added rounview.py

roundview.py

@@ -0,0 +1,179 @@
+from __future__ import division
+"""
+
+
+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
+
+
+   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 
+  [email protected]
+  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__ = "[email protected]"
+__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)