doc: remove warnings about duplicate object description

modules/bindings/doc/tmtools.rst

modules/db/doc/db.rst

modules/gui/doc/layout.rst

modules/mol/alg/doc/lddt_deprecated.rst

modules/mol/mm/doc/simulation.rst

modules/mol/mm/doc/topology.rst

modules/seq/alg/doc/seqalg.rst

modules/seq/base/doc/seq.rst