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Confab unable to read sdf, pdb, and mol2 files #4

Open GoogleCodeExporter opened 8 years ago

GoogleCodeExporter commented 8 years ago 
What steps will reproduce the problem?
1. Execution of Confab

What is the expected output? What do you see instead?
I expected to see conformations produced by confab, instead I see: 
confab: cannot read input format!

What version of the product are you using? On what operating system?
I am using Ubuntu 12

Please provide any additional information below.
This was the output from confab using pdb, mol2, and sdf files produced by 
various applications (Pymol, openbabel, etc.).

Original issue reported on code.google.com by mla...@gmail.com on 2 Oct 2012 at 7:25

GoogleCodeExporter commented 8 years ago 
I have the same issue with Mac OS X 10.7.5 - I compiled locally, and don't see 
any errors as such, but lines such as:
Linking CXX shared module ../../lib/cdxmlformat.so
appear in red.
Any idea what might be wrong?

Original comment by xn.h...@gmail.com on 19 Nov 2012 at 4:09

GoogleCodeExporter commented 8 years ago 
Just to check, did you run "make install" and install locally?

Original comment by baoille...@gmail.com on 19 Nov 2012 at 4:17

GoogleCodeExporter commented 8 years ago 
Yup - My steps were:
$ cmake ../Confab-1.0.1 -DCMAKE_INSTALL_PREFIX=~/confab 
-DCMAKE_BUILD_TYPE=DEBUG -DEIGEN2_INCLUDE_DIR=../eigen-eigen-b23437e61a07/
... blah blah blah .. GUI will not be built ...
-- Build files have been written to: /Users/my_username/src/Confab-1.0.1-build
$ make
... lots of green "Building ..." along with stuff like:
Linking CXX shared library ../lib/libopenbabel.dylib
[ 87%] Built target openbabel
Scanning dependencies of target cdxmlformat
[ 88%] Building CXX object 
src/formats/CMakeFiles/cdxmlformat.dir/xml/cdxmlformat.o
[ 89%] Building CXX object src/formats/CMakeFiles/cdxmlformat.dir/xml/xml.o
Linking CXX shared module ../../lib/cdxmlformat.so
[ 89%] Built target cdxmlformat
...
[100%] Built target confab
$ make install
... blah blah blah ... installing ...
My LD_LIBRARY_PATH (and DYLD_LIBRARY_PATH) is /Users/my_username/confab/lib and 
BABEL_DATADIR is /Users/my_username/confab/share/openbabel/2.2.99

Original comment by xn.h...@gmail.com on 19 Nov 2012 at 4:26

GoogleCodeExporter commented 8 years ago 
Well, it should be working based on the info you've provided. It seems to have 
compiled fine. I presume you've set the environment variables with the "export" 
command, right? You can also try setting BABEL_LIBDIR to the directory with the 
file format plugins, but this shouldn't be necessary to be honest.

Original comment by baoille...@gmail.com on 21 Nov 2012 at 1:16