Hi Edward,
That is the problem. In the xyz file you can probably have several
molecules, but you can not recognized that. There is no parameter to
define the molecule or the residue like in the pdb file.
Best,
Han
On Jun 20, 2011, at 10:41 AM, Edward d'Auvergne wrote:
Hi Han,
It's now working, your ssh access :) I was just wondering why you had
the statement:
if mol_index==0:
This could be problematic if you have multiple molecules in the XYZ
file. Is it possible to have more than one in the format?
Cheers,
Edward
On 20 June 2011 10:07, <[email protected]> wrote:
Author: han87
Date: Mon Jun 20 10:07:35 2011
New Revision: 13121
URL: http://svn.gna.org/viewcvs/relax?rev=13121&view=rev
Log:
Debugging the user functions load_xyz() and test_read_xyz_internal2
().
The user functions load_xyz() in 'generic_fns/structure/
internal.py' and test_read_xyz_internal2() in 'test_suite/
system_tests/structure.py' have been changed so that the molecule
name can be read properly.
Modified:
branches/xyz/generic_fns/structure/internal.py
branches/xyz/test_suite/system_tests/structure.py
Modified: branches/xyz/generic_fns/structure/internal.py
URL: http://svn.gna.org/viewcvs/relax/branches/xyz/generic_fns/
structure/internal.py?rev=13121&r1=13120&r2=13121&view=diff
=====================================================================
=========
--- branches/xyz/generic_fns/structure/internal.py (original)
+++ branches/xyz/generic_fns/structure/internal.py Mon Jun 20
10:07:35 2011
@@ -853,8 +853,9 @@
if set_mol_name:
new_mol_name.append(set_mol_name[mol_index])
else:
- # Set the name to the file name plus the
structure number.
- new_mol_name.append(file_root(file) + '_mol' +
repr(mol_index))
+ if mol_index==0:
+ #Set the name to the file name plus the
structure number.
+ new_mol_name.append(file_root(file) + '_mol' +
repr(mol_index+1))
# Store the original mol number.
orig_mol_num.append(mol_index)
@@ -874,7 +875,8 @@
# Increment the model index.
model_index = model_index + 1
-
+
+ orig_mol_num=[0]
# Create the structural data data structures.
self.pack_structs(mol_conts,
orig_model_num=orig_model_num, set_model_num=set_model_num,
orig_mol_num=orig_mol_num, set_mol_name=new_mol_name,
file_name=file, file_path=path)
Modified: branches/xyz/test_suite/system_tests/structure.py
URL: http://svn.gna.org/viewcvs/relax/branches/xyz/test_suite/
system_tests/structure.py?rev=13121&r1=13120&r2=13121&view=diff
=====================================================================
=========
--- branches/xyz/test_suite/system_tests/structure.py (original)
+++ branches/xyz/test_suite/system_tests/structure.py Mon Jun 20
10:07:35 2011
@@ -659,10 +659,10 @@
self.interpreter.structure.read_xyz(file='SSS-cluster4-new-
test.xyz', dir=path)
# Test the molecule name.
- self.assertEqual(cdp.structure.structural_data[0].mol
[0].mol_name, 'SSS-cluster4-new-test')
+ self.assertEqual(cdp.structure.structural_data[0].mol
[0].mol_name, 'SSS-cluster4-new-test_mol1')
# Load a single atom and test it.
- self.interpreter.structure.load_spins('SSS-cluster4-new-
test:3@C')
+ self.interpreter.structure.load_spins('SSS-cluster4-new-
test_mol1:@C')
self.assertEqual(count_spins(), 1)
# Try loading a few protons.
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