Manual Python 3 port of doc example code

modules/base/doc/generic.rst

modules/base/doc/logging.rst

modules/bindings/doc/dssp.rst

modules/bindings/doc/hhblits.rst

modules/bindings/doc/tmtools.rst

modules/conop/doc/compoundlib.rst

modules/doc/external.rst

modules/doc/intro-01.rst

modules/doc/intro-02.rst

modules/doc/table.rst

modules/geom/doc/mat.rst

modules/geom/doc/vec.rst

modules/gui/doc/python_cpp.rst

modules/img/base/doc/point-size-extent.rst

modules/io/doc/io.rst

modules/mol/alg/doc/lddt.rst

modules/mol/alg/doc/molalg.rst

modules/mol/base/doc/entity.rst

modules/seq/alg/doc/seqalg.rst

modules/seq/base/doc/seq.rst