Author: bugman
Date: Mon May 19 12:30:52 2014
New Revision: 23237
URL: http://svn.gna.org/viewcvs/relax?rev=23237&view=rev
Log:
Merged revisions 23234-23236 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
r23234 | bugman | 2014-05-19 12:21:31 +0200 (Mon, 19 May 2014) | 5 lines
The new structure.delete 'verbosity' argument is now propagated into the
structural object.
This allows the printouts to now be completely suppressed.
........
r23235 | bugman | 2014-05-19 12:25:49 +0200 (Mon, 19 May 2014) | 5 lines
The structure.read_* user function 'verbosity' argument is now passed into
the structural object.
This allows another printout to be silenced.
........
r23236 | bugman | 2014-05-19 12:29:36 +0200 (Mon, 19 May 2014) | 5 lines
The structure.read_* user function 'verbosity' argument is now passed into
lib.io.open_read_file().
This allows all printouts from these three user functions to be suppressed.
........
Modified:
branches/frame_order_cleanup/ (props changed)
branches/frame_order_cleanup/lib/structure/internal/object.py
branches/frame_order_cleanup/pipe_control/structure/main.py
Propchange: branches/frame_order_cleanup/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Mon May 19 12:30:52 2014
@@ -1 +1 @@
-/trunk:1-23232
+/trunk:1-23236
Modified: branches/frame_order_cleanup/lib/structure/internal/object.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/lib/structure/internal/object.py?rev=23237&r1=23236&r2=23237&view=diff
==============================================================================
--- branches/frame_order_cleanup/lib/structure/internal/object.py
(original)
+++ branches/frame_order_cleanup/lib/structure/internal/object.py Mon
May 19 12:30:52 2014
@@ -240,17 +240,19 @@
return 'Average vector'
- def _parse_models_gaussian(self, file_path):
+ def _parse_models_gaussian(self, file_path, verbosity=1):
"""Generator function for looping over the models in the Gaussian
log file.
@param file_path: The full path of the Gaussian log file.
@type file_path: str
@return: The model number and all the records for that
model.
@rtype: tuple of int and array of str
+ @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
"""
# Open the file.
- file = open_read_file(file_path)
+ file = open_read_file(file_path, verbosity=verbosity)
lines = file.readlines()
file.close()
@@ -580,17 +582,19 @@
return lines[i:]
- def _parse_models_xyz(self, file_path):
+ def _parse_models_xyz(self, file_path, verbosity=1):
"""Generator function for looping over the models in the XYZ file.
@param file_path: The full path of the XYZ file.
@type file_path: str
+ @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
@return: The model number and all the records for that
model.
@rtype: tuple of int and array of str
"""
# Open the file.
- file = open_read_file(file_path)
+ file = open_read_file(file_path, verbosity=verbosity)
lines = file.readlines()
file.close()
@@ -1499,18 +1503,21 @@
mol.atom_connect(index1=index1, index2=index2)
- def delete(self, atom_id=None):
+ def delete(self, atom_id=None, verbosity=1):
"""Deletion of structural information.
@keyword atom_id: The molecule, residue, and atom identifier
string. This matches the spin ID string format. If not given, then all
structural data will be deleted.
@type atom_id: str or None
+ @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
"""
# All data.
if atom_id == None:
- # Print out.
- print("Deleting the following structural data:\n")
- print(self.structural_data)
+ # Printout.
+ if verbosity:
+ print("Deleting the following structural data:\n")
+ print(self.structural_data)
# Delete the structural data.
del self.structural_data
@@ -1795,7 +1802,7 @@
set_model_num = [1]
# Loop over all models in the Gaussian log file, doing nothing so
the last model records are stored.
- for model_records in self._parse_models_gaussian(file_path):
+ for model_records in self._parse_models_gaussian(file_path,
verbosity=verbosity):
pass
# Generate the molecule container.
@@ -1805,7 +1812,7 @@
mol.fill_object_from_gaussian(model_records)
# Create the structural data data structures.
- self.pack_structs([[mol]], orig_model_num=[1],
set_model_num=set_model_num, orig_mol_num=[0], set_mol_name=set_mol_name,
file_name=file_name, file_path=path, file_path_abs=path_abs)
+ self.pack_structs([[mol]], orig_model_num=[1],
set_model_num=set_model_num, orig_mol_num=[0], set_mol_name=set_mol_name,
file_name=file_name, file_path=path, file_path_abs=path_abs,
verbosity=verbosity)
# Loading worked.
return True
@@ -1860,7 +1867,7 @@
set_model_num = [set_model_num]
# Open the PDB file.
- pdb_file = open_read_file(file_path)
+ pdb_file = open_read_file(file_path, verbosity=verbosity)
pdb_lines = pdb_file.readlines()
pdb_file.close()
@@ -1938,7 +1945,7 @@
return False
# 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,
file_path_abs=path_abs, merge=merge)
+ 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,
file_path_abs=path_abs, merge=merge, verbosity=verbosity)
# Loading worked.
return True
@@ -1996,7 +2003,7 @@
mol_conts = []
orig_mol_num = []
new_mol_name = []
- for model_records in self._parse_models_xyz(file_path):
+ for model_records in self._parse_models_xyz(file_path,
verbosity=verbosity):
# Increment the xyz_model_increment
xyz_model_increment = xyz_model_increment +1
@@ -2040,7 +2047,7 @@
# Create the structural data data structures.
orig_mol_num = [0]
- 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,
file_path_abs=path_abs)
+ 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,
file_path_abs=path_abs, verbosity=verbosity)
# Loading worked.
return True
@@ -2114,7 +2121,7 @@
return len(self.structural_data[0].mol)
- def pack_structs(self, data_matrix, orig_model_num=None,
set_model_num=None, orig_mol_num=None, set_mol_name=None, file_name=None,
file_path=None, file_path_abs=None, merge=False):
+ def pack_structs(self, data_matrix, orig_model_num=None,
set_model_num=None, orig_mol_num=None, set_mol_name=None, file_name=None,
file_path=None, file_path_abs=None, verbosity=1, merge=False):
"""From the given structural data, expand the structural data data
structure.
@param data_matrix: A matrix of structural objects.
@@ -2133,6 +2140,8 @@
@type file_path: None or str
@keyword file_path_abs: The absolute path to the file specified
by 'file_name'. This is a fallback mechanism in case results or save files
are located somewhere other than the working directory.
@type file_path_abs: None or str
+ @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
@keyword merge: A flag which if set to True will try to
merge the structure into the currently loaded structures.
@type merge: bool
"""
@@ -2189,11 +2198,12 @@
# Loop over the molecules.
for j in range(len(set_mol_name)):
- # Print out.
- if merge:
- print("Merging with model %s of molecule '%s' (from the
original molecule number %s of model %s)" % (set_model_num[i],
set_mol_name[j], orig_mol_num[j], orig_model_num[i]))
- else:
- print("Adding molecule '%s' to model %s (from the
original molecule number %s of model %s)" % (set_mol_name[j],
set_model_num[i], orig_mol_num[j], orig_model_num[i]))
+ # Printout.
+ if verbosity:
+ if merge:
+ print("Merging with model %s of molecule '%s' (from
the original molecule number %s of model %s)" % (set_model_num[i],
set_mol_name[j], orig_mol_num[j], orig_model_num[i]))
+ else:
+ print("Adding molecule '%s' to model %s (from the
original molecule number %s of model %s)" % (set_mol_name[j],
set_model_num[i], orig_mol_num[j], orig_model_num[i]))
# The index of the new molecule to add or merge.
index = len(model.mol)
Modified: branches/frame_order_cleanup/pipe_control/structure/main.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/pipe_control/structure/main.py?rev=23237&r1=23236&r2=23237&view=diff
==============================================================================
--- branches/frame_order_cleanup/pipe_control/structure/main.py (original)
+++ branches/frame_order_cleanup/pipe_control/structure/main.py Mon May 19
12:30:52 2014
@@ -311,7 +311,7 @@
if hasattr(cdp, 'structure'):
if verbosity:
print("Deleting structural data from the current pipe.")
- cdp.structure.delete(atom_id=atom_id)
+ cdp.structure.delete(atom_id=atom_id, verbosity=verbosity)
elif verbosity:
print("No structures are present.")
r23237 - in /branches/frame_order_cleanup: ./ lib/structure/internal/object.py pipe_control/structure/main.py