Author: bugman
Date: Fri Jan 30 16:27:19 2015
New Revision: 27394
URL: http://svn.gna.org/viewcvs/relax?rev=27394&view=rev
Log:
Modified the assemble_coordinates() function of the
pipe_control.structure.main module.
The function has been renamed to assemble_structural_objects(). The call to
the
lib.structure.internal.coordinates.assemble_coord_array() function has also
been shifted out of
assemble_structural_objects() to simplify the logic and decrease the amount
of arguments passed
around.
Modified:
trunk/pipe_control/structure/main.py
Modified: trunk/pipe_control/structure/main.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/pipe_control/structure/main.py?rev=27394&r1=27393&r2=27394&view=diff
==============================================================================
--- trunk/pipe_control/structure/main.py (original)
+++ trunk/pipe_control/structure/main.py Fri Jan 30 16:27:19 2015
@@ -165,8 +165,11 @@
if end_gap_extend_penalty < 0.0:
raise RelaxError("The end gap extension penalty %s must be a
positive number." % end_gap_extend_penalty)
- # Assemble the atomic coordinates and obtain the corresponding element
information.
- coord, ids, mol_names, res_names, res_nums, atom_names, elements =
assemble_coordinates(pipes=pipes, molecules=molecules, models=models,
atom_id=atom_id, algorithm=algorithm, matrix=matrix,
gap_open_penalty=gap_open_penalty, gap_extend_penalty=gap_extend_penalty,
end_gap_open_penalty=end_gap_open_penalty,
end_gap_extend_penalty=end_gap_extend_penalty, seq_info_flag=True)
+ # Assemble the structural objects.
+ objects, object_names, pipes = assemble_structural_objects(pipes=pipes,
models=models, molecules=molecules)
+
+ # Assemble the atomic coordinates.
+ coord, ids, mol_names, res_names, res_nums, atom_names, elements =
assemble_coord_array(objects=objects, object_names=object_names,
models=models, molecules=molecules, atom_id=atom_id, algorithm=algorithm,
matrix=matrix, gap_open_penalty=gap_open_penalty,
gap_extend_penalty=gap_extend_penalty,
end_gap_open_penalty=end_gap_open_penalty,
end_gap_extend_penalty=end_gap_extend_penalty, seq_info_flag=True)
# Catch missing data.
if len(coord[0]) == 0:
@@ -184,7 +187,7 @@
# Loop over all pipes, models, and molecules.
i = 0
- for pipe_index, model_num, mol_name in structure_loop(pipes=pipes,
molecules=molecules, models=models, atom_id=atom_id):
+ for pipe_index, model_num, mol_name in structure_loop(pipes=pipes,
models=models, molecules=molecules, atom_id=atom_id):
# The current displacement ID.
curr_displace_id = None
if isinstance(displace_id, str):
@@ -214,7 +217,7 @@
i += 1
-def assemble_coordinates(pipes=None, molecules=None, models=None,
atom_id=None, algorithm='NW70', matrix='BLOSUM62', gap_open_penalty=1.0,
gap_extend_penalty=1.0, end_gap_open_penalty=0.0, end_gap_extend_penalty=0.0,
seq_info_flag=False):
+def assemble_structural_objects(pipes=None, models=None, molecules=None):
"""Assemble the atomic coordinates.
@keyword pipes: The data pipes to assemble the
coordinates from.
@@ -223,24 +226,8 @@
@type models: None or list of lists of int
@keyword molecules: The list of molecules for each data
pipe. The number of elements must match the pipes argument.
@type molecules: None or list of lists of str
- @keyword atom_id: The molecule, residue, and atom
identifier string of the coordinates of interest. This matches the spin ID
string format.
- @type atom_id: None or str
- @keyword algorithm: The pairwise sequence alignment
algorithm to use. If set to None, then no alignment will be performed.
- @type algorithm: str or None
- @keyword matrix: The substitution matrix to use.
- @type matrix: str
- @keyword gap_open_penalty: The penalty for introducing gaps, as
a positive number.
- @type gap_open_penalty: float
- @keyword gap_extend_penalty: The penalty for extending a gap, as
a positive number.
- @type gap_extend_penalty: float
- @keyword end_gap_open_penalty: The optional penalty for opening a
gap at the end of a sequence.
- @type end_gap_open_penalty: float
- @keyword end_gap_extend_penalty: The optional penalty for extending a
gap at the end of a sequence.
- @type end_gap_extend_penalty: float
- @keyword seq_info_flag: A flag which if True will cause the
atomic sequence information to be assembled and returned. This includes the
molecule names, residue names, residue numbers, atom names, and elements.
- @type seq_info_flag: bool
- @return: The array of atomic coordinates
(first dimension is the model and/or molecule, the second are the atoms, and
the third are the coordinates); a list of unique IDs for each structural
object, model, and molecule; the common list of molecule names (if the
seq_info_flag is set); the common list of residue names (if the seq_info_flag
is set); the common list of residue numbers (if the seq_info_flag is set);
the common list of atom names (if the seq_info_flag is set); the common list
of element names (if the seq_info_flag is set).
- @rtype: numpy rank-3 float64 array, list of
str, list of str, list of str, list of int, list of str, list of str
+ @return: The structural objects, structural
object names, and data pipes list.
+ @rtype: list of
lib.structure.internal.object.Internal instances, list of str, list of str
"""
# The data pipes to use.
@@ -268,8 +255,8 @@
objects.append(dp.structure)
object_names.append(pipes[pipe_index])
- # Call the library method to do all of the work.
- return assemble_coord_array(objects=objects, object_names=object_names,
molecules=molecules, models=models, atom_id=atom_id, algorithm=algorithm,
matrix=matrix, gap_open_penalty=gap_open_penalty,
gap_extend_penalty=gap_extend_penalty,
end_gap_open_penalty=end_gap_open_penalty,
end_gap_extend_penalty=end_gap_extend_penalty, seq_info_flag=seq_info_flag)
+ # Return the structural objects, object names, and the new pipes list.
+ return objects, object_names, pipes
def atomic_fluctuations(pipes=None, models=None, molecules=None,
atom_id=None, measure='distance', file=None, format='text', dir=None,
force=False):
@@ -302,8 +289,11 @@
if measure not in allowed_measures:
raise RelaxError("The measure '%s' must be one of %s." % (measure,
allowed_measures))
+ # Assemble the structural objects.
+ objects, object_names, pipes = assemble_structural_objects(pipes=pipes,
models=models, molecules=molecules)
+
# Assemble the atomic coordinates.
- coord, ids, mol_names, res_names, res_nums, atom_names, elements =
assemble_coordinates(pipes=pipes, molecules=molecules, models=models,
atom_id=atom_id, seq_info_flag=True)
+ coord, ids, mol_names, res_names, res_nums, atom_names, elements =
assemble_coord_array(objects=objects, object_names=object_names,
models=models, molecules=molecules, atom_id=atom_id, seq_info_flag=True)
# The number of dimensions.
n = len(atom_names)
@@ -623,8 +613,11 @@
# Test if the current data pipe exists.
check_pipe()
+ # Assemble the structural objects.
+ objects, object_names, pipes = assemble_structural_objects(pipes=pipes,
models=models, molecules=molecules)
+
# Assemble the atomic coordinates.
- coord, ids = assemble_coordinates(pipes=pipes, molecules=molecules,
models=models, atom_id=atom_id)
+ coord, ids = assemble_coord_array(objects=objects,
object_names=object_names, models=models, molecules=molecules,
atom_id=atom_id)
# Initialise the data structure.
if not hasattr(cdp.structure, 'displacments'):
@@ -666,8 +659,11 @@
init_pos = zeros(3, float64)
init_pos = array(init_pos)
+ # Assemble the structural objects.
+ objects, object_names, pipes = assemble_structural_objects(pipes=pipes,
models=models, molecules=molecules)
+
# Assemble the atomic coordinates.
- coord, ids = assemble_coordinates(pipes=pipes, molecules=molecules,
models=models, atom_id=atom_id)
+ coord, ids = assemble_coord_array(objects=objects,
object_names=object_names, models=models, molecules=molecules,
atom_id=atom_id)
# Linear constraints for the pivot position (between -1000 and 1000
Angstrom).
A = zeros((6, 3), float64)
@@ -1200,8 +1196,11 @@
# Test if the current data pipe exists.
check_pipe()
+ # Assemble the structural objects.
+ objects, object_names, pipes = assemble_structural_objects(pipes=pipes,
models=models, molecules=molecules)
+
# Assemble the atomic coordinates.
- coord, ids = assemble_coordinates(pipes=pipes, molecules=molecules,
models=models, atom_id=atom_id)
+ coord, ids = assemble_coord_array(objects=objects,
object_names=object_names, models=models, molecules=molecules,
atom_id=atom_id)
# Calculate the RMSD.
cdp.structure.rmsd = atomic_rmsd(coord, verbosity=1)
@@ -1307,7 +1306,7 @@
objects.append(dp.structure)
# Call the library method to do all of the work.
- for pipe_index, model_num, mol_name in
loop_coord_structures(objects=objects, molecules=molecules, models=models,
atom_id=atom_id):
+ for pipe_index, model_num, mol_name in
loop_coord_structures(objects=objects, models=models, molecules=molecules,
atom_id=atom_id):
yield pipe_index, model_num, mol_name
@@ -1342,8 +1341,11 @@
if models == None:
models = cdp.structure.model_list()
- # Assemble the atomic coordinates and obtain the corresponding element
information.
- coord, ids, mol_names, res_names, res_nums, atom_names, elements =
assemble_coordinates(models=[models], atom_id=atom_id, seq_info_flag=True)
+ # Assemble the structural objects.
+ objects, object_names, pipes =
assemble_structural_objects(models=[models])
+
+ # Assemble the atomic coordinates.
+ coord, ids, mol_names, res_names, res_nums, atom_names, elements =
assemble_coord_array(objects=objects, object_names=object_names,
models=[models], atom_id=atom_id, seq_info_flag=True)
# The different algorithms.
if method == 'fit to mean':
@@ -1566,8 +1568,11 @@
check_pipe()
check_structure()
+ # Assemble the structural objects.
+ objects, object_names, pipes = assemble_structural_objects(pipes=pipes,
models=models, molecules=molecules)
+
# Assemble the atomic coordinates.
- coord, ids, mol_names, res_names, res_nums, atom_names, elements =
assemble_coordinates(pipes=pipes, molecules=molecules, models=models,
atom_id=atom_id, seq_info_flag=True)
+ coord, ids, mol_names, res_names, res_nums, atom_names, elements =
assemble_coord_array(objects=objects, object_names=object_names,
models=models, molecules=molecules, atom_id=atom_id, seq_info_flag=True)
# Check that more than one structure is present.
if not len(coord) > 1:
r27394 - /trunk/pipe_control/structure/main.py