pinang

Description

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.

Installation

Please change compiler confirgurations in src/Makefile, then run

make
make install

By default, all the tools will be moved to the bin/ directory.

Prerequisites

The Boost C++ Libraries are reqired.

Tools

Command	Description
p_cafemol_ts_read	Simplely read CafeMol .ts files.
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.

Dangerous Traps

PDB format

• 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”.