Voronota version 1.29

Commands:

get-balls-from-atoms-file
calculate-vertices
calculate-vertices-in-parallel
calculate-contacts
query-balls
query-contacts
draw-contacts
score-contacts-energy
score-contacts-quality
score-contacts-potential
compare-contacts
write-balls-to-atoms-file
query-balls-clashes
run-script
expand-descriptors

Command 'get-balls-from-atoms-file' options:
--annotated                                 flag to enable annotated mode
--include-heteroatoms                       flag to include heteroatoms
--include-hydrogens                         flag to include hydrogen atoms
--multimodel-chains                         flag to read multiple models in PDB format and rename chains accordingly
--input-format                  string      input format, variants are: 'pdb' (default), 'mmcif', 'detect'
--radii-file                    string      path to radii configuration file
--default-radius                number      default atomic radius
--only-default-radius                       flag to make all radii equal to the default radius
--hull-offset                   number      positive offset distance enables adding artificial hull balls
--help                                      flag to print usage help to stdout and exit
stdin   <-  file in PDB or mmCIF format
stdout  ->  list of balls
              (default mode line format: 'x y z r # atomSerial chainID resSeq resName atomName altLoc iCode')
              (annotated mode line format: 'annotation x y z r tags adjuncts')

Command 'calculate-vertices' options:
--print-log                                 flag to print log of calculations
--exclude-hidden-balls                      flag to exclude hidden input balls
--include-surplus-quadruples                flag to include surplus quadruples
--link                                      flag to output links between vertices
--init-radius-for-BSH           number      initial radius for bounding sphere hierarchy
--check                                     flag to slowly check the resulting vertices (used only for testing)
--help                                      flag to print usage help to stdout and exit
stdin   <-  list of balls (line format: 'x y z r')
stdout  ->  list of Voronoi vertices, i.e. quadruples with tangent spheres (line format: 'q1 q2 q3 q4 x y z r')

Command 'calculate-vertices-in-parallel' options:
--method                        string   *  parallelization method name, variants are: 'simulated'
--parts                         number   *  number of parts for splitting, must be power of 2
--print-log                                 flag to print log of calculations
--include-surplus-quadruples                flag to include surplus quadruples
--link                                      flag to output links between vertices
--init-radius-for-BSH           number      initial radius for bounding sphere hierarchy
--help                                      flag to print usage help to stdout and exit
stdin   <-  list of balls (line format: 'x y z r')
stdout  ->  list of Voronoi vertices, i.e. quadruples with tangent spheres (line format: 'q1 q2 q3 q4 x y z r')

Command 'calculate-contacts' options:
--annotated                                 flag to enable annotated mode
--probe                         number      probe radius
--exclude-hidden-balls                      flag to exclude hidden input balls
--step                          number      curve step length
--projections                   number      curve optimization depth
--sih-depth                     number      spherical surface optimization depth
--add-mirrored                              flag to add mirrored contacts to non-annnotated output
--draw                                      flag to output graphics for annotated contacts
--tag-centrality                            flag to tag contacts centrality
--tag-peripherial                           flag to tag peripherial contacts
--old-contacts-output           string      file path to output spherical contacts
--volumes-output                string      file path to output constrained cells volumes
--help                                      flag to print usage help to stdout and exit
stdin   <-  list of balls
              (default mode line format: 'x y z r')
              (annotated mode line format: 'annotation x y z r tags adjuncts')
stdout  ->  list of contacts
              (default mode line format: 'b1 b2 area')
              (annotated mode line format: 'annotation1 annotation2 area distance tags adjuncts [graphics]')

Command 'query-balls' options:
--match                         string      selection
--match-not                     string      negative selection
--match-tags                    string      tags to match
--match-tags-not                string      tags to not match
--match-adjuncts                string      adjuncts intervals to match
--match-adjuncts-not            string      adjuncts intervals to not match
--match-external-annotations    string      file path to input matchable annotations
--invert                                    flag to invert selection
--whole-residues                            flag to select whole residues
--drop-atom-serials                         flag to drop atom serial numbers from input
--drop-altloc-indicators                    flag to drop alternate location indicators from input
--drop-tags                                 flag to drop all tags from input
--drop-adjuncts                             flag to drop all adjuncts from input
--set-tags                      string      set tags instead of filtering
--set-dssp-info                 string      file path to input DSSP file
--set-adjuncts                  string      set adjuncts instead of filtering
--set-external-adjuncts         string      file path to input external adjuncts
--set-external-adjuncts-name    string      name for external adjuncts
--rename-chains                             flag to rename input chains to be in interval from 'A' to 'Z'
--guess-chain-names                         flag to assign input chain names based on residue numbering
--renumber-from-adjunct         string      adjunct name to use for input residue renumbering
--renumber-positively                       flag to increment residue numbers to make them positive
--reset-serials                             flag to reset atom serial numbers
--set-seq-pos-adjunct                       flag to set normalized sequence position adjunct
--set-ref-seq-num-adjunct       string      file path to input reference sequence
--ref-seq-alignment             string      file path to output alignment with reference
--seq-output                    string      file path to output query result sequence string
--chains-summary-output         string      file path to output chains summary
--chains-seq-identity           number      sequence identity threshold for chains summary, default is 0.9
--help                                      flag to print usage help to stdout and exit
stdin   <-  list of balls (line format: 'annotation x y z r tags adjuncts')
stdout  ->  list of balls (line format: 'annotation x y z r tags adjuncts')

Command 'query-contacts' options:
--match-first                   string      selection for first contacting group
--match-first-not               string      negative selection for first contacting group
--match-second                  string      selection for second contacting group
--match-second-not              string      negative selection for second contacting group
--match-min-seq-sep             number      minimum residue sequence separation
--match-max-seq-sep             number      maximum residue sequence separation
--match-min-area                number      minimum contact area
--match-max-area                number      maximum contact area
--match-min-dist                number      minimum distance
--match-max-dist                number      maximum distance
--match-tags                    string      tags to match
--match-tags-not                string      tags to not match
--match-adjuncts                string      adjuncts intervals to match
--match-adjuncts-not            string      adjuncts intervals to not match
--match-external-first          string      file path to input matchable annotations
--match-external-second         string      file path to input matchable annotations
--match-external-pairs          string      file path to input matchable annotation pairs
--no-solvent                                flag to not include solvent accessible areas
--ignore-dist-for-solvent                   flag to ignore distance for solvent contacts
--ignore-seq-sep-for-solvent                flag to ignore sequence separation for solvent contacts
--no-same-chain                             flag to not include same chain contacts
--no-poly-bonds                             flag to not include peptide and nucleic polymerization bonds
--invert                                    flag to invert selection
--drop-tags                                 flag to drop all tags from input
--drop-adjuncts                             flag to drop all adjuncts from input
--set-tags                      string      set tags instead of filtering
--set-hbplus-tags               string      file path to input HBPLUS file
--set-distance-bins-tags        string      list of distance thresholds
--inter-residue-hbplus-tags                 flag to set inter-residue H-bond tags
--set-adjuncts                  string      set adjuncts instead of filtering
--set-external-adjuncts         string      file path to input external adjuncts
--set-external-adjuncts-name    string      name for external adjuncts
--set-external-means            string      file path to input external values for averaging
--set-external-means-name       string      name for external means
--renaming-map                  string      file path to input atoms renaming map
--inter-residue                             flag to convert input to inter-residue contacts
--inter-residue-after                       flag to convert output to inter-residue contacts
--summing-exceptions            string      file path to input inter-residue summing exceptions annotations
--summarize                                 flag to output only summary of matched contacts
--summarize-by-first                        flag to output only summary of matched contacts by first identifier
--preserve-graphics                         flag to preserve graphics in output
--help                                      flag to print usage help to stdout and exit
stdin   <-  list of contacts (line format: 'annotation1 annotation2 area distance tags adjuncts [graphics]')
stdout  ->  list of contacts (line format: 'annotation1 annotation2 area distance tags adjuncts [graphics]')

Command 'draw-contacts' options:
--drawing-for-pymol             string      file path to output drawing as pymol script
--drawing-for-jmol              string      file path to output drawing as jmol script
--drawing-for-scenejs           string      file path to output drawing as scenejs script
--drawing-for-chimera           string      file path to output drawing as chimera bild script
--drawing-name                  string      graphics object name for drawing output
--default-color                 string      default color for drawing output, in hex format, white is 0xFFFFFF
--adjunct-gradient              string      adjunct name to use for gradient-based coloring
--adjunct-gradient-blue         number      blue adjunct gradient value
--adjunct-gradient-red          number      red adjunct gradient value
--adjuncts-rgb                              flag to use RGB color values from adjuncts
--random-colors                             flag to use random color for each drawn contact
--alpha                         number      alpha opacity value for drawing output
--use-labels                                flag to use labels in drawing if possible
--help                                      flag to print usage help to stdout and exit
stdin   <-  list of contacts (line format: 'annotation1 annotation2 area distance tags adjuncts graphics')
stdout  ->  list of contacts (line format: 'annotation1 annotation2 area distance tags adjuncts graphics')

Command 'score-contacts-energy' options:
--potential-file                string   *  file path to input potential values
--ignorable-max-seq-sep         number      maximum residue sequence separation for ignorable contacts
--inter-atom-scores-file        string      file path to output inter-atom scores
--atom-scores-file              string      file path to output atom scores
--depth                         number      neighborhood normalization depth
--help                                      flag to print usage help to stdout and exit
stdin   <-  list of contacts (line format: 'annotation1 annotation2 conditions area')
stdout  ->  global scores

Command 'score-contacts-quality' options:
--default-mean                  number      default mean parameter
--default-sd                    number      default standard deviation parameter
--means-and-sds-file            string      file path to input atomic mean and sd parameters
--mean-shift                    number      mean shift in standard deviations
--external-weights-file         string      file path to input external weights for global scoring
--smoothing-window              number      window to smooth residue quality scores along sequence
--atom-scores-file              string      file path to output atom scores
--residue-scores-file           string      file path to output residue scores
--help                                      flag to print usage help to stdout and exit
stdin   <-  list of atom energy descriptors
stdout  ->  weighted average local score

Command 'score-contacts-potential' options:
--input-file-list                           flag to read file list from stdin
--input-contributions           string      file path to input contact types contributions
--input-fixed-types             string      file path to input fixed types
--input-seq-pairs-stats         string      file path to input sequence pairings statistics
--potential-file                string      file path to output potential values
--probabilities-file            string      file path to output observed and expected probabilities
--single-areas-file             string      file path to output single type total areas
--contributions-file            string      file path to output contact types contributions
--multiply-areas                number      coefficient to multiply output areas
--toggling-list                 string      list of toggling subtags
--help                                      flag to print usage help to stdout and exit
stdin   <-  list of contacts (line format: 'annotation1 annotation2 conditions area')
stdout  ->  line of contact type area summaries (line format: 'annotation1 annotation2 conditions area')

Command 'compare-contacts' options:
--target-contacts-file          string   *  file path to input target contacts
--inter-atom-scores-file        string      file path to output inter-atom scores
--inter-residue-scores-file     string      file path to output inter-residue scores
--atom-scores-file              string      file path to output atom scores
--residue-scores-file           string      file path to output residue scores
--depth                         number      local neighborhood depth
--smoothing-window              number      window to smooth residue scores along sequence
--smoothed-scores-file          string      file path to output smoothed residue scores
--ignore-residue-names                      flag to consider just residue numbers and ignore residue names
--residue-level-only                        flag to output only residue-level results
--detailed-output                           flag to enable detailed output
--chains-renaming-file          string      file path to input chains renaming
--remap-chains                              flag to calculate optimal chains remapping
--remap-chains-log                          flag output remapping progress to stderr
--remapped-chains-file          string      file path to output calculated chains remapping
--help                                      flag to print usage help to stdout and exit
stdin   <-  list of model contacts (line format: 'annotation1 annotation2 area')
stdout  ->  global scores (atom-level and residue-level)

Command 'write-balls-to-atoms-file' options:
--pdb-output                    string      file path to output query result in PDB format
--pdb-output-b-factor           string      name of adjunct to output as B-factor in PDB format
--pdb-output-template           string      file path to input template for B-factor insertions
--add-chain-terminators                     flag to add TER lines after chains
--help                                      flag to print usage help to stdout and exit
stdin   <-  list of balls (line format: 'annotation x y z r tags adjuncts')
stdout  ->  list of balls (line format: 'annotation x y z r tags adjuncts')

Command 'query-balls-clashes' options:
--clash-distance                number      clash distance threshold in angstroms, default is 3.0
--min-seq-sep                   number      minimum residue sequence separation, default is 2
--init-radius-for-BSH           number      initial radius for bounding sphere hierarchy
--help                                      flag to print usage help to stdout and exit
stdin   <-  list of balls (line format: 'annotation x y z r')
stdout  ->  list of clashes (line format: 'annotation1 annotation2 distance min-distance-between-balls')

Command 'run-script' options:
--interactive                               flag for interactive mode
--exit-on-first-failure                     flag to terminate script when a command fails
--max-unfolding                 number      maximum level of output unfolding, default is 6
--help                                      flag to print usage help to stdout and exit
stdin   <-  script as plain text
stdout  ->  output of script execution

Command 'expand-descriptors' options:
--help                                      flag to print usage help to stdout and exit
stdin   <-  any text containing atom descriptors
stdout  ->  text with each atom descriptor expanded to 'chainID resSeq iCode serial altLoc resName name'

