Author: bugman
Date: Mon Jan 26 17:44:46 2015
New Revision: 27313
URL: http://svn.gna.org/viewcvs/relax?rev=27313&view=rev
Log:
The pairwise sequence alignment is now active in the structure.align user
function.
This is implemented in the
lib.structure.internal.coordinates.assemble_coord_array() function for
assembling atomic coordinates. It will also automatically be used by many of
the structure user
functions which operate on multiple structures.
The atomic coordinate assembly logic has been completely changed. Instead of
grouping atomic
information by the molecule, it is now grouped per residue. This allows the
residue based sequence
alignments to find matching coordinate information.
The assemble_coord_array() function will also handle the algorithm argument set
to None and assume
that the residue sequences are identical between the structures, but this
should be avoided.
A new function, common_residues() has been created as a work-around for not
having a multiple
sequence alignment implementation. It will take the pairwise sequence
alignment information and
construct a special data structure specifying which residues are present in all
structures.
The logic for skipping missing atoms remains in place, but it now operates on
the residue rather
than molecule level and simply uses the atom name rather than atom ID to
identify common atoms.
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=27313&r1=27312&r2=27313&view=diff
==============================================================================
--- trunk/lib/structure/internal/coordinates.py (original)
+++ trunk/lib/structure/internal/coordinates.py Mon Jan 26 17:44:46 2015
@@ -24,8 +24,10 @@
# Python module imports.
from numpy import array, float64
+import sys
# relax module imports.
+from lib.errors import RelaxFault
from lib.sequence_alignment.align_protein import align_pairwise
@@ -42,8 +44,8 @@
@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.
- @type algorithm: 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.
@@ -106,17 +108,18 @@
# Extend the lists.
if molecules == None:
+ atom_names.append([])
atom_ids.append([])
- atom_pos.append({})
+ atom_pos.append([])
if seq_info_flag:
- mol_names.append({})
- res_names.append({})
- res_nums.append({})
- atom_names.append({})
- elements.append({})
+ mol_names.append([])
+ res_names.append([])
+ res_nums.append([])
+ elements.append([])
# Add all coordinates and elements.
current_mol = ''
+ current_res = None
for mol_name, res_num, res_name, atom_name, elem, pos in
objects[struct_index].atom_loop(selection=selection, model_num=model.num,
mol_name_flag=True, res_num_flag=True, res_name_flag=True, atom_name_flag=True,
pos_flag=True, element_flag=True):
# No molecule match, so skip.
if molecules != None and mol_name not in
molecules[struct_index]:
@@ -127,22 +130,23 @@
# Printout.
print(" Molecule: %s" % mol_name)
- # Change the current molecule name.
+ # Change the current molecule name and residue number.
current_mol = mol_name
+ current_res = None
# Store the one letter codes for sequence alignment.
one_letter_codes.append(objects[struct_index].one_letter_codes(mol_name=mol_name))
# Extend the lists.
if molecules != None:
+ atom_names.append([])
atom_ids.append([])
- atom_pos.append({})
+ atom_pos.append([])
if seq_info_flag:
- mol_names.append({})
- res_names.append({})
- res_nums.append({})
- atom_names.append({})
- elements.append({})
+ mol_names.append([])
+ res_names.append([])
+ res_nums.append([])
+ elements.append([])
# Create a new structure ID.
if molecules != None:
@@ -155,6 +159,21 @@
else:
ids.append('%s' % mol_name)
+ # A new residue.
+ if res_num != current_res:
+ # Change the current residue
+ current_res = res_num
+
+ # Extend the lists.
+ atom_names[-1].append([])
+ atom_ids[-1].append({})
+ atom_pos[-1].append({})
+ if seq_info_flag:
+ mol_names[-1].append({})
+ res_names[-1].append({})
+ res_nums[-1].append({})
+ elements[-1].append({})
+
# A unique identifier.
if molecules != None:
id = ":%s&%s@%s" % (res_num, res_name, atom_name)
@@ -162,60 +181,100 @@
id = "#%s:%s&%s@%s" % (mol_name, res_num, res_name,
atom_name)
# Store the per-structure ID and coordinate.
- atom_ids[-1].append(id)
- atom_pos[-1][id] = pos[0]
+ atom_names[-1][-1].append(atom_name)
+ atom_ids[-1][-1][atom_name] = id
+ atom_pos[-1][-1][atom_name] = pos[0]
# Store the per-structure sequence information.
if seq_info_flag:
- mol_names[-1][id] = mol_name
- res_names[-1][id] = res_name
- res_nums[-1][id] = res_num
- atom_names[-1][id] = atom_name
- elements[-1][id] = elem
+ mol_names[-1][-1][atom_name] = mol_name
+ res_names[-1][-1][atom_name] = res_name
+ res_nums[-1][-1][atom_name] = res_num
+ elements[-1][-1][atom_name] = elem
+
+ # The total number of molecules.
+ num_mols = len(atom_ids)
# Sequence alignment.
- print("\nPairwise sequence alignment to the first molecule:\n")
- gap_matrices = []
- for i in range(1, len(one_letter_codes)):
- print("Molecules 1-%i" % (i+1))
- align1, align2, gaps = align_pairwise(one_letter_codes[0],
one_letter_codes[i], matrix='BLOSUM62', gap_open_penalty=5.0,
gap_extend_penalty=1.0)
- gap_matrices.append(gaps)
-
- # Set up the structures for the superimposition algorithm.
- num = len(atom_ids)
+ 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.
+ else:
+ # Create
+ skip = []
+ for mol_index in range(num_mols):
+ skip.append([])
+ for res_index in range(len(one_letter_codes[mol_index])):
+ skip[mol_index].append(0)
+
+ # Set up the structures for common coordinates.
coord = []
mol_name_common = []
res_name_common = []
res_num_common = []
atom_name_common = []
element_common = []
- for i in range(num):
+ for mol_index in range(num_mols):
coord.append([])
# Find the common atoms and create the coordinate data structure.
- for id in atom_ids[0]:
- # Is the atom ID present in all other structures?
- present = True
- for i in range(num):
- if id not in atom_ids[i]:
- present = False
- break
-
- # Not present, so skip the atom.
- if not present:
- continue
-
- # Add the atomic position to the coordinate list and the element to
the element list.
- for i in range(num):
- coord[i].append(atom_pos[i][id])
-
- # The common sequence information.
- if seq_info_flag:
- mol_name_common.append(mol_names[0][id])
- res_name_common.append(res_names[0][id])
- res_num_common.append(res_nums[0][id])
- atom_name_common.append(atom_names[0][id])
- element_common.append(elements[0][id])
+ res_indices = [-1]*num_mols
+ max_res = -1
+ for mol_index in range(num_mols):
+ if len(one_letter_codes[mol_index]) > max_res:
+ max_res = len(one_letter_codes[mol_index])
+ while 1:
+ # Move to the next non-skipped residues in each molecule.
+ for mol_index in range(num_mols):
+ terminate = False
+ while 1:
+ res_indices[mol_index] += 1
+ if res_indices[mol_index] >= len(skip[mol_index]):
+ terminate = True
+ break
+ if not skip[mol_index][res_indices[mol_index]]:
+ break
+
+ # Termination.
+ for mol_index in range(num_mols):
+ if res_indices[mol_index] > len(atom_names[0]):
+ terminate = True
+ if terminate:
+ break
+
+ # Loop over the residue atoms in the first molecule.
+ for atom_name in atom_names[0][res_indices[0]]:
+ # Is the atom ID present in all other structures?
+ present = True
+ for mol_index in range(1, num_mols):
+ if atom_name not in
atom_names[mol_index][res_indices[mol_index]]:
+ present = False
+ break
+
+ # Not present, so skip the atom.
+ if not present:
+ continue
+
+ # Add the atomic position to the coordinate list and the element
to the element list.
+ for mol_index in range(num_mols):
+
coord[mol_index].append(atom_pos[mol_index][res_indices[mol_index]][atom_name])
+
+ # The common sequence information.
+ if seq_info_flag:
+ mol_name_common.append(mol_names[0][res_indices[0]][atom_name])
+ res_name_common.append(res_names[0][res_indices[0]][atom_name])
+ res_num_common.append(res_nums[0][res_indices[0]][atom_name])
+ atom_name_common.append(atom_name)
+ element_common.append(elements[0][res_indices[0]][atom_name])
# Convert to a numpy array.
coord = array(coord, float64)
@@ -225,6 +284,130 @@
return coord, ids, mol_name_common, res_name_common, res_num_common,
atom_name_common, element_common
else:
return coord, ids
+
+
+def common_residues(gap_matrices=None, one_letter_codes=None):
+ """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
+ @return: The residue skipping data structure. The
first dimension corresponds to the molecule, 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 = []
+ res_counts = []
+ for mol_index in range(num_mols):
+ res_counts.append(len(one_letter_codes[mol_index]))
+ skip_counts.append(0)
+ 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
+
+ # Printout.
+ sys.stdout.write("Shared residues:\n")
+ sys.stdout.write("Molecule %3i: " % 1)
+ for j in range(max(res_counts)):
+ # No more residues.
+ if j >= res_counts[0]:
+ sys.stdout.write("-")
+ continue
+
+ # A skip.
+ if skip[0][j]:
+ sys.stdout.write("-")
+
+ # Keep the residue.
+ else:
+ sys.stdout.write(one_letter_codes[0][j])
+ sys.stdout.write("\n")
+
+ # 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):
+ # Printout.
+ sys.stdout.write("Molecule %3i: " % (mol_index+1))
+
+ # Loop over the residues of alignment mol_index.
+ seq1_index = -1
+ seq2_index = -1
+ for j in range(max(res_counts)):
+ # No more residues.
+ if j >= len(gap_matrices[mol_index-1][1]):
+ sys.stdout.write("-")
+ continue
+
+ # 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
+ sys.stdout.write("-")
+
+ # 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
+ sys.stdout.write("-")
+
+ # 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
+ sys.stdout.write("-")
+
+ # Skipped in the second molecule.
+ elif gap_matrices[mol_index-1][1, j]:
+ sys.stdout.write("-")
+
+ # Print out the one letter code.
+ else:
+ sys.stdout.write(one_letter_codes[mol_index][seq2_index])
+
+ # EOL.
+ sys.stdout.write("\n")
+
+ # 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.
+ return skip
def loop_coord_structures(objects=None, molecules=None, models=None,
atom_id=None):
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