initial commit with only vector3 library
added copyright notice
Added skeleton to deal with atom entries in PDB files.

Needs more infrastructure before it can be tested or compiled.
Began coding pdb-parser etc. Not even tried to compile it yet.
Some refactoring. Now compiles without warnings. No tests yet.
added som additional asserts
cleaned up indentation and whitespace
Now reads pdb correctly

formalize testing?
Typed in skeleton for Shrake and Rupley calculation based on old code. Not tested in any way yet.
SR-calculation compiles, runs and gives data that look ok, still needs to be verified more closely.

Added test-program.
Added forgotten probe radius and some debug code to visualize surface.
Fixed serious bug in SASA calculation. Now results make sense.
Added basic application for calculations. Have not decided how to present output yet, i.e. the program does the calculation but prints nothing.
Added help message to main application.
added short help message too.
moved atom-code into protein to reduce exposure of implementation
added some getter and setter functions
Refactored again. Now the mapping of atom-type to radius is a separate function, that can be customized.

Before the exclusion of some atoms was completely automatic because only one definition of atom types was allowed, now it is less straightforward. For now hydrogens are excluded when a whole PDB-file is read, but when they are added manually one by one, it is assumed that users know what they're doing.