pymol

.pymol/startup/centroid.py

@@ -0,0 +1,66 @@
+'''
+See more here: http://www.pymolwiki.org/index.php/centroid
+
+DESCRIPTION
+        get the centroid (geometric center) of a selection or move selection to the origin.
+
+ARGUMENTS
+        selection = string: a valid PyMOL selection {default: all}
+        center = 0 or 1: if center=1 center the selection {default: 0}
+        returns: centroid: [ x, y, z ]
+
+SEE ALSO
+        get_extent, get_position, http://pymolwiki.org/index.php/Center_Of_Mass
+
+# @AUTHOR: Jason Vertrees
+# Copyright (c) 2008, Jason Vertrees
+# All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following
+# conditions are met:
+#
+#     * Redistributions of source code must retain the above copyright notice, this list of conditions and the following
+#     * disclaimer.
+#     * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following
+#     * disclaimer in the documentation and/or other materials provided with the distribution.
+#     * Neither the name of the <ORGANIZATION> nor the names of its contributors may be used to endorse or promote products derived
+#     * from this software without specific prior written permission.
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT
+# NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL
+# THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
+# OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+#
+# DATE  : 2008-09-26
+# REV   : 1
+
+'''
+from __future__ import print_function
+from pymol import cmd
+from pymol import stored
+from chempy import cpv
+
+
+def centroid(selection='all', center=0, quiet=1):
+
+    model = cmd.get_model(selection)
+    nAtom = len(model.atom)
+
+    centroid = cpv.get_null()
+
+    for a in model.atom:
+        centroid = cpv.add(centroid, a.coord)
+    centroid = cpv.scale(centroid, 1. / nAtom)
+
+    if not int(quiet):
+        print(' centroid: [%8.3f,%8.3f,%8.3f]' % tuple(centroid))
+
+    if int(center):
+        cmd.alter_state(1, selection, "(x,y,z)=sub((x,y,z), centroid)",
+                        space={'centroid': centroid, 'sub': cpv.sub})
+
+    return centroid
+
+cmd.extend("centroid", centroid)

.pymolrc

@@ -1,4 +1,21 @@
+set fetch_path, /tmp
+set async_builds, on
+set max_threads, 16
+set cache_mode 
+
 set opaque_background, 0
 log_open /tmp/pymol_log.pml
 set cartoon_side_chain_helper, 1
 set cartoon_highlight_color, grey50
+
+set_key F1, as lines, solvent
+set_key F2, hide everything, solvent
+set_key F3, as spheres, inorganic and (n. NA or n. K or n. CL or n. CA or n. XE or n. RN)
+set_key F4, hide everything, inorganic and (n. NA or n. K or n. CL or n. CA or n. XE or n. RN)
+set_key F5, as sticks, organic
+set_key F6, hide everything, organic
+
+set_key F9, set orthoscopic
+set_key F10, set orthoscopic, off
+set_key F11, ray
+set_key F12, ray 1600,1600