reorganize dotfiles

profiles/pymol/.pymol/startup/spectrum_states.py

@@ -0,0 +1,92 @@
+'''
+http://pymolwiki.org/index.php/spectrum_states
+
+(c) 2011 Takanori Nakane and Thomas Holder
+
+License: BSD-2-Clause
+'''
+
+from __future__ import print_function
+
+from pymol import cmd, CmdException
+
+
+def spectrum_states(selection='all', representations='cartoon ribbon',
+                    color_list='blue cyan green yellow orange red',
+                    first=1, last=0, quiet=1):
+    '''
+DESCRIPTION
+
+    Color each state in a multi-state object different.
+
+USAGE
+
+    spectrum_states [ selection [, representations [, color_list [, first [, last ]]]]]
+
+ARGUMENTS
+
+    selection = string: object names (works with complete objects only)
+    {default: all}
+
+    representations = string: space separated list of representations
+    {default: cartoon ribbon}
+
+    color_list = string: space separated list of colors {default: blue cyan
+    green yellow orange red}
+
+SEE ALSO
+
+    spectrum, spectrumany
+    '''
+    from math import floor, ceil
+
+    first, last, quiet = int(first), int(last), int(quiet)
+    colors = color_list.split()
+    if len(colors) < 2:
+        print(' Error: please provide at least 2 colors')
+        raise CmdException
+
+    colvec = [cmd.get_color_tuple(i) for i in colors]
+
+    # filter for valid <repr>_color settings
+    settings = []
+    for r in representations.split():
+        if r[-1] == 's':
+            r = r[:-1]
+        s = r + '_color'
+        if s in cmd.setting.name_list:
+            settings.append(s)
+        elif not quiet:
+            print(' Warning: no such setting:', s)
+
+    # object names only
+    selection = ' '.join(cmd.get_object_list('(' + selection + ')'))
+    if cmd.count_atoms(selection) == 0:
+        print(' Error: empty selection')
+        raise CmdException
+
+    if last < 1:
+        last = cmd.count_states(selection)
+
+    val_range = int(last - first + 1)
+    if val_range < 2:
+        print(' Error: no spectrum possible, need more than 1 state')
+        raise CmdException
+
+    for i in range(val_range):
+        p = float(i) / (val_range - 1) * (len(colvec) - 1)
+        p0, p1 = int(floor(p)), int(ceil(p))
+        ii = (p - p0)
+        col_list = [colvec[p1][j] * ii + colvec[p0][j] * (1.0 - ii) for j in range(3)]
+        col_name = '0x%02x%02x%02x' % (col_list[0] * 255, col_list[1] * 255, col_list[2] * 255)
+        for s in settings:
+            cmd.set(s, col_name, selection, state=i + first)
+
+cmd.extend('spectrum_states', spectrum_states)
+
+# tab-completion of arguments
+cmd.auto_arg[0]['spectrum_states'] = cmd.auto_arg[0]['disable']
+cmd.auto_arg[1]['spectrum_states'] = [cmd.auto_arg[0]['show'][0], 'representation', ' ']
+cmd.auto_arg[2]['spectrum_states'] = [cmd.auto_arg[0]['color'][0], 'color', ' ']
+
+# vi:expandtab:smarttab