r13122 - /branches/xyz/prompt/structure.py -- June 20, 2011 - 15:52

Author: han87
Date: Mon Jun 20 15:52:58 2011
New Revision: 13122

URL: http://svn.gna.org/viewcvs/relax?rev=13122&view=rev
Log:
changing the description in the user functions load_spins() and read_xyz(). 

An example for loading the spins for xyz file format was added in the 
description of the user function load_spins() and the description of the user 
function read_xyz() was changed. Both user functions are located in 
'prompt/structure.py'. 


Modified:
    branches/xyz/prompt/structure.py

Modified: branches/xyz/prompt/structure.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/xyz/prompt/structure.py?rev=13122&r1=13121&r2=13122&view=diff
==============================================================================
--- branches/xyz/prompt/structure.py (original)
+++ branches/xyz/prompt/structure.py Mon Jun 20 15:52:58 2011
@@ -334,7 +334,18 @@
 
         relax> for id in [":A@C8", ":A@C2", ":G@C8", ":G@N1", ":C@C5", 
":C@C6", ":U@N3", ":U@C5", ":U@C6"]:
         relax>     structure.load_spins(spin_id=id)
-        """
+
+
+
+        Example for xyz file
+        To load all C atoms from the 'test.xyz' (which is a single 
molecule), type the following two user functions:
+
+        relax> structure.read_xyz('test.xyz')
+        relax> structure.load_spins(spin_id='@C')
+
+        To load only the third atom from the xyz file, type the following 
user function:
+        relax> structure.load_spins(spin_id='@3')
+"""
 
         # Function intro text.
         if self._exec_info.intro:
@@ -493,13 +504,11 @@
         Description
         ~~~~~~~~~~~
 
-        The reading of XYZ files into relax is quite a flexible procedure 
allowing for both models,
-        defined as an ensemble of the same molecule but with different 
atomic positions, and
-        different molecules within the same model.  One of more molecules 
can exist in one or more
-        models.  The flexibility allows XYZ models to be converted into 
different molecules and
-        different XYZ files loaded as the same molecule but as different 
models.  This flexibility
-        is controlled by the four keyword arguments 'read_mol', 
'set_mol_name', 'read_model', and
-        'set_model_num'.
+        The XYZ files with different models, which defined as an ensemble of 
the same molecule but with 
+        different atomic positions, can be read into relax. If there are 
several molecules in one xyz file, 
+        please seperate them into different files and then load them 
individually. Loading different models
+        and different molecules is controlled by the four keyword arguments 
'read_mol', 'set_mol_name', 
+        'read_model', and 'set_model_num'.
 
 
         The 'set_mol_name' argument is used to name the molecules within the 
XYZ (within one
@@ -533,17 +542,16 @@
         relax> structure.read_xyz('test.xyz', set_mol_name=['CaM_1', 
'CaM_2'], read_model=[1, 5],
                                   set_model_num=[1, 1])
 
-        To load the files 'lactose_MCMM4_S1_1.xyz', 'lactose_MCMM4_S1_2.xyz',
-        'lactose_MCMM4_S1_3.xyz' and 'lactose_MCMM4_S1_4.xyz' as models, 
type the following sequence
-        of commands:
-
-        relax> structure.read_xyz('lactose_MCMM4_S1_1.xyz', 
set_mol_name='lactose_MCMM4_S1',
+        To load the files 'test_1.xyz', 'test_2.xyz','test_3.xyz' and 
'test_4.xyz' as models, type the 
+        following sequence of commands:
+
+        relax> structure.read_xyz('test_1.xyz', set_mol_name='test_1',
                                   set_model_num=1)
-        relax> structure.read_xyz('lactose_MCMM4_S1_2.xyz', 
set_mol_name='lactose_MCMM4_S1',
+        relax> structure.read_xyz('test_2.xyz', set_mol_name='test_2',
                                   set_model_num=2)
-        relax> structure.read_xyz('lactose_MCMM4_S1_3.xyz', 
set_mol_name='lactose_MCMM4_S1',
+        relax> structure.read_xyz('test_3.xyz', set_mol_name='test_3',
                                   set_model_num=3)
-        relax> structure.read_xyz('lactose_MCMM4_S1_4.xyz', 
set_mol_name='lactose_MCMM4_S1',
+        relax> structure.read_xyz('test_4.xyz', set_mol_name='test_4',
                                   set_model_num=4)
         """