Decide how to determine where to insert rotations and flips

[russell-taylor]

This currently depends on looking at the hydrogen placement plan information and at the covalent bonding structure.

            HET dict comes from the PDB but it is not being updated
                    There is a more complicated replacement for it now
                    They run a script to remove hydrogens from Phosphates
                    There are now some other changes
            Consider pulling ever more things into the geostd library
            x       Probably not
            Consider keeping our table of rotations and flips (or at least their types) to have for the standard residues
                    then look up in geostd and/or the monomer library
                    then look up in the CIF files
                    Enable a CIF file to override
            ***     It may be that we can run the same HET code on the standard residues to get the same types
                            Problem when dealing with disulfide bonds and other things, where constraints can change

[russell-taylor]

Dorothee's script reports the number of rotatable Hydrogens that it finds. Perhaps we can get the information we need on where there can be flips and rotations that way.

run_table_info.zip

[russell-taylor]

Decided and implemented.