XRNA xml format

There are five sections in this simple example





Header
< ComplexDocument Name='e.coli_5s'/>
< SceneNodeGeom CenterX='-357.51' CenterY='324.24' />
< Complex Name='e.coli_5s'>
< RNAMolecule Name='e.coli_5s'>


NucListData
contains X-Y positions of nucleotides in sequence

< NucListData StartNucID='1' DataType='NucChar.XPos.YPos'>
U 165.66 -138.34
...
U 132.34 -159.03
< /NucListData>


Nuc
LabelList and RefID are defined in this section. 
RefID's are assigned a default font. This is the font for the ATGC's. 
Each RefID can be also be assigned additional other labels. 
In this example every tenth base is labeled. The font for each label (10,20,etc) is set individually.

< Nuc RefIDs='1-120' Color='0' FontID='0' FontSize='14' />
< Nuc RefIDs='1-120' IsSchematic='false' SchematicColor='0' SchematicLineWidth='1.5' SchematicBPLineWidth='1.0' />
< Nuc RefID='120' FormatType='9' />
< Nuc RefID='10'>
< LabelList>
s 5.53 21.99 0.0 12 0 0 "10"
l 2.31 7.35 4.11 15.14 0.2 0 0 0 0 0 0
< /LabelList>
< /Nuc>
...
In this example, positions are indicated every 10 bases
...
< Nuc RefID='110'>
< LabelList>
s -28.9 -6.99 0.0 12 0 0 "110"
l -7.17 -2.47 -14.73 -5.09 0.2 0 0 0 0 0 0
< /LabelList>
< /Nuc>

s=symbol
s xposition yposition unused fontsize unused unused "text"

l=line
l xposition_start yposition_start xposition_end yposition_end thickness unused unused unused unused unused 


Basepair Helixes

< BasePairs nucID='1' length='10' bpNucID='119' />
...
In this example nucleotide 1 is paired with 119.
A length of 10 means this is continued for 10 bases
2 is paired with 118, 
3 is paired with 117, 
4 is paired with 116, 
5 is paired with 115, 
6 is paired with 114, 
7 is paired with 113, 
8 is paired with 112, 
9 is paired with 111, 
10 is paired with 110 
...

< BasePairs nucID='79' length='8' bpNucID='97' />


Footer
< /RNAMolecule>
< /Complex>
< /ComplexDocument>