Clarifying DNAEdge base class units

[shanilpanara]

Summary

Thus far, I have always been a little confused to the units of our DNAedge objects. Having started to review code I implemented over the summer, I have found a few errors, although they are easily fixed.

I would like to update this base class. But would first like to check with you @debeshmandal that it won't break any code you/chris/fiona are working on.

e.g. if node1=[0,0,0] node2=[5,0,0] i would like to make updates such that the following would be true

• DNAEdge.length=6 the length of edge in the number of nucleotides
• DNAEdge.nt_length=5*2.45 the distance from the first nucleotide to last nucleotide in oxDNA units

Details

Essentially, when generating DNA strands between the DNANodes of a LatticeRoute, the edge lengths are already in terms of the number of nucleotides. When we generate the strands, we are setting the number of nucleotides, n to the nt_length of the edge. This takes the length of the edge and multiplies it by 2.45 (oxDNA distance between two nucleotides) and hence it gives the distance in oxDNA units. Instead, what we should be doing is setting the number of nucleotides, n, to the corresponding length of a DNAEdge.

Also, if DNAedge.length is supposedly in units of nucleotides, it has been calculated wrong (see updated version below)

Currently

Code extract from route.py -> update_strands()

...
# generate strand above that's going in opposite direction
strand = generate_helix(n=int(self.edges[i].nt_length),
                        start_position=start,
                        direction=direction,
                        a1=a1)[0]
strands.append(strand)
...

tools.py -> DNAEdge()

@property
def length(self):
    """The length of the edge in oxdna units (i think)"""
    return np.linalg.norm(self.vector)

@property
def nt_length(self):
    """The length of the edge in units of nucleotides"""
    return int(self.length * 2.45)

Updated code:

route.py -> update_strands()

...
# generate strand above that's going in opposite direction
strand = generate_helix(n=int(self.edges[i].length),
                        start_position=start,

tools.py -> DNAEdge()

@property
def length(self):
    """The length of the edge in units of nucleotides"""
    return int(np.linalg.norm(self.vector)+1)

@property
def nt_length(self):
    """The distance from the first nucleotide to last nucleotide in oxDNA units"""
    return int((self.length-1) * 2.45)

[shanilpanara]

Having reviewed this after your comments in our meeting @debeshmandal , I think I may have been overthinking it. Having said that, I have updated the descriptions and added a new property number_of_nt. Will push changes for review soon :)