e2pathwalker

usage: e2pathwalker.py [options] <pdb file>

	Find paths between two atoms in a PDB model. You can also specify two PDB files to calculate an RMSD.
	
	Use "--solve=<solver>" to run the TSP solver and save the output.
	Use "--output" to save the output to a PDB file.
	Use "--mapfile" to input the density map.

	Pathwalker wiki:
		http://blake.bcm.edu/emanwiki/Pathwalker

Option	Type	Description
--version	None	show program's version number and exit
--output	str	Output file
--mapfile	str	Density map file
--start	int	Start ATOM
--end	int	End ATOM
--average	float	Average Ca-Ca length
--mapweight	float	Weight of density, to balance between geometry and density score
--mapthresh	float	Density threshold, bonds on density lower than threshold is not prefered
--dmin	float	Mininum Ca-Ca length
--dmax	float	Maximum Ca-Ca length
--noise	float	Add Gaussian Noise
--solver	str	Run TSP Solver: concorde or lkh
--atomtype	str	Load Atom Type. Default: 'CA'. Options: 'C' or 'all'
--chain	str	Load Chain. Default: load all chains
--edgefile	str	Load fixed fragment file; one sequence of forced connections per line, separated by space.
-e, --edge	None	Forced edge: e.g. -e1,3
--fixed	str	Same as --edgefile.
--iterations	int	Iterations
--json	int	If writing output pdb, also write JSON metadata. Default: 1. Options: 0, 1
--overwrite	None	Overwrite files without prompting
--verbose, -v	int	verbose level [0-9], higher number means higher level of verboseness
--ppid	int	Set the PID of the parent process, used for cross platform PPID
--subunit	int	Number of subunits.