Merge pull request #228 from RosettaCommons/jkleman/mp_updates
MP_UPDATES:
* compute_structure_based_membrane_position: makes sure the embeddings show in positive z direction
* EmbeddingDef:
= constructor now takes a boolean whether the embeddings should show in positive z direction
= implemented invert function that inverts the normal
* Embedding:
= constructor from pose and topology makes sure total embedding normal always shows in positive z direction
= implemented invert function that inverts the normals of all EmbeddingDefs
* AddMembraneMover:
= debug check_pdb_for_mem to read in MEM in PDB file; it now goes through every residue in the pose to identify the MEM residue and matches that up with the user input; this means that reading in a membrane residue from the commandline works now
* Types:
= created core/conformation/membrane/types file that contains all membrane default values
= replaced (hopefully) all instances with the default values in types
* moved membrane_axis from docking into protocols3/membrane/geometry/util
* MEM.params:
= for fullatom, changed normal to length 15
* Conformation:
= update_membrane_position now normalizes first and sets the points from the vectors - this is correct behavior: this function should now always be called with the vector for the normal and not with the point
Unit tests: pass
Integration tests: expected changes