great if I can have a list of generated conformers
which I can later write them in an SDF file?
Below is the java code, by the way with this code, writes only one
generated conformer to the output file.
System.loadLibrary("openbabel_java");
OBMol mol = new OBMol();
OBConformerSearch conformer = new OBConformerSearch();
OBConversion conv = new OBConversion();
conv.ReadFile(mol,"input.mol");
conv.SetOutFormat("sdf");
conformer.Setup(mol,5);
conformer.GetConformers(mol);
conv.WriteFile(mol, "conformers.sdf");
I have seen a similar post
(
http://forums.openbabel.org/Generating-a-diverse-set-of-conformers-td4656011.html
)
in python but there seems to be no answer.
Any suggestion in the right direction is highly appreciated. Thank you.
--
Regards
Vinothkumar Mohanakrishnan
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Re: [Open Babel] Reg: Conformer Search Write Conformers as SDF File
Dear Noel
Thanks a lot for your valuable hint and it works, I created a loop and
wrote the conformers as individual SDF file (code below), then I combine
all the individual SDF files into one using Openbabel GUI (not an ideal way
to do),
conformer.Setup(mol,5);
conformer.GetConformers(mol);
for(int i=1;i<6;i++) {
mol.SetConformer(i);
String fileName = "fileName"+ i +".sdf";
conv.WriteFile(mol,fileName); //
}
Is there a way that I could do it programmatically to combine all the
individual files into a single SDF file? any hints? Thank you.
On Wed, Dec 20, 2017 at 2:12 PM, Noel O'Boyle wrote:
> Have you tried SetConformer(int n)? This switches the coordinates of the
> molecule between the available conformers.
>
> On 20 December 2017 at 12:35, Vinothkumar Mohanakrishnan <
> kmvin...@gmail.com> wrote:
>
>> Dear OpenBabelers
>>
>> I am using OpenBabel in my Java application.I would like to generate set
>> of conformers for my molecule using Openbabel and write the generated
>> conformers to an output file (SDF format).
>>
>> I am able to generate the conformers using GetConformers method in
>> OBConformerSearch class, Since, the return type of the method is void, I am
>> not able to get hold of the generated conformers and write them to the
>> output file. It would be great if I can have a list of generated conformers
>> which I can later write them in an SDF file?
>>
>> Below is the java code, by the way with this code, writes only one
>> generated conformer to the output file.
>>
>> System.loadLibrary("openbabel_java");
>>
>> OBMol mol = new OBMol();
>>
>> OBConformerSearch conformer = new OBConformerSearch();
>>
>> OBConversion conv = new OBConversion();
>>
>> conv.ReadFile(mol,"input.mol");
>>
>> conv.SetOutFormat("sdf");
>>
>> conformer.Setup(mol,5);
>>
>> conformer.GetConformers(mol);
>>
>> conv.WriteFile(mol, "conformers.sdf");
>>
>>
>> I have seen a similar post
>>
>> (
>> http://forums.openbabel.org/Generating-a-diverse-set-of-conf
>> ormers-td4656011.html
>> )
>> in python but there seems to be no answer.
>> Any suggestion in the right direction is highly appreciated. Thank you.
>>
>> --
>> Regards
>> Vinothkumar Mohanakrishnan
>>
>>
>> --------
>> --
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>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
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>>
>>
>
--
Regards
Vinothkumar Mohanakrishnan
--
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[Open Babel] Reg: Packing openbabel along with my Java application
Dear OpenBabel Users
I am developing a Java application (GUI) which uses OpenBabel in the
backend. I want to pack this application so that users can use in different
operating systems like Windows, Linux, MacOS.
Right now, In my development environment, I am using
System.loadlibrary("openbabel_java"). This works fine.
This will break down when I pack my application (myapp.jar) for another
computer or another operating system (in spite of having OpenBabel.jar in
my application).
I would like to know how can one pack OpenBabel in a third party
application? I am pretty sure I am not the first one to have this question,
any hints in the right direction(like some workflow) are highly
appreciated.
Just a small suggestion, It would be a nice idea to have a page
describing, packing
OpenBabel along with custom application in the documentation of OpenBabel.Thank
you.
--
Regards
Vinothkumar Mohanakrishnan
--
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[Open Babel] Java bindings undefined symbol: _ZTVN9OpenBabel30OBMinimizingRMSDConformerScoreE
Dear OPenBabel Users
I am using OpenBabel in my (Java) application and want to pack this
application and use it in different operating systems like Windows, Linux,
and MacOs.
I have compiled JAVA bindings for OpenBabel using the command
*sudo cmake
/home/vin/openbabel2.4-DCMAKE_INSTALL_PREFIX=~/Tools-DCMAKE_BUILD_TYPE=DEBUG-DJAVA_BINDINGS=ON-DEIGEN3_INCLUDE_DIR=/home/vin/Eigen3-DSWIG_EXECUTABLE=/usr/bin/swig-DRUN_SWIG=ONsudo
make*
The compilation went well and took the libopenbabel_java.so and
libopenbabel.so from the build directory and packed it along with my
application in the directory (app/rescources) and specified the path to the
app/resources directory in the source code
(system.load("/home/vin/app/resources/libopenbabel_java.so")) of my
application for performing an openbabel task.
When I run my application jar file (app.jar) and perform an openbabel task
(generate conformers) I am getting the below error
Exception in thread "AWT-EventQueue-0" java.lang.UnsatisfiedLinkError:
/home/praktikant/OPAS_ALPHA_1.0/resources/libopenbabel_java.so:
*/home/vin/app_ALPHA_1.0/resources/libopenbabel_java.so:
undefined symbol: _ZTVN9OpenBabel30OBMinimizingRMSDConformerScoreE*
By the way, my application runs perfectly fine where OpenBabel is already
installed (like in my development environment). Any hints in the right
direction is highly appreciated. Thank you.
--
Regards
Vinothkumar Mohanakrishnan
--
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