Package: drawtetrado
Project descriptionDrawTetrado is a Python application to visualize quadruplexes and
G4-helices in DNA and RNA structures. It generates publication-quality
SVG files containing layer diagrams. They show the tetrads as a stack,
with each position having four nucleobases colored according to anti or
syn conformation. In addition, DrawTetrado visualizes the strands with
arrows for an accessible overview of their directionality and visual
determination of loop types.DrawTetrado automatically optimizes the layout. The result is a visually
pleasing and readable image, even for the most complex cases like
V-loops and G4-helices (dimers).Installationpip install drawtetradoDependenciesThe project is written in Python 3.6+ and requirespycairo,svgwrite, andorjsonandElTetrado(Zoket al., 2022;
Popendaet al., 2020; Zoket al., 2020). The internal
optimization routine is written in C++ and requiresCythonand a C++20-compliant compiler (e.g. GCC
8+).DrawTetrado parses the output ofElTetrado. It can also process PDB or
PDBx/mmCIF files which will be first analyzed internally with ElTetrado.Usageusage: drawtetrado [-h] [-i INPUT] [-o OUTPUT_TEMPLATE] [--config CONFIG]
                   [-m MODEL] [--stacking-mismatch STACKING_MISMATCH] [--strict]
                   [--no-reorder]

options:
  -h, --help            show this help message and exit
  -i INPUT, --input INPUT
                        path to input PDB, PDBx/mmCIF file or JSON generated by
                        ElTetrado. If PDB or PDBx/mmCIF file is provided, it will
                        be first analyzed using ElTetrado.
  -o OUTPUT_TEMPLATE, --output-template OUTPUT_TEMPLATE
                        (optional) path to output SVG file template
                        [default=input file path and basename]
  --config CONFIG       (optional) JSON config file containing all parameter
                        changes and individual nucleotide coloring overrides
  -m MODEL, --model MODEL
                        (optional, ElTetrado) model number to process
  --stacking-mismatch STACKING_MISMATCH
                        (optional, ElTetrado) a perfect tetrad stacking covers 4
                        nucleotides; this option can be used with values 1 or 2 to
                        allow this number of nucleotides to be non-stacked with
                        otherwise well aligned tetrad [default=2]
  --strict              (optional, ElTetrado) nucleotides in tetrad are found
                        when linked only by cWH pairing
  --no-reorder          (optional, ElTetrado) chains of bi- and tetramolecular
                        quadruplexes should be reordered to be able to have them
                        classified; when this is set, chains will be processed in
                        the original order, which for bi-/tetramolecular means that
                        they will likely be misclassified; use with care!

The output path is a template. The program will generate drawings for each individual
quadruplex in each helix as well as each full helix. If we have a file with 2
helices with 2 quadruplexes each, if no output_template value is provided, path
and basename of the input file will be used. If it is provided,
output_template=/tmp/out, the resulting files will be /tmp/out_0.svg, with full
helix 0, /tmp/out_0_0.svg and /tmp/out_0_1.svg for each quadruplex in helix 0.
Similar files will be created for helix 1 with /tmp/out_1.svg and
/tmp/out_1_0.svg, /tmp/out_1_1.svg.Visual customizationDrawTetrado allows for a wide variety of changes to the visual representation of
the resulting drawing.All modifications to visual aspects of the drawing can be done using JSON
formatted config file. Example config.json is available in the repository with
all possible parameters and their default values.{"_comment0":"Example config.json with all available parameters default values.","_comment1":"All parameters explained in README","scale":1.0,"nucl-longer":100.0,"nucl-shorter":70.0,"nucl-spacing":10.0,"angle":50.0,"tetrad-spacing":50.0,"line-stroke":3.0,"point-size":6.0,"point-stroke":2.0,"se-label-spacing":20.0,"se-label-font-size":24.0,"font-family":"Arial, Helvetica","label-font-size":20.0,"tilted_labels":true,"label-chain":true,"label-nucl-name":true,"label-nucl-fullname":true,"label-number":true,"_comment2":"Colors in RGBA hex. If only RGB is provided, alpha of 1.0 is used","_comment3":"for anything other than ONZ colors. Those default to 0.85.","colors":{"connection":"#000000FF","border":"#E23D28FF","text":"#000000FF","point":"#FFFFFFFF","anti":"#FFFFFFFF","syn":"#000000FF","n/a":"#606060FF","onz_default":"#646464D9","o_plus":"#1F78B4D9","o_minus":"#A6CEE3D9","n_plus":"#33A02CD9","n_minus":"#B2DF8AD9","z_plus":"#FF7F00D9","z_minus":"#FDBF6FD9"},"_comment3":"dictionary of nucleotide full name to desired color in RGBA hex.","_comment4":"If only RGB is provided, alpha of 0.85 (aka. D9) is used.","_comment_example":"'A.DG12': '#E23D28AA'","nucl-color-override":{}}Nucleotide labels are made from 3 parts:A.DG12
  A  - Chain of the nucleotide. If label-chain is set to false, this information (and .)
       is not included in the creation of the labels.
  DG - Full name of the nucleotide. Setting label-nucl-fullname to false will result
       in normal short names like A, C, T, G. label-nucl-name to false will remove
       nucleotide name part altogether.
  12 - Index of the nucleotide. Can be removed with label-number set to false.Examples of how A.DG12 label would look like with different label options:A.DG12 - Default - All label parameters as true.
A.G12  - "label-nucl-fullname": false
A.12   - "label-nucl-name": false
DG12   - "label-chain": false
A.DG   - "label-number": false
A      - "label-number": false, "label-nucleotide": falseExamplesHuman telomere DNA quadruplexClick to see the input JSON{"metals":[],"nucleotides":[{"index":1,"model":1,"chain":"A","number":1,"icode":" ","molecule":"DNA","fullName":"A.DA1","shortName":"A","chi":22.308,"glycosidicBond":"syn"},{"index":2,"model":1,"chain":"A","number":2,"icode":" ","molecule":"DNA","fullName":"A.DA2","shortName":"A","chi":-123.055,"glycosidicBond":"anti"},{"index":3,"model":1,"chain":"A","number":3,"icode":" ","molecule":"DNA","fullName":"A.DA3","shortName":"A","chi":-94.966,"glycosidicBond":"anti"},{"index":4,"model":1,"chain":"A","number":4,"icode":" ","molecule":"DNA","fullName":"A.DG4","shortName":"G","chi":79.284,"glycosidicBond":"syn"},{"index":5,"model":1,"chain":"A","number":5,"icode":" ","molecule":"DNA","fullName":"A.DG5","shortName":"G","chi":-126.017,"glycosidicBond":"anti"},{"index":6,"model":1,"chain":"A","number":6,"icode":" ","molecule":"DNA","fullName":"A.DG6","shortName":"G","chi":-127.267,"glycosidicBond":"anti"},{"index":7,"model":1,"chain":"A","number":7,"icode":" ","molecule":"DNA","fullName":"A.DT7","shortName":"T","chi":-63.108,"glycosidicBond":"syn"},{"index":8,"model":1,"chain":"A","number":8,"icode":" ","molecule":"DNA","fullName":"A.DT8","shortName":"T","chi":-138.795,"glycosidicBond":"anti"},{"index":9,"model":1,"chain":"A","number":9,"icode":" ","molecule":"DNA","fullName":"A.DA9","shortName":"A","chi":-148.84,"glycosidicBond":"anti"},{"index":10,"model":1,"chain":"A","number":10,"icode":" ","molecule":"DNA","fullName":"A.DG10","shortName":"G","chi":58.779,"glycosidicBond":"syn"},{"index":11,"model":1,"chain":"A","number":11,"icode":" ","molecule":"DNA","fullName":"A.DG11","shortName":"G","chi":-123.857,"glycosidicBond":"anti"},{"index":12,"model":1,"chain":"A","number":12,"icode":" ","molecule":"DNA","fullName":"A.DG12","shortName":"G","chi":-84.367,"glycosidicBond":"syn"},{"index":13,"model":1,"chain":"A","number":13,"icode":" ","molecule":"DNA","fullName":"A.DT13","shortName":"T","chi":-30.819,"glycosidicBond":"syn"},{"index":14,"model":1,"chain":"A","number":14,"icode":" ","molecule":"DNA","fullName":"A.DT14","shortName":"T","chi":-168.518,"glycosidicBond":"anti"},{"index":15,"model":1,"chain":"A","number":15,"icode":" ","molecule":"DNA","fullName":"A.DA15","shortName":"A","chi":-105.729,"glycosidicBond":"anti"},{"index":16,"model":1,"chain":"A","number":16,"icode":" ","molecule":"DNA","fullName":"A.DG16","shortName":"G","chi":74.323,"glycosidicBond":"syn"},{"index":17,"model":1,"chain":"A","number":17,"icode":" ","molecule":"DNA","fullName":"A.DG17","shortName":"G","chi":81.084,"glycosidicBond":"syn"},{"index":18,"model":1,"chain":"A","number":18,"icode":" ","molecule":"DNA","fullName":"A.DG18","shortName":"G","chi":-122.904,"glycosidicBond":"anti"},{"index":19,"model":1,"chain":"A","number":19,"icode":" ","molecule":"DNA","fullName":"A.DT19","shortName":"T","chi":-102.982,"glycosidicBond":"anti"},{"index":20,"model":1,"chain":"A","number":20,"icode":" ","molecule":"DNA","fullName":"A.DT20","shortName":"T","chi":-112.151,"glycosidicBond":"anti"},{"index":21,"model":1,"chain":"A","number":21,"icode":" ","molecule":"DNA","fullName":"A.DA21","shortName":"A","chi":-89.071,"glycosidicBond":"syn"},{"index":22,"model":1,"chain":"A","number":22,"icode":" ","molecule":"DNA","fullName":"A.DG22","shortName":"G","chi":83.443,"glycosidicBond":"syn"},{"index":23,"model":1,"chain":"A","number":23,"icode":" ","molecule":"DNA","fullName":"A.DG23","shortName":"G","chi":-115.412,"glycosidicBond":"anti"},{"index":24,"model":1,"chain":"A","number":24,"icode":" ","molecule":"DNA","fullName":"A.DG24","shortName":"G","chi":-111.148,"glycosidicBond":"anti"},{"index":25,"model":1,"chain":"A","number":25,"icode":" ","molecule":"DNA","fullName":"A.DA25","shortName":"A","chi":-58.324,"glycosidicBond":"syn"},{"index":26,"model":1,"chain":"A","number":26,"icode":" ","molecule":"DNA","fullName":"A.DA26","shortName":"A","chi":-90.841,"glycosidicBond":"anti"}],"basePairs":[{"nt1":"A.DA2","nt2":"A.DT20","stericity":"cis","edge5":"Hoogsteen","edge3":"Watson-Crick"},{"nt1":"A.DT20","nt2":"A.DA2","stericity":"cis","edge5":"Watson-Crick","edge3":"Hoogsteen"},{"nt1":"A.DA3","nt2":"A.DA21","stericity":"cis","edge5":"Hoogsteen","edge3":"Watson-Crick"},{"nt1":"A.DA21","nt2":"A.DA3","stericity":"cis","edge5":"Watson-Crick","edge3":"Hoogsteen"},{"nt1":"A.DG4","nt2":"A.DT7","stericity":"cis","edge5":"Hoogsteen","edge3":"Watson-Crick"},{"nt1":"A.DT7","nt2":"A.DG4","stericity":"cis","edge5":"Watson-Crick","edge3":"Hoogsteen"},{"nt1":"A.DG4","nt2":"A.DG10","stericity":"cis","edge5":"Hoogsteen","edge3":"Watson-Crick"},{"nt1":"A.DG10","nt2":"A.DG4","stericity":"cis","edge5":"Watson-Crick","edge3":"Hoogsteen"},{"nt1":"A.DG4","nt2":"A.DG22","stericity":"cis","edge5":"Watson-Crick","edge3":"Hoogsteen"},{"nt1":"A.DG22","nt2":"A.DG4","stericity":"cis","edge5":"Hoogsteen","edge3":"Watson-Crick"},{"nt1":"A.DG5","nt2":"A.DG11","stericity":"cis","edge5":"Watson-Crick","edge3":"Hoogsteen"},{"nt1":"A.DG11","nt2":"A.DG5","stericity":"cis","edge5":"Hoogsteen","edge3":"Watson-Crick"},{"nt1":"A.DG5","nt2":"A.DG23","stericity":"cis","edge5":"Hoogsteen","edge3":"Watson-Crick"},{"nt1":"A.DG23","nt2":"A.DG5","stericity":"cis","edge5":"Watson-Crick","edge3":"Hoogsteen"},{"nt1":"A.DG6","nt2":"A.DG12","stericity":"cis","edge5":"Watson-Crick","edge3":"Hoogsteen"},{"nt1":"A.DG12","nt2":"A.DG6","stericity":"cis","edge5":"Hoogsteen","edge3":"Watson-Crick"},{"nt1":"A.DG6","nt2":"A.DG24","stericity":"cis","edge5":"Hoogsteen","edge3":"Watson-Crick"},{"nt1":"A.DG24","nt2":"A.DG6","stericity":"cis","edge5":"Watson-Crick","edge3":"Hoogsteen"},{"nt1":"A.DT7","nt2":"A.DG10","stericity":"cis","edge5":"Hoogsteen","edge3":"Sugar"},{"nt1":"A.DG10","nt2":"A.DT7","stericity":"cis","edge5":"Sugar","edge3":"Hoogsteen"},{"nt1":"A.DG10","nt2":"A.DG18","stericity":"cis","edge5":"Hoogsteen","edge3":"Watson-Crick"},{"nt1":"A.DG18","nt2":"A.DG10","stericity":"cis","edge5":"Watson-Crick","edge3":"Hoogsteen"},{"nt1":"A.DG11","nt2":"A.DG17","stericity":"cis","edge5":"Watson-Crick","edge3":"Hoogsteen"},{"nt1":"A.DG17","nt2":"A.DG11","stericity":"cis","edge5":"Hoogsteen","edge3":"Watson-Crick"},{"nt1":"A.DG12","nt2":"A.DG16","stericity":"cis","edge5":"Watson-Crick","edge3":"Hoogsteen"},{"nt1":"A.DG16","nt2":"A.DG12","stericity":"cis","edge5":"Hoogsteen","edge3":"Watson-Crick"},{"nt1":"A.DT14","nt2":"A.DA25","stericity":"trans","edge5":"Watson-Crick","edge3":"Watson-Crick"},{"nt1":"A.DA25","nt2":"A.DT14","stericity":"trans","edge5":"Watson-Crick","edge3":"Watson-Crick"},{"nt1":"A.DA15","nt2":"A.DA25","stericity":"trans","edge5":"Sugar","edge3":"Watson-Crick"},{"nt1":"A.DA25","nt2":"A.DA15","stericity":"trans","edge5":"Watson-Crick","edge3":"Sugar"},{"nt1":"A.DG16","nt2":"A.DG24","stericity":"cis","edge5":"Watson-Crick","edge3":"Hoogsteen"},{"nt1":"A.DG24","nt2":"A.DG16","stericity":"cis","edge5":"Hoogsteen","edge3":"Watson-Crick"},{"nt1":"A.DG17","nt2":"A.DG23","stericity":"cis","edge5":"Watson-Crick","edge3":"Hoogsteen"},{"nt1":"A.DG23","nt2":"A.DG17","stericity":"cis","edge5":"Hoogsteen","edge3":"Watson-Crick"},{"nt1":"A.DG18","nt2":"A.DG22","stericity":"cis","edge5":"Hoogsteen","edge3":"Watson-Crick"},{"nt1":"A.DG22","nt2":"A.DG18","stericity":"cis","edge5":"Watson-Crick","edge3":"Hoogsteen"}],"helices":[{"quadruplexes":[{"tetrads":[{"id":"A.DG6-A.DG12-A.DG16-A.DG24","nt1":"A.DG6","nt2":"A.DG12","nt3":"A.DG16","nt4":"A.DG24","onz":"O+","gbaClassification":"VIa","planarityDeviation":0.1829350977806063,"ionsChannel":[],"ionsOutside":[]},{"id":"A.DG5-A.DG11-A.DG17-A.DG23","nt1":"A.DG5","nt2":"A.DG11","nt3":"A.DG17","nt4":"A.DG23","onz":"O+","gbaClassification":"Va","planarityDeviation":0.10474313820007491,"ionsChannel":[],"ionsOutside":[]},{"id":"A.DG4-A.DG22-A.DG18-A.DG10","nt1":"A.DG4","nt2":"A.DG22","nt3":"A.DG18","nt4":"A.DG10","onz":"O-","gbaClassification":"Vb","planarityDeviation":0.17372283960377813,"ionsChannel":[],"ionsOutside":[]}],"onzm":"Oh*","loopClassification":"9a","gbaClassification":["V","VI"],"tracts":[["A.DG16","A.DG17","A.DG18"],["A.DG24","A.DG23","A.DG22"],["A.DG6","A.DG5","A.DG4"],["A.DG12","A.DG11","A.DG10"]],"loops":[{"type":"propeller-","nucleotides":["A.DT7","A.DT8","A.DA9"]},{"type":"lateral-","nucleotides":["A.DT13","A.DT14","A.DA15"]},{"type":"lateral+","nucleotides":["A.DT19","A.DT20","A.DA21"]}]}],"tetradPairs":[{"tetrad1":"A.DG6-A.DG12-A.DG16-A.DG24","tetrad2":"A.DG5-A.DG11-A.DG17-A.DG23","direction":"hybrid","rise":3.1149939255558747,"twist":27.111587838260725},{"tetrad1":"A.DG5-A.DG11-A.DG17-A.DG23","tetrad2":"A.DG4-A.DG22-A.DG18-A.DG10","direction":"hybrid","rise":3.2109650905140654,"twist":20.409525129779524}]}]}V-loopClick to see the input JSON{"metals":[],"nucleotides":[{"index":1,"model":1,"chain":"A","number":1,"icode":" ","molecule":"DNA","fullName":"A.DG1","shortName":"G","chi":54.111,"glycosidicBond":"syn"},{"index":2,"model":1,"chain":"A","number":2,"icode":" ","molecule":"DNA","fullName":"A.DG2","shortName":"G","chi":83.093,"glycosidicBond":"syn"},{"index":3,"model":1,"chain":"A","number":3,"icode":" ","molecule":"DNA","fullName":"A.DG3","shortName":"G","chi":-120.17,"glycosidicBond":"anti"},{"index":4,"model":1,"chain":"A","number":4,"icode":" ","molecule":"DNA","fullName":"A.DA4","shortName":"A","chi":-111.874,"glycosidicBond":"anti"},{"index":5,"model":1,"chain":"A","number":5,"icode":" ","molecule":"DNA","fullName":"A.DT5","shortName":"T","chi":-153.281,"glycosidicBond":"anti"},{"index":6,"model":1,"chain":"A","number":6,"icode":" ","molecule":"DNA","fullName":"A.DG6","shortName":"G","chi":-106.483,"glycosidicBond":"anti"},{"index":7,"model":1,"chain":"A","number":7,"icode":" ","molecule":"DNA","fullName":"A.DG7","shortName":"G","chi":-122.668,"glycosidicBond":"anti"},{"index":8,"model":1,"chain":"A","number":8,"icode":" ","molecule":"DNA","fullName":"A.DG8","shortName":"G","chi":-125.241,"glycosidicBond":"anti"},{"index":9,"model":1,"chain":"A","number":9,"icode":" ","molecule":"DNA","fullName":"A.DA9","shortName":"A","chi":-90.027,"glycosidicBond":"anti"},{"index":10,"model":1,"chain":"A","number":10,"icode":" ","molecule":"DNA","fullName":"A.DC10","shortName":"C","chi":-144.141,"glycosidicBond":"anti"},{"index":11,"model":1,"chain":"A","number":11,"icode":" ","molecule":"DNA","fullName":"A.DA11","shortName":"A","chi":-139.299,"glycosidicBond":"anti"},{"index":12,"model":1,"chain":"A","number":12,"icode":" ","molecule":"DNA","fullName":"A.DC12","shortName":"C","chi":-89.925,"glycosidicBond":"syn"},{"index":13,"model":1,"chain":"A","number":13,"icode":" ","molecule":"DNA","fullName":"A.DA13","shortName":"A","chi":-116.926,"glycosidicBond":"anti"},{"index":14,"model":1,"chain":"A","number":14,"icode":" ","molecule":"Other","fullName":"A.GF2/14","shortName":"g","chi":75.041,"glycosidicBond":"syn"},{"index":15,"model":1,"chain":"A","number":15,"icode":" ","molecule":"Other","fullName":"A.GFL15","shortName":"g","chi":-167.524,"glycosidicBond":"anti"},{"index":16,"model":1,"chain":"A","number":16,"icode":" ","molecule":"DNA","fullName":"A.DG16","shortName":"G","chi":-100.43,"glycosidicBond":"anti"},{"index":17,"model":1,"chain":"A","number":17,"icode":" ","molecule":"DNA","fullName":"A.DG17","shortName":"G","chi":-140.143,"glycosidicBond":"anti"},{"index":18,"model":1,"chain":"A","number":18,"icode":" ","molecule":"DNA","fullName":"A.DA18","shortName":"A","chi":-100.903,"glycosidicBond":"anti"},{"index":19,"model":1,"chain":"A","number":19,"icode":" ","molecule":"DNA","fullName":"A.DC19","shortName":"C","chi":-131.147,"glycosidicBond":"anti"},{"index":20,"model":1,"chain":"A","number":20,"icode":" ","molecule":"DNA","fullName":"A.DG20","shortName":"G","chi":-169.165,"glycosidicBond":"anti"},{"index":21,"model":1,"chain":"A","number":21,"icode":" ","molecule":"DNA","fullName":"A.DG21","shortName":"G","chi":-105.18,"glycosidicBond":"anti"},{"index":22,"model":1,"chain":"A","number":22,"icode":" ","molecule":"DNA","fullName":"A.DG22","shortName":"G","chi":-106.1,"glycosidicBond":"anti"}],"basePairs":[{"nt1":"A.DG1","nt2":"A.DG7","stericity":"cis","edge5":"Hoogsteen","edge3":"Watson-Crick"},{"nt1":"A.DG7","nt2":"A.DG1","stericity":"cis","edge5":"Watson-Crick","edge3":"Hoogsteen"},{"nt1":"A.DG1","nt2":"A.DG16","stericity":"cis","edge5":"Watson-Crick","edge3":"Hoogsteen"},{"nt1":"A.DG16","nt2":"A.DG1","stericity":"cis","edge5":"Hoogsteen","edge3":"Watson-Crick"},{"nt1":"A.DG2","nt2":"A.DG6","stericity":"cis","edge5":"Hoogsteen","edge3":"Watson-Crick"},{"nt1":"A.DG6","nt2":"A.DG2","stericity":"cis","edge5":"Watson-Crick","edge3":"Hoogsteen"},{"nt1":"A.DG2","nt2":"A.GFL15","stericity":"cis","edge5":"Watson-Crick","edge3":"Hoogsteen"},{"nt1":"A.GFL15","nt2":"A.DG2","stericity":"cis","edge5":"Hoogsteen","edge3":"Watson-Crick"},{"nt1":"A.DG3","nt2":"A.DG6","stericity":"cis","edge5":"Sugar","edge3":"Watson-Crick"},{"nt1":"A.DG6","nt2":"A.DG3","stericity":"cis","edge5":"Watson-Crick","edge3":"Sugar"},{"nt1":"A.DG3","nt2":"A.DG20","stericity":"cis","edge5":"Watson-Crick","edge3":"Watson-Crick"},{"nt1":"A.DG20","nt2":"A.DG3","stericity":"cis","edge5":"Watson-Crick","edge3":"Watson-Crick"},{"nt1":"A.DG6","nt2":"A.DG20","stericity":"cis","edge5":"Hoogsteen","edge3":"Watson-Crick"},{"nt1":"A.DG20","nt2":"A.DG6","stericity":"cis","edge5":"Watson-Crick","edge3":"Hoogsteen"},{"nt1":"A.DG7","nt2":"A.DG21","stericity":"cis","edge5":"Hoogsteen","edge3":"Watson-Crick"},{"nt1":"A.DG21","nt2":"A.DG7","stericity":"cis","edge5":"Watson-Crick","edge3":"Hoogsteen"},{"nt1":"A.DG8","nt2":"A.GF2/14","stericity":"cis","edge5":"Watson-Crick","edge3":"Hoogsteen"},{"nt1":"A.GF2/14","nt2":"A.DG8","stericity":"cis","edge5":"Hoogsteen","edge3":"Watson-Crick"},{"nt1":"A.DG8","nt2":"A.DG22","stericity":"cis","edge5":"Hoogsteen","edge3":"Watson-Crick"},{"nt1":"A.DG22","nt2":"A.DG8","stericity":"cis","edge5":"Watson-Crick","edge3":"Hoogsteen"},{"nt1":"A.DC12","nt2":"A.DA13","stericity":"cis","edge5":"Sugar","edge3":"Hoogsteen"},{"nt1":"A.DA13","nt2":"A.DC12","stericity":"cis","edge5":"Hoogsteen","edge3":"Sugar"},{"nt1":"A.GF2/14","nt2":"A.DG17","stericity":"cis","edge5":"Watson-Crick","edge3":"Hoogsteen"},{"nt1":"A.DG17","nt2":"A.GF2/14","stericity":"cis","edge5":"Hoogsteen","edge3":"Watson-Crick"},{"nt1":"A.GFL15","nt2":"A.DG20","stericity":"cis","edge5":"Watson-Crick","edge3":"Hoogsteen"},{"nt1":"A.DG20","nt2":"A.GFL15","stericity":"cis","edge5":"Hoogsteen","edge3":"Watson-Crick"},{"nt1":"A.DG16","nt2":"A.DA18","stericity":"trans","edge5":"Sugar","edge3":"Hoogsteen"},{"nt1":"A.DA18","nt2":"A.DG16","stericity":"trans","edge5":"Hoogsteen","edge3":"Sugar"},{"nt1":"A.DG16","nt2":"A.DG21","stericity":"cis","edge5":"Watson-Crick","edge3":"Hoogsteen"},{"nt1":"A.DG21","nt2":"A.DG16","stericity":"cis","edge5":"Hoogsteen","edge3":"Watson-Crick"},{"nt1":"A.DG17","nt2":"A.DG22","stericity":"cis","edge5":"Watson-Crick","edge3":"Hoogsteen"},{"nt1":"A.DG22","nt2":"A.DG17","stericity":"cis","edge5":"Hoogsteen","edge3":"Watson-Crick"}],"helices":[{"quadruplexes":[{"tetrads":[{"id":"A.DG2-A.GFL15-A.DG20-A.DG6","nt1":"A.DG2","nt2":"A.GFL15","nt3":"A.DG20","nt4":"A.DG6","onz":"N-","gbaClassification":"VIIb","planarityDeviation":0.2180730955436729,"ionsChannel":[],"ionsOutside":[]},{"id":"A.DG1-A.DG16-A.DG21-A.DG7","nt1":"A.DG1","nt2":"A.DG16","nt3":"A.DG21","nt4":"A.DG7","onz":"N-","gbaClassification":"VIIb","planarityDeviation":0.23623267132215198,"ionsChannel":[],"ionsOutside":[]},{"id":"A.DG8-A.GF2/14-A.DG17-A.DG22","nt1":"A.DG8","nt2":"A.GF2/14","nt3":"A.DG17","nt4":"A.DG22","onz":"O+","gbaClassification":"IIIa","planarityDeviation":0.12292426530184954,"ionsChannel":[],"ionsOutside":[]}],"onzm":"Mh*","loopClassification":"7b","gbaClassification":["III","VII"],"tracts":[["A.DG20","A.DG21","A.DG22"],["A.DG6","A.DG7","A.DG8"],["A.DG2","A.DG1","A.GF2/14"],["A.GFL15","A.DG16","A.DG17"]],"loops":[{"type":"lateral+","nucleotides":["A.DG3","A.DA4","A.DT5"]},{"type":"lateral-","nucleotides":["A.DA9","A.DC10","A.DA11","A.DC12","A.DA13"]},{"type":"propeller-","nucleotides":["A.DA18","A.DC19"]}]}],"tetradPairs":[{"tetrad1":"A.DG2-A.GFL15-A.DG20-A.DG6","tetrad2":"A.DG1-A.DG16-A.DG21-A.DG7","direction":"hybrid","rise":3.4053905200064882,"twist":32.09137702765124},{"tetrad1":"A.DG1-A.DG16-A.DG21-A.DG7","tetrad2":"A.DG8-A.GF2/14-A.DG17-A.DG22","direction":"parallel","rise":3.4862467282164604,"twist":29.215089333872314}]}]}G4-helix (dimer)Click to see the input JSON{"metals":[],"nucleotides":[{"index":1,"model":1,"chain":"A","number":1,"icode":" ","molecule":"DNA","fullName":"A.DG1","shortName":"G","chi":-109.42,"glycosidicBond":"anti"},{"index":2,"model":1,"chain":"A","number":2,"icode":" ","molecule":"DNA","fullName":"A.DG2","shortName":"G","chi":-128.871,"glycosidicBond":"anti"},{"index":3,"model":1,"chain":"A","number":3,"icode":" ","molecule":"DNA","fullName":"A.DA3","shortName":"A","chi":-56.59,"glycosidicBond":"syn"},{"index":4,"model":1,"chain":"A","number":4,"icode":" ","molecule":"DNA","fullName":"A.DG4","shortName":"G","chi":-171.001,"glycosidicBond":"anti"},{"index":5,"model":1,"chain":"A","number":5,"icode":" ","molecule":"DNA","fullName":"A.DG5","shortName":"G","chi":-127.906,"glycosidicBond":"anti"},{"index":6,"model":1,"chain":"A","number":6,"icode":" ","molecule":"DNA","fullName":"A.DA6","shortName":"A","chi":-87.061,"glycosidicBond":"syn"},{"index":7,"model":1,"chain":"A","number":7,"icode":" ","molecule":"DNA","fullName":"A.DG7","shortName":"G","chi":-159.577,"glycosidicBond":"anti"},{"index":8,"model":1,"chain":"A","number":8,"icode":" ","molecule":"DNA","fullName":"A.DG8","shortName":"G","chi":-135.751,"glycosidicBond":"anti"},{"index":9,"model":1,"chain":"A","number":9,"icode":" ","molecule":"DNA","fullName":"A.DA9","shortName":"A","chi":-50.982,"glycosidicBond":"syn"},{"index":10,"model":1,"chain":"A","number":10,"icode":" ","molecule":"DNA","fullName":"A.DG10","shortName":"G","chi":-135.29,"glycosidicBond":"anti"},{"index":11,"model":1,"chain":"A","number":11,"icode":" ","molecule":"DNA","fullName":"A.DG11","shortName":"G","chi":-113.575,"glycosidicBond":"anti"},{"index":12,"model":1,"chain":"A","number":12,"icode":" ","molecule":"DNA","fullName":"A.DA12","shortName":"A","chi":-110.595,"glycosidicBond":"anti"},{"index":13,"model":1,"chain":"B","number":13,"icode":" ","molecule":"DNA","fullName":"B.DG13","shortName":"G","chi":-112.685,"glycosidicBond":"anti"},{"index":14,"model":1,"chain":"B","number":14,"icode":" ","molecule":"DNA","fullName":"B.DG14","shortName":"G","chi":-136.989,"glycosidicBond":"anti"},{"index":15,"model":1,"chain":"B","number":15,"icode":" ","molecule":"DNA","fullName":"B.DA15","shortName":"A","chi":-57.076,"glycosidicBond":"syn"},{"index":16,"model":1,"chain":"B","number":16,"icode":" ","molecule":"DNA","fullName":"B.DG16","shortName":"G","chi":-169.156,"glycosidicBond":"anti"},{"index":17,"model":1,"chain":"B","number":17,"icode":" ","molecule":"DNA","fullName":"B.DG17","shortName":"G","chi":-124.27,"glycosidicBond":"anti"},{"index":18,"model":1,"chain":"B","number":18,"icode":" ","molecule":"DNA","fullName":"B.DA18","shortName":"A","chi":-84.463,"glycosidicBond":"syn"},{"index":19,"model":1,"chain":"B","number":19,"icode":" ","molecule":"DNA","fullName":"B.DG19","shortName":"G","chi":-164.508,"glycosidicBond":"anti"},{"index":20,"model":1,"chain":"B","number":20,"icode":" ","molecule":"DNA","fullName":"B.DG20","shortName":"G","chi":-141.652,"glycosidicBond":"anti"},{"index":21,"model":1,"chain":"B","number":21,"icode":" ","molecule":"DNA","fullName":"B.DA21","shortName":"A","chi":-59.955,"glycosidicBond":"syn"},{"index":22,"model":1,"chain":"B","number":22,"icode":" ","molecule":"DNA","fullName":"B.DG22","shortName":"G","chi":-128.818,"glycosidicBond":"anti"},{"index":23,"model":1,"chain":"B","number":23,"icode":" ","molecule":"DNA","fullName":"B.DG23","shortName":"G","chi":-108.407,"glycosidicBond":"anti"},{"index":24,"model":1,"chain":"B","number":24,"icode":" ","molecule":"DNA","fullName":"B.DA24","shortName":"A","chi":-115.199,"glycosidicBond":"anti"}],"basePairs":[{"nt1":"A.DG1","nt2":"A.DA3","stericity":"trans","edge5":"Sugar","edge3":"Hoogsteen"},{"nt1":"A.DA3","nt2":"A.DG1","stericity":"trans","edge5":"Hoogsteen","edge3":"Sugar"},{"nt1":"A.DG1","nt2":"A.DG4","stericity":"cis","edge5":"Watson-Crick","edge3":"Hoogsteen"},{"nt1":"A.DG4","nt2":"A.DG1","stericity":"cis","edge5":"Hoogsteen","edge3":"Watson-Crick"},{"nt1":"A.DG1","nt2":"A.DG10","stericity":"cis","edge5":"Hoogsteen","edge3":"Watson-Crick"},{"nt1":"A.DG10","nt2":"A.DG1","stericity":"cis","edge5":"Watson-Crick","edge3":"Hoogsteen"},{"nt1":"A.DG2","nt2":"A.DG5","stericity":"cis","edge5":"Watson-Crick","edge3":"Hoogsteen"},{"nt1":"A.DG5","nt2":"A.DG2","stericity":"cis","edge5":"Hoogsteen","edge3":"Watson-Crick"},{"nt1":"A.DG2","nt2":"A.DG11","stericity":"cis","edge5":"Hoogsteen","edge3":"Watson-Crick"},{"nt1":"A.DG11","nt2":"A.DG2","stericity":"cis","edge5":"Watson-Crick","edge3":"Hoogsteen"},{"nt1":"A.DG2","nt2":"A.DA12","stericity":"cis","edge5":"Hoogsteen","edge3":"Watson-Crick"},{"nt1":"A.DA12","nt2":"A.DG2","stericity":"cis","edge5":"Watson-Crick","edge3":"Hoogsteen"},{"nt1":"A.DA3","nt2":"A.DG4","stericity":"cis","edge5":"Hoogsteen","edge3":"Hoogsteen"},{"nt1":"A.DG4","nt2":"A.DA3","stericity":"cis","edge5":"Hoogsteen","edge3":"Hoogsteen"},{"nt1":"A.DG4","nt2":"A.DA6","stericity":"cis","edge5":"Sugar","edge3":"Hoogsteen"},{"nt1":"A.DA6","nt2":"A.DG4","stericity":"cis","edge5":"Hoogsteen","edge3":"Sugar"},{"nt1":"A.DG4","nt2":"A.DG7","stericity":"cis","edge5":"Watson-Crick","edge3":"Hoogsteen"},{"nt1":"A.DG7","nt2":"A.DG4","stericity":"cis","edge5":"Hoogsteen","edge3":"Watson-Crick"},{"nt1":"A.DG4","nt2":"B.DG22","stericity":"cis","edge5":"Hoogsteen","edge3":"Hoogsteen"},{"nt1":"B.DG22","nt2":"A.DG4","stericity":"cis","edge5":"Hoogsteen","edge3":"Hoogsteen"},{"nt1":"A.DG5","nt2":"A.DG8","stericity":"cis","edge5":"Watson-Crick","edge3":"Hoogsteen"},{"nt1":"A.DG8","nt2":"A.DG5","stericity":"cis","edge5":"Hoogsteen","edge3":"Watson-Crick"},{"nt1":"A.DA6","nt2":"A.DG7","stericity":"cis","edge5":"Hoogsteen","edge3":"Hoogsteen"},{"nt1":"A.DG7","nt2":"A.DA6","stericity":"cis","edge5":"Hoogsteen","edge3":"Hoogsteen"},{"nt1":"A.DG7","nt2":"A.DA9","stericity":"trans","edge5":"Sugar","edge3":"Hoogsteen"},{"nt1":"A.DA9","nt2":"A.DG7","stericity":"trans","edge5":"Hoogsteen","edge3":"Sugar"},{"nt1":"A.DG7","nt2":"A.DG10","stericity":"cis","edge5":"Watson-Crick","edge3":"Hoogsteen"},{"nt1":"A.DG10","nt2":"A.DG7","stericity":"cis","edge5":"Hoogsteen","edge3":"Watson-Crick"},{"nt1":"A.DG8","nt2":"A.DG11","stericity":"cis","edge5":"Watson-Crick","edge3":"Hoogsteen"},{"nt1":"A.DG11","nt2":"A.DG8","stericity":"cis","edge5":"Hoogsteen","edge3":"Watson-Crick"},{"nt1":"A.DG8","nt2":"A.DA12","stericity":"cis","edge5":"Watson-Crick","edge3":"Hoogsteen"},{"nt1":"A.DA12","nt2":"A.DG8","stericity":"cis","edge5":"Hoogsteen","edge3":"Watson-Crick"},{"nt1":"A.DG10","nt2":"B.DG16","stericity":"cis","edge5":"Hoogsteen","edge3":"Hoogsteen"},{"nt1":"B.DG16","nt2":"A.DG10","stericity":"cis","edge5":"Hoogsteen","edge3":"Hoogsteen"},{"nt1":"A.DG10","nt2":"B.DG22","stericity":"cis","edge5":"Watson-Crick","edge3":"Watson-Crick"},{"nt1":"B.DG22","nt2":"A.DG10","stericity":"cis","edge5":"Watson-Crick","edge3":"Watson-Crick"},{"nt1":"B.DG13","nt2":"B.DA15","stericity":"trans","edge5":"Sugar","edge3":"Hoogsteen"},{"nt1":"B.DA15","nt2":"B.DG13","stericity":"trans","edge5":"Hoogsteen","edge3":"Sugar"},{"nt1":"B.DG13","nt2":"B.DG16","stericity":"cis","edge5":"Watson-Crick","edge3":"Hoogsteen"},{"nt1":"B.DG16","nt2":"B.DG13","stericity":"cis","edge5":"Hoogsteen","edge3":"Watson-Crick"},{"nt1":"B.DG13","nt2":"B.DG22","stericity":"cis","edge5":"Hoogsteen","edge3":"Watson-Crick"},{"nt1":"B.DG22","nt2":"B.DG13","stericity":"cis","edge5":"Watson-Crick","edge3":"Hoogsteen"},{"nt1":"B.DG14","nt2":"B.DG17","stericity":"cis","edge5":"Watson-Crick","edge3":"Hoogsteen"},{"nt1":"B.DG17","nt2":"B.DG14","stericity":"cis","edge5":"Hoogsteen","edge3":"Watson-Crick"},{"nt1":"B.DG14","nt2":"B.DG23","stericity":"cis","edge5":"Hoogsteen","edge3":"Watson-Crick"},{"nt1":"B.DG23","nt2":"B.DG14","stericity":"cis","edge5":"Watson-Crick","edge3":"Hoogsteen"},{"nt1":"B.DG14","nt2":"B.DA24","stericity":"cis","edge5":"Hoogsteen","edge3":"Watson-Crick"},{"nt1":"B.DA24","nt2":"B.DG14","stericity":"cis","edge5":"Watson-Crick","edge3":"Hoogsteen"},{"nt1":"B.DA15","nt2":"B.DG16","stericity":"cis","edge5":"Hoogsteen","edge3":"Hoogsteen"},{"nt1":"B.DG16","nt2":"B.DA15","stericity":"cis","edge5":"Hoogsteen","edge3":"Hoogsteen"},{"nt1":"B.DG16","nt2":"B.DA18","stericity":"cis","edge5":"Sugar","edge3":"Hoogsteen"},{"nt1":"B.DA18","nt2":"B.DG16","stericity":"cis","edge5":"Hoogsteen","edge3":"Sugar"},{"nt1":"B.DG16","nt2":"B.DG19","stericity":"cis","edge5":"Watson-Crick","edge3":"Hoogsteen"},{"nt1":"B.DG19","nt2":"B.DG16","stericity":"cis","edge5":"Hoogsteen","edge3":"Watson-Crick"},{"nt1":"B.DG17","nt2":"B.DG20","stericity":"cis","edge5":"Watson-Crick","edge3":"Hoogsteen"},{"nt1":"B.DG20","nt2":"B.DG17","stericity":"cis","edge5":"Hoogsteen","edge3":"Watson-Crick"},{"nt1":"B.DA18","nt2":"B.DG19","stericity":"cis","edge5":"Hoogsteen","edge3":"Hoogsteen"},{"nt1":"B.DG19","nt2":"B.DA18","stericity":"cis","edge5":"Hoogsteen","edge3":"Hoogsteen"},{"nt1":"B.DG19","nt2":"B.DA21","stericity":"trans","edge5":"Sugar","edge3":"Hoogsteen"},{"nt1":"B.DA21","nt2":"B.DG19","stericity":"trans","edge5":"Hoogsteen","edge3":"Sugar"},{"nt1":"B.DG19","nt2":"B.DG22","stericity":"cis","edge5":"Watson-Crick","edge3":"Hoogsteen"},{"nt1":"B.DG22","nt2":"B.DG19","stericity":"cis","edge5":"Hoogsteen","edge3":"Watson-Crick"},{"nt1":"B.DG20","nt2":"B.DG23","stericity":"cis","edge5":"Watson-Crick","edge3":"Hoogsteen"},{"nt1":"B.DG23","nt2":"B.DG20","stericity":"cis","edge5":"Hoogsteen","edge3":"Watson-Crick"}],"helices":[{"quadruplexes":[{"tetrads":[{"id":"B.DG14-B.DG17-B.DG20-B.DG23","nt1":"B.DG14","nt2":"B.DG17","nt3":"B.DG20","nt4":"B.DG23","onz":"O+","gbaClassification":"VIIIa","planarityDeviation":0.16023147318800904,"ionsChannel":[],"ionsOutside":[]},{"id":"B.DG13-B.DG16-B.DG19-B.DG22","nt1":"B.DG13","nt2":"B.DG16","nt3":"B.DG19","nt4":"B.DG22","onz":"O+","gbaClassification":"VIIIa","planarityDeviation":0.45582726991701444,"ionsChannel":[],"ionsOutside":[]}],"onzm":"Op+","loopClassification":"1a","gbaClassification":["VIII"],"tracts":[["B.DG23","B.DG22"],["B.DG14","B.DG13"],["B.DG17","B.DG16"],["B.DG20","B.DG19"]],"loops":[{"type":"propeller-","nucleotides":["B.DA15"]},{"type":"propeller-","nucleotides":["B.DA18"]},{"type":"propeller-","nucleotides":["B.DA21"]}]},{"tetrads":[{"id":"A.DG1-A.DG4-A.DG7-A.DG10","nt1":"A.DG1","nt2":"A.DG4","nt3":"A.DG7","nt4":"A.DG10","onz":"O+","gbaClassification":"VIIIa","planarityDeviation":0.5675509888987945,"ionsChannel":[],"ionsOutside":[]},{"id":"A.DG2-A.DG5-A.DG8-A.DA12","nt1":"A.DG2","nt2":"A.DG5","nt3":"A.DG8","nt4":"A.DA12","onz":"O+","gbaClassification":"VIIIa","planarityDeviation":0.7820234571290057,"ionsChannel":[],"ionsOutside":[]}],"onzm":"Op+","loopClassification":"1a","gbaClassification":["VIII"],"tracts":[["A.DG7","A.DG8"],["A.DG10","A.DA12"],["A.DG1","A.DG2"],["A.DG4","A.DG5"]],"loops":[{"type":"propeller-","nucleotides":["A.DA3"]},{"type":"propeller-","nucleotides":["A.DA6"]},{"type":"propeller-","nucleotides":["A.DA9"]}]}],"tetradPairs":[{"tetrad1":"B.DG14-B.DG17-B.DG20-B.DG23","tetrad2":"B.DG13-B.DG16-B.DG19-B.DG22","direction":"parallel","rise":3.4598098620083153,"twist":26.65295578601502},{"tetrad1":"B.DG13-B.DG16-B.DG19-B.DG22","tetrad2":"A.DG1-A.DG4-A.DG7-A.DG10","direction":"parallel","rise":3.1498276292124316,"twist":7.769329062763674},{"tetrad1":"A.DG1-A.DG4-A.DG7-A.DG10","tetrad2":"A.DG2-A.DG5-A.DG8-A.DA12","direction":"parallel","rise":4.363977409213413,"twist":53.69239641441069}]}]}BibliographyONQUADRO: a database of experimentally determined quadruplex
structures. T. Zok, N. Kraszewska, J. Miskiewicz, P. Pielacinska, M.
Zurkowski, M. Szachniuk.Nucleic Acids Research. 2022.
50(D1):D253–D258.
doi:10.1093/nar/gkab1118Topology-based classification of tetrads and quadruplex
structures. M. Popenda, J. Miskiewicz, J. Sarzynska, T. Zok, M.
Szachniuk.Bioinformatics. 2020. 36(4):1129–1134.
doi:10.1093/bioinformatics/btz738ElTetrado: a tool for identification and classification of tetrads
and quadruplexes. T. Zok, M. Popenda, M. Szachniuk.BMC
Bioinformatics. 2020. 21(1):40.
doi:10.1186/s12859-020-3385-1