=============================
Lipid Height Calculations
=============================

The HeightPlotter code calculates the average height of lipids (Phosphate or C2 to midplane distance)
and the bilayer thickness. The output contains three figures: one for the builayer thickness, one 
for the upper leaflet height, and one for the lower leflet height. The lipids heights are averages over 
a specified block of simualtion time (trjst to trjsp). If this time is too short, then area on the 
plots will have a height of zero. If blocks are too short, then peptides may blur as averages flatten. 

.. figure:: run57-76_skip20.png


Minimum Requirements
====================
Calculations require:
 * System PSF
 * System trajectory files
 * `matplotlib <http://matplotlib.org/>`_ 
 * `MDAnalysis <https://code.google.com/p/mdanalysis/>`_

Notes
====================

Assumptions:
    Two-component bilayer (for 1 component system, set both LipidA and LipidB to same peptide.
    Trajectory name is dyn$N.trj, where $N is a number between TrjSt and TrjSp or, if 'path'
    ends with '.trj' or '.dcd', read only that file.

Peptides are colored as gray, purple (Charged), and white (Histidine) circles. This should be easy to modify in furture versions.



Optional Keywords for the Input File 
====================================

================= ========================================================================================
Keyword           Values
================= ========================================================================================
**Title**         Title on figures
**PSF**           Location of psf
**path**          Path for trajectory files
**LipidA**        Residue name for lipid A
**LipidB**        Residue name for lipid B (use same as Lipid B no Lipid A)
**trjst**         Number of first trajectory file
**trjsp**         Number of last trajectory file
**out**           Output file name
**Translate**     If *True*, translate each frame so N-termini are at center  
**Rotate**        If *True*, rotate each frame so N-termmini is at the 6 o'clock
                  Position and the C-termini is at the 12 o'clock position. This is best
                  Used when 'Translate' is also True
**pbcsym**        Symmetry of unit cell, *P1* or *P21* only
**phosphates**    If *True*, use phosphates to determine lipid height. If *False*, use C2 of sn-2 chain.
**plottype**      *ColorMap*, *Contour*, or *Voronoi*. Voronoi currenty not working. 
**EmptyCell**     If cell has zero population, 'Zero' keeps a zero value and 'Neighbors'
                  Fills the cell with an average of neighboring cells. If all neighboring
                  Cells are empty, the program will crash!
**ShowNeighbors** If *True*, show image peptides. If *False*, don't.
**IncludeHist**   If *True*, include histograms of tilt, depths of insertion, and rotation. 
                  All three properties must be calculated beforehand.
================= ========================================================================================


Example Input File::

     Title         p1 3:1 PC/PG P21                                                                 
     PSF           /u/bsp6/Proj/piscidin/DMPC_DMPG_FEP1/SetupPcPgP1_FREE/pcpgp1_p21_mini_free.psf   
     path          /u/bsp6/Proj/piscidin/DMPC_DMPG_FEP1/DynPcPgP1_FREE/                             
     LipidA        DMPC                                                                             
     LipidB        DMPG                                                                             
     trjst         43                                                                               
     trjsp         62                                                                               
     out           run43-62_skip20                                                                  
     Translate     True                                                                             
     Rotate        True                                                                             
     pbcsym        P21                                                                              
     phosphates    False                                                                            
     plottype      ColorMap                                                                         
     EmptyCell     Neighbors                                                                        
     ShowNeighbors False                                                                            
     IncludeHist   True