Author: bugman
Date: Fri Jan 30 17:20:04 2015
New Revision: 27396
URL: http://svn.gna.org/viewcvs/relax?rev=27396&view=rev
Log:
Implemented the backend of the structure.sequence_alignment user function.
This checks some of the input parameters, assembles the structural objects then
the atomic
coordinate information, performs the multiple sequence alignment, and then
stores the results.
Modified:
trunk/pipe_control/structure/main.py
trunk/user_functions/structure.py
Modified: trunk/pipe_control/structure/main.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/pipe_control/structure/main.py?rev=27396&r1=27395&r2=27396&view=diff
==============================================================================
--- trunk/pipe_control/structure/main.py (original)
+++ trunk/pipe_control/structure/main.py Fri Jan 30 17:20:04 2015
@@ -29,6 +29,8 @@
from warnings import warn
# relax module imports.
+from data_store import Relax_data_store; ds = Relax_data_store()
+from data_store.seq_align import Sequence_alignments
from lib.check_types import is_float
from lib.errors import RelaxError, RelaxFileError
from lib.geometry.vectors import vector_angle_atan2
@@ -36,7 +38,8 @@
from lib.plotting.api import correlation_matrix
from lib.selection import tokenise
from lib.sequence import write_spin_data
-from lib.structure.internal.coordinates import assemble_coord_array,
loop_coord_structures
+from lib.sequence_alignment.msa import central_star
+from lib.structure.internal.coordinates import assemble_atomic_coordinates,
assemble_coord_array, loop_coord_structures
from lib.structure.internal.displacements import Displacements
from lib.structure.internal.object import Internal
from lib.structure.represent.diffusion_tensor import diffusion_tensor
@@ -1254,6 +1257,71 @@
print("Rotated %i atoms." % selection.count_atoms())
+def sequence_alignment(pipes=None, models=None, molecules=None,
msa_algorithm='Central Star', pairwise_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):
+ """Superimpose a set of related, but not identical structures.
+
+ @keyword pipes: The data pipes to include in the
alignment and superimposition.
+ @type pipes: None or list of str
+ @keyword models: The list of models to for each data
pipe superimpose. The number of elements must match the pipes argument. If
set to None, then all models will be used.
+ @type models: list of lists of int or None
+ @keyword molecules: The molecule names to include in the
alignment and superimposition. The number of elements must match the pipes
argument.
+ @type molecules: None or list of str
+ @keyword msa_algorithm: The multiple sequence alignment (MSA)
algorithm to use.
+ @type msa_algorithm: str
+ @keyword pairwise_algorithm: The pairwise sequence alignment
algorithm to use.
+ @type pairwise_algorithm: str
+ @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
+ """
+
+ # Check the penalty arguments.
+ if gap_open_penalty != None:
+ if gap_open_penalty < 0.0:
+ raise RelaxError("The gap opening penalty %s must be a positive
number." % gap_open_penalty)
+ if gap_extend_penalty != None:
+ if gap_extend_penalty < 0.0:
+ raise RelaxError("The gap extension penalty %s must be a positive
number." % gap_extend_penalty)
+ if end_gap_open_penalty != None:
+ if end_gap_open_penalty < 0.0:
+ raise RelaxError("The end gap opening penalty %s must be a
positive number." % end_gap_open_penalty)
+ if end_gap_extend_penalty != None:
+ 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 structural objects.
+ objects, object_names, pipes = assemble_structural_objects(pipes=pipes,
models=models, molecules=molecules)
+
+ # Assemble the atomic coordinates of all structures.
+ ids, atom_pos, mol_names, res_names, res_nums, atom_names, elements,
one_letter_codes, num_mols = assemble_atomic_coordinates(objects=objects,
object_names=object_names, molecules=molecules, models=models)
+
+ # MSA.
+ if msa_algorithm == 'Central Star':
+ # Use the central star multiple alignment algorithm.
+ strings, gaps = central_star(one_letter_codes,
algorithm=pairwise_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)
+
+ # Set up the data store object.
+ if not hasattr(ds, 'sequence_alignment'):
+ ds.sequence_alignment = Sequence_alignments()
+
+ # Flatten the lists.
+ flat_models = []
+ flat_molecules = []
+ for i in range(len(pipes)):
+ flat_models += models[i]
+ flat_molecules += molecules[i]
+
+ # Store the alignment.
+ ds.sequence_alignment.add(object_ids=ids, models=flat_models,
molecules=flat_molecules, sequences=one_letter_codes, strings=strings,
gaps=gaps, msa_algorithm=msa_algorithm, pairwise_algorithm=pairwise_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)
+
+
def set_vector(spin=None, xh_vect=None):
"""Place the XH unit vector into the spin container object.
Modified: trunk/user_functions/structure.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/user_functions/structure.py?rev=27396&r1=27395&r2=27396&view=diff
==============================================================================
--- trunk/user_functions/structure.py (original)
+++ trunk/user_functions/structure.py Fri Jan 30 17:20:04 2015
@@ -1400,7 +1400,7 @@
uf.desc.append(Desc_container("Prompt examples"))
uf.desc[-1].add_paragraph("To superimpose the structures in the 'A' data pipe
onto the structures of the 'B' data pipe using backbone heavy atoms, type:")
uf.desc[-1].add_prompt("relax> structure.sequence_alignment(pipes=['B', 'A'],
atom_id='@N,C,CA,O')")
-uf.backend = pipe_control.structure.main.align
+uf.backend = pipe_control.structure.main.sequence_alignment
uf.menu_text = "&sequence_alignment"
uf.wizard_apply_button = False
uf.wizard_height_desc = 320
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