DynoPlot - Revision history

Pyadmin: 23 revisions

2014-03-28T02:18:17Z

23 revisions

Tlinnet at 15:13, 15 January 2012

2012-01-15T15:13:49Z

Tlinnet at 22:07, 11 December 2011

2011-12-11T22:07:02Z

Tlinnet at 22:06, 11 December 2011

2011-12-11T22:06:40Z

Speleo3: Infobox script-repo

2011-12-09T09:43:12Z

Infobox script-repo

Tlinnet: /* SCRIPTS (DynoPlot.py) */

2011-12-06T02:29:11Z

SCRIPTS (DynoPlot.py)

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Speleo3: postscript dump

2011-11-18T09:38:02Z

postscript dump

Speleo3: color support

2011-11-17T17:46:10Z

color support

Speleo3: description update

2011-09-20T17:53:46Z

description update

Speleo3: general overhaul of the script

2011-09-20T17:43:13Z

general overhaul of the script

Show changes

← Older revision		Revision as of 15:13, 15 January 2012
Line 50:		Line 50:
	[[Category:Script_Library\|DynoPlot]]		[[Category:Script_Library\|DynoPlot]]
	[[Category:Structural_Biology_Scripts\|DynoPlot]]		[[Category:Structural_Biology_Scripts\|DynoPlot]]
		+	[[Category:Pymol-script-repo]]

@@ Line 5: / Line 5: @@
 |license   = -
 }}
+== Introduction ==
 This script was setup to do generic plotting, that is given a set of data and axis labels it would create a plot. Initially, I had it setup to draw the plot directly in the PyMol window (allowing for both 2D and 3D style plots), but because I couldn't figure out how to billboard CGO objects (Warren told me at the time that it couldn't be done) I took a different approach.  The plot now exists in it's own window and can only do 2D plots.  It is however interactive.  I only have here a Rama.(phi,psi) plot, but the code can be easily extended to other types of data.  For instance, I had this working for an energy vs distance data that I had generated by another script.

@@ Line 1: / Line 1: @@
 {{Infobox script-repo
-|type      = PyMOL Plugin
+|type      = plugin
 |filename  = plugins/dynoplot.py
-|author    = Dan Kulp
+|author    = [[User:Tmwsiy|Dan Kulp]]
-|license   =
+|license   = -
 }}

@@ Line 1: / Line 1: @@
 This script was setup to do generic plotting, that is given a set of data and axis labels it would create a plot. Initially, I had it setup to draw the plot directly in the PyMol window (allowing for both 2D and 3D style plots), but because I couldn't figure out how to billboard CGO objects (Warren told me at the time that it couldn't be done) I took a different approach.  The plot now exists in it's own window and can only do 2D plots.  It is however interactive.  I only have here a Rama.(phi,psi) plot, but the code can be easily extended to other types of data.  For instance, I had this working for an energy vs distance data that I had generated by another script.
@@ Line 40: / Line 47: @@
 rama ss S,    none, aa, /tmp/canvasdump_sheet.ps
 </source>
 [[Category:Script_Library|DynoPlot]]
 [[Category:Structural_Biology_Scripts|DynoPlot]]

@@ Line 18: / Line 18: @@
 ===USAGE===
-rama SELECTION
 ===EXAMPLES===
-*load pdb file 1ENV (download it or use the PDB loader plugin)
-*select sel01, resi 129-136
+<source lang="python">
-*rama sel01
+fetch 1ENV, async=0 # (download it or use the PDB loader plugin)
-*rock   # the object needs to be moving in order for the angles to be updated.
+select sel01, resi 129-136
 ===SCRIPTS (DynoPlot.py)===
@@ Line 70: / Line 85: @@
          self.shapes = {}    # store plot data, x,y etc..
          self.idx2resn = {}  # residue name mapping
      def axis(self,xmin=40,xmax=300,ymin=10,ymax=290,xint=290,yint=40,xlabels=[],ylabels=[]):
@@ Line 115: / Line 131: @@
          resn, color, ss = self.idx2resn.get(meta)
-         if True:
+         if self.symbols == 0:
              # symbols by amino acid (G/P/other)
              mark = {'GLY': 'Tri', 'PRO': 'Rect'}.get(resn, 'Oval')
@@ Line 293: / Line 309: @@
 # New Callback object, so that we can update the structure when phi,psi points are moved.
 class DynoRamaObject:
-     def __init__(self, selection=None, name=None):
+     def __init__(self, selection=None, name=None, symbols=''):
          from pymol import _ext_gui as pmgapp
          if pmgapp is not None:
@@ Line 314: / Line 330: @@
                  ylabels=[-180,-150,-120,-90,-60,-30,0,30,60,90,120,150,180])
          canvas.update()
          if name is None:
@@ Line 357: / Line 376: @@
          if self.lock:
              return
          # Loop through each item on plot to see if updated
          for value in self.canvas.shapes.itervalues():
@@ Line 367: / Line 387: @@
                  value[2] = 0
-def rama(sel='(all)', name=None):
+def rama(sel='(all)', name=None, symbols='aa', filename=None):
      '''
 DESCRIPTION
@@ Line 381: / Line 401: @@
      angles when canvas points are dragged, or 'none' to not create a callback
      object {default: DynoRamaObject}
      '''
-     DynoRamaObject(sel, name)
+     dyno = DynoRamaObject(sel, name, symbols)
 # Extend these commands

← Older revision	Revision as of 02:18, 28 March 2014
(No difference)

@@ Line 34: / Line 34: @@
 #  Creation Date: 8/29/05
+#
-#  Modified 2011-09-20 by Thomas Holder
+#  Modified 2011-11-17 by Thomas Holder
+#
 #  Notes:
@@ Line 54: / Line 54: @@
      # Class variables
      mark_size = 4
@@ Line 114: / Line 113: @@
          y = self.convertToPixel("Y",yp)
-         resn = self.idx2resn.get(meta)
+         resn, color, ss = self.idx2resn.get(meta)
-         mark = {'GLY': 'Tri', 'PRO': 'Rect'}.get(resn, self.mark)
          if mark == 'Oval':
@@ Line 130: / Line 135: @@
              coords = [x-self.mark_size, y-self.mark_size,
                      x+self.mark_size, y+self.mark_size]
          oval = create_shape(*coords,
-                 width=1, outline="black", fill="SkyBlue2")
+                 width=1, outline="black", fill=color)
          self.shapes[oval] = [x,y,0,xp,yp,meta]
@@ Line 336: / Line 347: @@
      def start(self,sel):
          self.lock = 1
-         cmd.iterate('(%s) and name CA' % sel, 'idx2resn[model,index] = resn',
+         cmd.iterate('(%s) and name CA' % sel,'idx2resn[model,index] = (resn, color, ss)',
                  space={'idx2resn': self.canvas.idx2resn})
          for model_index, (phi,psi) in cmd.get_phipsi(sel).iteritems():

@@ Line 1: / Line 1: @@
 This script was setup to do generic plotting, that is given a set of data and axis labels it would create a plot. Initially, I had it setup to draw the plot directly in the PyMol window (allowing for both 2D and 3D style plots), but because I couldn't figure out how to billboard CGO objects (Warren told me at the time that it couldn't be done) I took a different approach.  The plot now exists in it's own window and can only do 2D plots.  It is however interactive.  I only have here a Rama.(phi,psi) plot, but the code can be easily extended to other types of data.  For instance, I had this working for an energy vs distance data that I had generated by another script.
@@ Line 11: / Line 10: @@
 ===SETUP===
-place the DynoPlot.py script into the appropriate startup directory then restart PyMol
+Install from the plugins menu with ''Plugin > Manage Plugins > Install ...'' or just [[run]] the script.
 ===NOTES / STATUS===
-*Tested on Windows, PyMol version 0.97
+*Tested on Linux, PyMol version 1.4
 *Left, Right mouse buttons do different things; Right = identify data point, Left = drag data point around
 *Post comments/questions or send them to: dwkulp@mail.med.upenn.edu
@@ Line 36: / Line 22: @@
 ===EXAMPLES===
 *load pdb file 1ENV (download it or use the PDB loader plugin)
-*select resi 129-136
+*select sel01, resi 129-136
 *rama sel01
 *rock   # the object needs to be moving in order for the angles to be updated.
 ===SCRIPTS (DynoPlot.py)===