Ejemplo n.º 1
0
def makeMutationAddendum(target=None, template=None, options=None):
    """
    converting two residue labels to a mutation tag
    """
    if target == "   gap   " or template == "   gap   ":
      return  None
    else:
      code1, resName = convertResidueCode(resName=target[:3])
      code2, resName = convertResidueCode(resName=template[:3])
      resNumb = int(target[3:7])
    
      return  "%s%d%s" % (code1, resNumb, code2)
Ejemplo n.º 2
0
def makeMutationAddendum(target=None, template=None, options=None):
    """
    converting two residue labels to a mutation tag
    """
    if target == "   gap   " or template == "   gap   ":
        return None
    else:
        code1, resName = convertResidueCode(resName=target[:3])
        code2, resName = convertResidueCode(resName=template[:3])
        resNumb = int(target[3:7])

        return "%s%d%s" % (code1, resNumb, code2)
Ejemplo n.º 3
0
    def makeSequence(self, mutation=None):
        """
        creates a sequence from the chain object to be used in Scwrl-mutations
        """
        sequence = ""
        for residue in self.residues:
          if residue.resName in lib.residueList("standard"):
            if   mutation == None:
              code, resName = lib.convertResidueCode(resName=residue.resName)
              sequence += code.lower()
            elif residue.label in mutation:
              new_label = mutation[residue.label]['label']
              code, resName = lib.convertResidueCode(resName=new_label[:3])
              sequence += code.upper()
            else:
              code, resName = lib.convertResidueCode(resName=residue.resName)
              sequence += code.lower()

        return sequence
Ejemplo n.º 4
0
    def makeSequence(self, mutation=None):
        """
        creates a sequence from the chain object to be used in Scwrl-mutations
        """
        sequence = ""
        for residue in self.residues:
            if residue.resName in lib.residueList("standard"):
                if mutation == None:
                    code, resName = lib.convertResidueCode(
                        resName=residue.resName)
                    sequence += code.lower()
                elif residue.label in mutation:
                    new_label = mutation[residue.label]['label']
                    code, resName = lib.convertResidueCode(
                        resName=new_label[:3])
                    sequence += code.upper()
                else:
                    code, resName = lib.convertResidueCode(
                        resName=residue.resName)
                    sequence += code.lower()

        return sequence
Ejemplo n.º 5
0
 def setAlignment(self, alignment=None):
     """
     Sets the alignment information (from self)
     """
     if alignment == None:
       print("setting alignment according to protein")
       self.alignment = ""
       for residue in self.residues:
         if residue.resName != "N+ " and residue.resName != "C- ":
           code, resName = lib.convertResidueCode(resName=residue.resName)
           if code in "ARNDCQEGHILKMFPSTWYV":
             self.alignment += (code)
       print(self.alignment)
       print( len(self.alignment) )
     else:
       self.alignment = alignment
Ejemplo n.º 6
0
 def setAlignment(self, alignment=None):
     """
     Sets the alignment information (from self)
     """
     if alignment == None:
         pka_print("setting alignment according to protein")
         self.alignment = ""
         for residue in self.residues:
             if residue.resName != "N+ " and residue.resName != "C- ":
                 code, resName = lib.convertResidueCode(
                     resName=residue.resName)
                 if code in "ARNDCQEGHILKMFPSTWYV":
                     self.alignment += (code)
         pka_print(self.alignment)
         pka_print(len(self.alignment))
     else:
         self.alignment = alignment