[IMP-dev] molecular hierarchy helper methods

We have been kind of inconsistent about molecularhierarchy-related helper methods, for example molecular_hierarchy_get_by_type. Some of the methods have a molecular_hierarchy_ prefix and some not. I propose (as was Ben's preference when this was discussed before) to remove the prefix from the methods which have it: molecular_hierarchy_get_by_type becomes get_by_type and molecular_hiearchy_get_residue becomes get_residue