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67 lines
2.7 KiB
Python
67 lines
2.7 KiB
Python
'''
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See more here: http://www.pymolwiki.org/index.php/centroid
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DESCRIPTION
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get the centroid (geometric center) of a selection or move selection to the origin.
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ARGUMENTS
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selection = string: a valid PyMOL selection {default: all}
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center = 0 or 1: if center=1 center the selection {default: 0}
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returns: centroid: [ x, y, z ]
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SEE ALSO
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get_extent, get_position, http://pymolwiki.org/index.php/Center_Of_Mass
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# @AUTHOR: Jason Vertrees
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# Copyright (c) 2008, Jason Vertrees
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# All rights reserved.
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#
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# Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following
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# conditions are met:
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#
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# * Redistributions of source code must retain the above copyright notice, this list of conditions and the following
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# * disclaimer.
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# * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following
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# * disclaimer in the documentation and/or other materials provided with the distribution.
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# * Neither the name of the <ORGANIZATION> nor the names of its contributors may be used to endorse or promote products derived
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# * from this software without specific prior written permission.
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#
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# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT
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# NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL
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# THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
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# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
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# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
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# OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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#
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# DATE : 2008-09-26
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# REV : 1
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'''
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from __future__ import print_function
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from pymol import cmd
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from pymol import stored
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from chempy import cpv
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def centroid(selection='all', center=0, quiet=1):
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model = cmd.get_model(selection)
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nAtom = len(model.atom)
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centroid = cpv.get_null()
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for a in model.atom:
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centroid = cpv.add(centroid, a.coord)
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centroid = cpv.scale(centroid, 1. / nAtom)
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if not int(quiet):
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print(' centroid: [%8.3f,%8.3f,%8.3f]' % tuple(centroid))
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if int(center):
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cmd.alter_state(1, selection, "(x,y,z)=sub((x,y,z), centroid)",
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space={'centroid': centroid, 'sub': cpv.sub})
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return centroid
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cmd.extend("centroid", centroid)
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