Convert DNA sequencesto PDB files and spatially wrangle them.
Useful for simulation input data.
Conceived to be the basis of a cadnano 2.5
*.json converter, which is now in that repo as createPDB.py.
The core data structure is a stripped down version of ProDy's
AtomGroup class
dependencies: numpy
Should be Python 2/3 compatible
RNA is not supported yet, but totally could be.
Base data pdb's were sourced from Avogadro 1.1.1 / OpenBabel output and an effort is made to come as close to the spatial output for double stranded DNA as would be generated from Avogadro 1.1.1.
""" create a strand that double backs on itself
"""
from na2pdb import AtomicSequence
aseq = AtomicSequence("ACGTACGT", name="not_useful")
aseq.transformBases(4, 8, 0, 0, 0, False)
# 1. Get base separation
aseq.linearize()
# 2. do all rotations
aseq.applyReverseQueue()
aseq.applyTwist()
# 3. move to position
aseq.applyTransformQueue()
out_file = 'test_file.pdb'
aseq.toPDB(out_file)