Author: bugman
Date: Thu Jan 29 16:19:17 2015
New Revision: 27359
URL: http://svn.gna.org/viewcvs/relax?rev=27359&view=rev
Log:
The assemble_coord_array() function is now using the central star multiple
sequence alignment.
This is the function from the lib.structure.internal.coordinates module used to
assemble common
atomic coordinate information, used by the structure.align,
structure.atomic_fluctuations,
structure.com, structure.displacement, structure.find_pivot, structure.mean,
structure.rmsd,
structure.superimpose and structure.web_of_motion user functions.
The non-functional lib.structure.internal.coordinates.common_residues()
function has been removed as
the lib.sequence_alignment.msa.central_star() function performs this
functionality correctly.
Modified:
trunk/lib/structure/internal/coordinates.py
Modified: trunk/lib/structure/internal/coordinates.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/structure/internal/coordinates.py?rev=27359&r1=27358&r2=27359&view=diff
==============================================================================
--- trunk/lib/structure/internal/coordinates.py (original)
+++ trunk/lib/structure/internal/coordinates.py Thu Jan 29 16:19:17 2015
@@ -27,7 +27,7 @@
# relax module imports.
from lib.errors import RelaxFault
-from lib.sequence_alignment.align_protein import align_pairwise
+from lib.sequence_alignment.msa import central_star
def assemble_coord_array(objects=None, object_names=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):
@@ -160,21 +160,35 @@
# The total number of molecules.
num_mols = len(atom_names)
- # Sequence alignment.
- if algorithm == 'NW70':
- print("\nPairwise sequence alignment to the first molecule:\n")
- gap_matrices = []
- for mol_index in range(1, num_mols):
- print("Molecules 1-%i" % (mol_index+1))
- align1, align2, gaps = align_pairwise(one_letter_codes[0],
one_letter_codes[mol_index], 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)
- gap_matrices.append(gaps)
-
- # Determine the residues in common.
- skip = common_residues(gap_matrices=gap_matrices,
one_letter_codes=one_letter_codes)
-
- # No alignment, so create an empty residue skipping data structure.
+ # Multiple sequence alignment.
+ if algorithm != None:
+ # Use the central star multiple alignment algorithm.
+ strings, gaps = central_star(one_letter_codes, 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)
+
+ # Create the residue skipping data structure.
+ skip = []
+ for mol_index in range(num_mols):
+ skip.append([])
+ for i in range(len(strings[0])):
+ # No residue in the current sequence.
+ if gaps[mol_index][i]:
+ continue
+
+ # A gap in one of the other sequences.
+ gap = False
+ for mol_index2 in range(num_mols):
+ if gaps[mol_index2][i]:
+ gap = True
+
+ # Skip the residue.
+ if gap:
+ skip[mol_index].append(1)
+ else:
+ skip[mol_index].append(0)
+
+ # No alignment.
else:
- # Create
+ # Create an empty residue skipping data structure.
skip = []
for mol_index in range(num_mols):
skip.append([])
@@ -253,145 +267,6 @@
return coord, ids
-def common_residues(gap_matrices=None, one_letter_codes=None, seq=False):
- """Determine the common residues between all the pairwise alignments.
-
- @keyword gap_matrices: The list of gap matrices from the pairwise
alignments.
- @type gap_matrices: list of numpy rank-2 arrays.
- @keyword one_letter_codes: The list of strings of one letter residue
codes for each molecule.
- @type one_letter_codes: list of str
- @keyword seq: A flag which if True will cause the gapped
sequence strings to be returned.
- @type seq: bool
- @return: The residue skipping data structure and the
optional gapped sequence strings. For the skipping structure, the first
dimension corresponds to the molecule and the second to the residue. A one
means the residue should be skipped, whereas zero means keep the residue.
- @rtype: list of list of int
- """
-
- # The number of molecules.
- num_mols = len(gap_matrices) + 1
-
- # Initialise the residue skipping structures.
- skip = []
- skip_counts = zeros(num_mols, int16)
- res_counts = zeros(num_mols, int16)
- for mol_index in range(num_mols):
- res_counts[mol_index] = len(one_letter_codes[mol_index])
- skip.append([])
- for j in range(res_counts[mol_index]):
- skip[mol_index].append(0)
-
- # Update the residue skipping structures for the first molecule.
- for mol_index in range(num_mols-1):
- # Loop over the residues of alignment i.
- seq_index = -1
- for j in range(len(gap_matrices[mol_index][0])):
- # Increment the sequence index.
- if not gap_matrices[mol_index][0, j]:
- seq_index += 1
-
- # A gap in the second sequence, so skip the residue.
- if gap_matrices[mol_index][1, j]:
- skip[0][seq_index] = 1
-
- # Initialise the gapped strings data structure for the first molecule.
- gapped_strings = ['']
- string_length = max(res_counts)
- offsets = zeros((num_mols-1), int16)
- prev_offsets = zeros((num_mols-1), int16)
- for seq_index in range(res_counts[0]):
- # Increment the offsets indices.
- for mol_index in range(1, num_mols):
- while gap_matrices[mol_index-1][0, seq_index+offsets[mol_index-1]]:
- offsets[mol_index-1] += 1
-
- # A gap.
- for i in range(max(offsets - prev_offsets)):
- gapped_strings[0] += "-"
-
- # Missing in one of the other molecule.
- missing = False
- for mol_index in range(1, num_mols):
- if gap_matrices[mol_index-1][1, seq_index+offsets[mol_index-1]]:
- missing = True
- if missing:
- gapped_strings[0] += "-"
-
- # Keep the residue.
- else:
- gapped_strings[0] += one_letter_codes[0][seq_index]
-
- # Store the old offsets.
- prev_offsets = offsets * 1
-
- # Final padding.
- for j in range(max(res_counts) - res_counts[0] - 1):
- gapped_strings[0] += "-"
-
- # Update the first molecule skip counts.
- skip_counts[0] = sum(skip[0])
-
- # Update the residue skipping structures for all other molecules.
- for mol_index in range(1, num_mols):
- # Loop over the residues of alignment mol_index.
- seq1_index = -1
- seq2_index = -1
- gapped_strings.append('')
- for j in range(len(gap_matrices[mol_index-1][0])):
- # Increment the sequence indices.
- if not gap_matrices[mol_index-1][0, j]:
- seq1_index += 1
- if not gap_matrices[mol_index-1][1, j]:
- seq2_index += 1
-
- # End condition for the first molecule.
- if seq1_index >= res_counts[0]:
- # Skip the rest of the second molecule.
- for k in range(seq2_index, res_counts[mol_index]):
- skip[mol_index][k] = 1
- skip_counts[mol_index] += 1
- gapped_strings[mol_index] += "-"
-
- # Terminate the loop.
- break
-
- # A gap in the first sequence, so skip the residue.
- if gap_matrices[mol_index-1][0, j]:
- skip[mol_index][seq2_index] = 1
- skip_counts[mol_index] += 1
- gapped_strings[mol_index] += "-"
-
- # Already skipped in the first molecule.
- elif skip[0][seq1_index] and not gap_matrices[mol_index-1][1, j]:
- skip[mol_index][seq2_index] = 1
- skip_counts[mol_index] += 1
- gapped_strings[mol_index] += "-"
-
- # Skipped in the second molecule.
- elif gap_matrices[mol_index-1][1, j]:
- gapped_strings[mol_index] += "-"
-
- # Print out the one letter code.
- else:
- gapped_strings[mol_index] +=
one_letter_codes[mol_index][seq2_index]
-
- # Printout.
- print("Shared residues:")
- for mol_index in range(num_mols):
- print("Molecule %3i: %s" % (mol_index, gapped_strings[mol_index]))
-
- # Sanity checks.
- total = res_counts[0] - skip_counts[0]
- for mol_index in range(1, num_mols):
- if total != res_counts[mol_index] - skip_counts[mol_index]:
- print("\nThe total shared residue counts between molcule 1 and %i
of %i and %i respectively do not match." % ((mol_index+1), total,
res_counts[mol_index] - skip_counts[mol_index]))
- raise RelaxFault
-
- # Return the skipping data structure.
- if seq:
- return skip, gapped_strings
- else:
- return skip
-
-
def loop_coord_structures(objects=None, molecules=None, models=None,
atom_id=None):
"""Generator function for looping over all internal structural objects,
models and molecules.
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