DPDchrom is developed to reconstruct 3D chromatin conformation using a single-cell Hi-C contact map. This method is based on DPD [1]. Previous version with manual preparation published [2] and available here. It means that the thermostat is embedded into a motion calculation. A solvent is taken into account explicitly. Due to the soft repulsion, one can use a large integration time step, dt=0.04. This software takes the contact matrix as an input and produces chromatin conformation as an output.
To install DPDchrom, put in the same folder makefile and DPDchrom.f90, then compile the Fortran code with any Fortran compiler.
make
DPDchrom is ready to run.
In the test folder there is an example of input 37420_*.csv [3]. The format of the file is:
chr1,chr2,start1,end1,start2,end2,count
1,1,3200000,3400000,3200000,3400000,1
To perform calculations execute DPDchrom in the command line passing 3 arguments, /path/to/file, resolution in bp, and chain length. Path to file and resolution are self-descriptive. If you want to reconstruct a single chain with a fixed length, then pass the number of beads. When you don't want to define chain length or have several chains, please, pass 0. Example of the command to reconstruct conformation using file myfile at resolution 100 Kb:
./DPDchrom /home/work/myfile 100000 0
The format of the output file with conformation is custom. In order to convert it to mol2 format, there is a script rst2mol2.py in py_script folder. Moreover, there is an opportunity to remove periodic boundary conditions properly.
To compare structures with each other, there is a script imj_acc.py provided as a template to calculate similarity (reconstruction accuracy) as the Modified Jaccard Index.
In the folder cmd you can find input files for CMD calculations for LAMMPS.
- Groot, Robert D., and Patrick B. Warren. "Dissipative particle dynamics: Bridging the gap between atomistic and mesoscopic simulation." The Journal of chemical physics 107.11 (1997): 4423-4435.
- Ulianov, Sergey V., et al. "Order and stochasticity in the folding of individual Drosophila genomes." Nature Communications 12.1 (2021): 1-17.
- Flyamer, Ilya M., et al. "Single-nucleus Hi-C reveals unique chromatin reorganization at oocyte-to-zygote transition." Nature 544.7648 (2017): 110-114.