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Steven E. Wheeler edited this page Jul 2, 2018 · 25 revisions

AaronTools provides a collection of tools for automating routine tasks encountered when running quantum chemistry computations.

These tools can be used either directly with a Perl script using AaronTools objects, or via a series of command-line scripts.

These scripts can be used on the command-line or incorporated into other workflows.

The scripts currently available are:

Table of Contents

angle 

 Options:
     -a, --atoms
         Specify the atoms to find the angle between
 
     -r, --radians
         Use radians for ANGLE units (default is degrees)
 
     -h, --help
         Print this help message and exit

cat_substitute 

 Options:
     -l target=sub, --ligand target=sub
         Replace target (atom or substituent) on ligand with specified substituent
 
     -s target=sub, --substrate target=sub
         Replace target (atom or substituent) on substrate with specified substituent
 
     -r, --relnum
         Use relative ligand/substrate based numbering instead of absolute 1-indexed numbering
 
     -o outfile, --output outfile
         Output to file instead of STDOUT
 
     -h, --help
         Print this help message and exit

dihedral 

 Options:
     -c ATOM1 ATOM2 ANGLE, --change ATOM1 ATOM2 ANGLE
         Change dihedral about ATOM1-ATOM2 (1-indexed) bond by ANGLE
 
     -p ATOM1 ATOM2 ATOM3 ATOM4, --print ATOM1 ATOM2 ATOM3 ATOM4
         Print current ATOM1-ATOM2-ATOM3-ATOM4 (1-indexed) dihedral to STDOUT
 
     -s ATOM1 ATOM2 ATOM3 ATOM4 ANGLE, --set ATOM1 ATOM2 ATOM3 ATOM4 ANGLE
         Set new ATOM1-ATOM2-ATOM3-ATOM4 (1-indexed) dihedral to ANGLE
 
     -o outfile.xyz, --output outfile.xyz
         Write new geometry output to xyz-file instead of STDOUT
 
     -r, --radians
         Use radians for ANGLE units (default is degrees)
 
     -h, --help
         Print this help message and exit

genrotate 

     genrotate [options] -v x y z -n rotations file [file2 file3 ...]
 
 Options:
     -v x y z, --vector x y z
         The rotation vector defined by the points (0, 0, 0), (x, y, z).
         Should be space separated.
 
     -a angle, --angle angle
         Rotate by ANGLE degrees.
 
     -n num, --nrot num
         If used with --angle specified, repeats the rotation NUM times.
         Otherwise, performs NUM equally spaced rotations (implies ANGLE=360/NUM).
 
     -t list, --targets list
         List of atom numbers to rotate (1-indexed). Defaults to all atoms.
 
     -r, --radians
         Angle specified in radians (default is degrees).
 
     -w [directory], --write [directory]
         Write new geometry output to INFILE_genrotate_AXIS_ANGLE.xyz instead of STDOUT.
         Directory defaults to current working directory.
 
     -h, --help
         Print this help message and exit.

genshift 

 Options:
     -v x y z, --vector x y z
         Shift the molecule (or target fragment) by the vector (x, y, z)
 
     -n num, --nshift num
         Repeat the shift n times
 
     -t list, --targets list
         List of atom numbers to shift (1-indexed). Defaults to all atoms.
 
     -w [directory], --write [directory]
         Write new geometry output to INFILE-NAME_shift_VECTOR.xyz instead of STDOUT.
         Directory defaults to current working directory.
 
     -h, --help
         Print this help message and exit

grab_thermo 

 Options:
     -o FILENAME, --output FILENAME
         Write output to FILENAME (in csv format)
 
     -h, --help
         Print this help message and exit

map_ligand 

 Options:
     -l target_ligand, --ligand target_ligand
         Specify ligands to map to reference structure. Multiple ligands can be specified.
         May be xyz file or name of AARON built-in.
 
     -w [directory], --write [directory]
         Save files instead of printing to STDOUT. Defaults to current directory.
 
     -h, --help
         Print this help message and exit

mirror 

 Options:
     -x x, --axis x
         Specify cartesian axis perpendicular to reflection plane (defaults to X).
 
     -w [directory], --write [directory]
         Write new geometry output to INFILE_mirror.xyz instead of STDOUT.
         Directory defaults to current working directory.
 
     -h, --help
         Print this help message and exit

grab_coords 

     Extracts final geometry from <filename> and prints as XYZ coordinates

rmsd_align 

     Aligns [specified atoms in] target_geom to [specified atoms in] reference_geom.
 
 Options:
     -ha, --heavyatoms
         Only align heavy atoms.
 
     -r atomlist, --refatoms atomlist
         List of atoms in reference geometry to align to (1-indexed).
 
     -t atomlist, --targetatoms atomlist
         List of atoms in target geometry to align (1-indexed).
 
     -o outfile, --output outfile
         Write aligned geometry to OUTFILE instead of STDOUT
 
     -h, --help
         Print this help message and exit

rotate 

     rotate [options] -x x|y|z -n rotations file [file2 file3 ...]
 
 Options:
     -x axis, --axis axis
         Specify rotation about x, y, or z axis.
 
     -a angle, --angle angle
         Specify the angle to rotate.
 
     -n num, --nrot num
         If used with --angle specified, repeats the rotation NUM times.
         Otherwise, performs NUM equally spaced rotations (implies angle=360/num).
 
     -r, --radians
         Angle specified in radians (default is degrees)
 
     -w [directory], --write [directory]
         Write new geometry output to INFILE-NAME_rotate_AXIS_ANGLE.xyz instead of STDOUT. 
         Directory defaults to current working directory.
 
     -h, --help
         Print this help message and exit.

substitute 

 Options:
     -s atom=sub, --sub atom=sub
         Location of substituent (1-indexed) and requested substituent using
         key=value notation.
 
     -m, --minimize
         Rotate new substituent to minimize LJ potential
 
     -w [directory], --write [directory]
         Write new geometry output to INFILE-NAME_TARGET-ATOM_SUB-NAME.xyz instead of STDOUT. 
         Directory defaults to current working directory.
 
     -h, --help
         Print this help message and exit
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