diff --git a/modules/seq/alg/pymod/renumber.py b/modules/seq/alg/pymod/renumber.py
index ceb3a0113f3ca1bc6931ff56a2884902b232c63a..39ea9fb489949845fb65681ac1cbb6f000f4e56e 100644
--- a/modules/seq/alg/pymod/renumber.py
+++ b/modules/seq/alg/pymod/renumber.py
@@ -1,4 +1,5 @@
from ost import io, seq, mol, conop
+import ost
def Renumber(seq_handle):
"""
@@ -19,32 +20,30 @@ def Renumber(seq_handle):
io.SavePDB(e, "renum.pdb")
"""
- if seq_handle.HasAttachedView==False:
+ if seq_handle.HasAttachedView()==False:
raise RuntimeError, "Sequence Handle has no attached view"
- counter=0
changed_residue_count=0
- renumberingFlag = 0
+ renumberingFlag = False
ent_n=mol.CreateEntity()
ed=ent_n.RequestXCSEditor()
c=ed.InsertChain(" ")
for pos in range(len(seq_handle)):
if seq_handle[pos]!='-':
- r=seq_handle.attached_view.residues[counter]
+ r=seq_handle.GetResidue(pos)
if r.IsValid():
#print seq_handle[pos],r.number.num,pos+1
if r.number.num!=pos+1:
changed_residue_count+=1
- renumberingFlag = 1
+ renumberingFlag = True
r_n=ed.AppendResidue(c,r.name, mol.ResNum(pos+1))
for atom in r.atoms:
ed.InsertAtom(r_n,atom.name,atom.pos,atom.prop)
else:
err='Error: renumbering failed at position %s' %pos
raise RuntimeError, err
- counter+=1
- if renumberingFlag == 1:
+ if renumberingFlag == True:
err = 'Warning: %s residues have been renumbered!' %changed_residue_count
- print err
+ ost.LogMessage(err)
conop.ConnectAll(ent_n)
return ent_n