The analysis of macromolecular structures often requires a comprehensive definition of atomic neighborhoods. Such a definition can be based on the Voronoi diagram of balls, where each ball represents an atom of some van der Waals radius. Voronota is a software tool for finding all the vertices of the Voronoi diagram of balls. Such vertices correspond to the centers of the empty tangent spheres defined by quadruples of balls. Voronota is especially suitable for processing three-dimensional structures of biological macromolecules such as proteins and RNA.
Since version 1.2 Voronota also uses the Voronoi vertices to construct inter-atom contact surfaces and solvent accessible surfaces. Voronota provides tools to query contacts, generate contacts graphics, compare contacts and evaluate quality of protein structural models using contacts.
Voronota is developed by Kliment Olechnovic (kliment.olechnovic@bti.vu.lt).
Below are several commands that install the latest version of Voronota and its expansions for the command line use in Unix-like systems.
# download the latest package
wget https://github.com/kliment-olechnovic/voronota/releases/download/v1.28.4132/voronota_1.28.4132.tar.gz
# unpack the package
tar -xf ./voronota_1.28.4132.tar.gz
# change to the package directory
cd ./voronota_1.28.4132
# run CMake
cmake . -DEXPANSION_JS=ON -DEXPANSION_LT=ON
# compile everything
make
# install everything
sudo make installThe installed files are listed in the ‘install_manifest.txt’ file. They can be uninstalled by running
sudo xargs rm < ./install_manifest.txtCurrently there are three expansions of Voronota: Voronota-JS, Voronota-LT and Voronota-GL.
The expansions need to be built separately in their subdirectories. Alternatively, they can be built by appending -DEXPANSION_JS=ON and/or -DEXPANSION_LT=ON and/or -DEXPANSION_GL=ON to the CMake command call.
The expansions have separate dedicated documentation pages.
Voronota-JS expansion is located in the ‘expansion_js’ subdirectory of the Voronota package.
Voronota-JS provides a way to write JavaScript scripts for the comprehensive analysis of macromolecular structures, including the Voronoi tesselation-based analysis. Currently, the Voronota-JS package contains several executables:
Voronota-LT expansion is located in the ‘expansion_lt’ subdirectory of the Voronota package.
Voronota-LT (pronounced ‘voronota lite’) is an alternative version of Voronota for constructing tessellation-derived atomic contact areas and volumes. Voronota-LT was written from scratch and does not use any external code, even from the core Voronota. The primary motivation for creating Voronota-LT was drastically increasing the speed of computing tessellation-based atom-atom contact areas and atom solvent-accessible surface areas. Like Voronota, Voronota-LT can compute contact areas derived from the additively weighted Voronoi tessellation, but the main increase in speed comes when utilizing a simpler, radical tessellation variant, also known as Laguerre-Laguerre tessellation or power diagram.
Voronota-GL expansion is located in the ‘expansion_gl’ subdirectory of the Voronota package
Voronota-GL is a visual tool for the comprehensive interactive analysis of macromolecular structures, including the Voronoi tesselation-based analysis.
Download the latest archive from the official downloads page: https://github.com/kliment-olechnovic/voronota/releases.
The archive contains ready-to-use statically compiled ‘voronota’ program for 64 bit Linux systems. This executable can be rebuilt from the provided source code to work on any modern Linux, macOS or Windows operating systems.
On Ubuntu 18.04 and newer it is possible to install Voronota using ‘apt’ command:
sudo apt install voronotaOn Windows 10 operating system the easiest way to run Voronota is to use Windows Subsystem for Linux (WSL).
Voronota has no required external dependencies, only a standard-compliant C++ compiler is needed to build it.
You can build using CMake for makefile generation. Starting in the directory containing “CMakeLists.txt” file, run the sequence of commands:
cmake ./
makeAlternatively, to keep files more organized, CMake can be run in a separate “build” directory:
mkdir build
cd build
cmake ../
make
cp ./voronota ../voronotaFor example, “voronota” executable can be built from the sources in “src” directory using GNU C++ compiler:
g++ -O3 -std=c++11 -o voronota $(find ./src/ -name '*.cpp')To allow the usage of OpenMP when calling the “calculate-vertices-in-parallel” command, the “-fopenmp” flag needs to be set when building.
When building using C++ compiler directly, just add “-fopenmp”:
g++ -O3 -std=c++11 -fopenmp -o voronota $(find ./src/ -name '*.cpp')When using CMake, set the CMAKE_CXX_FLAGS variable:
cmake -DCMAKE_CXX_FLAGS="-fopenmp" ./
makeTo allow the usage of MPI when calling the “calculate-vertices-in-parallel” command, you can use mpic++ compiler wrapper and define “ENABLE_MPI” macro when buiding:
mpic++ -O3 -std=c++11 -DENABLE_MPI -o voronota ./$(find ./src/ -name '*.cpp')Voronota can be built with either modern C++ compilers or pre-C++11 compilers that support C++ Technical Report 1 (TR1) features. The voronota code has preprocessor-based checks to find out if C++ TR1 namespace is available and needs to be used. If compilation fails, it may mean that these checks failed. To troubleshoot this, try setting the value of the “USE_TR1” macro to 0 (to not use TR1 and to rely on C++11 standard) or 1 (to use TR1) when compiling, for example:
g++ -O3 -DUSE_TR1=1 -o voronota $(find ./src/ -name '*.cpp')or
g++ -O3 -std=c++11 -DUSE_TR1=0 -o voronota $(find ./src/ -name '*.cpp')Here is a basic example of computing Voronoi vertices for a structure in a PDB file:
./voronota get-balls-from-atoms-file < input.pdb > balls.txt
./voronota calculate-vertices < balls.txt > vertices.txtThe first command reads a PDB file “input.pdb” and outputs a file “balls.txt” that contains balls corresponding to the atoms in “input.pdb” (by default, Voronota ignores all heteroatoms and all hydrogen atoms when reading PDB files: this behavior can be altered using command-line options). The second command reads “balls.txt” and outputs a file “vertices.txt” that contains a quadruples and empty tangent spheres that correspond to the vertices of the Voronoi diagram of the input balls. The formats of “balls.txt” and “vertices.txt” are described below.
In “balls.txt” the line format is “x y z r # comments”. The first four values (x, y, z, r) are atomic ball coordinates and radius. Comments are not needed for further calculations, they are to assist human readers. For example, below is a part of some possible “balls.txt”:
28.888 9.409 52.301 1.7 # 1 A 2 SER N
27.638 10.125 52.516 1.9 # 2 A 2 SER CA
26.499 9.639 51.644 1.75 # 3 A 2 SER C
26.606 8.656 50.915 1.49 # 4 A 2 SER O
27.783 11.635 52.378 1.91 # 5 A 2 SER CB
27.69 12.033 51.012 1.54 # 6 A 2 SER OGIn “vertices.txt” the line format is “q1 q2 q3 q4 x y z r”. The first four numbers (q1, q2, q3, q4) are numbers of atomic records in “balls.txt”, starting from 0. The remaining four values (x, y, z, r) are the coordinates and the radius of an empty tangent sphere of the quadruple of atoms. For example, below is a part of some possible “vertices.txt”:
0 1 2 3 27.761 8.691 51.553 -0.169
0 1 2 23 28.275 9.804 50.131 0.588
0 1 3 1438 24.793 -3.225 60.761 14.047
0 1 4 5 28.785 10.604 50.721 0.283
0 1 4 1453 30.018 10.901 55.386 1.908
0 1 5 23 28.544 10.254 50.194 0.595Taking the “balls.txt” file described in the previous section, here is a basic example of computing inter-atom contacts:
./voronota calculate-contacts < balls.txt > contacts.txtIn “contacts.txt” file the line format is “b1 b2 area”. The first two numbers (b1 and b2) are numbers of atomic records in “balls.txt”, starting from 0. If b1 does not equal b2, then the ‘area’ value is the area of contact between atoms b1 and b2. If b1 equals b2, then the ‘area’ value is the solvent-accessible area of atom b1. For example, below is a part of some possible “contacts.txt”:
0 0 35.440
0 1 15.908
0 2 0.167
0 3 7.025
0 4 7.021
0 5 0.624
0 23 2.849
0 25 0.008
0 26 11.323
0 1454 0.021
1 1 16.448
1 2 11.608
1 3 0.327
1 4 14.170
1 5 0.820
1 6 3.902
1 23 0.081
2 2 3.591
2 3 11.714
2 4 0.305
2 5 2.019Here is a basic example of computing annotated inter-atom contacts:
./voronota get-balls-from-atoms-file --annotated < input.pdb > annotated_balls.txt
./voronota calculate-contacts --annotated < annotated_balls.txt > annotated_contacts.txtIn “annotated_contacts.txt” the line format is “annotation1 annotation2 area distance tags adjuncts [graphics]”. The strings ‘annotation1’ and ‘annotation2’ describe contacting atoms, the ‘area’ value is the area of contact between the two atoms, the ‘distance’ value is the distance between the centers of the contacting atoms. If ‘annotation2’ contains string “solvent”, then the ‘area’ value is the solvent-accessible area of the atom described by ‘annotation1’. The remaining part of the line is used by Voronota querying and drawing commands that are not covered in this section. Below is a part of some possible “annotated_contacts.txt” (with text fields aligned using “column -t” command):
c<A>r<2>a<1>R<SER>A<N> c<A>r<2>a<2>R<SER>A<CA> 15.908 1.456 . .
c<A>r<2>a<1>R<SER>A<N> c<A>r<2>a<3>R<SER>A<C> 0.167 2.488 . .
c<A>r<2>a<1>R<SER>A<N> c<A>r<2>a<4>R<SER>A<O> 7.025 2.774 . .
c<A>r<2>a<1>R<SER>A<N> c<A>r<2>a<5>R<SER>A<CB> 7.021 2.486 . .
c<A>r<2>a<1>R<SER>A<N> c<A>r<2>a<6>R<SER>A<OG> 0.624 3.159 . .
c<A>r<2>a<1>R<SER>A<N> c<A>r<5>a<24>R<GLU>A<CB> 2.849 4.628 . .
c<A>r<2>a<1>R<SER>A<N> c<A>r<5>a<26>R<GLU>A<CD> 0.008 4.792 . .
c<A>r<2>a<1>R<SER>A<N> c<A>r<5>a<27>R<GLU>A<OE1> 11.323 3.932 . .
c<A>r<2>a<1>R<SER>A<N> c<A>r<194>a<1501>R<LEU>A<CD2> 0.021 5.465 . .
c<A>r<2>a<1>R<SER>A<N> c<solvent> 35.440 5.9 . .
c<A>r<2>a<2>R<SER>A<CA> c<A>r<2>a<3>R<SER>A<C> 11.608 1.514 . .
c<A>r<2>a<2>R<SER>A<CA> c<A>r<2>a<4>R<SER>A<O> 0.327 2.405 . .
c<A>r<2>a<2>R<SER>A<CA> c<A>r<2>a<5>R<SER>A<CB> 14.170 1.523 . .
c<A>r<2>a<2>R<SER>A<CA> c<A>r<2>a<6>R<SER>A<OG> 0.820 2.430 . .
c<A>r<2>a<2>R<SER>A<CA> c<A>r<3>a<7>R<LYS>A<N> 3.902 2.371 . .
c<A>r<2>a<2>R<SER>A<CA> c<A>r<5>a<24>R<GLU>A<CB> 0.081 4.954 . .
c<A>r<2>a<2>R<SER>A<CA> c<solvent> 16.448 6.1 . .Each atomic descriptor in the above text can be transformed into a space-separated list (chainID resSeq iCode serial altLoc resName name) using “voronota expand-descriptors” command:
cat annotated_contacts.txt | voronota expand-descriptors | column -t > expanded_table_of_contacts.txtBelow is a part of some possible “expanded_table_of_contacts.txt”:
A 2 . 1 . SER N A 2 . 2 . SER CA 15.908 1.456 . .
A 2 . 1 . SER N A 2 . 3 . SER C 0.167 2.488 . .
A 2 . 1 . SER N A 2 . 4 . SER O 7.025 2.774 . .
A 2 . 1 . SER N A 2 . 5 . SER CB 7.021 2.486 . .
A 2 . 1 . SER N A 2 . 6 . SER OG 0.624 3.159 . .
A 2 . 1 . SER N A 5 . 24 . GLU CB 2.849 4.628 . .
A 2 . 1 . SER N A 5 . 26 . GLU CD 0.008 4.792 . .
A 2 . 1 . SER N A 5 . 27 . GLU OE1 11.323 3.932 . .
A 2 . 1 . SER N A 194 . 1501 . LEU CD2 0.021 5.465 . .
A 2 . 1 . SER N solvent . . . . . . 35.440 5.9 . .
A 2 . 2 . SER CA A 2 . 3 . SER C 11.608 1.514 . .
A 2 . 2 . SER CA A 2 . 4 . SER O 0.327 2.405 . .
A 2 . 2 . SER CA A 2 . 5 . SER CB 14.170 1.523 . .
A 2 . 2 . SER CA A 2 . 6 . SER OG 0.820 2.430 . .
A 2 . 2 . SER CA A 3 . 7 . LYS N 3.902 2.371 . .
A 2 . 2 . SER CA A 5 . 24 . GLU CB 0.081 4.954 . .
A 2 . 2 . SER CA solvent . . . . . . 16.448 6.1 . .The “voronota query-contacts” command can be used to query and manipulate computed annotated contacts. For example, below is the command that selects contacts that probably correspond to salt bridges:
cat annotated_contacts.txt | voronota query-contacts --match-first 'R<ASP,GLU>&A<OD1,OD2,OE1,OE2,OXT>' --match-second 'R<ARG,HIS,LYS>&A<NH1,NH2,ND1,NE2,NZ>' --match-max-dist 4.0The support/generate-arguments-for-query-contacts.html file in the Voronota package provides a graphical interface for generating sets of arguments for the “voronota query-contacts” command: it serves as an interactive documentation. A similar interface for the “voronota query-balls” command is provided by the support/generate-arguments-for-query-balls.html file.
The list of all available Voronota commands is displayed when executing Voronota without any parameters.
Command help is shown when “–help” command line option is present, for example:
./voronota calculate-vertices --helpUsing “–help” option without specific command results in printing help for all commands:
./voronota --helpName Type Description
------------------------------- ------ ---- ------------------------------------------------------------------------
--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 exitfile in PDB or mmCIF formatlist 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'Name Type Description
------------------------------- ------ ---- ------------------------------------------------------------------------
--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 exitlist of balls (line format: 'x y z r')list of Voronoi vertices, i.e. quadruples with tangent spheres (line format: 'q1 q2 q3 q4 x y z r')Name Type Description
------------------------------- ------ ---- ------------------------------------------------------------------------
--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 exitlist of balls (line format: 'x y z r')list of Voronoi vertices, i.e. quadruples with tangent spheres (line format: 'q1 q2 q3 q4 x y z r')Name Type Description
------------------------------- ------ ---- ------------------------------------------------------------------------
--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 exitlist of balls
default mode line format: 'x y z r'
annotated mode line format: 'annotation x y z r tags adjuncts'list of contacts
default mode line format: 'b1 b2 area'
annotated mode line format: 'annotation1 annotation2 area distance tags adjuncts [graphics]'Name Type Description
------------------------------- ------ ---- ------------------------------------------------------------------------
--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 exitlist of balls (line format: 'annotation x y z r tags adjuncts')list of balls (line format: 'annotation x y z r tags adjuncts')Name Type Description
------------------------------- ------ ---- ------------------------------------------------------------------------
--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 exitlist of contacts (line format: 'annotation1 annotation2 area distance tags adjuncts [graphics]')list of contacts (line format: 'annotation1 annotation2 area distance tags adjuncts [graphics]')Name Type Description
------------------------------- ------ ---- ------------------------------------------------------------------------
--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 exitlist of contacts (line format: 'annotation1 annotation2 area distance tags adjuncts graphics')list of contacts (line format: 'annotation1 annotation2 area distance tags adjuncts graphics')Name Type Description
------------------------------- ------ ---- ------------------------------------------------------------------------
--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 exitlist of contacts (line format: 'annotation1 annotation2 conditions area')global scoresName Type Description
------------------------------- ------ ---- ------------------------------------------------------------------------
--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 exitlist of atom energy descriptorsweighted average local scoreName Type Description
------------------------------- ------ ---- ------------------------------------------------------------------------
--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 exitlist of contacts (line format: 'annotation1 annotation2 conditions area')line of contact type area summaries (line format: 'annotation1 annotation2 conditions area')Name Type Description
------------------------------- ------ ---- ------------------------------------------------------------------------
--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 exitlist of model contacts (line format: 'annotation1 annotation2 area')global scores (atom-level and residue-level)Name Type Description
------------------------------- ------ ---- ------------------------------------------------------------------------
--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 exitlist of balls (line format: 'annotation x y z r tags adjuncts')list of balls (line format: 'annotation x y z r tags adjuncts')Name Type Description
------------------------------- ------ ---- ------------------------------------------------------------------------
--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 exitlist of balls (line format: 'annotation x y z r')list of clashes (line format: 'annotation1 annotation2 distance min-distance-between-balls')Name Type Description
------------------------------- ------ ---- ------------------------------------------------------------------------
--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 exitscript as plain textoutput of script executionName Type Description
------------------------------- ------ ---- ------------------------------------------------------------------------
--help flag to print usage help to stdout and exitany text containing atom descriptorstext with each atom descriptor expanded to 'chainID resSeq iCode serial altLoc resName name'‘voronota-voromqa’ script is an implementation of VoroMQA (Voronoi diagram-based Model Quality Assessment) method using Voronota. The script interface is presented below:
Basic options:
--input | -i string input structure file in PDB or mmCIF format
--input-filter-query string input atoms filtering query parameters
--output-atom-scores string output text file with atom scores
--output-atom-scores-pdb string output PDB file with atom scores as B-factors
--output-residue-scores string output text file with residue scores
--output-residue-scores-pdb string output PDB file with residue scores as B-factors
--output-residue-scores-plot string output PNG image file with residue scores plot, requires R
--help | -h flag to display help message and exit
Advanced options:
--cache-dir string path to cache directory
--smoothing-window number residue scores smoothing window size, default is 5
--atoms-query string atoms query parameters to define selection
--contacts-query string contacts query parameters to define selection
--output-selected-scores string output text file with selected atom scores
--reference-sequence string sequence file or string for residue renumbering
--output-sequence-alignment string output text file with sequence alignment
--print-header flag to print output header
--multiple-models flag to handle multiple models in PDB file
--score-inter-chain flag to output inter-chain interface scores
--list-all-options flag to display list of all command line options and exit
Standard output (one line):
{input file path} {global score} {number of residues} {number of atoms} [ {selection score} {number of selected atoms} ]All options of ‘voronota-voromqa’ script, in alphabetical order:
--add-hydrogens string command to add hydrogens
--atoms-query string atoms query parameters to define selection
--cache-dir string path to cache directory
--contacts-query string contacts query parameters to define selection
--energy-input-potential string path to custom potential file
--energy-input-statistics string path to custom energy statistics file
--energy-mode string energy mode name
--help flag to display help message and exit
--highlight-selection-in-plot flag to highlight selection in plot
--input-filter-query string input atoms filtering query parameters
--input-is-list flag to treat input as a list of files
--input-is-structure flag to treat input as a PDB file
--input string input structure file in PDB format
--more-logging flag to enable more logging
--multiple-energy-modes string list of energy modes
--multiple-models flag to handle multiple models in PDB file
--mutation-goal string three-letter residue code
--mutation-query string atoms query parameters to define residues to mutate
--neglect-SAS flag to discard solvent-accessible surface
--no-multiple-energy-modes flag to not use multiple energy modes
--no-split-into-models flag to not split input into separate models
--no-use-slurm flag to not use Slurm
--options-for-calculating-contacts string custom options for calculating contacts
--output-atom-depth-values string output file with atom depth values
--output-atom-energies string output file with atom energy values
--output-atom-scores-pdb string output PDB file with atom scores as B-factors
--output-atom-scores string output text file with atom scores
--output-balls string output file with balls
--output-contacts-map-svg string output file with contact map image
--output-contacts string output file with contacts
--output-cutting-suggestions string output file with chain cutting suggestions
--output-directory-for-global-scores string output directory for global scores
--output-residue-scores-for-CAMEO string output file with output for CAMEO
--output-residue-scores-like-for-CASP string output file with output like for CASP
--output-residue-scores-pdb string output PDB file with residue scores as B-factors
--output-residue-scores-plot string output PNG image file with residue scores plot, requires R
--output-residue-scores string output text file with residue scores
--output-scores-for-CASP-log string output file with logs generated in CASP mode
--output-scores-for-CASP-pdb string output file with structure generated in CASP mode
--output-scores-for-CASP string output file with scores generated in CASP mode
--output-screenshot string output file with screenshot
--output-selected-scores string output text file with selected atom scores
--output-selected-scores-by-residue string output text file with selected scores summed by residue
--output-sequence-alignment string output text file with sequence alignment
--output-summary-for-potential string output file with statistics of contact
--print-clash-score-of-contacts-selection flag to print clash score of contacts selection
--print-energy-of-contacts-selection flag to print energy of contacts selection
--print-header flag to print output header
--print-horizontally flag to print output horizontally
--print-vertically flag to print output vertically
--probe-radius number probe radius for defining contacts
--processors number maximum number of processors to use
--rebuild-sidechains string command to rebuild side-chains
--reference-sequence string sequence file or string for residue renumbering
--reinterpret-SAS flag to interpret solvent as hydrophobic atoms
--sbatch-parameters string parameters for sbatch when using slurm
--score-inter-chain flag to output inter-chain interface scores
--screenshot-background string screenshot background color
--screenshot-height number screenshot image height
--screenshot-width number screenshot image width
--small-plot flag to generate smaller residue scores plot
--smoothing-window number residue scores smoothing window size, default is 5
--split-into-models string path to directory for storing extracted models
--strip-rotamers flag to remove sidechains
--surface-craving-atoms-energies-output string output text file with surface frustration results
--surface-craving-atoms-energies-pdb string output PDB file with surface frustration results
--surface-craving-atoms-output-pdb string output PDB file with atom scores as B-factors
--surface-craving-atoms-output string output text file with atom scores
--surface-craving-depth-value number depth for surface frustration calculation, default is 3
--surface-craving-residues-output-pdb string output PDB file with residue scores as B-factors
--surface-craving-residues-output string output text file with residue scores
--w-surface-craving-residues-output-pdb string output PDB file with residue scores as B-factors
--w-surface-craving-residues-output string output text file with residue scores
--tag-peripheral-contacts flag to tag peripheral contacts
--unteaching-dir string path to directory with potential-defining files
--use-slurm string path to directory to use for Slurm logs‘voronota-cadscore’ script is an implementation of CAD-score (Contact Area Difference score) method using Voronota. The script interface is presented below:
Basic options:
--input-target | -t string * input target structure file in PDB or mmCIF format
--input-model | -m string * input model structure file in PDB format
--input-filter-query string input atoms filtering query parameters
--filter-model-by-target flag to filter model residues by the set of target residue IDs
--output-residue-scores string output text file with residue scores
--output-residue-scores-pdb-t string output target PDB file with residue scores as B-factors
--output-residue-scores-pdb-m string output model PDB file with residue scores as B-factors
--smoothing-window number residue scores smoothing window size, default is 0
--contacts-query string contacts query parameters
--contacts-query-inter-chain flag to consider only inter-chain contacts
--contacts-query-by-code string contacts query code, possible codes are AA, AS, SS, AM, MM, MS
--use-all-query-codes flag to output global scores for all query codes, one line per code
--cache-dir string path to cache directory
--output-header flag to output header before result line
--help | -h flag to display help message and exit
Advanced options:
--ignore-residue-names flag to consider just residue numbers and ignore residue names
--enable-site-based-scoring flag to enable site-based scoring
--multiple-models flag to handle multiple models in PDB file as an assembly
--input-model-chains-renaming input text file with renaming rules for chains
--remap-chains flag to automatically rearrange chain names for higher scores
--remap-chains-output string output file with chain names rearrangement
--neighborhood-depth number number of layers to for per-residue scoring, default is 0
--old-regime flag to calculate areas as in pre-Voronota CAD-score
Standard output (one line):
{target file path} {model file path} {query code} {number of residues} {global score} {target total area} {corresponding model total area}
[ {site-based number of residues} {site-based global score} {site-based target total area} {corresponding site-based model total area} ]‘voronota-contacts’ script provides a way for calculating and querying interatomic contacts with just one command (without the need to construct a pipeline from ‘voronota’ calls).
Basic options:
--input | -i string * input structure file in PDB or mmCIF format
--input-filter-query string input atoms filtering query parameters
--contacts-query string contacts query parameters
--contacts-query-additional string additional, preceeding query parameters, default is '--match-min-seq-sep 1'
--cache-dir string path to cache directory
--sum-at-end flag to print sum of areas as the last line in output
--tsv-output flag to output table in tab-separated values format with header
--help | -h flag to display help message and exit
Advanced options:
--output-drawing string output file with drawing script for PyMol
--drawing-parameters string drawing parameters
--wireframe-drawing flag to draw wireframe representation of contacts
--multiple-models flag to handle multiple models in PDB file
--use-hbplus flag to run 'hbplus' to tag H-bonds
Standard output (multiple lines):
{contacting atom} {contacting atom} {contact area} {distance between atoms centers} {tags} {adjunct values}‘voronota-volumes’ script provides a way for calculating and querying atomic volumes with just one command (without the need to construct a pipeline from ‘voronota’ calls).
Basic options:
--input | -i string * input structure file in PDB or mmCIF format
--input-filter-query string input atoms filtering query parameters
--cache-dir string path to cache directory
--sum-at-end flag to print sum of areas as the last line in output
--help | -h flag to display help message and exit
Advanced options:
--atoms-query string atoms query parameters
--per-residue flag to output per-residue results
--multiple-models flag to handle multiple models in PDB file
Standard output (multiple lines):
{name} {volume}‘voronota-pocket’ script provides a way for identifying and describing pockets, cavities and channels using the Voronoi tessellation vertices.
Options:
--input | -i string * input structure file in PDB or mmCIF format
--input-filter-query string input atoms filtering query, default is '--match-tags-not het'
--probe-min number scanning probe radius minimum, default is 2.0
--probe-max number scanning probe radius maximum, default is 30.0
--buriedness-core number buriedness minimum for pocket start, default is 0.7
--buriedness-rim number buriedness maximum for pocket end, default is 0.4
--subpockets number number of sorted subpockets to include, default is 999999
--tangent-leeway number tangent sphere radius expansion for atom checks, default is 0.5
--tangent-radius-min number tanget sphere radius minimum, default is 1.4
--tetrahedron-edge-max number tetrahedron edge maximum, default is 999999
--voxelization-factor number voxelization factor, default is 1.0
--output-atoms string file to output analyzed atoms with annotations
--output-buriedness-pdb string file to output PDB file with buriedness in b-factors
--output-pocketness-pdb string file to output PDB file with pocketness in b-factors
--output-vertices string file to output Voronoi vertices of pocket
--output-voxels-pdb string file to output voxels as PDB file
--draw-tetrahedrons string file to output PyMol script for drawing pocket tetrahedrons
--draw-spheres string file to output PyMol script for drawing pocket spheres
--output-log string file to output detailed log on calculations
--output-header flag to output header before result line
--help | -h flag to display help message and exit
Standard output (one line):
{input file} {max buriedness} {all atoms} {all vertices} {pocket atoms} {pocket vertices} {volume of pocket tetrahedrons}
Suggested parameters
for pocket analysis:
--probe-min 2 --probe-max 30 --buriedness-core 0.7 --buriedness-rim 0.4
for large channel analysis:
--probe-min 5 --probe-max 30 --buriedness-core 0.8 --buriedness-rim 0.6
Other suggestions:
For large pockets or channels the spheres drawing option may
produce very large files (too large for PyMol).‘voronota-membrane’ script provides a way for fitting a membrane for a protein struture using VoroMQA-based surface frustration analysis.
Options:
--input | -i string * input structure file in PDB or mmCIF format
--input-filter-query string input atoms filtering query, default is ''
--membrane-width number membrane width, default is 30.0
--output-atoms string file to output analyzed atoms with annotations
--output-membraneness-pdb string file to output PDB file with membraneness in b-factors
--output-log string file to output detailed log on calculations
--output-header flag to output header before result line
--help | -h flag to display help message and exit
Standard output (one line):
{input file} {membrane fitting score} {direction x} {direction y} {direction z} {center projection}