Fix PQR file output

Fix PQR file output

PQR files from editconf were always written as fixed format PDB files
with just the field information added. As pointed out in the linked
redmine, this can violate the PQR file standard if the field lengths are
too long, even though the file would still be a valid PDB.

This adds a slightly different form of the writeout that has a flexible,
PQR conform format.

Fixes #2511

Change-Id: I626380b642a0214970753da289e9c969ce411ea7