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Commit c0340350 authored by pascal's avatar pascal
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minor modifications to lower the WTF number

git-svn-id: https://dng.biozentrum.unibas.ch/svn/openstructure/trunk@2697 5a81b35b-ba03-0410-adc8-b2c5c5119f08
parent e0634f2d
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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
......
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