erix, with great respect for your habit of providing actual solutions, this falls short:

Is your data PDB? ... Chemistry::File::PDB.

At most that will allow the OP to read his data files.

But then, the format is so simple that the relevant parts can be read using single lines of Perl code:

## Load line data
my @linePts = map[ (split)[ 5,6,7 ] ], split "\n", <DATA>; # pp \@line
+Pts;

## Load the "rotatable" points
my @rotPts  = map[ (split)[ 6,7,8 ] ], split "\n", <DATA>; # pp \@rotP
+ts;

## Load the stop points.
my @stopPts = map[ (split)[ 7,8,9 ] ], split "\n", <DATA>; # pp \@stop
+Pts;
[download]

I'm also wondering whether existing GIS software (postgis for postgresql comes to mind, or even plain vanilla postgresql geometric datatypes) might not already contain what you need, although admittedly it's probably a bit of a learning curve.

To the best of my ability to discern (you weren't kidding about the learning curce), postgis only deals with 2D data which wouldn't help for this.

At most that will allow the OP to read his data files.

Well, it was also meant for others, and as a hint to the OP. Whatever the precise question; it is useful to know if a widely used format is being discussed. Taking myself as example: to realise that this data is PDB (I had to look up the format at the PDB site) got *me* interested -- and perhaps I'll give it a try with postgres/postgis later on (I think there is actually quite a bit of 3d stuff available between them).

The advantage would mainly be indexing, I think, so if a database approach can be made to work at all, it would mostly be useful if one wanted to look at many proteins.