roundview.py

from __future__ import division
from __future__ import print_function
# -*- coding: utf-8 -*-

"""

version 1.0         26 October 2015
    Posted in github for first time.

version 1.1         23 November 2015
    Corrected description of the rounding off the matrix elements.
    Corrected hard wrapped text the broke the script. 
    Added example of running program as a horizontal script.
    Made code pep8 compliant (changed use of blank lines, 
        removed whitespaces in defualt arguments assignments, 
        inserted whitespaces after commas in lists, 
        removed whitespaces at the ends of lines).
    Added version number.

version 1.2         23 May 2016
    Edited copyright notice.
    Corrected typos
    
version 1.3         23 July 2016
    Added missing parenthesis at end of file.
    

   Copyright Notice
  ================
  
     Copyright (C) 2016  Blaine Mooers

    This program is free software: you can redistribute it and/or modify
    it under the terms of the GNU General Public License as published by
    the Free Software Foundation, either version 3 of the License.

    This program is distributed in the hope that it will be useful,
    but WITHOUT ANY WARRANTY; without even the implied warranty of
    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  
    See the GNU General Public License for more details:
    http://www.gnu.org/licenses/.

  The source code in this file is copyrighted, but you can
  freely use and copy it as long as you don't change or remove any of
  the copyright notices.
  
  Blaine Mooers, PhD 
  blaine-mooers@ouhsc.edu
  975 NE 10th St, BRC 466
  University of Oklahoma Health Sciences Center, 
  Oklahoma City, OK, USA 73104

 """
from pymol import stored, cmd
__author__ = "Blaine Mooers"
__copyright__ = "Blaine Mooers, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA 73104"
__license__ = "GPL-3"
__version__ = "1.0.2"
__credits__ = ["William Beasley","Chiedza Kanyumbu"] 
# people who reported bug fixes, made suggestions, etc. 
__date__ = "30 May 2016"
__maintainer__ = "Blaine Mooers"
__email__ = "blaine-mooers@ouhsc.edu"
__status__ = "Production" 


def roundview(StoredView=0, decimal_places=2, outname="roundedview.txt"):

    """
    DESCRIPTION

    Adds the command "roundview" that gets a view (default is 0,
    the current view; you can get a stored view assigned to some
    other digit with the view command) and rounds to two decimal
    places (two digits to the right of the decimal point) the
    viewpoint matrix elements and rewrites the matrix elements
    on a single line with no whitespaces and a semicolon at the
    end. The saved space eases the making of a single line of
    PyMOL commands separated by semicolons. This enables rapid
    and interactive editing of chunks of PyMOL commands. The
    viewpoints are appended to the bottom of a text file in the
    present working directory called "roundedview.txt". The line
    could be easier to copy from this file than from the command
    history window in the external gui. A semicolon with nothing
    to the right of it at the end of a line of grouped commands
    is harmless.


    USAGE
     
    roundview [view, decimal_places, outname] 

    Note that the values in the [] are optional.

    The default values  for the arguments of the function
    are "0,2, roundedview.txt". 

    Simple one-line example with roundview.py script in current working
    directory--check by typing 'pwd' and 'ls *.py' on the command line. PyMOL
    should return 'roundview.py' in the lisf of files in the external (top) gui.
    Next, paste the following command on the external (top) commandline, hit
    return, and wait 5-10 seconds:

    fetch 1lw9, async=0; run roundview.py; roundview 0,1


    The following view setting will be returned without the blackslash.

    set_view (1.0,0.0,0.0,0.0,1.0,0.0,0.0,0.0,1.0,0.0,0.0,-155.2,35.1,11.5,9.7,122.3,188.0,-20.0);

    Advanced option:

    Copy roundview.py to the folder ~/.pymol/startup and then
    the command will always be accessible. You may have to 
    create these directories. 


    18 elements of the view matrix (0-17)

    0 - 8 = column-major 3x3 matrix that rotates the model axes
    to camera axes 

    9 - 11 = origin of rotation relative to the camera
    in camera space

    12 - 14 = origin of rotation in model space

    15 = front plane distance from the camera

    16 = rear plane distance from the camera

    17 = orthoscopic flag 
    (not implemented in older versions)
    
    """
    
    #convert the commandline arguments from strings to integers

    StoredView = int(StoredView)
    decimal_places = int(decimal_places)
    
    
    #call the get_view function

    m = cmd.get_view(StoredView)


    #Make a list of the elements in the orientation matrix.

    myList = [m[0], m[1], m[2], m[3], m[4], m[5], m[6],
        m[7], m[8], m[9], m[10], m[11], m[12], m[13], m[14],
        m[15], m[16], m[17]]


    #Round off the matrix elements to two decimal places (two fractional places)
    #This rounding approach solved the problem of unwanted
    #whitespaces when I tried using a string format statement

    myRoundedList = [ round(elem, decimal_places) for elem in myList]
    
    
    #x is the format of the output. The whitespace is required
    #between the "set_view" and "(".
    
    x = 'set_view ({0},{1},{2},{3},{4},{5},{6},{7},\
{8},{9},{10},{11},{12},{13},{14},{15},{16},{17});'


    #print to the external gui.

    print x.format(*myRoundedList)


    #Write to a text file.

    myFile = open("roundedview.txt", "a")
    myFile.write(x.format(*myRoundedList) + "\n")
    myFile.close()
    return


    #The extend command makes roundview into a PyMOL command.

cmd.extend("roundview", roundview)