
Voronota-LT version 0.9.5

'voronota-lt' executable constructs a radical Voronoi tessellation (also known as a Laguerre-Voronoi diagram or a power diagram)
of atomic balls of van der Waals radii constrained inside a solvent-accessible surface defined by a rolling probe.
The software computes inter-atom contact areas, per-cell solvent accessible surface areas, per-cell constrained volumes.
'voronota-lt' is very fast when used on molecular data with a not large rolling probe radius (less than 2.0 angstroms, 1.4 is recommended)
and can be made even faster by running it using multiple processors.

Options:
    --probe                                          number     rolling probe radius, default is 1.4
    --processors                                     number     maximum number of OpenMP threads to use, default is 2
    --compute-only-inter-residue-contacts                       flag to only compute inter-residue contacts, turns off per-cell summaries
    --compute-only-inter-chain-contacts                         flag to only compute inter-chain contacts, turns off per-cell summaries
    --run-in-aw-diagram-regime                                  flag to run construct a simplified additively weighted Voronoi diagram, turns off per-cell summaries
    --input | -i                                     string     input file path to use instead of standard input, or '_stdin' to still use standard input
    --periodic-box-directions                        numbers    coordinates of three vectors (x1 y1 z1 x2 y2 z2 x3 y3 z3) to define and use a periodic box
    --periodic-box-corners                           numbers    coordinates of two corners (x1 y1 z1 x2 y2 z2) to define and use a periodic box
    --pdb-or-mmcif-heteroatoms                                  flag to include heteroatoms when reading input in PDB or mmCIF format
    --pdb-or-mmcif-hydrogens                                    flag to include hydrogen atoms when reading input in PDB or mmCIF format
    --pdb-or-mmcif-join-models                                  flag to join multiple models into an assembly when reading input in PDB or mmCIF format
    --print-contacts                                            flag to print table of contacts to stdout
    --print-contacts-residue-level                              flag to print residue-level grouped contacts to stdout
    --print-contacts-chain-level                                flag to print chain-level grouped contacts to stdout
    --print-cells                                               flag to print table of per-cell summaries to stdout
    --print-cells-residue-level                                 flag to print residue-level grouped per-cell summaries to stdout
    --print-cells-chain-level                                   flag to print chain-level grouped per-cell summaries to stdout
    --print-everything                                          flag to print everything to stdout, terminate if printing everything is not possible
    --write-input-balls-to-file                                 output file path to write input balls to file
    --write-contacts-to-file                         string     output file path to write table of contacts
    --write-contacts-residue-level-to-file           string     output file path to write residue-level grouped contacts
    --write-contacts-chain-level-to-file             string     output file path to write chain-level grouped contacts
    --write-cells-to-file                            string     output file path to write of per-cell summaries
    --write-cells-residue-level-to-file              string     output file path to write residue-level grouped per-cell summaries
    --write-cells-chain-level-to-file                string     output file path to write chain-level grouped per-cell summaries
    --write-tessellation-edges-to-file               string     output file path to write generating IDs and lengths of SAS-constrained tessellation edges
    --write-tessellation-vertices-to-file            string     output file path to write generating IDs and positions of SAS-constrained tessellation vertices
    --graphics-output-file                           string     output file path to write contacts drawing .py script to run in PyMol
    --graphics-*                                     various    other graphics output configuration options, can be listed with '--help-full' flag
    --mesh-output-obj-file                           string     output file path to write contacts surfaces mesh .obj file
    --mesh-print-topology-summary                               flag to print mesh topology summary
    --measure-running-time                                      flag to measure and output running times
    --write-log-to-file                              string     output file path to write global log, does not turn off printing log to stderr
    --help-full                                                 flag to print full help (for all options) to stderr and exit
    --help | -h                                                 flag to print help (for basic options) to stderr and exit

Standard input stream:
    Several input formats are supported:
      a) Space-separated or tab-separated header-less table of balls, one of the following line formats possible:
             x y z radius
             chainID x y z radius
             chainID residueID x y z radius
             chainID residueID atomName x y z radius
      b) Output of 'voronota get-balls-from-atoms-file' is acceptable, where line format is:
             x y z radius # atomSerial chainID resSeq resName atomName altLoc iCode
      c) PDB file
      d) mmCIF file

Standard output stream:
    Requested tables with headers, with column values tab-separated

Standard error output stream:
    Log (a name-value pair line), error messages

Usage examples:

    cat ./2zsk.pdb | voronota-lt --print-contacts

    voronota-lt -i ./2zsk.pdb --print-contacts

    voronota-lt --input ./2zsk.pdb --print-contacts-residue-level --compute-only-inter-residue-contacts

    voronota-lt --input ./balls.xyzr --processors 8 --write-contacts-to-file ./contacts.tsv --write-cells-to-file ./cells.tsv

    voronota-lt -i ./balls.xyzr --probe 2 --periodic-box-corners 0 0 0 100 100 300 --processors 8 --write-cells-to-file ./cells.tsv

