binding to call external USalign executable

modules/bindings/doc/tmtools.rst

@@ -5,7 +5,7 @@
   :synopsis: Sequence dependent and independent structure superposition
 
 The :mod:`~ost.bindings.tmtools` module provides access to the structural 
-superposition programs TMscore, Tmalign and MMalign developed by Y. Zhang 
+superposition programs TMscore and Tmalign developed by Y. Zhang 
 and J. Skolnick. These programs superpose a model onto a reference structure, 
 using the positions of the Calpha atoms only. While at their core, these 
 programs essentially use the same algorithm, they differ on how the Calphas are 
@@ -17,14 +17,15 @@ Citation:
   Yang Zhang and Jeffrey Skolnick, Proteins 2004 57: 702-710
   Y. Zhang and J. Skolnick, Nucl. Acids Res. 2005 33, 2302-9
 
-Besides using the standalone TM-align program, ost also provides a wrapper 
+Besides using the standalone TM-align program, ost also provides wrappers 
 around USalign as published in:
 
   Chengxin Zhang, Morgan Shine, Anna Marie Pyle, Yang Zhang
   (2022) Nat Methods
 
-The advantage is that no intermediate files must be generated, a wrapper on the
-c++ layer is used instead. 
+USalign can be used as external standalone tool. Alternatively, ost allows to
+directly inject structural data in the USAlign c++ layer. The advantage of that
+is that no intermediate files must be generated. 
 
 
 Distance measures used by TMscore
@@ -77,15 +78,27 @@ Usage of TMscore
 
 .. autoclass:: ost.bindings.tmtools.TMScoreResult
 
+Usage of USalign
+--------------------------------------------------------------------------------
+
+For higher order complexes, ost provides access to USalign. This corresponds to
+calling USalign with the preferred way of comparing full biounits:
+
+.. code-block:: bash
+
+  USalign mdl.pdb ref.pdb -mm 1 -ter 0
+
+.. autofunction:: ost.bindings.tmtools.USAlign
 
-TMalign C++ wrapper
+
+C++ wrappers
 --------------------------------------------------------------------------------
 
 .. currentmodule:: ost.bindings
 
-Instead of calling the TMalign executable, ost also provides a wrapper around
-its C++ implementation. The advantage is that no intermediate files need to be 
-generated in order to call the executable.
+Instead of calling the external executables, ost also provides a wrapper around
+the USalign c++ implementation which is shipped with the ost source code.
+The advantage is that no intermediate files need to be  generated.
 
 .. code-block:: python
 
@@ -118,8 +131,8 @@ generated in order to call the executable.
 
 .. method:: WrappedTMAlign(chain1, chain2, [fast=False])
 
-  Takes two chain views and runs TMalign with *chain2* as reference.
-  The positions and sequences are directly extracted from the chain
+  Takes two chain views and runs TMalign from USAlign with *chain2* as
+  reference. The positions and sequences are directly extracted from the chain
   residues for every residue that fulfills:
   
     * peptide linking and valid CA atom OR nucleotide linking and valid C3'
@@ -161,13 +174,7 @@ generated in order to call the executable.
                         respectively are not consistent in size.
 
 For higher order complexes, ost provides access to the MMalign functionality
-from USalign. This corresponds to calling USalign with the preferred way of
-comparing full biounits:
-
-.. code-block:: bash
-
-  USalign mdl.pdb ref.pdb -mm 1 -ter 0
-
+from USalign. 
 
 .. class:: MMAlignResult(rmsd, tm_score, transform, aligned_length, alignments,\
                          ent1_mapped_chains, ent2_mapped_chains)

modules/bindings/pymod/tmtools.py

@@ -73,6 +73,90 @@ def _ParseTmAlign(lines,lines_matrix):
   return ost.bindings.TMAlignResult(rmsd, tm_score, tm_score_swapped,
                                     aln_length, tf, alignment)
 
+def _ParseUSAlign(lines,lines_matrix):
+
+  # stuff that is immediately parsed
+  rmsd = None
+  tm_score = None
+  tm_score_swapped = None
+  aligned_length = None
+
+  # first goes into intermediate data structures
+  aln_data = list()
+  mapping_data1 = list()
+  mapping_data2 = list()
+  in_aln = False
+
+  for line in lines:
+    if in_aln:
+      if len(line.strip()) == 0:
+        in_aln = False
+      else:
+        aln_data.append(line.strip('*'))
+    elif line.startswith("Name of Structure_1:"):
+      tmp = [item.strip() for item in line.split()[3].split(':')[1:]]
+      for item in tmp:
+        if len(item) > 0:
+          mapping_data1.append(item.split(',')[1])
+        else:
+          mapping_data1.append("")
+    elif line.startswith("Name of Structure_2:"):
+      tmp = [item.strip() for item in line.split()[3].split(':')[1:]]
+      for item in tmp:
+        if len(item) > 0:
+          mapping_data2.append(item.split(',')[1])
+        else:
+          mapping_data2.append("")
+    elif line.startswith("Aligned length="):
+      data = [item.strip() for item in line.split(',')]
+      for item in data:
+        if item.startswith("Aligned length="):
+          aligned_length = int(item.split("=")[1])
+        elif item.startswith("RMSD="):
+          rmsd = float(item.split("=")[1])
+    elif line.startswith("TM-score="):
+      if "(normalized by length of Structure_1" in line:
+        tm_score_swapped = float(line.split('(')[0].split('=')[1].strip())
+      elif "(normalized by length of Structure_2" in line:
+        tm_score = float(line.split('(')[0].split('=')[1].strip())
+    elif line.startswith("(\":\" denotes residue pairs of"):
+      in_aln = True
+
+  assert(len(aln_data)==3)
+  aln_sequences1 = aln_data[0].split('*')
+  aln_sequences2 = aln_data[2].split('*')
+
+  # do mapping/aln data
+  alns = ost.seq.AlignmentList()
+  ent1_mapped_chains = ost.StringList()
+  ent2_mapped_chains = ost.StringList()
+  assert(len(mapping_data1) == len(mapping_data2))
+  assert(len(aln_sequences1) == len(aln_sequences2))
+  assert(len(mapping_data1) == len(aln_sequences1))
+  for a, b, c, d in zip(mapping_data1, mapping_data2,
+                        aln_sequences1, aln_sequences2):
+    if len(a) > 0 and len(b) > 0:
+      ent1_mapped_chains.append(a)
+      ent2_mapped_chains.append(b)
+      assert(len(c) == len(d))
+      aln = seq.CreateAlignment()
+      aln.AddSequence(seq.CreateSequence(a, c))
+      aln.AddSequence(seq.CreateSequence(b, d))
+      alns.append(aln)
+
+  # parse transformation matrix
+  tf1=[float(i.strip()) for i in lines_matrix[2].split()[1:]]
+  tf2=[float(i.strip()) for i in lines_matrix[3].split()[1:]]
+  tf3=[float(i.strip()) for i in lines_matrix[4].split()[1:]]
+  mat = geom.Mat4(tf1[0], tf1[1], tf1[2], tf1[3],
+                  tf2[0], tf2[1], tf2[2], tf2[3],
+                  tf3[0], tf3[1], tf3[2], tf3[3],
+                  0.0,    0.0,    0.0,    1.0)
+
+  return ost.bindings.MMAlignResult(rmsd, tm_score, tm_score_swapped,
+                                    aligned_length, mat, alns,
+                                    ent1_mapped_chains, ent2_mapped_chains)
+
 def _RunTmAlign(tmalign, tmp_dir):
   model1_filename=os.path.join(tmp_dir, 'model01.pdb')
   model2_filename=os.path.join(tmp_dir, 'model02.pdb')
@@ -93,6 +177,21 @@ def _RunTmAlign(tmalign, tmp_dir):
   matrix_file.close() 
   return _ParseTmAlign(lines,lines_matrix)
 
+def _RunUSAlign(usalign, tmp_dir):
+  model1_filename=os.path.join(tmp_dir, 'model01.pdb')
+  model2_filename=os.path.join(tmp_dir, 'model02.pdb')
+  mat_filename = os.path.join(tmp_dir, "mat.txt")
+  usalign_path=settings.Locate('USalign', explicit_file_name=usalign)  
+  command = f"{usalign_path} {model1_filename} {model2_filename}  -mm 1 -ter 0 -m {mat_filename}"
+  ps=subprocess.Popen(command, shell=True, stdout=subprocess.PIPE)
+  stdout,_=ps.communicate()
+  lines=stdout.decode().splitlines()
+  if (len(lines))<22:
+    _CleanupFiles(tmp_dir)
+    raise RuntimeError("USalign superposition failed")
+  with open(mat_filename) as fh:
+    lines_matrix = fh.readlines()
+  return _ParseUSAlign(lines,lines_matrix)
 
 class TMScoreResult:
   """
@@ -218,3 +317,31 @@ def TMScore(model1, model2, tmscore=None):
   model1.handle.EditXCS().ApplyTransform(result.transform)  
   _CleanupFiles(tmp_dir_name)
   return result
+
+
+def USAlign(model1, model2, usalign=None):
+  """
+  Performs a sequence independent superposition of model1 onto model2, the 
+  reference. Can deal with multimeric complexes and RNA.
+
+  Creates temporary model files on disk and runs USalign with:
+  ``USalign model1.pdb model2.pdb -mm 1 -ter 0 -m rotmat.txt``
+  
+  :param model1: The model structure. If the superposition is successful, will 
+                 be superposed onto the reference structure
+  :type model1: :class:`~ost.mol.EntityView` or :class:`~ost.mol.EntityHandle`
+  :param model2: The reference structure
+  :type model2: :class:`~ost.mol.EntityView` or :class:`~ost.mol.EntityHandle`
+  :param usalign: If not None, the path to the USalign executable. Searches
+                  for executable with name ``USalign`` in PATH if not given.
+  :returns: The result of the superposition
+  :rtype: :class:`ost.bindings.MMAlignResult`
+  
+  :raises: :class:`~ost.settings.FileNotFound` if executable could not be located.
+  :raises: :class:`RuntimeError` if the superposition failed
+  """
+  tmp_dir_name=_SetupFiles((model1, model2))
+  result=_RunUSAlign(usalign, tmp_dir_name)
+  model1.handle.EditXCS().ApplyTransform(result.transform)
+  _CleanupFiles(tmp_dir_name)
+  return result