This is a package consisting of several small handy tools for analyzing biomolecule structures (protein, RNA, DNA) or MD trajectories.
At the current stage, these tools are mainly used for analyzing CafeMol MD results.
Please change compiler confirgurations in
src/Makefile, then run
make make install
By default, all the tools will be moved to the
The Boost C++ Libraries are reqired.
|p_cafemol_ts_read||Simplely read CafeMol |
|p_dcd_angle_com||Calculate angle between three COMs (center of masses).|
|p_dcd_base_pairing_percentage||Calculate base pairing percentage for DNA.|
|p_dcd_contact_number||Calculate contact number between biomolecule chains.|
|p_dcd_distance_*||Calculate distances between atoms/COM/specified groups.|
|p_dcd_dna_curvature||Calculate DNA curvature from trajectories.|
|p_dcd_interface_scan||Find inter-chain interface in MD trajectories.|
|p_dcd_persistence_length||Calculate DNA persistence length from MD trajectories.|
|p_pdb_PDI_st||Statistics of protein-DNA interactions from PDB structures.|
|p_pdb_R_g||Calculate radius of gyration \(R_g\) of molecules from PDB.|
|p_pdb_cat||Re-output PDB coordinates.|
|p_pdb_cg_top||Generate topology file from PDB file.|
|p_pdb_dna_curvature||Calculate DNA curvature and other structural information from PDB.|
|p_pdb_get_sequence||Output sequence of molecules in PDB.|
- DNA residues should have name “DA”, “DT”, “DC”, or “DG”.
- If the user want to include ions into CG models, change atom record name from “HETATM” to “ATOM”.