README.md

resdata

resdata is a tool that calculates residue wise interatomic distances and contact probabilities probabilities accounting for symmetric molecules . It works using the GROMACS API.

Installation

To install it you need to compile and install GROMACS (2023/2024) using -DGMX_INSTALL_LEGACY_API=ON -DBUILD_SHARED_LIBS=ON -DGMX_INSTALL_NBLIB_API=ON. Then in a local subfolder (e.g., build, run cmake .. then make and make install).

Usage

resdata calculates a residue wise contact and distance matrix for complex system. It can Calculate block averages of probabilities It takes in input an index (only hole molecules can be removed otherwise an error is raised)

Usage: cmdata [OPTION...]
  -f, --traj=FILE               Trajectory file
  -s, --top=FILE                Topology file
  -b, --t_begin[=FLOAT]         Start time
  -e, --t_end[=FLOAT]           End time
  -o, --out[=STRING]            Output prefix
  -n, --index[=STRING]          Index file
      --dt[=INT]                Time step
      --cutoff[=DOUBLE]         Cutoff distance
      --mol_cutoff[=DOUBLE]     Molecule cutoff distance
      --nskip[=INT]             Number of frames to skip
      --num_threads[=INT]       Number of threads
      --mode[=STRING]           Mode of operation
      --weights[=FILE]          Weights file
      --no_pbc                  Ignore pbcs
      --blk_avg                 Calculates block average for probabili

Help options:
  -?, --help                    Show this help message
      --usage                   Display brief usage message