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'
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