relative paths

The Transform class was moved from the mol module to the geom module. A typedef
was put into the mol namespace in C++, and a similar alias was put into the
mol python module, with an added deprecation warning.

folder because it breaks the make clean command

added cmake option to set hidden visibility for gcc compiles; fixed several missing visibility declarations

Fixes BZDNG-385

Mainly Marco's work

to check for breaking of the in_sequence property.
Added an SetInSequence() function to the ChainHandle to check and update
the in_sequence property

1. Option to move libexec to lib/openstructure/libexec
2. Gosty moved to libexec

Version is now defined only in the CMakeList.txt at the top level. Everything in OpenStructure picks it up from there

The main purpose of this commit is to test the jira/git
integration, so I'm just randomly mentioning a bug report
that exists in the develop instance of jira: BZDNG-9.

Any project dependent on OST will also need to do the boost initialization, therefore moving it to a macro avoids code duplication.

changed cmake scripts to allow building as subproject / moved common configuration from startup scripts to separate script

Added support for Homebrew MacOSX packaging system and for Eigen3 (in Eigen2 compatibility mode)

Added support for Homebrew MacOSX packaging system and for Eigen3 (in Eigen2 compatibility mode)

This is very useful when deploying a single program building
on the C++ libraries only.

ENABLE_GUI not ENABLE_UI


git-svn-id: https://dng.biozentrum.unibas.ch/svn/openstructure/trunk@2701 5a81b35b-ba03-0410-adc8-b2c5c5119f08