cubeWorks

The cubeWorks package contains a group of programs to perform operations on files in the Gaussian cube format. This format (initially developed for electron densities) is used for multiple output files by 3D-2PT.

Installation

UNIX Terminal

• download and unzip the source code
• enter cubeWorks directory, e.g.
  cd cubeWorks-1.0 or cd cubeWorks-main
• compile with GNU make
  • type make to compile all programs (requires float version of FFTW3)
    or
  • type make noFT to compile without -lfftw3f (skips compilation of cubeFilter)
• make cubeWorks binaries findable
  • add cubeWorks/bin to $PATH:
    dir=$(pwd)
echo "export PATH=\$PATH:${dir}/bin" >> ~/.bash_profile
    or
  • copy contents of cubeWorks/bin to usr/local/bin:
    sudo cp bin/* usr/local/bin/
    or
  • ...

Using cubeWorks

All cubeWorks programs print a short usage message, e.g.

[user@localhost:~]$ cubeAdd
usage: cubeAdd A.cube B.cube output.cube [output_title]
output.cube = A.cube + B.cube

Command line arguments in square brackets ([ ]) are optional.

Short Description of Each Program

cube2dat

usage: cube2dat input.cube [output_filename] [scaling factor] ["output_title"]

• converts file input.cube into ASCII data file with explicitly written x, y and z coordinates
• if output_filename is not specified, the .cube extension of the input file is replaced by .dat
• volume data in input.cube can be scaled with scaling_factor
• A title is written in first of 3 header lines of output file. By default, title is taken from header of input.cube file, but optionally a new title can be provided on command line (white spaces in output_title currently not supported)

cubeAdd

usage: cubeAdd A.cube B.cube output.cube [output_title]
output.cube = A.cube + B.cube

• adds data in cube files A.cube and B.cube and writes result into output.cube
• title in header of output.cube is taken from A.cube or can be provided with output_title (white spaces in title currently not supported)

cubeAver

usage: cubeAver A.cube B.cube ... output.cube
output.cube = (A.cube + B.cube + ...) / N

• averages data in cube files A.cube, B.cube, ... (no explicit limit on number of cube input files that can be specified) and writes result into output.cube (last command line argument)

cubeCenter

usage: cubeCenter input.cube output.cube [output title]

• ensures that the center of the grid is located at 0 0 0 (atom coordinates are moved as well)
• title in header of output.cube is taken from A.cube or can be provided with output_title (white spaces in title currently not supported)

cubeDiv

usage: cubeDiv A.cube B.cube output.cube [escape]
output.cube = A.cube / B.cube
escape: result of division by zero

• divides data in cube files A.cube by data in B.cube and writes result into output.cube
• if division by zero is encountered, the result can be defined with escape (0 by default)

cubeFilter

usage: cubeFilter input.cube sigma
input.cube: cube file to apply filter on
sigma : sigma of Gaussian filter (Angstrom)

• applies 3D Gaussian blur filter on data in input.cube to suppress noise
• sigma specifies the kernel width of the filter in Angstrom
  • small sigma:
• output is written to cube file with name derived from input.cube and sigma, e.g. input_f-1.00A.cube

cubeMax

usage: cubeMax input.cube
input.cube: cube file with density

• identifies all local maxima in the density stored in input.cube
• results are stored in a formatted ASCII file that conatins:
  • coordinates of the maxima
  • 1D indices of corresponding voxels
  • peak intensities
  • peak integrals (sum over voxels belonging to maximum)
  • number of voxels belonging to peak
  • indices of all voxels associated with each peak
• output file name derived from input.cube, e.g. input_maxima.dat

cubeMirror

usage: cubeMirror input.cube plane output.cube [output_title]

• computes tha average of mirror images associated with a selected mirror plane
• resulting data will be symmetric with respect to selected mirror plane
• useful to reduce noise in symmetric systems
• available mirror planes: XY, XZ, YZ
• mirror operation is performed using indices in a 3D array storing the data, not actual coordinates (relevant if cube voxels not aligned with x,y,z axes -> triggers WARNING message)
• title in header of output.cube is taken from A.cube or can be provided with output_title (white spaces in title currently not supported)

cubeMove

usage: cubeMove input.cube dX dY dZ output.cube [output_title]
output.cube = input.cube + (dX dY dZ)

• translates input.cube according to vector (dX dY dZ) (in Angstroms) and writes result to output.cube
• translation is applied to grid points and atoms sepcified in input.cube
• title in header of output.cube is taken from A.cube or can be provided with output_title (white spaces in title currently not supported)

cubeMult

usage: cubeMult A.cube B.cube output.cube [output_title]
output.cube = A.cube * B.cube

• multiplies data in cube files A.cube by data in B.cube and writes result into output.cube
• title in header of output.cube is taken from A.cube or can be provided with output_title (white spaces in title currently not supported)

cubeRot

usage: cubeRot A.cube axisX axisY axisZ angle_degree output.cube [output_title]
output.cube = rot(axis,angle) @ input.cube

• rotates input.cube around axis (axisX axisY axisZ) by specified angle in degrees and writes result to output.cube
• rotation axis does not need to be normalized
• rotation is applied to grid points and atoms sepcified in input.cube
• title in header of output.cube is taken from A.cube or can be provided with output_title (white spaces in title currently not supported)

cubeScale

usage: cubeScale input.cube scale output.cube [output_title]
output.cube = scale * input.cube

• multiplies data in cube file A.cube by scale and writes result into output.cube
• title in header of output.cube is taken from A.cube or can be provided with output_title (white spaces in title currently not supported)

cubeScaleInv

usage: cubeScaleInv input.cube scale output.cube [output_title]
output.cube = input.cube / scale

• divides data in cube file A.cube by scale and writes result into output.cube
• title in header of output.cube is taken from A.cube or can be provided with output_title (white spaces in title currently not supported)

cubeSub

usage: cubeSub A.cube B.cube output.cube [output_title]
output.cube = A.cube - B.cube

• subtracts data in cube file B.cube from data in A.cube and writes result into output.cube
• title in header of output.cube is taken from A.cube or can be provided with output_title (white spaces in title currently not supported)

cubeSum

usage: cubeSum A.cube B.cube ... output.cube
output.cube = A.cube + B.cube + ...

• sums data in cube files A.cube, B.cube, ... (no explicit limit on number of cube input files that can be specified) and writes result into output.cube (last command line argument)

cubeTitle

usage: cubeTitle input.cube new_title

• replaces title in header of input.cube with new_title (white spaces in new_title currently not supported)
• overwrites input.cube

resolvate

usage: resolvate input.pdb input.cube dist
input.pdb : structure file to be solvated
input.cube: cube file with water density

• assumes that input.cube contains a water density
• identifies all local maxima of density in input.cube
• results are stored in a formatted ASCII file that conatins:
  • coordinates of the maxima
  • 1D indices of corresponding voxels
  • peak intensities
  • peak integrals (sum over voxels belonging to maximum)
  • number of voxels belonging to peak
  • indices of all voxels associated with each peak
• output file name derived from input.cube, e.g. input_maxima.dat
• identifies all maxima within distance dist of any atom in input.pdb
• write PDB file with HETATM entries for water oxygens associated position of all density maxima within distance dist
• occupancy field of new HETATM entires correspond to peak integrals
• PDB output file name derived from input.cube and dist, e.g. input+shell-5.00A.pdb