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DefineStructureXML.py.bak
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from Structure import Structure
#from xml.etree.ElementTree import ElementTree, Element, SubElement, Comment, tostring, dump
from lxml import etree
def WriteStructureXML(structure, path):
tree = etree.Element('structure')
if(structure.residue_path!=None):
Xresidue_path = etree.Element('residuePath')
Xresidue_path.text = structure.residue_path
tree.append(Xresidue_path)
Xaliases = etree.Element('alias')
for key, values in structure.alias.iteritems():
Xalias = etree.Element('element')
Xalias.set('name',key)
Xalone = etree.Element('alone')
Xalone.text = values[0]
Xalias.append(Xalone)
Xstart = etree.Element('start')
Xstart.text = values[1]
Xalias.append(Xstart)
Xmiddle = etree.Element('middle')
Xmiddle.text = values[2]
Xalias.append(Xmiddle)
Xend = etree.Element('end')
Xend.text = values[3]
Xalias.append(Xend)
#append alias element to the list of aliases.
Xaliases.append(Xalias)
tree.append(Xaliases)
for name in structure.residue_names:
Xresidue = etree.Element('residue')
Xresidue.set('name', name)
Xresidue.set('length', str(structure.residue_length[name]))
#Adding append/prepend connects
connect = structure.connect[name]
Xappend = etree.Element('append')
Xprepend = etree.Element('prepend')
XappNewFatom = etree.Element('newFirstAtom')
XappNewFatom.text = str(connect[0][0])
XappOldLatom = etree.Element('oldLastAtom')
XappOldLatom.text = str(connect[0][1])
XappBondL = etree.Element('bondLength')
XappBondL.text = str(connect[2])
Xappend.append(XappNewFatom)
Xappend.append(XappOldLatom)
Xappend.append(XappBondL)
XprpNewLatom = etree.Element('newLastAtom')
XprpNewLatom.text = str(connect[1][0])
XprpOldFatom = etree.Element('oldFirstAtom')
XprpOldFatom.text = str(connect[1][1])
XprpBondL = etree.Element('bondLength')
XprpBondL.text = str(connect[3])
Xprepend.append(XprpNewLatom)
Xprepend.append(XprpOldFatom)
Xprepend.append(XprpBondL)
Xresidue.append(Xappend)
Xresidue.append(Xprepend)
#Adding backbone information
backbone = structure.backbone_elements[name]
if backbone != None:
#INFO: [[start, middle_pre, bond], [middle_post, end]]
Xbackbone = etree.Element('backbone')
Xbbstart = etree.Element('start')
Xbbstart.text = str(backbone[0][0])
Xbackbone.append(Xbbstart)
Xbbmiddle_pre = etree.Element('middle_pre')
Xbbmiddle_pre.text = str(backbone[0][1])
Xbackbone.append(Xbbmiddle_pre)
Xbbbond = etree.Element('bond')
Xbbbond.text = str(backbone[0][2])
Xbackbone.append(Xbbbond)
Xbbmiddle_post = etree.Element('middle_post')
Xbbmiddle_post.text = str(backbone[1][0])
Xbackbone.append(Xbbmiddle_post)
Xbbend = etree.Element('end')
Xbbend.text = str(backbone[1][1])
Xbackbone.append(Xbbend)
Xresidue.append(Xbackbone)
#Adding rotating elements
i = 0
for rotation in structure.rotating_elements[name]:
if rotation != [None]:
Xrotation = etree.Element('rotation')
#Vorschlag Rotationen indizieren
Xrotation.set('index', str(i))
i += 1
Xstart = etree.Element('start')
Xstart.text = str(rotation[0])
Xrotation.append(Xstart)
Xbond = etree.Element('bond')
Xbond.text = str(rotation[1])
Xrotation.append(Xbond)
#Handling the special 'end' property of the end rotation tag
Xend = etree.Element('end')
if rotation[2] == None:
Xend.text = 'end'
else:
Xend.text = str(rotation[2])
Xrotation.append(Xend)
Xresidue.append(Xrotation)
#append complete residue definition to tree
tree.append(Xresidue)
#nice output using lxml
result = etree.tostring(tree, pretty_print=True)
#Writes the output tree to the given path. Implement error handling?
file = open(path, "w")
file.write(result)
file.close()
#Specification of DNA-residues begins here ---------------------------------------------------------------------------------------#
DNAresidues = ["DGN", "DAN", "DTN", "DCN",
"DG", "DA", "DT", "DC",
"DG5", "DA5", "DT5", "DC5",
"DG3", "DA3", "DT3", "DC3"]
DNAphosphate = [["DGN", 0, 1, None],
["DAN", 0, 1, None],
["DTN", 0, 1, None],
["DCN", 0, 1, None],
["DG5", 0, 1, None],
["DA5", 0, 1, None],
["DT5", 0, 1, None],
["DC5", 0, 1, None],
["DG", 0, 3, None],
["DA", 0, 3, None],
["DT", 0, 3, None],
["DC", 0, 3, None],
["DG3", 0, 3, None],
["DA3", 0, 3, None],
["DT3", 0, 3, None],
["DC3", 0, 3, None]]
DNAoc5 = [["DGN", 1, 2, None],
["DAN", 1, 2, None],
["DTN", 1, 2, None],
["DCN", 1, 2, None],
["DG5", 1, 2, None],
["DA5", 1, 2, None],
["DT5", 1, 2, None],
["DC5", 1, 2, None],
["DG", 3, 4, None],
["DA", 3, 4, None],
["DT", 3, 4, None],
["DC", 3, 4, None],
["DG3", 3, 4, None],
["DA3", 3, 4, None],
["DT3", 3, 4, None],
["DC3", 3, 4, None]]
DNAbase = [["DGN", 8, 10, -7],
["DAN", 8, 10, -7],
["DTN", 8, 10, -7],
["DCN", 8, 10, -7],
["DG5", 8, 10, -6],
["DA5", 8, 10, -6],
["DT5", 8, 10, -6],
["DC5", 8, 10, -6],
["DG", 10, 12, -6],
["DA", 10, 12, -6],
["DT", 10, 12, -6],
["DC", 10, 12, -6],
["DG3", 10, 12, -7],
["DA3", 10, 12, -7],
["DT3", 10, 12, -7],
["DC3", 10, 12, -7]]
DNAoc3 = [["DGN", -4, -2, None],
["DAN", -4, -2, None],
["DTN", -4, -2, None],
["DCN", -4, -2, None],
["DG5", -3, -1, None],
["DA5", -3, -1, None],
["DT5", -3, -1, None],
["DC5", -3, -1, None],
["DG", -3, -1, None],
["DA", -3, -1, None],
["DT", -3, -1, None],
["DC", -3, -1, None],
["DG3", -4, -2, None],
["DA3", -4, -2, None],
["DT3", -4, -2, None],
["DC3", -4, -2, None]]
DNAbackbone = [["DGN", 0, 8, 10, -7, -1],
["DAN", 0, 8, 10, -7, -1],
["DTN", 0, 8, 10, -7, -1],
["DCN", 0, 8, 10, -7, -1],
["DG5", 0, 8, 10, -6, -1],
["DA5", 0, 8, 10, -6, -1],
["DT5", 0, 8, 10, -6, -1],
["DC5", 0, 8, 10, -6, -1],
["DG", 0, 10, 12, -6, -1],
["DA", 0, 10, 12, -6, -1],
["DT", 0, 10, 12, -6, -1],
["DC", 0, 10, 12, -6, -1],
["DG3", 0, 10, 12, -7, -1],
["DA3", 0, 10, 12, -7, -1],
["DT3", 0, 10, 12, -7, -1],
["DC3", 0, 10, 12, -7, -1]]
DNAlengths = [32, 31, 31, 29,
33, 32, 32, 30,
31, 30, 30, 28,
34, 33, 33, 31]
DNAalias = [["DGN","DGN","DG5","DG","DG3"],["DAN","DAN","DA5","DA","DA3"],["DTN","DTN","DT5","DT","DT3"],["DCN","DCN","DC5","DC","DC3"],
["DG3","DG3","DG","DG","DG3"],["DA3","DA3","DA","DA","DA3"],["DT3","DT3","DT","DT","DT3"],["DC3","DC3","DC","DC","DC3"],
["DG5","DG5","DG5","DG","DG"],["DA5","DA5","DA5","DA","DA"],["DT5","DT5","DT5","DT","DT"],["DC5","DC5","DC5","DC","DC"],
["G","DGN","DG5","DG","DG3"],["A","DAN","DA5","DA","DA3"],["T","DTN","DT5","DT","DT3"],["C","DCN","DC5","DC","DC3"]]
#Specification of DNA-residues ends here -----------------------------------------------------------------------------------------#
#Build Structure-object for DNA residues
DNA = Structure(DNAresidues,
residue_length=DNAlengths,
rotating_elements=DNAphosphate+DNAoc5+DNAbase+DNAoc3,
backbone_elements=DNAbackbone,
alias=DNAalias)
WriteStructureXML(DNA,"DNA.xml")