Source code for view

from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
#from __future__ import unicode_literals
#
#   SASMOL: Copyright (C) 2011 Joseph E. Curtis, Ph.D. 
#
#    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, or
#    (at your option) any later version.
#
#    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.
#
#    You should have received a copy of the GNU General Public License
#    along with this program.  If not, see <http://www.gnu.org/licenses/>.
#
#	VIEW
#
#	11/27/2013	--	initial coding			:	jc
#	12/29/2015	--	refactored for release  :   jc
#	08/19/2016	--	added doc strings       :   jc
#
# LC	 1         2         3         4         5         6         7
# LC4567890123456789012345678901234567890123456789012345678901234567890123456789
#								       *      **
'''
	View is the main module that contains the base classes that 
	read and write atomic information from and to external viewers
	such as vmd and others in the future (PyMol, etc.).
	
	To view the coordinates the viewer needs to be open and controlled
	external to view / sasmol.  These methods merely allow 
	coordinates to be passed between programs.

	These classes are accessed by system objects

'''

import os
import sys
import string
import locale
import struct
import numpy
import time
import sasmol.view_vmd

class View(object):

    """ 

        View is the main module that contains the base classes that 
	    read and write atomic information from and to external viewers
	    such as vmd and others in the future (PyMol, etc.).
	
	    To view the coordinates the viewer needs to be open and controlled
	    external to view / sasmol.  These methods merely allow 
	    coordinates to be passed between programs.

	    See the following sites for the IMD format:
    
	    http://www.ks.uiuc.edu/Research/vmd/
	    http://www.ks.uiuc.edu/Research/namd/
    
	    This class is accessed by system objects

        Examples
        ========

        How to use send coordinates to VMD 

        >>> import sasmol.system as system
        >>> molecule = system.Molecule('hiv1_gag.pdb')
        >>> flag = False
        >>> molecule.send_coordinates_to_vmd(1085, flag)

        Note
        ----
    
        `self` parameter is not shown in the ``Parameters`` section in the documentation

    """ 

    def send_coordinates_to_vmd(self, port, flag, **kwargs):
        """
        This method opens a socket to send and receive coordinates
        by calling a pre-compiled C module (view_vmd).

        
        Parameters
        ----------
        port 
            integer : port number to communicate 

        flag
            boolean : True to close existing connection

        kwargs 
            optional future arguments
                                                                                     
        Returns
        -------
        None

        Examples
        ========

        How to use send coordinates to VMD 

        >>> import sasmol.system as system
        >>> molecule = system.Molecule('hiv1_gag.pdb')
        >>> flag = False
        >>> molecule.send_coordinates_to_vmd(1085, flag)

        Note
        ----
        VMD needs to be open with your molecule already loaded for the
        coordinates to be accepted via IMD.

        """

        natoms = self._coor[0, :, 0].shape[0]
        frame = 0
        tx = self._coor[frame, :, 0].astype(numpy.float32)
        ty = self._coor[frame, :, 1].astype(numpy.float32)
        tz = self._coor[frame, :, 2].astype(numpy.float32)

        result = view_vmd.send_coordinates_to_vmd(tx, ty, tz, port, flag)

        return