diff --git a/requirements.txt b/requirements.txt index 9609bee..c9068de 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,4 +1,4 @@ mmcif==0.90.0 numpy==1.26.4 orjson==3.10.11 -rnapolis==0.3.17 +rnapolis==0.4.7 diff --git a/src/eltetrado/VERSION b/src/eltetrado/VERSION index 26c185e..83d4cf8 100644 --- a/src/eltetrado/VERSION +++ b/src/eltetrado/VERSION @@ -1 +1 @@ -1.5.17 +1.5.18 diff --git a/src/eltetrado/analysis.py b/src/eltetrado/analysis.py index 1d6a51a..2a84d98 100644 --- a/src/eltetrado/analysis.py +++ b/src/eltetrado/analysis.py @@ -8,7 +8,6 @@ import tempfile from collections import Counter, defaultdict from dataclasses import dataclass, field -from functools import lru_cache from typing import IO, Dict, FrozenSet, Iterable, List, Optional, Set, Tuple import numpy @@ -30,69 +29,6 @@ logging.basicConfig(level=os.environ.get("LOGLEVEL", "INFO")) -@lru_cache(maxsize=None) -def is_nucleotide(nt): - phosphate_atoms = {"P", "OP1", "OP2", "O3'", "O5'"} - sugar_atoms = {"C1'", "C2'", "C3'", "C4'", "C5'", "O4'"} - adenine_atoms = {"N1", "C2", "N3", "C4", "C5", "C6", "N6", "N7", "C8", "N9"} - guanine_atoms = {"N1", "C2", "N2", "N3", "C4", "C5", "C6", "O6", "N7", "C8", "N9"} - cytosine_atoms = {"N1", "C2", "O2", "N3", "C4", "N4", "C5", "C6"} - thymine_atoms = {"N1", "C2", "O2", "N3", "C4", "O4", "C5", "C5M", "C6"} - uracil_atoms = {"N1", "C2", "O2", "N3", "C4", "O4", "C5", "C6"} - scores = {"phosphate": 0.0, "sugar": 0.0, "base": 0.0, "connections": 0.0} - weights = {"phosphate": 0.25, "sugar": 0.25, "base": 0.25, "connections": 0.25} - - residue_atoms = {atom.name for atom in nt.atoms} - - phosphate_match = len(residue_atoms.intersection(phosphate_atoms)) - scores["phosphate"] = phosphate_match / len(phosphate_atoms) - - sugar_match = len(residue_atoms.intersection(sugar_atoms)) - scores["sugar"] = sugar_match / len(sugar_atoms) - - matches = { - "A": len(residue_atoms.intersection(adenine_atoms)) / len(adenine_atoms), - "G": len(residue_atoms.intersection(guanine_atoms)) / len(guanine_atoms), - "C": len(residue_atoms.intersection(cytosine_atoms)) / len(cytosine_atoms), - "T": len(residue_atoms.intersection(thymine_atoms)) / len(thymine_atoms), - "U": len(residue_atoms.intersection(uracil_atoms)) / len(uracil_atoms), - } - best_match = max(matches.items(), key=lambda x: x[1]) - scores["base"] = best_match[1] - - connection_score = 0.0 - distance_threshold = 2.0 - - if "P" in residue_atoms and "O5'" in residue_atoms: - p_atom = next(atom for atom in nt.atoms if atom.name == "P") - o5_atom = next(atom for atom in nt.atoms if atom.name == "O5'") - if ( - numpy.linalg.norm(p_atom.coordinates - o5_atom.coordinates) - <= distance_threshold - ): - connection_score += 0.5 - if "C1'" in residue_atoms: - c1_atom = next(atom for atom in nt.atoms if atom.name == "C1'") - for base_connection in ["N9", "N1"]: - if base_connection in residue_atoms: - base_atom = next( - atom for atom in nt.atoms if atom.name == base_connection - ) - if ( - numpy.linalg.norm(c1_atom.coordinates - base_atom.coordinates) - <= distance_threshold - ): - connection_score += 0.5 - break - - scores["connections"] = connection_score - - probability = sum( - scores[component] * weights[component] for component in scores.keys() - ) - return probability > 0.5 - - @dataclass(order=True) class Tetrad: @staticmethod @@ -590,7 +526,7 @@ def __find_loops(self) -> List[Loop]: else: nts = list( filter( - lambda nt: is_nucleotide(nt) + lambda nt: nt.is_nucleotide and self.global_index[nprev] < self.global_index[nt] < self.global_index[ncur], @@ -1286,7 +1222,7 @@ def __dot_bracket(self, pairs: List[BasePair3D]) -> Tuple[str, str]: i = 1 for nt in sorted( - filter(lambda nt: is_nucleotide(nt), self.structure3d.residues), + filter(lambda nt: nt.is_nucleotide, self.structure3d.residues), key=lambda nt: self.global_index[nt], ): if chain and chain != nt.chain: @@ -1330,7 +1266,7 @@ def __str__(self): def __chain_order(self) -> List[str]: only_nucleic_acids = filter( - lambda nt: is_nucleotide(nt), self.structure3d.residues + lambda nt: nt.is_nucleotide, self.structure3d.residues ) return list( { @@ -1451,7 +1387,7 @@ def __to_helix( ONZ.Z_MINUS: 6, } nucleotides = [ - nt for nt in self.analysis.structure3d.residues if is_nucleotide(nt) + nt for nt in self.analysis.structure3d.residues if nt.is_nucleotide ] chain = None shifts = dict() diff --git a/src/eltetrado/dto.py b/src/eltetrado/dto.py index 3420982..5b3cfdd 100644 --- a/src/eltetrado/dto.py +++ b/src/eltetrado/dto.py @@ -3,7 +3,7 @@ from dataclasses import dataclass from typing import List, Optional -from eltetrado.analysis import Analysis, Quadruplex, TetradPair, is_nucleotide +from eltetrado.analysis import Analysis, Quadruplex, TetradPair from eltetrado.model import Ion @@ -127,7 +127,7 @@ def convert_nucleotides(analysis: Analysis) -> List[NucleotideDTO]: nt.chi_class.value if nt.chi_class else None, ) for nt in analysis.structure3d.residues - if is_nucleotide(nt) + if nt.is_nucleotide ] diff --git a/tests/files/6a85-assembly1.cif.gz b/tests/files/6a85-assembly1.cif.gz new file mode 100644 index 0000000..77965ab Binary files /dev/null and b/tests/files/6a85-assembly1.cif.gz differ diff --git a/tests/files/6a85-assembly1.json b/tests/files/6a85-assembly1.json new file mode 100644 index 0000000..dd463dd --- /dev/null +++ b/tests/files/6a85-assembly1.json @@ -0,0 +1 @@ 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Nucleic Acids Res., 43(21):e142 [doi:10.1093/nar/gkv716].","command":"x3dna-dssr -i=/tmp/tmp.i8QALHTIfm.cif --format=mmcif --json --nmr -o=/tmp/tmp.SgHGOJTyK1.json","input_file":"/tmp/tmp.i8QALHTIfm.cif","str_id":"tmp.i8QALHTIfm","num_naChains":4,"naChains":"A=17,B=17,A-2=17,B-2=17","num_atoms":1756,"num_waters":302,"num_metals":28,"metals_desc":"Li=4,Na=22,Pb=2","num_notes":52,"notes":[{"Aminors":"A-minor interactions (including types I and II)"},{"Cstem_index":"stem index of the 'Canonical' helix in k-turn"},{"Cstem_pair":"Cstem bp delineating the k-turn internal loop"},{"Dp":"perpendicular distance of the 3' P atom to the glycosidic bond"},{"GA_pair":"sheared G-A pair in k-turn"},{"HtypePknot":"H-type pseudoknot"},{"Kturn":"kink-turn (k-turn)"},{"LW":"Leontis-Westhof"},{"NCstem_index":"stem index of the 'Non-Canonical' helix in k-turn"},{"NCstem_pair":"NCstem bp delineating the k-turn internal loop"},{"Uturn":"U-turn of the UNR- or GNRA-type"},{"aa":"amino acid"},{"atom_pair":"symbols of the two atoms involved in an H-bond"},{"auxfiles":"auxiliary files"},{"glyco_bond":"conformation of base related to sugar (syn or anti)"},{"bb_type":"backbone conformation, BI or BII"},{"bending_angle":"angle between two helical axes"},{"bp":"base pair"},{"bseq":"base sequence in one-letter code"},{"bulge":"bulge loop"},{"coaxStacks":"coaxial stacking of stems within a helix"},{"dbn":"dot bracket notation"},{"desc":"description"},{"donAcc_type":"donor/acceptor type of the atom pair in an H-bond"},{"epsilon_zeta":"difference between epsilon and zeta torsion angles"},{"hairpin":"hairpin loop"},{"hbond":"hydrogen bond (H-bond)"},{"helix":"defined by base-stacking interactions, regardless of bp type and backbone connectivity"},{"id":"identifier"},{"iloop":"internal loop"},{"index":"serial number"},{"isoCanonPairs":"isolated canonical pairs"},{"junction":"(multi-branched) junction loop"},{"kissingLoop":"kissing loop"},{"multiplet":"3+ bases in a coplanar geometry"},{"na":"nucleic acid"},{"nonPair":"two nts not forming a pair, but with H-bonding/stacking interactions"},{"nonStack":"nucleotide not involved in stacking interactions"},{"nt":"nucleotide"},{"num":"number"},{"oArea":"overlap areas between two bases, including exocyclic atoms"},{"oArea_ring":"overlap areas between two bases, including only ring atoms"},{"phosContacts":"H-bonding and atom-capping interactions involving a phosphate"},{"residue_pair":"types of the two residues involved in an H-bond"},{"rmsd":"root-mean-squares deviation"},{"serNum":"serial number"},{"ssSegments":"single-stranded segments not involved in loops"},{"ssZp":"Z-coordinate of the 3' phosphorus atom with reference to the 5' base plane"},{"sstr":"secondary structure in dbn"},{"stem":"helix consisting of only canonical pairs, with a continuous backbone"},{"str_id":"structure identifier, derived from inpfile with extension removed"},{"vert_dist":"vertical distance from an atom to a base plane"}],"start_at":"Sun Oct 15 07:42:04 2023","finish_at":"Sun Oct 15 07:42:06 2023","time_used":"00:00:00:01"}}}],"start_at":"Sun Oct 15 07:42:04 2023","finish_at":"Sun Oct 15 07:42:06 2023","time_used":"00:00:00:01"} \ No newline at end of file diff --git a/tests/test_dto.py b/tests/test_dto.py index ce0d734..3783e9a 100644 --- a/tests/test_dto.py +++ b/tests/test_dto.py @@ -109,3 +109,28 @@ def test_5v3f(): ) assert dto.dotBracket.line1 == ".......([{..)].(.[{.).]}.}....-.([{..)].(.[{.).]}.}" assert dto.dotBracket.line2 == ".......([(..[{.).]}.{.)].}....-.([(..[{.).]}.{.)].}" + + +def test_6a85(): + """ + In 6A85 the two-line dot-bracket notation requires more than 10 different bracket levels + """ + cif = handle_input_file("tests/files/6a85-assembly1.cif.gz") + structure3d = rnapolis.parser.read_3d_structure(cif, 1) + structure2d = read_secondary_structure_from_dssr( + structure3d, 1, "tests/files/6a85-assembly1.json" + ) + analysis = eltetrado(structure2d, structure3d, False, False, 2) + dto = generate_dto(analysis) + assert ( + dto.dotBracket.sequence + == "AGAGAGATGGGTGCGT-TAGAGAGATGGGTGCGT-TAGAGAGATGGGTGCGT-TAGAGAGATGGGTGCGTT" + ) + assert ( + dto.dotBracket.line1 + == ".([[{{.abcde.f.-..{)(]<.ABCDEF.G.-..}])}>.abcdef.g.." + ) + assert ( + dto.dotBracket.line2 + == ".(([[{.abcde.f.-..)}]g}.>abcde.f.." + )