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eltetrado's Introduction

Project description

This is an application to analyze base pairing patterns of DNA/RNA 3D structures to find and classify tetrads and quadruplexes. ElTetrado assigns tetrads to one of the ONZ classes (O, N, Z) alongside with the directionality of the tetrad (+/-) determined by the bonds between bases and their non-canonical interactions. The interactions follow Leontis/Westhof classification (Leontis and Westhof, 2001). Watson-Crick (W) edge of first base in the tetrad structure exposed to the Hoogsteen (H) edge of the next nucleobase from the same tetrad sets the tetrad directionality, clockwise (+) or anticlockwise (-). For more details, please refer to Zok et al. (2020) and Popenda et al. (2020)

Installation

Please run:

pip install eltetrado

If you have both Python 2 and Python 3 installed, you need to explicitly call pip3:

pip3 install eltetrado

Dependencies

The project is written in Python 3.6+ and requires Biopython and NumPy in to run.

ElTetrado depends on DSSR (Lu et al., 2015) in terms of detection of base pairing and stacking. The binary x3dna-dssr can be downloaded and it needs to be put in $PATH i.e. typically in /usr/bin. Alternatively, one can pre-process the 3D data with x3dna-dssr --json and provide the path to a JSON result as an input to ElTetrado (see Usage section below).

Visualization is created by R 3.6+ script which uses R4RNA (Lai et al., 2012) library. The dependency will be automatically installed if not present.

Usage

ElTetrado is a command line application, which requires to be provided with:

  • either --dssr-json and the path to JSON generated with x3dna-dssr --json (fast, but quadruplex parameters like rise or twist are not calculated)
  • or --pdb and the path to PDB or PDBx/mmCIF file (slow, because the execution time is a sum of ElTetrado and DSSR times)
  • or both --pdb and --dssr-json (recommended, all analyses are made and only ElTetrado is executed while DSSR results are read from the file)

By default, ElTetrado outputs textual results on the standard output. A JSON version of the output can be obtained with --output switch followed by a path where the file is supposed to be created.

ElTetrado prepares visualization of the whole structure and of each N4-helices, quadruplexes and tetrads. This can be supplemented with canonical base pairs visualization when --complete-2d is set. All color settings are located in the first several lines of the quadraw.R file, you can easily change them without knowledge of R language. If you want ElTetrado to not visualize anything, pass --no-image switch to it.

Chains reorder

ElTetrado keeps a global and unique 5’-3’ index for every nucleotide which is independent from residue numbers. For example, if a structure has chain M with 60 nucleotides and chain N with 15 nucleotides, then ElTetrado will keep index between 0 and 74 which uniquely identifies every nucleotide. Initially, ElTetrado assigns this indices according to the order of chains in the input file. Therefore, if M preceded N then nucleotides in M will be indexed from 0 to 59 and in N from 60 to 74. Otherwise, nucleotides in N will be indexed from 0 to 14 and in M from 15 to 74.

When --no-reorder is present, this initial assignment is used. Otherwise, ElTetrado exhaustively checks all permutations of chains’ orders. Every permutation check induces recalculation of the global and unique 5’-3’ index and in effect it changes ONZ classification of tetrads.

ElTetrado keeps a table of tetrad classification scores according to these rules:

  • Type preference: O > N > Z
  • Direction preference: + > -

The table keeps low values for preferred classes i.e. O+ is 0, O- is 1 and so on up to Z- with score 5. For every permutation of chain orders, ElTetrado computes sum of scores for tetrads classification induced by 5’-3’ indexing. We select permutation with the minimum value.

Examples

1MY9: Solution structure of a K+ cation stabilized dimeric RNA quadruplex containing two G:G(:A):G:G(:A) hexads, G:G:G:G tetrads and UUUU loops

$ curl ftp://ftp.wwpdb.org/pub/pdb/data/structures/divided/mmCIF/my/1my9.cif.gz | gzip -d > 1my9.cif
$ ./eltetrado --pdb 1my9.cif --output 1my9.json

Chain order: A, B
n4-helix with 4 tetrads
  Op+ VIII 1a quadruplex with 2 tetrads
    B.G16 B.G19 B.G25 B.G28 cWH-cWH-cWH-cWH O+ VIIIa planarity=0.31 ions_channel= ions_outside={}
      direction=parallel rise=4.21 twist=33.45
    B.G15 B.G18 B.G24 B.G27 cWH-cWH-cWH-cWH O+ VIIIa planarity=0.26 ions_channel= ions_outside={}

    Tracts:
      B.G25, B.G24
      B.G28, B.G27
      B.G16, B.G15
      B.G19, B.G18

    Loops:
      propeller- B.A17
      propeller- B.U20, B.U21, B.U22, B.U23
      propeller- B.A26

  Op+ VIII 1a quadruplex with 2 tetrads
    A.G1 A.G4 A.G10 A.G13 cWH-cWH-cWH-cWH O+ VIIIa planarity=0.63 ions_channel= ions_outside={}
      direction=parallel rise=4.12 twist=27.15
    A.G2 A.G5 A.G11 A.G14 cWH-cWH-cWH-cWH O+ VIIIa planarity=0.5 ions_channel= ions_outside={}

    Tracts:
      A.G4, A.G5
      A.G10, A.G11
      A.G13, A.G14
      A.G1, A.G2

    Loops:
      propeller- A.A3
      propeller- A.U6, A.U7, A.U8, A.U9
      propeller- A.A12


GGAGGUUUUGGAGG-GGAGGUUUUGGAGG
([.)]....([.)]-([.)]....([.)]
([.([....)].)]-([.([....)].)]
Click to see the output JSON 
{
  "metals": "",
  "nucleotides": {
    "A.G1": {
      "index": 1,
      "model": 1,
      "chain": "A",
      "number": 1,
      "icode": " ",
      "molecule": "RNA",
      "full_name": "A.G1",
      "short_name": "G",
      "chi": -114.063,
      "glycosidic_bond": "anti"
    },
    "A.G2": {
      "index": 2,
      "model": 1,
      "chain": "A",
      "number": 2,
      "icode": " ",
      "molecule": "RNA",
      "full_name": "A.G2",
      "short_name": "G",
      "chi": -136.905,
      "glycosidic_bond": "anti"
    },
    "A.A3": {
      "index": 3,
      "model": 1,
      "chain": "A",
      "number": 3,
      "icode": " ",
      "molecule": "RNA",
      "full_name": "A.A3",
      "short_name": "A",
      "chi": -53.884,
      "glycosidic_bond": "syn"
    },
    "A.G4": {
      "index": 4,
      "model": 1,
      "chain": "A",
      "number": 4,
      "icode": " ",
      "molecule": "RNA",
      "full_name": "A.G4",
      "short_name": "G",
      "chi": 167.763,
      "glycosidic_bond": "anti"
    },
    "A.G5": {
      "index": 5,
      "model": 1,
      "chain": "A",
      "number": 5,
      "icode": " ",
      "molecule": "RNA",
      "full_name": "A.G5",
      "short_name": "G",
      "chi": -98.198,
      "glycosidic_bond": "anti"
    },
    "A.U6": {
      "index": 6,
      "model": 1,
      "chain": "A",
      "number": 6,
      "icode": " ",
      "molecule": "RNA",
      "full_name": "A.U6",
      "short_name": "U",
      "chi": -150.069,
      "glycosidic_bond": "anti"
    },
    "A.U7": {
      "index": 7,
      "model": 1,
      "chain": "A",
      "number": 7,
      "icode": " ",
      "molecule": "RNA",
      "full_name": "A.U7",
      "short_name": "U",
      "chi": -130.523,
      "glycosidic_bond": "anti"
    },
    "A.U8": {
      "index": 8,
      "model": 1,
      "chain": "A",
      "number": 8,
      "icode": " ",
      "molecule": "RNA",
      "full_name": "A.U8",
      "short_name": "U",
      "chi": -158.504,
      "glycosidic_bond": "anti"
    },
    "A.U9": {
      "index": 9,
      "model": 1,
      "chain": "A",
      "number": 9,
      "icode": " ",
      "molecule": "RNA",
      "full_name": "A.U9",
      "short_name": "U",
      "chi": -149.743,
      "glycosidic_bond": "anti"
    },
    "A.G10": {
      "index": 10,
      "model": 1,
      "chain": "A",
      "number": 10,
      "icode": " ",
      "molecule": "RNA",
      "full_name": "A.G10",
      "short_name": "G",
      "chi": -113.245,
      "glycosidic_bond": "anti"
    },
    "A.G11": {
      "index": 11,
      "model": 1,
      "chain": "A",
      "number": 11,
      "icode": " ",
      "molecule": "RNA",
      "full_name": "A.G11",
      "short_name": "G",
      "chi": -138.466,
      "glycosidic_bond": "anti"
    },
    "A.A12": {
      "index": 12,
      "model": 1,
      "chain": "A",
      "number": 12,
      "icode": " ",
      "molecule": "RNA",
      "full_name": "A.A12",
      "short_name": "A",
      "chi": -70.627,
      "glycosidic_bond": "syn"
    },
    "A.G13": {
      "index": 13,
      "model": 1,
      "chain": "A",
      "number": 13,
      "icode": " ",
      "molecule": "RNA",
      "full_name": "A.G13",
      "short_name": "G",
      "chi": 150.585,
      "glycosidic_bond": "anti"
    },
    "A.G14": {
      "index": 14,
      "model": 1,
      "chain": "A",
      "number": 14,
      "icode": " ",
      "molecule": "RNA",
      "full_name": "A.G14",
      "short_name": "G",
      "chi": -158.594,
      "glycosidic_bond": "anti"
    },
    "B.G15": {
      "index": 15,
      "model": 1,
      "chain": "B",
      "number": 15,
      "icode": " ",
      "molecule": "RNA",
      "full_name": "B.G15",
      "short_name": "G",
      "chi": -114.303,
      "glycosidic_bond": "anti"
    },
    "B.G16": {
      "index": 16,
      "model": 1,
      "chain": "B",
      "number": 16,
      "icode": " ",
      "molecule": "RNA",
      "full_name": "B.G16",
      "short_name": "G",
      "chi": -134.388,
      "glycosidic_bond": "anti"
    },
    "B.A17": {
      "index": 17,
      "model": 1,
      "chain": "B",
      "number": 17,
      "icode": " ",
      "molecule": "RNA",
      "full_name": "B.A17",
      "short_name": "A",
      "chi": -52.702,
      "glycosidic_bond": "syn"
    },
    "B.G18": {
      "index": 18,
      "model": 1,
      "chain": "B",
      "number": 18,
      "icode": " ",
      "molecule": "RNA",
      "full_name": "B.G18",
      "short_name": "G",
      "chi": 156.482,
      "glycosidic_bond": "anti"
    },
    "B.G19": {
      "index": 19,
      "model": 1,
      "chain": "B",
      "number": 19,
      "icode": " ",
      "molecule": "RNA",
      "full_name": "B.G19",
      "short_name": "G",
      "chi": -100.234,
      "glycosidic_bond": "anti"
    },
    "B.U20": {
      "index": 20,
      "model": 1,
      "chain": "B",
      "number": 20,
      "icode": " ",
      "molecule": "RNA",
      "full_name": "B.U20",
      "short_name": "U",
      "chi": -146.822,
      "glycosidic_bond": "anti"
    },
    "B.U21": {
      "index": 21,
      "model": 1,
      "chain": "B",
      "number": 21,
      "icode": " ",
      "molecule": "RNA",
      "full_name": "B.U21",
      "short_name": "U",
      "chi": -144.09,
      "glycosidic_bond": "anti"
    },
    "B.U22": {
      "index": 22,
      "model": 1,
      "chain": "B",
      "number": 22,
      "icode": " ",
      "molecule": "RNA",
      "full_name": "B.U22",
      "short_name": "U",
      "chi": -160.945,
      "glycosidic_bond": "anti"
    },
    "B.U23": {
      "index": 23,
      "model": 1,
      "chain": "B",
      "number": 23,
      "icode": " ",
      "molecule": "RNA",
      "full_name": "B.U23",
      "short_name": "U",
      "chi": -144.171,
      "glycosidic_bond": "anti"
    },
    "B.G24": {
      "index": 24,
      "model": 1,
      "chain": "B",
      "number": 24,
      "icode": " ",
      "molecule": "RNA",
      "full_name": "B.G24",
      "short_name": "G",
      "chi": -121.507,
      "glycosidic_bond": "anti"
    },
    "B.G25": {
      "index": 25,
      "model": 1,
      "chain": "B",
      "number": 25,
      "icode": " ",
      "molecule": "RNA",
      "full_name": "B.G25",
      "short_name": "G",
      "chi": -132.739,
      "glycosidic_bond": "anti"
    },
    "B.A26": {
      "index": 26,
      "model": 1,
      "chain": "B",
      "number": 26,
      "icode": " ",
      "molecule": "RNA",
      "full_name": "B.A26",
      "short_name": "A",
      "chi": -72.432,
      "glycosidic_bond": "syn"
    },
    "B.G27": {
      "index": 27,
      "model": 1,
      "chain": "B",
      "number": 27,
      "icode": " ",
      "molecule": "RNA",
      "full_name": "B.G27",
      "short_name": "G",
      "chi": -178.717,
      "glycosidic_bond": "anti"
    },
    "B.G28": {
      "index": 28,
      "model": 1,
      "chain": "B",
      "number": 28,
      "icode": " ",
      "molecule": "RNA",
      "full_name": "B.G28",
      "short_name": "G",
      "chi": -130.902,
      "glycosidic_bond": "anti"
    }
  },
  "base_pairs": [
    {
      "nt1": "A.G1",
      "nt2": "A.A3",
      "stericity": "trans",
      "edge5": "Sugar",
      "edge3": "Hoogsteen"
    },
    {
      "nt1": "A.A3",
      "nt2": "A.G1",
      "stericity": "trans",
      "edge5": "Hoogsteen",
      "edge3": "Sugar"
    },
    {
      "nt1": "A.G1",
      "nt2": "A.G4",
      "stericity": "cis",
      "edge5": "Watson-Crick",
      "edge3": "Hoogsteen"
    },
    {
      "nt1": "A.G4",
      "nt2": "A.G1",
      "stericity": "cis",
      "edge5": "Hoogsteen",
      "edge3": "Watson-Crick"
    },
    {
      "nt1": "A.G1",
      "nt2": "A.G13",
      "stericity": "cis",
      "edge5": "Hoogsteen",
      "edge3": "Watson-Crick"
    },
    {
      "nt1": "A.G13",
      "nt2": "A.G1",
      "stericity": "cis",
      "edge5": "Watson-Crick",
      "edge3": "Hoogsteen"
    },
    {
      "nt1": "A.G2",
      "nt2": "A.G5",
      "stericity": "cis",
      "edge5": "Watson-Crick",
      "edge3": "Hoogsteen"
    },
    {
      "nt1": "A.G5",
      "nt2": "A.G2",
      "stericity": "cis",
      "edge5": "Hoogsteen",
      "edge3": "Watson-Crick"
    },
    {
      "nt1": "A.G2",
      "nt2": "A.G11",
      "stericity": "trans",
      "edge5": "Watson-Crick",
      "edge3": "Watson-Crick"
    },
    {
      "nt1": "A.G11",
      "nt2": "A.G2",
      "stericity": "trans",
      "edge5": "Watson-Crick",
      "edge3": "Watson-Crick"
    },
    {
      "nt1": "A.G2",
      "nt2": "A.G14",
      "stericity": "cis",
      "edge5": "Hoogsteen",
      "edge3": "Watson-Crick"
    },
    {
      "nt1": "A.G14",
      "nt2": "A.G2",
      "stericity": "cis",
      "edge5": "Watson-Crick",
      "edge3": "Hoogsteen"
    },
    {
      "nt1": "A.G4",
      "nt2": "A.G10",
      "stericity": "cis",
      "edge5": "Watson-Crick",
      "edge3": "Hoogsteen"
    },
    {
      "nt1": "A.G10",
      "nt2": "A.G4",
      "stericity": "cis",
      "edge5": "Hoogsteen",
      "edge3": "Watson-Crick"
    },
    {
      "nt1": "A.G4",
      "nt2": "B.A17",
      "stericity": "trans",
      "edge5": "Hoogsteen",
      "edge3": "Hoogsteen"
    },
    {
      "nt1": "B.A17",
      "nt2": "A.G4",
      "stericity": "trans",
      "edge5": "Hoogsteen",
      "edge3": "Hoogsteen"
    },
    {
      "nt1": "A.G5",
      "nt2": "A.G11",
      "stericity": "cis",
      "edge5": "Watson-Crick",
      "edge3": "Hoogsteen"
    },
    {
      "nt1": "A.G11",
      "nt2": "A.G5",
      "stericity": "cis",
      "edge5": "Hoogsteen",
      "edge3": "Watson-Crick"
    },
    {
      "nt1": "A.G10",
      "nt2": "A.A12",
      "stericity": "trans",
      "edge5": "Sugar",
      "edge3": "Hoogsteen"
    },
    {
      "nt1": "A.A12",
      "nt2": "A.G10",
      "stericity": "trans",
      "edge5": "Hoogsteen",
      "edge3": "Sugar"
    },
    {
      "nt1": "A.G10",
      "nt2": "A.G13",
      "stericity": "cis",
      "edge5": "Watson-Crick",
      "edge3": "Hoogsteen"
    },
    {
      "nt1": "A.G13",
      "nt2": "A.G10",
      "stericity": "cis",
      "edge5": "Hoogsteen",
      "edge3": "Watson-Crick"
    },
    {
      "nt1": "A.G11",
      "nt2": "A.G14",
      "stericity": "cis",
      "edge5": "Watson-Crick",
      "edge3": "Hoogsteen"
    },
    {
      "nt1": "A.G14",
      "nt2": "A.G11",
      "stericity": "cis",
      "edge5": "Hoogsteen",
      "edge3": "Watson-Crick"
    },
    {
      "nt1": "A.G13",
      "nt2": "B.G27",
      "stericity": "cis",
      "edge5": "Hoogsteen",
      "edge3": "Hoogsteen"
    },
    {
      "nt1": "B.G27",
      "nt2": "A.G13",
      "stericity": "cis",
      "edge5": "Hoogsteen",
      "edge3": "Hoogsteen"
    },
    {
      "nt1": "B.G15",
      "nt2": "B.A17",
      "stericity": "trans",
      "edge5": "Sugar",
      "edge3": "Hoogsteen"
    },
    {
      "nt1": "B.A17",
      "nt2": "B.G15",
      "stericity": "trans",
      "edge5": "Hoogsteen",
      "edge3": "Sugar"
    },
    {
      "nt1": "B.G15",
      "nt2": "B.G18",
      "stericity": "cis",
      "edge5": "Watson-Crick",
      "edge3": "Hoogsteen"
    },
    {
      "nt1": "B.G18",
      "nt2": "B.G15",
      "stericity": "cis",
      "edge5": "Hoogsteen",
      "edge3": "Watson-Crick"
    },
    {
      "nt1": "B.G15",
      "nt2": "B.G27",
      "stericity": "cis",
      "edge5": "Hoogsteen",
      "edge3": "Watson-Crick"
    },
    {
      "nt1": "B.G27",
      "nt2": "B.G15",
      "stericity": "cis",
      "edge5": "Watson-Crick",
      "edge3": "Hoogsteen"
    },
    {
      "nt1": "B.G16",
      "nt2": "B.G19",
      "stericity": "cis",
      "edge5": "Watson-Crick",
      "edge3": "Hoogsteen"
    },
    {
      "nt1": "B.G19",
      "nt2": "B.G16",
      "stericity": "cis",
      "edge5": "Hoogsteen",
      "edge3": "Watson-Crick"
    },
    {
      "nt1": "B.G16",
      "nt2": "B.G28",
      "stericity": "cis",
      "edge5": "Hoogsteen",
      "edge3": "Watson-Crick"
    },
    {
      "nt1": "B.G28",
      "nt2": "B.G16",
      "stericity": "cis",
      "edge5": "Watson-Crick",
      "edge3": "Hoogsteen"
    },
    {
      "nt1": "B.G18",
      "nt2": "B.G24",
      "stericity": "cis",
      "edge5": "Watson-Crick",
      "edge3": "Hoogsteen"
    },
    {
      "nt1": "B.G24",
      "nt2": "B.G18",
      "stericity": "cis",
      "edge5": "Hoogsteen",
      "edge3": "Watson-Crick"
    },
    {
      "nt1": "B.G19",
      "nt2": "B.G25",
      "stericity": "cis",
      "edge5": "Watson-Crick",
      "edge3": "Hoogsteen"
    },
    {
      "nt1": "B.G25",
      "nt2": "B.G19",
      "stericity": "cis",
      "edge5": "Hoogsteen",
      "edge3": "Watson-Crick"
    },
    {
      "nt1": "B.G24",
      "nt2": "B.A26",
      "stericity": "trans",
      "edge5": "Sugar",
      "edge3": "Hoogsteen"
    },
    {
      "nt1": "B.A26",
      "nt2": "B.G24",
      "stericity": "trans",
      "edge5": "Hoogsteen",
      "edge3": "Sugar"
    },
    {
      "nt1": "B.G24",
      "nt2": "B.G27",
      "stericity": "cis",
      "edge5": "Watson-Crick",
      "edge3": "Hoogsteen"
    },
    {
      "nt1": "B.G27",
      "nt2": "B.G24",
      "stericity": "cis",
      "edge5": "Hoogsteen",
      "edge3": "Watson-Crick"
    },
    {
      "nt1": "B.G25",
      "nt2": "B.G28",
      "stericity": "cis",
      "edge5": "Watson-Crick",
      "edge3": "Hoogsteen"
    },
    {
      "nt1": "B.G28",
      "nt2": "B.G25",
      "stericity": "cis",
      "edge5": "Hoogsteen",
      "edge3": "Watson-Crick"
    }
  ],
  "helices": [
    {
      "quadruplexes": [
        {
          "tetrads": {
            "B.G16-B.G19-B.G25-B.G28": {
              "nt1": "B.G16",
              "nt2": "B.G19",
              "nt3": "B.G25",
              "nt4": "B.G28",
              "onz": "O+",
              "gba_classification": "VIIIa",
              "planarity_deviation": 0.31002684978384765,
              "ions_channel": [],
              "ions_outside": {}
            },
            "B.G15-B.G18-B.G24-B.G27": {
              "nt1": "B.G15",
              "nt2": "B.G18",
              "nt3": "B.G24",
              "nt4": "B.G27",
              "onz": "O+",
              "gba_classification": "VIIIa",
              "planarity_deviation": 0.2616979115189099,
              "ions_channel": [],
              "ions_outside": {}
            }
          },
          "onzm": "Op+",
          "loop_classification": "1a",
          "gba_classification": "VIII",
          "tracts": [
            [
              "B.G25",
              "B.G24"
            ],
            [
              "B.G28",
              "B.G27"
            ],
            [
              "B.G16",
              "B.G15"
            ],
            [
              "B.G19",
              "B.G18"
            ]
          ],
          "loops": [
            {
              "loop_type": "propeller-",
              "nucleotides": [
                "B.A17"
              ]
            },
            {
              "loop_type": "propeller-",
              "nucleotides": [
                "B.U20",
                "B.U21",
                "B.U22",
                "B.U23"
              ]
            },
            {
              "loop_type": "propeller-",
              "nucleotides": [
                "B.A26"
              ]
            }
          ]
        },
        {
          "tetrads": {
            "A.G1-A.G4-A.G10-A.G13": {
              "nt1": "A.G1",
              "nt2": "A.G4",
              "nt3": "A.G10",
              "nt4": "A.G13",
              "onz": "O+",
              "gba_classification": "VIIIa",
              "planarity_deviation": 0.6331163330540677,
              "ions_channel": [],
              "ions_outside": {}
            },
            "A.G2-A.G5-A.G11-A.G14": {
              "nt1": "A.G2",
              "nt2": "A.G5",
              "nt3": "A.G11",
              "nt4": "A.G14",
              "onz": "O+",
              "gba_classification": "VIIIa",
              "planarity_deviation": 0.49745503003636027,
              "ions_channel": [],
              "ions_outside": {}
            }
          },
          "onzm": "Op+",
          "loop_classification": "1a",
          "gba_classification": "VIII",
          "tracts": [
            [
              "A.G4",
              "A.G5"
            ],
            [
              "A.G10",
              "A.G11"
            ],
            [
              "A.G13",
              "A.G14"
            ],
            [
              "A.G1",
              "A.G2"
            ]
          ],
          "loops": [
            {
              "loop_type": "propeller-",
              "nucleotides": [
                "A.A3"
              ]
            },
            {
              "loop_type": "propeller-",
              "nucleotides": [
                "A.U6",
                "A.U7",
                "A.U8",
                "A.U9"
              ]
            },
            {
              "loop_type": "propeller-",
              "nucleotides": [
                "A.A12"
              ]
            }
          ]
        }
      ],
      "tetrad_pairs": [
        {
          "tetrad1": "B.G16-B.G19-B.G25-B.G28",
          "tetrad2": "B.G15-B.G18-B.G24-B.G27",
          "direction": "parallel",
          "rise": 4.211160689840694,
          "twist": 33.447063602481144
        },
        {
          "tetrad1": "B.G15-B.G18-B.G24-B.G27",
          "tetrad2": "A.G1-A.G4-A.G10-A.G13",
          "direction": "parallel",
          "rise": 3.184510351147094,
          "twist": 12.118860788156299
        },
        {
          "tetrad1": "A.G1-A.G4-A.G10-A.G13",
          "tetrad2": "A.G2-A.G5-A.G11-A.G14",
          "direction": "parallel",
          "rise": 4.121721871766505,
          "twist": 27.15182036694497
        }
      ]
    }
  ]
}

4RJ1: Structural variations and solvent structure of UGGGGU quadruplexes stabilized by Sr2+ ions

$ curl https://www.ebi.ac.uk/pdbe/static/entry/download/4rj1-assembly-1.cif.gz | gzip -d > 4rj1-1.cif
$ ./eltetrado --pdb 4rj1-1.cif --output 4rj1-1.json

Chain order: A, AB, AA, AC, B, BC, BA, BB
n4-helix with 10 tetrads
  Op* VIII n/a quadruplex with 5 tetrads
    A.U1006 AC.U1006 AA.U1006 AB.U1006 cWH-cWH-cWH-cWH O- VIIIa planarity=1.06 ions_channel= ions_outside={A.U1006: 'SR', AA.U1006: 'SR', AB.U1006: 'SR', AC.U1006: 'SR'}
      direction=parallel rise=3.37 twist=39.96
    A.G1005 AB.G1005 AA.G1005 AC.G1005 cWH-cWH-cWH-cWH O+ VIIIa planarity=0.8 ions_channel=SR ions_outside={}
      direction=parallel rise=3.31 twist=25.9
    A.G1004 AB.G1004 AA.G1004 AC.G1004 cWH-cWH-cWH-cWH O+ VIIIa planarity=0.41 ions_channel= ions_outside={}
      direction=parallel rise=3.34 twist=35.81
    A.G1003 AB.G1003 AA.G1003 AC.G1003 cWH-cWH-cWH-cWH O+ VIIIa planarity=0.56 ions_channel=SR ions_outside={}
      direction=parallel rise=3.29 twist=27.12
    A.G1002 AB.G1002 AA.G1002 AC.G1002 cWH-cWH-cWH-cWH O+ VIIIa planarity=0.54 ions_channel= ions_outside={}

    Tracts:
      AA.U1006, AA.G1005, AA.G1004, AA.G1003, AA.G1002
      AB.U1006, AB.G1005, AB.G1004, AB.G1003, AB.G1002
      A.U1006, A.G1005, A.G1004, A.G1003, A.G1002
      AC.U1006, AC.G1005, AC.G1004, AC.G1003, AC.G1002

  Op* VIII n/a quadruplex with 5 tetrads
    B.G2002 BC.G2002 BA.G2002 BB.G2002 cWH-cWH-cWH-cWH O+ VIIIa planarity=0.67 ions_channel= ions_outside={}
      direction=parallel rise=3.37 twist=27.41
    B.G2003 BC.G2003 BA.G2003 BB.G2003 cWH-cWH-cWH-cWH O+ VIIIa planarity=0.58 ions_channel=SR ions_outside={}
      direction=parallel rise=3.32 twist=35.04
    B.G2004 BC.G2004 BA.G2004 BB.G2004 cWH-cWH-cWH-cWH O+ VIIIa planarity=0.23 ions_channel=SR ions_outside={}
      direction=parallel rise=3.27 twist=25.15
    B.G2005 BC.G2005 BA.G2005 BB.G2005 cWH-cWH-cWH-cWH O+ VIIIa planarity=0.78 ions_channel= ions_outside={}
      direction=parallel rise=7.14 twist=43.41
    B.U2006 BB.U2006 BA.U2006 BC.U2006 cWH-cWH-cWH-cWH O- VIIIa planarity=1.58 ions_channel=NA,NA ions_outside={}

    Tracts:
      BC.G2002, BC.G2003, BC.G2004, BC.G2005, BC.U2006
      BA.G2002, BA.G2003, BA.G2004, BA.G2005, BA.U2006
      BB.G2002, BB.G2003, BB.G2004, BB.G2005, BB.U2006
      B.G2002, B.G2003, B.G2004, B.G2005, B.U2006


UGGGGU-UGGGGU-UGGGGU-UGGGGU-UGGGGU-UGGGGU-UGGGGU-UGGGGU
.([{<A-.)]}>A-.([{<a-.)]}>a-.([{<A-.)]}>A-.([{<a-.)]}>a
.([{<A-.([{<a-.)]}>A-.)]}>a-.([{<A-.([{<a-.)]}>A-.)]}>a
Click to see the output JSON 
{
  "metals": "Ca=12,Na=2,Sr=8",
  "nucleotides": {
    "A.U1001": {
      "index": 1,
      "model": 1,
      "chain": "A",
      "number": 1001,
      "icode": " ",
      "molecule": "RNA",
      "full_name": "A.U1001",
      "short_name": "U",
      "chi": -141.927,
      "glycosidic_bond": "anti"
    },
    "A.G1002": {
      "index": 2,
      "model": 1,
      "chain": "A",
      "number": 1002,
      "icode": " ",
      "molecule": "RNA",
      "full_name": "A.G1002",
      "short_name": "G",
      "chi": -165.93,
      "glycosidic_bond": "anti"
    },
    "A.G1003": {
      "index": 3,
      "model": 1,
      "chain": "A",
      "number": 1003,
      "icode": " ",
      "molecule": "RNA",
      "full_name": "A.G1003",
      "short_name": "G",
      "chi": -121.565,
      "glycosidic_bond": "anti"
    },
    "A.G1004": {
      "index": 4,
      "model": 1,
      "chain": "A",
      "number": 1004,
      "icode": " ",
      "molecule": "RNA",
      "full_name": "A.G1004",
      "short_name": "G",
      "chi": -156.01,
      "glycosidic_bond": "anti"
    },
    "A.G1005": {
      "index": 5,
      "model": 1,
      "chain": "A",
      "number": 1005,
      "icode": " ",
      "molecule": "RNA",
      "full_name": "A.G1005",
      "short_name": "G",
      "chi": -148.101,
      "glycosidic_bond": "anti"
    },
    "A.U1006": {
      "index": 6,
      "model": 1,
      "chain": "A",
      "number": 1006,
      "icode": " ",
      "molecule": "RNA",
      "full_name": "A.U1006",
      "short_name": "U",
      "chi": -137.28,
      "glycosidic_bond": "anti"
    },
    "AA.U1001": {
      "index": 13,
      "model": 1,
      "chain": "AA",
      "number": 1001,
      "icode": " ",
      "molecule": "RNA",
      "full_name": "AA.U1001",
      "short_name": "U",
      "chi": -141.927,
      "glycosidic_bond": "anti"
    },
    "AA.G1002": {
      "index": 14,
      "model": 1,
      "chain": "AA",
      "number": 1002,
      "icode": " ",
      "molecule": "RNA",
      "full_name": "AA.G1002",
      "short_name": "G",
      "chi": -165.93,
      "glycosidic_bond": "anti"
    },
    "AA.G1003": {
      "index": 15,
      "model": 1,
      "chain": "AA",
      "number": 1003,
      "icode": " ",
      "molecule": "RNA",
      "full_name": "AA.G1003",
      "short_name": "G",
      "chi": -121.565,
      "glycosidic_bond": "anti"
    },
    "AA.G1004": {
      "index": 16,
      "model": 1,
      "chain": "AA",
      "number": 1004,
      "icode": " ",
      "molecule": "RNA",
      "full_name": "AA.G1004",
      "short_name": "G",
      "chi": -156.01,
      "glycosidic_bond": "anti"
    },
    "AA.G1005": {
      "index": 17,
      "model": 1,
      "chain": "AA",
      "number": 1005,
      "icode": " ",
      "molecule": "RNA",
      "full_name": "AA.G1005",
      "short_name": "G",
      "chi": -148.101,
      "glycosidic_bond": "anti"
    },
    "AA.U1006": {
      "index": 18,
      "model": 1,
      "chain": "AA",
      "number": 1006,
      "icode": " ",
      "molecule": "RNA",
      "full_name": "AA.U1006",
      "short_name": "U",
      "chi": -137.28,
      "glycosidic_bond": "anti"
    },
    "AB.U1001": {
      "index": 7,
      "model": 1,
      "chain": "AB",
      "number": 1001,
      "icode": " ",
      "molecule": "RNA",
      "full_name": "AB.U1001",
      "short_name": "U",
      "chi": -141.927,
      "glycosidic_bond": "anti"
    },
    "AB.G1002": {
      "index": 8,
      "model": 1,
      "chain": "AB",
      "number": 1002,
      "icode": " ",
      "molecule": "RNA",
      "full_name": "AB.G1002",
      "short_name": "G",
      "chi": -165.93,
      "glycosidic_bond": "anti"
    },
    "AB.G1003": {
      "index": 9,
      "model": 1,
      "chain": "AB",
      "number": 1003,
      "icode": " ",
      "molecule": "RNA",
      "full_name": "AB.G1003",
      "short_name": "G",
      "chi": -121.565,
      "glycosidic_bond": "anti"
    },
    "AB.G1004": {
      "index": 10,
      "model": 1,
      "chain": "AB",
      "number": 1004,
      "icode": " ",
      "molecule": "RNA",
      "full_name": "AB.G1004",
      "short_name": "G",
      "chi": -156.01,
      "glycosidic_bond": "anti"
    },
    "AB.G1005": {
      "index": 11,
      "model": 1,
      "chain": "AB",
      "number": 1005,
      "icode": " ",
      "molecule": "RNA",
      "full_name": "AB.G1005",
      "short_name": "G",
      "chi": -148.101,
      "glycosidic_bond": "anti"
    },
    "AB.U1006": {
      "index": 12,
      "model": 1,
      "chain": "AB",
      "number": 1006,
      "icode": " ",
      "molecule": "RNA",
      "full_name": "AB.U1006",
      "short_name": "U",
      "chi": -137.28,
      "glycosidic_bond": "anti"
    },
    "AC.U1001": {
      "index": 19,
      "model": 1,
      "chain": "AC",
      "number": 1001,
      "icode": " ",
      "molecule": "RNA",
      "full_name": "AC.U1001",
      "short_name": "U",
      "chi": -141.927,
      "glycosidic_bond": "anti"
    },
    "AC.G1002": {
      "index": 20,
      "model": 1,
      "chain": "AC",
      "number": 1002,
      "icode": " ",
      "molecule": "RNA",
      "full_name": "AC.G1002",
      "short_name": "G",
      "chi": -165.93,
      "glycosidic_bond": "anti"
    },
    "AC.G1003": {
      "index": 21,
      "model": 1,
      "chain": "AC",
      "number": 1003,
      "icode": " ",
      "molecule": "RNA",
      "full_name": "AC.G1003",
      "short_name": "G",
      "chi": -121.565,
      "glycosidic_bond": "anti"
    },
    "AC.G1004": {
      "index": 22,
      "model": 1,
      "chain": "AC",
      "number": 1004,
      "icode": " ",
      "molecule": "RNA",
      "full_name": "AC.G1004",
      "short_name": "G",
      "chi": -156.01,
      "glycosidic_bond": "anti"
    },
    "AC.G1005": {
      "index": 23,
      "model": 1,
      "chain": "AC",
      "number": 1005,
      "icode": " ",
      "molecule": "RNA",
      "full_name": "AC.G1005",
      "short_name": "G",
      "chi": -148.101,
      "glycosidic_bond": "anti"
    },
    "AC.U1006": {
      "index": 24,
      "model": 1,
      "chain": "AC",
      "number": 1006,
      "icode": " ",
      "molecule": "RNA",
      "full_name": "AC.U1006",
      "short_name": "U",
      "chi": -137.28,
      "glycosidic_bond": "anti"
    },
    "B.U2001": {
      "index": 25,
      "model": 1,
      "chain": "B",
      "number": 2001,
      "icode": " ",
      "molecule": "RNA",
      "full_name": "B.U2001",
      "short_name": "U",
      "chi": -146.462,
      "glycosidic_bond": "anti"
    },
    "B.G2002": {
      "index": 26,
      "model": 1,
      "chain": "B",
      "number": 2002,
      "icode": " ",
      "molecule": "RNA",
      "full_name": "B.G2002",
      "short_name": "G",
      "chi": -170.797,
      "glycosidic_bond": "anti"
    },
    "B.G2003": {
      "index": 27,
      "model": 1,
      "chain": "B",
      "number": 2003,
      "icode": " ",
      "molecule": "RNA",
      "full_name": "B.G2003",
      "short_name": "G",
      "chi": -117.687,
      "glycosidic_bond": "anti"
    },
    "B.G2004": {
      "index": 28,
      "model": 1,
      "chain": "B",
      "number": 2004,
      "icode": " ",
      "molecule": "RNA",
      "full_name": "B.G2004",
      "short_name": "G",
      "chi": -153.886,
      "glycosidic_bond": "anti"
    },
    "B.G2005": {
      "index": 29,
      "model": 1,
      "chain": "B",
      "number": 2005,
      "icode": " ",
      "molecule": "RNA",
      "full_name": "B.G2005",
      "short_name": "G",
      "chi": -148.852,
      "glycosidic_bond": "anti"
    },
    "B.U2006": {
      "index": 30,
      "model": 1,
      "chain": "B",
      "number": 2006,
      "icode": " ",
      "molecule": "RNA",
      "full_name": "B.U2006",
      "short_name": "U",
      "chi": -159.437,
      "glycosidic_bond": "anti"
    },
    "BA.U2001": {
      "index": 37,
      "model": 1,
      "chain": "BA",
      "number": 2001,
      "icode": " ",
      "molecule": "RNA",
      "full_name": "BA.U2001",
      "short_name": "U",
      "chi": -146.462,
      "glycosidic_bond": "anti"
    },
    "BA.G2002": {
      "index": 38,
      "model": 1,
      "chain": "BA",
      "number": 2002,
      "icode": " ",
      "molecule": "RNA",
      "full_name": "BA.G2002",
      "short_name": "G",
      "chi": -170.797,
      "glycosidic_bond": "anti"
    },
    "BA.G2003": {
      "index": 39,
      "model": 1,
      "chain": "BA",
      "number": 2003,
      "icode": " ",
      "molecule": "RNA",
      "full_name": "BA.G2003",
      "short_name": "G",
      "chi": -117.687,
      "glycosidic_bond": "anti"
    },
    "BA.G2004": {
      "index": 40,
      "model": 1,
      "chain": "BA",
      "number": 2004,
      "icode": " ",
      "molecule": "RNA",
      "full_name": "BA.G2004",
      "short_name": "G",
      "chi": -153.886,
      "glycosidic_bond": "anti"
    },
    "BA.G2005": {
      "index": 41,
      "model": 1,
      "chain": "BA",
      "number": 2005,
      "icode": " ",
      "molecule": "RNA",
      "full_name": "BA.G2005",
      "short_name": "G",
      "chi": -148.852,
      "glycosidic_bond": "anti"
    },
    "BA.U2006": {
      "index": 42,
      "model": 1,
      "chain": "BA",
      "number": 2006,
      "icode": " ",
      "molecule": "RNA",
      "full_name": "BA.U2006",
      "short_name": "U",
      "chi": -159.437,
      "glycosidic_bond": "anti"
    },
    "BB.U2001": {
      "index": 43,
      "model": 1,
      "chain": "BB",
      "number": 2001,
      "icode": " ",
      "molecule": "RNA",
      "full_name": "BB.U2001",
      "short_name": "U",
      "chi": -146.462,
      "glycosidic_bond": "anti"
    },
    "BB.G2002": {
      "index": 44,
      "model": 1,
      "chain": "BB",
      "number": 2002,
      "icode": " ",
      "molecule": "RNA",
      "full_name": "BB.G2002",
      "short_name": "G",
      "chi": -170.797,
      "glycosidic_bond": "anti"
    },
    "BB.G2003": {
      "index": 45,
      "model": 1,
      "chain": "BB",
      "number": 2003,
      "icode": " ",
      "molecule": "RNA",
      "full_name": "BB.G2003",
      "short_name": "G",
      "chi": -117.687,
      "glycosidic_bond": "anti"
    },
    "BB.G2004": {
      "index": 46,
      "model": 1,
      "chain": "BB",
      "number": 2004,
      "icode": " ",
      "molecule": "RNA",
      "full_name": "BB.G2004",
      "short_name": "G",
      "chi": -153.886,
      "glycosidic_bond": "anti"
    },
    "BB.G2005": {
      "index": 47,
      "model": 1,
      "chain": "BB",
      "number": 2005,
      "icode": " ",
      "molecule": "RNA",
      "full_name": "BB.G2005",
      "short_name": "G",
      "chi": -148.852,
      "glycosidic_bond": "anti"
    },
    "BB.U2006": {
      "index": 48,
      "model": 1,
      "chain": "BB",
      "number": 2006,
      "icode": " ",
      "molecule": "RNA",
      "full_name": "BB.U2006",
      "short_name": "U",
      "chi": -159.437,
      "glycosidic_bond": "anti"
    },
    "BC.U2001": {
      "index": 31,
      "model": 1,
      "chain": "BC",
      "number": 2001,
      "icode": " ",
      "molecule": "RNA",
      "full_name": "BC.U2001",
      "short_name": "U",
      "chi": -146.462,
      "glycosidic_bond": "anti"
    },
    "BC.G2002": {
      "index": 32,
      "model": 1,
      "chain": "BC",
      "number": 2002,
      "icode": " ",
      "molecule": "RNA",
      "full_name": "BC.G2002",
      "short_name": "G",
      "chi": -170.797,
      "glycosidic_bond": "anti"
    },
    "BC.G2003": {
      "index": 33,
      "model": 1,
      "chain": "BC",
      "number": 2003,
      "icode": " ",
      "molecule": "RNA",
      "full_name": "BC.G2003",
      "short_name": "G",
      "chi": -117.687,
      "glycosidic_bond": "anti"
    },
    "BC.G2004": {
      "index": 34,
      "model": 1,
      "chain": "BC",
      "number": 2004,
      "icode": " ",
      "molecule": "RNA",
      "full_name": "BC.G2004",
      "short_name": "G",
      "chi": -153.886,
      "glycosidic_bond": "anti"
    },
    "BC.G2005": {
      "index": 35,
      "model": 1,
      "chain": "BC",
      "number": 2005,
      "icode": " ",
      "molecule": "RNA",
      "full_name": "BC.G2005",
      "short_name": "G",
      "chi": -148.852,
      "glycosidic_bond": "anti"
    },
    "BC.U2006": {
      "index": 36,
      "model": 1,
      "chain": "BC",
      "number": 2006,
      "icode": " ",
      "molecule": "RNA",
      "full_name": "BC.U2006",
      "short_name": "U",
      "chi": -159.437,
      "glycosidic_bond": "anti"
    }
  },
  "base_pairs": [
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      "nt1": "A.U1001",
      "nt2": "B.G2003",
      "stericity": "cis",
      "edge5": "Sugar",
      "edge3": "Sugar"
    },
    {
      "nt1": "B.G2003",
      "nt2": "A.U1001",
      "stericity": "cis",
      "edge5": "Sugar",
      "edge3": "Sugar"
    },
    {
      "nt1": "A.G1002",
      "nt2": "AB.G1002",
      "stericity": "cis",
      "edge5": "Watson-Crick",
      "edge3": "Hoogsteen"
    },
    {
      "nt1": "AB.G1002",
      "nt2": "A.G1002",
      "stericity": "cis",
      "edge5": "Hoogsteen",
      "edge3": "Watson-Crick"
    },
    {
      "nt1": "A.G1002",
      "nt2": "AC.G1002",
      "stericity": "cis",
      "edge5": "Hoogsteen",
      "edge3": "Watson-Crick"
    },
    {
      "nt1": "AC.G1002",
      "nt2": "A.G1002",
      "stericity": "cis",
      "edge5": "Watson-Crick",
      "edge3": "Hoogsteen"
    },
    {
      "nt1": "A.G1003",
      "nt2": "AB.G1003",
      "stericity": "cis",
      "edge5": "Watson-Crick",
      "edge3": "Hoogsteen"
    },
    {
      "nt1": "AB.G1003",
      "nt2": "A.G1003",
      "stericity": "cis",
      "edge5": "Hoogsteen",
      "edge3": "Watson-Crick"
    },
    {
      "nt1": "A.G1003",
      "nt2": "AC.G1003",
      "stericity": "cis",
      "edge5": "Hoogsteen",
      "edge3": "Watson-Crick"
    },
    {
      "nt1": "AC.G1003",
      "nt2": "A.G1003",
      "stericity": "cis",
      "edge5": "Watson-Crick",
      "edge3": "Hoogsteen"
    },
    {
      "nt1": "A.G1003",
      "nt2": "B.U2001",
      "stericity": "cis",
      "edge5": "Sugar",
      "edge3": "Sugar"
    },
    {
      "nt1": "B.U2001",
      "nt2": "A.G1003",
      "stericity": "cis",
      "edge5": "Sugar",
      "edge3": "Sugar"
    },
    {
      "nt1": "A.G1004",
      "nt2": "AB.G1004",
      "stericity": "cis",
      "edge5": "Watson-Crick",
      "edge3": "Hoogsteen"
    },
    {
      "nt1": "AB.G1004",
      "nt2": "A.G1004",
      "stericity": "cis",
      "edge5": "Hoogsteen",
      "edge3": "Watson-Crick"
    },
    {
      "nt1": "A.G1004",
      "nt2": "AC.G1004",
      "stericity": "cis",
      "edge5": "Hoogsteen",
      "edge3": "Watson-Crick"
    },
    {
      "nt1": "AC.G1004",
      "nt2": "A.G1004",
      "stericity": "cis",
      "edge5": "Watson-Crick",
      "edge3": "Hoogsteen"
    },
    {
      "nt1": "A.G1005",
      "nt2": "AB.G1005",
      "stericity": "cis",
      "edge5": "Watson-Crick",
      "edge3": "Hoogsteen"
    },
    {
      "nt1": "AB.G1005",
      "nt2": "A.G1005",
      "stericity": "cis",
      "edge5": "Hoogsteen",
      "edge3": "Watson-Crick"
    },
    {
      "nt1": "A.G1005",
      "nt2": "AC.G1005",
      "stericity": "cis",
      "edge5": "Hoogsteen",
      "edge3": "Watson-Crick"
    },
    {
      "nt1": "AC.G1005",
      "nt2": "A.G1005",
      "stericity": "cis",
      "edge5": "Watson-Crick",
      "edge3": "Hoogsteen"
    },
    {
      "nt1": "A.U1006",
      "nt2": "AB.U1006",
      "stericity": "cis",
      "edge5": "Hoogsteen",
      "edge3": "Watson-Crick"
    },
    {
      "nt1": "AB.U1006",
      "nt2": "A.U1006",
      "stericity": "cis",
      "edge5": "Watson-Crick",
      "edge3": "Hoogsteen"
    },
    {
      "nt1": "A.U1006",
      "nt2": "AC.U1006",
      "stericity": "cis",
      "edge5": "Watson-Crick",
      "edge3": "Hoogsteen"
    },
    {
      "nt1": "AC.U1006",
      "nt2": "A.U1006",
      "stericity": "cis",
      "edge5": "Hoogsteen",
      "edge3": "Watson-Crick"
    },
    {
      "nt1": "AA.U1001",
      "nt2": "BA.G2003",
      "stericity": "cis",
      "edge5": "Sugar",
      "edge3": "Sugar"
    },
    {
      "nt1": "BA.G2003",
      "nt2": "AA.U1001",
      "stericity": "cis",
      "edge5": "Sugar",
      "edge3": "Sugar"
    },
    {
      "nt1": "AA.G1002",
      "nt2": "AB.G1002",
      "stericity": "cis",
      "edge5": "Hoogsteen",
      "edge3": "Watson-Crick"
    },
    {
      "nt1": "AB.G1002",
      "nt2": "AA.G1002",
      "stericity": "cis",
      "edge5": "Watson-Crick",
      "edge3": "Hoogsteen"
    },
    {
      "nt1": "AA.G1002",
      "nt2": "AC.G1002",
      "stericity": "cis",
      "edge5": "Watson-Crick",
      "edge3": "Hoogsteen"
    },
    {
      "nt1": "AC.G1002",
      "nt2": "AA.G1002",
      "stericity": "cis",
      "edge5": "Hoogsteen",
      "edge3": "Watson-Crick"
    },
    {
      "nt1": "AA.G1003",
      "nt2": "AB.G1003",
      "stericity": "cis",
      "edge5": "Hoogsteen",
      "edge3": "Watson-Crick"
    },
    {
      "nt1": "AB.G1003",
      "nt2": "AA.G1003",
      "stericity": "cis",
      "edge5": "Watson-Crick",
      "edge3": "Hoogsteen"
    },
    {
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      "nt2": "AC.G1003",
      "stericity": "cis",
      "edge5": "Watson-Crick",
      "edge3": "Hoogsteen"
    },
    {
      "nt1": "AC.G1003",
      "nt2": "AA.G1003",
      "stericity": "cis",
      "edge5": "Hoogsteen",
      "edge3": "Watson-Crick"
    },
    {
      "nt1": "AA.G1003",
      "nt2": "BA.U2001",
      "stericity": "cis",
      "edge5": "Sugar",
      "edge3": "Sugar"
    },
    {
      "nt1": "BA.U2001",
      "nt2": "AA.G1003",
      "stericity": "cis",
      "edge5": "Sugar",
      "edge3": "Sugar"
    },
    {
      "nt1": "AA.G1004",
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      "edge5": "Hoogsteen",
      "edge3": "Watson-Crick"
    },
    {
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      "edge5": "Watson-Crick",
      "edge3": "Hoogsteen"
    },
    {
      "nt1": "AA.G1004",
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      "edge5": "Watson-Crick",
      "edge3": "Hoogsteen"
    },
    {
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      "nt2": "AA.G1004",
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      "edge5": "Hoogsteen",
      "edge3": "Watson-Crick"
    },
    {
      "nt1": "AA.G1005",
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      "edge5": "Hoogsteen",
      "edge3": "Watson-Crick"
    },
    {
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      "nt2": "AA.G1005",
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    },
    {
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      "edge3": "Hoogsteen"
    },
    {
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      "nt2": "AA.G1005",
      "stericity": "cis",
      "edge5": "Hoogsteen",
      "edge3": "Watson-Crick"
    },
    {
      "nt1": "AA.U1006",
      "nt2": "AB.U1006",
      "stericity": "cis",
      "edge5": "Watson-Crick",
      "edge3": "Hoogsteen"
    },
    {
      "nt1": "AB.U1006",
      "nt2": "AA.U1006",
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      "edge3": "Watson-Crick"
    },
    {
      "nt1": "AA.U1006",
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    },
    {
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      "nt2": "AA.U1006",
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    },
    {
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      "nt2": "BB.G2003",
      "stericity": "cis",
      "edge5": "Sugar",
      "edge3": "Sugar"
    },
    {
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      "edge5": "Sugar",
      "edge3": "Sugar"
    },
    {
      "nt1": "AB.G1003",
      "nt2": "BB.U2001",
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      "edge5": "Sugar",
      "edge3": "Sugar"
    },
    {
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      "edge3": "Sugar"
    },
    {
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      "edge5": "Sugar",
      "edge3": "Sugar"
    },
    {
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      "edge5": "Sugar",
      "edge3": "Sugar"
    },
    {
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      "edge5": "Sugar",
      "edge3": "Sugar"
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    {
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      "edge5": "Sugar",
      "edge3": "Sugar"
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    {
      "nt1": "B.G2002",
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    },
    {
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      "edge3": "Hoogsteen"
    },
    {
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    },
    {
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      "edge3": "Watson-Crick"
    },
    {
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      "edge3": "Watson-Crick"
    },
    {
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      "edge3": "Hoogsteen"
    },
    {
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      "edge3": "Hoogsteen"
    },
    {
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      "stericity": "cis",
      "edge5": "Hoogsteen",
      "edge3": "Watson-Crick"
    },
    {
      "nt1": "B.G2004",
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      "edge5": "Hoogsteen",
      "edge3": "Watson-Crick"
    },
    {
      "nt1": "BB.G2004",
      "nt2": "B.G2004",
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      "edge5": "Watson-Crick",
      "edge3": "Hoogsteen"
    },
    {
      "nt1": "B.G2004",
      "nt2": "BC.G2004",
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      "edge5": "Watson-Crick",
      "edge3": "Hoogsteen"
    },
    {
      "nt1": "BC.G2004",
      "nt2": "B.G2004",
      "stericity": "cis",
      "edge5": "Hoogsteen",
      "edge3": "Watson-Crick"
    },
    {
      "nt1": "B.G2005",
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      "stericity": "cis",
      "edge5": "Hoogsteen",
      "edge3": "Watson-Crick"
    },
    {
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      "nt2": "B.G2005",
      "stericity": "cis",
      "edge5": "Watson-Crick",
      "edge3": "Hoogsteen"
    },
    {
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      "nt2": "BC.G2005",
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      "edge5": "Watson-Crick",
      "edge3": "Hoogsteen"
    },
    {
      "nt1": "BC.G2005",
      "nt2": "B.G2005",
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      "edge5": "Hoogsteen",
      "edge3": "Watson-Crick"
    },
    {
      "nt1": "B.U2006",
      "nt2": "BB.U2006",
      "stericity": "cis",
      "edge5": "Watson-Crick",
      "edge3": "Hoogsteen"
    },
    {
      "nt1": "BB.U2006",
      "nt2": "B.U2006",
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      "edge5": "Hoogsteen",
      "edge3": "Watson-Crick"
    },
    {
      "nt1": "B.U2006",
      "nt2": "BC.U2006",
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      "edge5": "Hoogsteen",
      "edge3": "Watson-Crick"
    },
    {
      "nt1": "BC.U2006",
      "nt2": "B.U2006",
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      "edge5": "Watson-Crick",
      "edge3": "Hoogsteen"
    },
    {
      "nt1": "BA.G2002",
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      "edge3": "Hoogsteen"
    },
    {
      "nt1": "BB.G2002",
      "nt2": "BA.G2002",
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      "edge3": "Watson-Crick"
    },
    {
      "nt1": "BA.G2002",
      "nt2": "BC.G2002",
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      "edge5": "Hoogsteen",
      "edge3": "Watson-Crick"
    },
    {
      "nt1": "BC.G2002",
      "nt2": "BA.G2002",
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      "edge5": "Watson-Crick",
      "edge3": "Hoogsteen"
    },
    {
      "nt1": "BA.G2003",
      "nt2": "BB.G2003",
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      "edge5": "Watson-Crick",
      "edge3": "Hoogsteen"
    },
    {
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      "edge3": "Watson-Crick"
    },
    {
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      "nt2": "BC.G2003",
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      "edge3": "Watson-Crick"
    },
    {
      "nt1": "BC.G2003",
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      "edge5": "Watson-Crick",
      "edge3": "Hoogsteen"
    },
    {
      "nt1": "BA.G2004",
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      "edge3": "Hoogsteen"
    },
    {
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      "edge3": "Watson-Crick"
    },
    {
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      "edge3": "Watson-Crick"
    },
    {
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      "edge3": "Hoogsteen"
    },
    {
      "nt1": "BA.G2005",
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      "edge3": "Hoogsteen"
    },
    {
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      "edge3": "Watson-Crick"
    },
    {
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      "edge3": "Watson-Crick"
    },
    {
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      "edge3": "Hoogsteen"
    },
    {
      "nt1": "BA.U2006",
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      "edge3": "Watson-Crick"
    },
    {
      "nt1": "BB.U2006",
      "nt2": "BA.U2006",
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      "edge3": "Hoogsteen"
    },
    {
      "nt1": "BA.U2006",
      "nt2": "BC.U2006",
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      "edge3": "Hoogsteen"
    },
    {
      "nt1": "BC.U2006",
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      "edge3": "Watson-Crick"
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      "quadruplexes": [
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              "nt4": "AB.U1006",
              "onz": "O-",
              "gba_classification": "VIIIa",
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                "AA.U1006": [
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                "AB.U1006": [
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                "AC.U1006": [
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            },
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              "nt1": "A.G1005",
              "nt2": "AB.G1005",
              "nt3": "AA.G1005",
              "nt4": "AC.G1005",
              "onz": "O+",
              "gba_classification": "VIIIa",
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              "nt2": "AB.G1004",
              "nt3": "AA.G1004",
              "nt4": "AC.G1004",
              "onz": "O+",
              "gba_classification": "VIIIa",
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              "nt1": "A.G1003",
              "nt2": "AB.G1003",
              "nt3": "AA.G1003",
              "nt4": "AC.G1003",
              "onz": "O+",
              "gba_classification": "VIIIa",
              "planarity_deviation": 0.5550003051758324,
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              "ions_outside": {}
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              "nt1": "A.G1002",
              "nt2": "AB.G1002",
              "nt3": "AA.G1002",
              "nt4": "AC.G1002",
              "onz": "O+",
              "gba_classification": "VIIIa",
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              "ions_outside": {}
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          },
          "onzm": "Op*",
          "loop_classification": "n/a",
          "gba_classification": "VIII",
          "tracts": [
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              "AA.G1005",
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              "AA.G1003",
              "AA.G1002"
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            [
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              "AB.G1005",
              "AB.G1004",
              "AB.G1003",
              "AB.G1002"
            ],
            [
              "A.U1006",
              "A.G1005",
              "A.G1004",
              "A.G1003",
              "A.G1002"
            ],
            [
              "AC.U1006",
              "AC.G1005",
              "AC.G1004",
              "AC.G1003",
              "AC.G1002"
            ]
          ],
          "loops": []
        },
        {
          "tetrads": {
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              "nt2": "BC.G2002",
              "nt3": "BA.G2002",
              "nt4": "BB.G2002",
              "onz": "O+",
              "gba_classification": "VIIIa",
              "planarity_deviation": 0.6730003356935284,
              "ions_channel": [],
              "ions_outside": {}
            },
            "B.G2003-BC.G2003-BA.G2003-BB.G2003": {
              "nt1": "B.G2003",
              "nt2": "BC.G2003",
              "nt3": "BA.G2003",
              "nt4": "BB.G2003",
              "onz": "O+",
              "gba_classification": "VIIIa",
              "planarity_deviation": 0.5770015716552734,
              "ions_channel": [
                "Sr"
              ],
              "ions_outside": {}
            },
            "B.G2004-BC.G2004-BA.G2004-BB.G2004": {
              "nt1": "B.G2004",
              "nt2": "BC.G2004",
              "nt3": "BA.G2004",
              "nt4": "BB.G2004",
              "onz": "O+",
              "gba_classification": "VIIIa",
              "planarity_deviation": 0.2290000915528585,
              "ions_channel": [
                "Sr"
              ],
              "ions_outside": {}
            },
            "B.G2005-BC.G2005-BA.G2005-BB.G2005": {
              "nt1": "B.G2005",
              "nt2": "BC.G2005",
              "nt3": "BA.G2005",
              "nt4": "BB.G2005",
              "onz": "O+",
              "gba_classification": "VIIIa",
              "planarity_deviation": 0.7810001373291016,
              "ions_channel": [],
              "ions_outside": {}
            },
            "B.U2006-BB.U2006-BA.U2006-BC.U2006": {
              "nt1": "B.U2006",
              "nt2": "BB.U2006",
              "nt3": "BA.U2006",
              "nt4": "BC.U2006",
              "onz": "O-",
              "gba_classification": "VIIIa",
              "planarity_deviation": 1.5839996337890805,
              "ions_channel": [
                "Na",
                "Na"
              ],
              "ions_outside": {}
            }
          },
          "onzm": "Op*",
          "loop_classification": "n/a",
          "gba_classification": "VIII",
          "tracts": [
            [
              "BC.G2002",
              "BC.G2003",
              "BC.G2004",
              "BC.G2005",
              "BC.U2006"
            ],
            [
              "BA.G2002",
              "BA.G2003",
              "BA.G2004",
              "BA.G2005",
              "BA.U2006"
            ],
            [
              "BB.G2002",
              "BB.G2003",
              "BB.G2004",
              "BB.G2005",
              "BB.U2006"
            ],
            [
              "B.G2002",
              "B.G2003",
              "B.G2004",
              "B.G2005",
              "B.U2006"
            ]
          ],
          "loops": []
        }
      ],
      "tetrad_pairs": [
        {
          "tetrad1": "A.U1006-AC.U1006-AA.U1006-AB.U1006",
          "tetrad2": "A.G1005-AB.G1005-AA.G1005-AC.G1005",
          "direction": "parallel",
          "rise": 3.3665008544921897,
          "twist": 39.962524289500855
        },
        {
          "tetrad1": "A.G1005-AB.G1005-AA.G1005-AC.G1005",
          "tetrad2": "A.G1004-AB.G1004-AA.G1004-AC.G1004",
          "direction": "parallel",
          "rise": 3.307998657226571,
          "twist": 25.896146524668296
        },
        {
          "tetrad1": "A.G1004-AB.G1004-AA.G1004-AC.G1004",
          "tetrad2": "A.G1003-AB.G1003-AA.G1003-AC.G1003",
          "direction": "parallel",
          "rise": 3.339500427246096,
          "twist": 35.811154582473115
        },
        {
          "tetrad1": "A.G1003-AB.G1003-AA.G1003-AC.G1003",
          "tetrad2": "A.G1002-AB.G1002-AA.G1002-AC.G1002",
          "direction": "parallel",
          "rise": 3.2864990234375084,
          "twist": 27.115165766478476
        },
        {
          "tetrad1": "A.G1002-AB.G1002-AA.G1002-AC.G1002",
          "tetrad2": "B.G2002-BC.G2002-BA.G2002-BB.G2002",
          "direction": "parallel",
          "rise": 3.3695011138916207,
          "twist": 28.99319277639063
        },
        {
          "tetrad1": "B.G2002-BC.G2002-BA.G2002-BB.G2002",
          "tetrad2": "B.G2003-BC.G2003-BA.G2003-BB.G2003",
          "direction": "parallel",
          "rise": 3.370999336242684,
          "twist": 27.410094298550373
        },
        {
          "tetrad1": "B.G2003-BC.G2003-BA.G2003-BB.G2003",
          "tetrad2": "B.G2004-BC.G2004-BA.G2004-BB.G2004",
          "direction": "parallel",
          "rise": 3.317999839782717,
          "twist": 35.04072151642772
        },
        {
          "tetrad1": "B.G2004-BC.G2004-BA.G2004-BB.G2004",
          "tetrad2": "B.G2005-BC.G2005-BA.G2005-BB.G2005",
          "direction": "parallel",
          "rise": 3.269000053405764,
          "twist": 25.149999240922924
        },
        {
          "tetrad1": "B.G2005-BC.G2005-BA.G2005-BB.G2005",
          "tetrad2": "B.U2006-BB.U2006-BA.U2006-BC.U2006",
          "direction": "parallel",
          "rise": 7.140500068664552,
          "twist": 43.406094327700266
        }
      ]
    }
  ]
}

Funding

This research was supported by the National Science Centre, Poland [2016/23/B/ST6/03931, 2019/35/B/ST6/03074] and Mloda Kadra project [09/91/SBAD/0684] from Poznan University of Technology, and carried out in the European Centre for Bioinformatics and Genomics (Poland). The authors also acknowledge partial support by the statutory funds of Poznan University of Technology, Polish Ministry of Science and Higher Education, and the Institute of Bioorganic Chemistry, PAS within intramural financing program.

Bibliography

  1. Topology-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/btz738

  2. ElTetrado: 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

  3. DSSR: An integrated software tool for dissecting the spatial structure of RNA. X.-J. Lu, H.J. Bussemaker, W.K. Olson. Nucleic Acids Research. 2015. 43(21):e142. doi:10.1093/nar/gkv716

  4. R-chie : A web server and R package for visualizing RNA secondary structures. D. Lai, J.R. Proctor, J.Y.A. Zhu, I.M. Meyer. Nucleic Acids Research. 2012. 40(12):e95. doi:10.1093/nar/gks241

  5. Geometric nomenclature and classification of RNA base pairs. N.B. Leontis, E. Westhof. RNA. 2001. 7(4):499–512. doi:10.1017/S1355838201002515

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