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@ibt.lt).
Download the latest archive from the official downloads page: https://bitbucket.org/kliment/voronota/downloads.
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, Mac OS X or Windows operating systems.
Packages in .deb or .rpm formats are currently not available. However, installing Voronota in Linux or Mac OS X is easy: just copy Voronota executable files ('voronota' program and, if needed, the wrapper scripts) to one of the directories listed in $PATH variable.
Voronota has no required external dependencies, only a standard-compliant C++ compiler is needed to build it.
For example, "voronota" executable can be built from the sources in "src" directory using GNU C++ compiler:
g++ -O3 -o voronota src/*.cpp
You can generate and use a makefile:
./configure
make
It allows to install and uninstall Voronota executables:
make install
make uninstall
You can build using CMake for makefile generation. Starting in the directory containing "CMakeLists.txt" file, run the sequence of commands:
cmake ./
make
To enable the usage of OpenMP for parallel processing when building using C++ compiler directly, add "-fopenmp" option:
g++ -O3 -fopenmp -o voronota src/*.cpp
When generating a makefile with a "configure" script, OpenMP usage can be enabled by setting CXXFLAGS variable:
./configure CXXFLAGS="-O3 -fopenmp"
make
When using CMake, OpenMP usage is enabled automatically if it is possible.
To enable the usage of MPI for parallel processing, you can use mpic++ compiler wrapper. You also need to define "ENABLE_MPI" macro when buiding:
mpic++ -O3 -DENABLE_MPI -o voronota ./src/*.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 src/*.cpp
or
g++ -O3 -std=c++11 -DUSE_TR1=0 -o voronota src/*.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.txt
The 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 OG
In "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 0.595
Taking 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.txt
In "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 2.019
Here 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.txt
In "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.txt
Below 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 4.0
The "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 --help
Using "--help" option without specific command results in printing help for all commands:
./voronota --help
Name 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
--mmcif flag to input in mmCIF format
--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
file in PDB or mmCIF format
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'
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 exit
list 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 exit
list 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 exit
list 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'
--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
list 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
--no-same-chain flag to not include same chain contacts
--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
list 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-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
list 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 exit
list of contacts (line format: 'annotation1 annotation2 conditions area')
global scores
Name 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 exit
list of atom energy descriptors
weighted average local score
Name 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 exit
list 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 exit
list 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
--help flag to print usage help to stdout and exit
list 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 exit
list of balls (line format: 'annotation x y z r')
list of clashes (line format: 'annotation1 annotation2 distance min-distance-between-balls')
Name Type Description
------------------------------- ------ ---- ------------------------------------------------------------------------
--help flag to print usage help to stdout and exit
any text containing atom descriptors
text 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 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
--multiple-models flag to handle multiple models in PDB file
Standard output (one line):
{input file path} {global score} {number of residues} {number of atoms} [ {selection score} {number of selected atoms} ]
'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 format
--input-model | -m string * input model structure file in PDB format
--input-filter-query string input atoms filtering query parameters
--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 falg to enable site-based scoring
--multiple-models flag to handle multiple models in PDB file
--remap-chains flag to automatically rearrange chain names for higher scores
--remap-chains-output string output file with chain names rearrangement
--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 format
--input-filter-query string input atoms filtering query parameters
--contacts-query string contacts query parameters
--contacts-query-additional string additional contacts 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:
--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
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 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}