moved ViewsFromSequences and ViewsFromAlignment over from scratch

git-svn-id: https://dng.biozentrum.unibas.ch/svn/openstructure/trunk@2140 5a81b35b-ba03-0410-adc8-b2c5c5119f08

modules/seq/base/pymod/__init__.py

@@ -18,3 +18,97 @@
 #------------------------------------------------------------------------------
 from _seq import *
 
+def ViewsFromAlignment(multi_seq_ali, ent_a, ent_b, include_atoms=True):
+  seq_a=multi_seq_ali.GetSequence(0)
+  seq_b=multi_seq_ali.GetSequence(1)
+
+  # set offset according to ent_a and ent_b
+
+
+  return ViewsFromSequences(seq_a, seq_b, ent_a, ent_b, include_atoms)
+
+def ViewsFromSequences(seq_a, seq_b, ent_a=None, ent_b=None,
+                       include_atoms=True):
+  ent_a=ent_a or seq_a.attached_view
+  ent_b=ent_b or seq_b.attached_view
+  if ent_a.chain_count>1:
+   raise RuntimeError("first entity contains more than one chain")
+  if ent_b.chain_count>1:
+   raise RuntimeError("second entity contains more than one chain")
+  is_ha=isinstance(ent_a, mol.EntityHandle)
+  is_hb=isinstance(ent_b, mol.EntityHandle)
+
+  ev_a= is_ha and ent_a.CreateEmptyView() or ent_a.handle.CreateEmptyView()
+  ev_b= is_hb and ent_b.CreateEmptyView() or ent_b.handle.CreateEmptyView()
+
+  flags=include_atoms and mol.ViewAddFlag.INCLUDE_ATOMS or 0
+  # get all residues
+  res_a=ent_a.residues
+  res_b=ent_b.residues
+
+  # map sequence onto
+  s1 = seq_a.gapless_string
+  s2 = seq_b.gapless_string
+
+  # get sequence of ent1
+  seq_ent_a = ""
+  seq_ent_b= ""
+
+  sub_a = ent_a.Select("peptide = 1")
+  sub_b = ent_b.Select("peptide = 1")
+  for res1 in sub_a.residues:
+      seq_ent_a = "%s%s" % (seq_ent_a, res1.one_letter_code)
+
+  seq_ent_b = ""
+  for res2 in sub_b.residues:
+      seq_ent_b = "%s%s" % (seq_ent_b, res2.one_letter_code)
+
+  #~ print seq_ent_a
+  #~ print s1
+
+  print seq_ent_a
+  print s1
+  off_a = seq_ent_a.index(s1)
+  off_b = seq_ent_b.index(s2)
+
+  #off_a=seq_a.GetSequenceOffset()
+  #off_b=seq_b.GetSequenceOffset()
+
+
+  index_a, index_b=(0, 0)
+  done=False
+
+  align_index = 0
+
+  # iterate over residues
+  while index_a<seq_a.GetLength() and index_b<seq_b.GetLength():
+      # print 'index',index_a, seq_a.GetLength(), index_b, seq_b.GetLength()
+   while seq_a.GetOneLetterCode(index_a)=='-':
+     index_a+=1
+     if seq_a.GetLength()<index_a:
+       done=True
+       break
+   while seq_b.GetOneLetterCode(index_b)=='-':
+     index_b+=1
+     if seq_b.GetLength()<index_b:
+       done=True
+       break
+   if done or len(res_a)<=off_a+index_b or len(res_b)<=off_b+index_a:
+     break
+   ra=res_a[off_a+index_b]
+   rb=res_b[off_b+index_a]
+   #ra = res_a[index_b]
+   #rb = res_a[index_a]
+   #~ print "set align_index %d for %s %s" % (align_index, ra, rb)
+   #ra.SetIntProp("align_index",align_index)
+   #rb.SetIntProp("align_index",align_index)
+   align_index += 1
+   ev_a.AddResidue(is_ha and ra or ra.handle, flags)
+   ev_b.AddResidue(is_hb and rb or rb.handle, flags)
+   index_a+=1
+   index_b+=1
+   eda=ev_a.handle.RequestXCSEditor()
+   eda.RenameChain(ent_a.chains[0].handle,ent_a.chains[0].name)
+   edb=ev_b.handle.RequestXCSEditor()
+   edb.RenameChain(ent_b.chains[0].handle, ent_b.chains[0].name)
+  return ev_a, ev_b