Author: bugman
Date: Fri Jun 10 15:08:46 2011
New Revision: 12968
URL: http://svn.gna.org/viewcvs/relax?rev=12968&view=rev
Log:
Generating new user function 'read_xyz()'.
This is Han's patch https://gna.org/task/download.php?file_id=13153 attached
to the task
http://gna.org/task/?7404.
The user function 'read_xyz()' was generated and modified in the
generic_fns/structure/main.py based
on the function 'read_pdb()'.
Modified:
branches/xyz/generic_fns/structure/main.py
Modified: branches/xyz/generic_fns/structure/main.py
URL:
http://svn.gna.org/viewcvs/relax/branches/xyz/generic_fns/structure/main.py?rev=12968&r1=12967&r2=12968&view=diff
==============================================================================
--- branches/xyz/generic_fns/structure/main.py (original)
+++ branches/xyz/generic_fns/structure/main.py Fri Jun 10 15:08:46 2011
@@ -364,6 +364,68 @@
molmol.open_pdb()
+def read_xyz(file=None, dir=None, read_mol=None, set_mol_name=None,
read_model=None, set_model_num=None, verbosity=1, fail=True):
+ """The XYZ loading function.
+
+
+ @keyword file: The name of the XYZ file to read.
+ @type file: str
+ @keyword dir: The directory where the XYZ file is located. If
set to None, then the
+ file will be searched for in the current
directory.
+ @type dir: str or None
+ @keyword read_mol: The molecule(s) to read from the file,
independent of model.
+ If set to None, then all molecules will be
loaded.
+ @type read_mol: None, int, or list of int
+ @keyword set_mol_name: Set the names of the molecules which are loaded.
If set to None, then
+ the molecules will be automatically labelled
based on the file name or
+ other information.
+ @type set_mol_name: None, str, or list of str
+ @keyword read_model: The XYZ model to extract from the file. If set
to None, then all models
+ will be loaded.
+ @type read_model: None, int, or list of int
+ @keyword set_model_num: Set the model number of the loaded molecule. If
set to None, then the
+ XYZ model numbers will be preserved, if they
exist.
+ @type set_model_num: None, int, or list of int
+ @keyword fail: A flag which, if True, will cause a RelaxError
to be raised if the XYZ
+ file does not exist. If False, then a
RelaxWarning will be trown
+ instead.
+ @type fail: bool
+ @keyword verbosity: The amount of information to print to screen.
Zero corresponds to
+ minimal output while higher values increase the
amount of output. The
+ default value is 1.
+ @type verbosity: int
+ @raise RelaxFileError: If the fail flag is set, then a RelaxError is
raised if the XYZ file
+ does not exist.
+ """
+
+ # Test if the current data pipe exists.
+ pipes.test()
+
+ # The file path.
+ file_path = get_file_path(file, dir)
+
+ # Try adding '.xyz' to the end of the file path, if the file can't be
found.
+ if not access(file_path, F_OK):
+ file_path_orig = file_path
+ file_path = file_path + '.xyz'
+
+ # Test if the file exists.
+ if not access(file_path, F_OK):
+ if fail:
+ raise RelaxFileError('XYZ', file_path_orig)
+ else:
+ warn(RelaxNoPDBFileWarning(file_path))
+ return
+
+
+ # Place the structural object into the relax data store.
+ if not hasattr(cdp, 'structure'):
+ cdp.structure = Internal()
+
+ # Load the structures.
+ cdp.structure.load_xyz(file_path, read_mol=read_mol,
set_mol_name=set_mol_name, read_model=read_model,
set_model_num=set_model_num, verbosity=verbosity)
+
+
def set_vector(spin=None, xh_vect=None):
"""Place the XH unit vector into the spin container object.
r12968 - /branches/xyz/generic_fns/structure/main.py