Author: tlinnet
Date: Mon May 19 13:49:04 2014
New Revision: 23238
URL: http://svn.gna.org/viewcvs/relax?rev=23238&view=rev
Log:
Merged revisions 23230,23232,23234-23236 via svnmerge from
svn+ssh://tlinnet@xxxxxxxxxxx/svn/relax/trunk
........
r23230 | bugman | 2014-05-19 11:57:56 +0200 (Mon, 19 May 2014) | 7 lines
Exposed the backend verbosity flag of the structure.read_* user functions.
This allows the user to silence these user functions, which can be very
useful when loading many
3D structures in the scripting UI mode. This change is for the
structure.read_gaussian,
structure.read_pdb, and structure.read_xyz user functions.
........
r23232 | bugman | 2014-05-19 12:09:17 +0200 (Mon, 19 May 2014) | 7 lines
Expanded the structure.delete user function to add the 'verbosity' and
'spin_info' arguments.
The verbosity argument, when set to zero, allows all output to be
suppressed. The spin_info flag
allows the deletion of spin and interatomic data to now be turned off, so
that only 3D data is
deleted.
........
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/disp_speed/ (props changed)
branches/disp_speed/lib/structure/internal/object.py
branches/disp_speed/pipe_control/structure/main.py
branches/disp_speed/user_functions/structure.py
Propchange: branches/disp_speed/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Mon May 19 13:49:04 2014
@@ -1 +1 @@
-/trunk:1-23213
+/trunk:1-23237
Modified: branches/disp_speed/lib/structure/internal/object.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_speed/lib/structure/internal/object.py?rev=23238&r1=23237&r2=23238&view=diff
==============================================================================
--- branches/disp_speed/lib/structure/internal/object.py (original)
+++ branches/disp_speed/lib/structure/internal/object.py Mon May 19
13:49:04 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/disp_speed/pipe_control/structure/main.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_speed/pipe_control/structure/main.py?rev=23238&r1=23237&r2=23238&view=diff
==============================================================================
--- branches/disp_speed/pipe_control/structure/main.py (original)
+++ branches/disp_speed/pipe_control/structure/main.py Mon May 19 13:49:04
2014
@@ -293,11 +293,15 @@
status.observers.result_file.notify()
-def delete(atom_id=None):
+def delete(atom_id=None, verbosity=1, spin_info=True):
"""Delete structural data.
@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
+ @keyword spin_info: A flag which if True will cause all structural
information in the spin containers and interatomic data containers to be
deleted as well. If False, then only the 3D structural data will be deleted.
+ @type spin_info: bool
"""
# Test if the current data pipe exists.
@@ -305,20 +309,27 @@
# Run the object method.
if hasattr(cdp, 'structure'):
- print("Deleting structural data from the current pipe.")
- cdp.structure.delete(atom_id=atom_id)
- else:
+ if verbosity:
+ print("Deleting structural data from the current pipe.")
+ cdp.structure.delete(atom_id=atom_id, verbosity=verbosity)
+ elif verbosity:
print("No structures are present.")
+ # Skip the rest.
+ if not spin_info:
+ return
+
# Then remove any spin specific structural info.
- print("Deleting all spin specific structural info.")
+ if verbosity:
+ print("Deleting all spin specific structural info.")
for spin in spin_loop(selection=atom_id):
# Delete positional information.
if hasattr(spin, 'pos'):
del spin.pos
# Then remove any interatomic vector structural info.
- print("Deleting all interatomic vectors.")
+ if verbosity:
+ print("Deleting all interatomic vectors.")
for interatom in interatomic_loop(selection1=atom_id):
# Delete bond vectors.
if hasattr(interatom, 'vector'):
Modified: branches/disp_speed/user_functions/structure.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_speed/user_functions/structure.py?rev=23238&r1=23237&r2=23238&view=diff
==============================================================================
--- branches/disp_speed/user_functions/structure.py (original)
+++ branches/disp_speed/user_functions/structure.py Mon May 19 13:49:04
2014
@@ -426,6 +426,20 @@
desc_short = "atom ID string",
desc = "The atom identification string.",
can_be_none = True
+)
+uf.add_keyarg(
+ name = "verbosity",
+ default = 1,
+ py_type = "int",
+ desc_short = "verbosity level",
+ desc = "The amount of information to print out. Set to zero to silence
the user function, or one to see all messages."
+)
+uf.add_keyarg(
+ name = "spin_info",
+ default = True,
+ py_type = "bool",
+ desc_short = "spin information flag",
+ desc = "A flag which if True will cause all structural information in
the spin containers and interatomic data containers to be deleted as well.
If False, then only the 3D structural data will be deleted."
)
# Description.
uf.desc.append(Desc_container())
@@ -644,6 +658,13 @@
desc = "Set the model numbers of the loaded molecules. This can be a
single number or list of numbers.",
can_be_none = True
)
+uf.add_keyarg(
+ name = "verbosity",
+ default = 1,
+ py_type = "int",
+ desc_short = "verbosity level",
+ desc = "The amount of information to print out. Set to zero to silence
the user function, or one to see all messages."
+)
# Description.
uf.desc.append(Desc_container())
uf.desc[-1].add_paragraph("The atomic positions from a Gaussian log file can
be read into relax. If optimisation has been preformed, the last set of
atomic coordinates from the log will be read to obtain the final structure.
The log file can be Gzip or Bzip2 compressed.")
@@ -716,6 +737,13 @@
desc_short = "alternate location indicator",
desc = "The PDB ATOM record 'Alternate location indicator' field value.",
can_be_none = True
+)
+uf.add_keyarg(
+ name = "verbosity",
+ default = 1,
+ py_type = "int",
+ desc_short = "verbosity level",
+ desc = "The amount of information to print out. Set to zero to silence
the user function, or one to see all messages."
)
uf.add_keyarg(
name = "merge",
@@ -805,6 +833,13 @@
desc = "Set the model numbers of the loaded molecules. If unset, then
the PDB model numbers will be preserved if they exist. This can be a single
number or list of numbers.",
can_be_none = True
)
+uf.add_keyarg(
+ name = "verbosity",
+ default = 1,
+ py_type = "int",
+ desc_short = "verbosity level",
+ desc = "The amount of information to print out. Set to zero to silence
the user function, or one to see all messages."
+)
# Description.
uf.desc.append(Desc_container())
uf.desc[-1].add_paragraph("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 separate them into different files and then load them
individually. Loading different models and different molecules is controlled
by specifying the molecule number read, setting the molecule names,
specifying which model to read, and setting the model numbers.")
r23238 - in /branches/disp_speed: ./ lib/structure/internal/ pipe_control/structure/ user_functions/