Changes and Updates For multiple Scripts.

[axiomcura]

Here's the lists of scripts and their suggested changes and updates it requires.

strip.py

• -r should not be required. Default should be removing everything
  but the protein. use -r for specific regions to conduct auto-imaging
• create a flag for atom selection (default: None)

get_tm_resids.py

• add help documentation
• add tabulated print statment
• add option to write out file -o (csv file)
• edit documentation
• Check PDBTM if it is being maintained

tm_consensus.py

• implement remove_outlier() function
• Check PDBTM if it is being maintained

traj2prmtop.py

• make output name required
• cpptraj executer block is hanging