r28098 - /trunk/user_functions/structure.py -- November 25, 2015 - 18:37

Author: bugman
Date: Wed Nov 25 18:37:55 2015
New Revision: 28098

URL: http://svn.gna.org/viewcvs/relax?rev=28098&view=rev
Log:
Created the structure.pca user function front end.

This is currently modelled on the structure.rmsd user function framework.

Modified:
    trunk/user_functions/structure.py

Modified: trunk/user_functions/structure.py
URL: 
http://svn.gna.org/viewcvs/relax/trunk/user_functions/structure.py?rev=28098&r1=28097&r2=28098&view=diff
==============================================================================
--- trunk/user_functions/structure.py   (original)
+++ trunk/user_functions/structure.py   Wed Nov 25 18:37:55 2015
@@ -863,6 +863,56 @@
 uf.menu_text = "&mean"
 uf.gui_icon = "oxygen.categories.applications-education"
 uf.wizard_size = (800, 600)
+uf.wizard_image = WIZARD_IMAGE_PATH + 'structure' + sep + '2JK4.png'
+
+
+# The structure.pca user function.
+uf = uf_info.add_uf('structure.pca')
+uf.title = "Principle component analysis (PCA) of the motions in an ensemble 
of structures."
+uf.title_short = "PCA analysis of structures."
+uf.add_keyarg(
+    name = "pipes",
+    py_type = "str_list",
+    desc_short = "data pipes",
+    desc = "The data pipes to determine the RMSD for.",
+    wiz_combo_iter = pipe_names,
+    wiz_read_only = False,
+    can_be_none = True
+)
+uf.add_keyarg(
+    name = "models",
+    py_type = "int_list_of_lists",
+    desc_short = "model list for each data pipe",
+    desc = "The list of models for each data pipe to determine the RMSD for. 
 The number of elements must match the pipes argument.  If no models are 
given, then all will be used.",
+    can_be_none = True
+)
+uf.add_keyarg(
+    name = "molecules",
+    py_type = "str_list_of_lists",
+    desc_short = "molecule list for each data pipe",
+    desc = "The list of molecules for each data pipe to determine the RMSD 
for.  The RMSD will only be calculated for atoms with identical residue name 
and number and atom name.  The number of elements must match the pipes 
argument.  If no molecules are given, then all will be used.",
+    can_be_none = True
+)
+uf.add_keyarg(
+    name = "atom_id",
+    py_type = "str",
+    desc_short = "atom identification string",
+    desc = "The atom identification string of the coordinates of interest.",
+    can_be_none = True
+)
+# Description.
+uf.desc.append(Desc_container())
+uf.desc[-1].add_paragraph("Perform a principle component analysis (PCA) for 
all the chosen structures.")
+uf.desc[-1].add_paragraph(paragraph_multi_struct)
+uf.desc[-1].add_paragraph(paragraph_atom_id)
+# Prompt examples.
+uf.desc.append(Desc_container("Prompt examples"))
+uf.desc[-1].add_paragraph("To determine the PCA modes of all models in the 
current data pipe, simply type:")
+uf.desc[-1].add_prompt("relax> structure.pcs()")
+uf.backend = pipe_control.structure.main.pcs
+uf.menu_text = "&pcs"
+uf.wizard_height_desc = 400
+uf.wizard_size = (900, 700)
 uf.wizard_image = WIZARD_IMAGE_PATH + 'structure' + sep + '2JK4.png'