PlecFinder

Python package for analyzing the topology of polymer configurations

Install

Required packages:

• numpy
• scipy
• numba
• cython
• matplolib

Package installation

git clone --recurse-submodules -j8 [email protected]:eskoruppa/PlecFinder.git
pip install PlecFinder/.

Example

python
import plecfinder as pf
pf.testrun()

How to use:

The core functionality is contained in the find_plectonemes function:

topol = pf.find_plecs((conf,min_writhe_density,plec_min_writhe ,disc_len=None, no_branch_overlap=True ,connect_dist=10.0, om0=1.76,include_wm=False))

Arguments:

conf : np.ndarray
    3D configruation, should be Nx3 numpy array containing the position vectors (dimension Nx3)

min_writhe_dens : float   
    minimum writhe density for a region to be detected as as plectonemic coil

plec_min_writhe : float
    minimum writhe for a coil to be identified as a plectoneme

disc_len :  float, optional       
    discretization length, if None discretization length will be calculated based on 
    provided configuration (default: None)

no_overlap: bool, optional
    remove overlap of neighboring branches (default: True)
    Note that no_overlap=True is required for building plectoneme structure

connect_dist: float, optional
    distance in nm for which neighboring points of sufficient writhedensity points are connected to form a branch (default: 10nm)

om0: float, optional
    intrinsic twist (default: 1.76 rad/nm)

include_wm: bool, optional
    include writhemap in return dictionary. This may lead to large memory consumption. (default: False)

Returns:

topology dictionary:

    ### Keys:
    - N :               int - number of chain segments
    - L :               float - Length of chain
    - disc_len :        float - discretization length (segment size)
    - wr :              float - total writhe in configuration
    - num_plecs :       int - number of plectonemes
    - num_branches :    list of branches
    - num_tracers :     list of tracers
    - plecs :           list of plectonemes
    - branches :        list of branches
    - tracers :         list of tracers
    - wm :              NxN ndarray - writhe map (this key is optional)
    - no_overlap :      bool - branch overlap removed

    Elements of the plectoneme list are dictionaries themselves. 
    ### Plectoneme Keys:
    - id1 :         entrance index
    - id2 :         exit index
    - wrdens :      writhe density within plectoneme
    - wr :          total writhe in plectoneme
    - num_segs :    number of contained segments
    - L :           length of plectoneme
    - branch_ids :  indices of branches and tracers contained in plectoneme

    Banches and Tracers are likewise dictionaries. 
    ### Branch keys:
    - id : index in branches list
    - x1 : entrance x id
    - x2 : exit x id
    - y1 : entrance y id
    - y2 : exit y id
    - wr : writhe within branch
    - wr_down : total writhe downstream relative to the given branch 

    ### Tracer keys:
    - id :      index in tracers list
    - points :  list of points tracing the branch, each of which contains an x index and y index for the two pairs consituting the two segments on opposing strands of the superhelix 

​

Writhe Map

Methods to calculate the writhe map are contained in the directory CalWM/. The is a cython, a numba and a bare python implementation of method 1 from Klenin et al (Ref. [1]). Cython is recommended as it is several times faster than the numba implementation but it requires compilation. To compile execute the bash script: ./compile.sh

1. Klenin, K., & Langowski, J. (2000). Computation of writhe in modeling of supercoiled DNA. Biopolymers, 54(5), 307–317. https://doi.org/10.1002/1097-0282(20001015)54:5<307::AID-BIP20>3.0.CO;2-Y