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.