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roundview.py for PyMOL

rounds off the viewport settings in PyMOL to 2 decimals places and returns on one line.
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// Enter here the actual content of the snippet. 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)
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