usage: translate.py [-h]
[-if {xyz,log,com,gjf,sd,sdf,mol,mol2,out,dat,fchk,crest,xtb,sqmout,47,31,qout}]
[-t atoms] [-f atoms] [-ct targets] [-v x y z]
[-d DISTANCE] [-dest x y z] [-com | -cent] [-o OUTFILE]
[input file [input file ...]]
move atoms along a vector
positional arguments:
input file a coordinate file
optional arguments:
-h, --help show this help message and exit
-if {xyz,log,com,gjf,sd,sdf,mol,mol2,out,dat,fchk,crest,xtb,sqmout,47,31,qout}, --input-format {xyz,log,com,gjf,sd,sdf,mol,mol2,out,dat,fchk,crest,xtb,sqmout,47,31,qout}
file format of input - xyz is assumed if input is stdin
-ct targets, --center-targets targets
target atoms for -com or -cent arguments
comma (,) and/or hyphen (-) separated list
hyphens denote a range of atoms
commas separate individual atoms or ranges
default: whole structure
-d DISTANCE, --distance DISTANCE
distance translated - only applies to --vector/-v
-o OUTFILE, --output OUTFILE
output destination
$INFILE will be replaced with the name of the input file
Default: stdout
atoms to move:
-t atoms, --targets atoms
move atoms with specified indices
Default: whole structure
-f atoms, --fragment atoms
move fragments containing specified atoms
Default: whole structure
translation mode (default: move centroid to origin):
-v x y z, --vector x y z
translate in direction of this vector
vector is normalized when --distance/-d is used
-dest x y z, --destination x y z
translate fragment to a point
center (default: centroid):
-com, --center-of-mass
translate the center of mass of the targets to the destination
-cent, --centroid translate the centroid of the targets to the destination