Author: bugman
Date: Fri Jun 10 12:13:16 2011
New Revision: 12958
URL: http://svn.gna.org/viewcvs/relax?rev=12958&view=rev
Log:
Generating new user function 'read_xyz()'.
This is Han's patch https://gna.org/task/download.php?file_id=13148 attached
to the task
http://gna.org/task/?7404.
The user function 'read_xyz()' was generated in the prompt/structure.py by
duplication of
'read_pdb()' and modified accordingly.
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=12958&r1=12957&r2=12958&view=diff
==============================================================================
--- branches/xyz/prompt/structure.py (original)
+++ branches/xyz/prompt/structure.py Fri Jun 10 12:13:16 2011
@@ -471,6 +471,107 @@
generic_fns.structure.main.read_pdb(file=file, dir=dir,
read_mol=read_mol, set_mol_name=set_mol_name, read_model=read_model,
set_model_num=set_model_num, parser=parser)
+ def read_xyz(self, file=None, dir=None, read_mol=None,
set_mol_name=None, read_model=None, set_model_num=None):
+ """The XYZ loading function.
+
+ Keyword Arguments
+ ~~~~~~~~~~~~~~~~~
+
+ file: The name of the XYZ file.
+
+ dir: The directory where the file is located.
+
+ read_mol: If set, only the given molecule(s) will be read.
+
+ set_mol_name: Set the names of the read molecules.
+
+ read_model: If set, only the given model number(s) from the XYZ
file will be read.
+
+ set_model_num: Set the model numbers of the read molecules.
+
+
+ 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 'set_mol_name' argument is used to name the molecules within the
XYZ (within one
+ model). If not set, then the molecules will be named after the file
name, with the molecule
+ number appended if more than one exists.
+
+ Note that relax will complain if it cannot work out what to do.
+
+
+ Examples
+ ~~~~~~~~
+
+ To load all structures from the XYZ file 'test.xyz' in the directory
'~/xyz', including all
+ models and all molecules, type one of:
+
+ relax> structure.read_xyz('test.xyz', '~/xyz')
+ relax> structure.read_xyz(file='test.xyz', dir='xyz')
+
+
+ To load the 10th model from the file 'test.xyz' and
+ naming it 'CaM', use one of:
+
+ relax> structure.read_xyz('test.xyz', read_model=10,
set_mol_name='CaM')
+ relax> structure.read_xyz(file='test.xyz', read_model=10,
set_mol_name='CaM')
+
+
+ To load models 1 and 5 from the file 'test.xyz' as two different
structures of the same
+ model, type one of:
+
+ relax> structure.read_xyz('test.xyz', read_model=[1, 5],
set_model_num=[1, 1])
+ 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',
+ set_model_num=1)
+ relax> structure.read_xyz('lactose_MCMM4_S1_2.xyz',
set_mol_name='lactose_MCMM4_S1',
+ set_model_num=2)
+ relax> structure.read_xyz('lactose_MCMM4_S1_3.xyz',
set_mol_name='lactose_MCMM4_S1',
+ set_model_num=3)
+ relax> structure.read_xyz('lactose_MCMM4_S1_4.xyz',
set_mol_name='lactose_MCMM4_S1',
+ set_model_num=4)
+ """
+
+ # Function intro text.
+ if self._exec_info.intro:
+ text = self._exec_info.ps3 + "structure.read_xyz("
+ text = text + "file=" + repr(file)
+ text = text + ", dir=" + repr(dir)
+ text = text + ", read_mol=" + repr(read_mol)
+ text = text + ", set_mol_name=" + repr(set_mol_name)
+ text = text + ", read_model=" + repr(read_model)
+ text = text + ", set_model_num=" + repr(set_model_num)
+ text = text + ")"
+ print(text)
+
+ # The argument checks.
+ arg_check.is_str(file, 'file name')
+ arg_check.is_str(dir, 'directory name', can_be_none=True)
+ arg_check.is_int_or_int_list(read_mol, 'read molecule number',
can_be_none=True)
+ arg_check.is_int_or_int_list(read_model, 'read model',
can_be_none=True)
+ arg_check.is_int_or_int_list(set_model_num, 'set model numbers',
can_be_none=True)
+ arg_check.is_str_or_str_list(set_mol_name, 'set molecule names',
can_be_none=True)
+
+ # Execute the functional code.
+ generic_fns.structure.main.read_xyz(file=file, dir=dir,
read_mol=read_mol, set_mol_name=set_mol_name, read_model=read_model,
set_model_num=set_model_num)
+
+
+
def vectors(self, attached='H', spin_id=None, model=None, verbosity=1,
ave=True, unit=True):
"""Extract and store the bond vectors from the loaded structures in
the spin container.
r12958 - /branches/xyz/prompt/structure.py