"""Test the libalign library.""" import os import tempfile from pathlib import Path import numpy as np import pytest from haddock.libs.libalign import ( ALIGNError, align_seq, calc_rmsd, centroid, check_chains, check_common_atoms, dump_as_izone, get_align, get_atoms, kabsch, load_coords, make_range, pdb2fastadic, rearrange_xyz_files, ) from . import golden_data def array_to_list(np_array): """Transform a numpy array in a nested list.""" return [list(e) for e in np_array] def test_kabsch(): """Test the Kabsch algorithm.""" P = [ [-3.811237974683542, -0.12069367088607574, 7.200868354430379], [-5.913237974683542, 8.536306329113923, 6.286868354430379], [12.839762025316457, 8.507306329113923, 4.5878683544303795], [4.856762025316458, -3.7666936708860748, -10.57713164556962], [-1.9222379746835419, -4.171693670886076, -6.596131645569622], [-12.186237974683543, -4.807693670886075, -10.77713164556962], [0.3087620253164576, -7.500693670886075, 8.632868354430379], [-0.08023797468354221, -7.218693670886075, 2.9678683544303794], [9.232762025316458, 18.419306329113926, 8.949868354430379], [-1.7482379746835424, -8.395693670886075, 7.604868354430379], ] Q = [ [6.0952658227848495, -5.630326582278489, 8.033610126582303], [0.5082658227848498, 1.733673417721512, 10.833610126582304], [7.42726582278485, 7.67067341772151, -5.757389873417694], [-12.59373417721515, -6.5263265822784895, 5.217610126582304], [-6.309734177215148, -4.75632658227849, 2.355610126582306], [-3.6647341772151485, -8.990326582278488, -8.014389873417695], [11.789265822784852, -10.62332658227849, 3.966610126582303], [6.895265822784854, -12.33832658227849, 1.2686101265823062], [5.7642658227848536, 16.110673417721507, 1.3446101265823032], [10.306265822784848, -12.226326582278489, 5.028610126582304], ] observed_U = kabsch(P, Q) expected_U = [ [0.38845040189428726, 0.38160307568742435, -0.8387403518932808], [-0.20700756088693778, 0.9230933741949091, 0.32410876608493205], [0.8979165634978604, 0.047725414019726436, 0.43757071411697324], ] np.testing.assert_allclose(np.asarray(expected_U), observed_U) def test_calc_rmsd(): """Test the RMSD calculation.""" V = [ [0.4975639180542826, 2.4634453459517913, 13.502915985158635], [11.227311917422782, 16.269820879072906, -3.962511851240976], [-7.0306634127649135, 4.226046643850031, -8.654935533437529], [-1.592886678968348, -10.874055594404654, -5.820287656251305], [-4.372921399498893, 2.094055858210638, -8.93135311766362], [-1.2876205748591463, -1.4125224802187486, 15.515992917804834], [6.43227627252424, 17.468089367358402, 11.04719510106607], [5.88420286284558, 9.382362089324166, -5.708004059876668], [4.238076687025332, 3.8305358597829944, -5.857279410346993], [5.145346893131023, -2.7233805318567046, 7.910771966100926], ] W = [ [-2.2927341772151664, 1.3226734177215107, 12.252610126582304], [8.353265822784834, 10.995673417721513, -7.888389873417699], [-12.224734177215169, -8.316326582278489, 6.479610126582301], [-6.9257341772151655, 6.939673417721508, -1.281389873417698], [-11.438734177215167, -5.325326582278489, 8.2086101265823], [-3.1317341772151686, -1.6973265822784924, 15.408610126582303], [-0.2497341772151671, 15.53367341772151, 4.4986101265822995], [5.965265822784836, 2.219673417721509, -7.501389873417699], [5.648265822784836, -3.0373265822784887, -4.8293898734177], [5.240265822784835, -3.3833265822784924, 9.9936101265823], ] rmsd = calc_rmsd(V, W) assert round(rmsd, 2) == 12.02 def test_centroid(): """Test the centroid calculation.""" X = [ [6.0952658227848495, -5.630326582278489, 8.033610126582303], [0.5082658227848498, 1.733673417721512, 10.833610126582304], [7.42726582278485, 7.67067341772151, -5.757389873417694], ] observed_centroid = centroid(X) observed_centroid = list(observed_centroid) expected_centroid = [ 4.6769324894515165, 1.2580067510548443, 4.369943459915638, ] assert observed_centroid == expected_centroid def test_load_coords(): """Test the loading of coordinates.""" # pdb_f = protprot_input_list[0] pdb_f = Path(golden_data, "protein.pdb") atoms = get_atoms(pdb_f) ( observed_coord_dic, observed_chain_ranges, ) = load_coords(pdb_f, atoms) observed_keys = list(observed_coord_dic.keys()) expected_keys = [ ("B", 1, "C"), ("B", 1, "O"), ("B", 1, "N"), ("B", 1, "CA"), ("B", 2, "N"), ("B", 2, "CA"), ("B", 2, "C"), ("B", 2, "O"), ("B", 3, "N"), ("B", 3, "CA"), ("B", 3, "C"), ("B", 3, "O"), ("B", 4, "N"), ("B", 4, "CA"), ("B", 4, "C"), ("B", 4, "O"), ("B", 5, "N"), ("B", 5, "CA"), ("B", 5, "C"), ("B", 5, "O"), ] assert observed_keys == expected_keys observed_coords = array_to_list(observed_coord_dic.values()) expected_coords = [ [2.76, 8.901, -10.955], [3.081, 10.085, -10.981], [3.315, 8.47, -13.254], [3.439, 7.91, -11.913], [1.846, 8.365, -10.156], [1.091, 9.158, -9.167], [1.355, 8.587, -7.772], [1.393, 7.371, -7.574], [1.625, 9.513, -6.851], [2.045, 9.187, -5.471], [1.203, 9.91, -4.411], [0.519, 10.884, -4.708], [1.149, 9.269, -3.244], [0.62, 9.867, -2.011], [1.447, 9.408, -0.806], [1.613, 8.206, -0.591], [2.009, 10.387, -0.089], [2.761, 10.16, 1.151], [1.832, 10.156, 2.373], [1.352, 11.174, 2.853], ] assert observed_coords == expected_coords expected_chain_ranges = {"B": (0, 19)} assert observed_chain_ranges == expected_chain_ranges def test_wrong_filtered_resid_error_load_coords(): """Test the residue matching error with an uncompatible resdic.""" filter_resdic_wrongres = {"B": [7, 8, 9]} # protein has only residues 1-5 pdb_f = Path(golden_data, "protein.pdb") atoms = get_atoms(pdb_f) with pytest.raises(ALIGNError): load_coords(pdb_f, atoms, filter_resdic=filter_resdic_wrongres) def test_wrong_filtered_chain_error_load_coords(): """Test the chain matching error with an uncompatible resdic.""" filter_resdic_wrongchain = {"A": [1, 2, 3]} # protein has only chain B pdb_f = Path(golden_data, "protein.pdb") atoms = get_atoms(pdb_f) with pytest.raises(ALIGNError): load_coords(pdb_f, atoms, filter_resdic=filter_resdic_wrongchain) def test_get_atoms(): """Test the identification of atoms.""" pdb_list = [ Path(golden_data, "protein.pdb"), Path(golden_data, "dna.pdb"), Path(golden_data, "ligand.pdb"), ] observed_atom_dic = {} for p in pdb_list: observed_atom_dic.update(get_atoms(p)) expected_atom_dic = { "ALA": ["C", "N", "CA", "O"], "ARG": ["C", "N", "CA", "O"], "ASN": ["C", "N", "CA", "O"], "ASP": ["C", "N", "CA", "O"], "CYS": ["C", "N", "CA", "O"], "GLN": ["C", "N", "CA", "O"], "GLU": ["C", "N", "CA", "O"], "GLY": ["C", "N", "CA", "O"], "HIS": ["C", "N", "CA", "O"], "ILE": ["C", "N", "CA", "O"], "LEU": ["C", "N", "CA", "O"], "LYS": ["C", "N", "CA", "O"], "MET": ["C", "N", "CA", "O"], "PHE": ["C", "N", "CA", "O"], "PRO": ["C", "N", "CA", "O"], "SER": ["C", "N", "CA", "O"], "THR": ["C", "N", "CA", "O"], "TRP": ["C", "N", "CA", "O"], "TYR": ["C", "N", "CA", "O"], "VAL": ["C", "N", "CA", "O"], "DA": [ "C5", "N9", "N2", "C8", "O2", "N4", "N7", "C7", "N1", "N6", "C2", "O4", "C6", "N3", "C4", "O6", ], "DC": [ "C5", "N9", "N2", "C8", "O2", "N4", "N7", "C7", "N1", "N6", "C2", "O4", "C6", "N3", "C4", "O6", ], "DT": [ "C5", "N9", "N2", "C8", "O2", "N4", "N7", "C7", "N1", "N6", "C2", "O4", "C6", "N3", "C4", "O6", ], "DG": [ "C5", "N9", "N2", "C8", "O2", "N4", "N7", "C7", "N1", "N6", "C2", "O4", "C6", "N3", "C4", "O6", ], "A": ["P", "O5'", "C5'", "C4'", "C3'", "O3'"], "G": ["P", "O5'", "C5'", "C4'", "C3'", "O3'"], "C": ["P", "O5'", "C5'", "C4'", "C3'", "O3'"], "U": ["P", "O5'", "C5'", "C4'", "C3'", "O3'"], "G39": [ "C1", "O1A", "O1B", "C2", "C3", "C4", "N4", "C5", "N5", "C6", "C7", "O7", "C8", "C9", "C10", "O10", "C11", "C81", "C82", "C91", ], } assert observed_atom_dic == expected_atom_dic def test_pdb2fastadic(): """Test the generation of the fastadic.""" protein_f = Path(golden_data, "protein.pdb") dna_f = Path(golden_data, "dna.pdb") ligand_f = Path(golden_data, "ligand.pdb") observed_prot_fastadic = pdb2fastadic(protein_f) expected_prot_fastadic = {"B": {1: "M", 2: "F", 3: "Q", 4: "Q", 5: "E"}} assert observed_prot_fastadic == expected_prot_fastadic observed_dna_fastadic = pdb2fastadic(dna_f) expected_dna_fastadic = { "B": { 1: "A", 2: "G", 3: "T", 4: "A", 5: "C", 28: "A", 29: "A", 30: "G", 31: "T", 32: "T", } } assert observed_dna_fastadic == expected_dna_fastadic observed_ligand_fastadic = pdb2fastadic(ligand_f) expected_ligand_fastadic = {"B": {500: "X"}} assert observed_ligand_fastadic == expected_ligand_fastadic def test_get_align(): """Test the selection of the align function.""" align_func = get_align(method="sequence", lovoalign_exec="") assert callable(align_func) align_func = get_align(method="structure", lovoalign_exec="") assert callable(align_func) # Need dependency to test this # def test_align_strct(): # pass def test_align_seq(): """Test the sequence alignment.""" ref = Path(golden_data, "protein.pdb") mod = Path(golden_data, "protein_renumb.pdb") with tempfile.TemporaryDirectory() as tmpdirname: observed_numb_dic, observed_chm_dict = align_seq(ref, mod, tmpdirname) expected_numb_dic = {"B": {101: 1, 102: 2, 110: 3, 112: 5}} expected_chm_dict = {"B": "B"} assert observed_numb_dic == expected_numb_dic assert observed_chm_dict == expected_chm_dict expected_aln_f = Path(tmpdirname, "blosum62_B.aln") assert expected_aln_f.exists() observed_aln = open(expected_aln_f).readlines() expected_aln = [ f"target 0 MFQQE 5{os.linesep}", f" 0 |||-| 5{os.linesep}", f"query 0 MFQ-E 4{os.linesep}", ] assert observed_aln == expected_aln def test_align_seq_chm(): """Test the sequence alignment with chain matching.""" ref = Path(golden_data, "protein.pdb") mod = Path(golden_data, "protein_segid.pdb") with tempfile.TemporaryDirectory() as tmpdirname: observed_numb_dic, observed_chm_dict = align_seq(ref, mod, tmpdirname) expected_numb_dic = {"B": {1: 1, 2: 2, 3: 3, 4: 4, 5: 5}} expected_chm_dict = {"X": "B"} assert observed_numb_dic == expected_numb_dic assert observed_chm_dict == expected_chm_dict def test_align_seq_inverted(): """Test the sequence alignment with inverted chain.""" ref = Path(golden_data, "protprot_complex_1.pdb") mod = Path(golden_data, "protprot_complex_2_inverted.pdb") with tempfile.TemporaryDirectory() as tmpdirname: observed_numb_dic, observed_chm_dict = align_seq(ref, mod, tmpdirname) expected_numb_keys = ["A", "B"] expected_chm_dict = {"A": "A", "B": "B"} assert list(observed_numb_dic.keys()) == expected_numb_keys assert observed_chm_dict == expected_chm_dict def test_make_range(): """Test the expansion of a chain dic into ranges.""" chain_range_dic = {"A": [1, 2, 4], "B": [100, 110, 200]} observed_range_dic = make_range(chain_range_dic) expected_range_dic = {"A": (1, 4), "B": (100, 200)} assert observed_range_dic == expected_range_dic def test_dump_as_izone(): """Test the generation of .izone file.""" numb_dic = {"B": {1: 101, 2: 102, 3: 110, 5: 112}} with tempfile.NamedTemporaryFile() as fp: dump_as_izone(fp.name, numb_dic) assert Path(fp.name).stat().st_size != 0 observed_izone = open(fp.name).readlines() expected_izone = [ f"ZONE B1:B101{os.linesep}", f"ZONE B2:B102{os.linesep}", f"ZONE B3:B110{os.linesep}", f"ZONE B5:B112{os.linesep}", ] assert observed_izone == expected_izone chm_ref2model_dict = {"B": "X"} with tempfile.NamedTemporaryFile() as fp: dump_as_izone(fp.name, numb_dic, chm_ref2model_dict) assert Path(fp.name).stat().st_size != 0 observed_izone = open(fp.name).readlines() expected_izone = [ f"ZONE B1:X101{os.linesep}", f"ZONE B2:X102{os.linesep}", f"ZONE B3:X110{os.linesep}", f"ZONE B5:X112{os.linesep}", ] assert observed_izone == expected_izone def test_check_common_atoms(): """Test the identification of common atoms.""" ref = Path(golden_data, "protprot_complex_1.pdb") mod = Path(golden_data, "protprot_complex_2.pdb") models = [ref, mod] n_atoms, obs_common_keys = check_common_atoms(models, None, False, 90.0) assert n_atoms == 950 assert len(obs_common_keys) == 950 assert ("B", 74, "N") in obs_common_keys models.append(Path(golden_data, "protein.pdb")) with pytest.raises(ALIGNError): n_atoms, obs_common_keys = check_common_atoms(models, None, False, 90.0) def test_rearrange_xyz_files(): """Test the rearrange_xyz_files function.""" with tempfile.TemporaryDirectory() as tmpdirname: ncores = 4 # Create a temporary directory with some files for i in range(ncores): with open(Path(tmpdirname, f"file_{i}.xyz"), "w") as f: f.write(f"{i} 0 0 0\n") # Test the function rearrange_xyz_files("file.xyz", path=tmpdirname, ncores=ncores) # Check the files have been renamed assert not Path(tmpdirname, "file_0.xyz").exists() assert Path(tmpdirname, "file.xyz").exists() # Check the content of the file with open(Path(tmpdirname, "file.xyz"), "r") as f: obs_content = f.read() exp_content = os.linesep.join([f"{i} 0 0 0" for i in range(ncores)]) exp_content += os.linesep assert obs_content == exp_content def test_check_chains(): """Test correct checking of chains.""" obs_ch = [ ["A", "C"], ["A", "B"], ["S", "E", "B", "A"], ["S", "E", "P", "A"], ["C", "D"], ] inp_receptor_chains = ["A", "A", "A", "A", "C"] inp_ligand_chains = [ [], [], ["B", "E"], ["B"], ["B"], ] # assuming exp chains are A and B exp_ch = [ ["A", ["C"]], # C becomes the ligand ["A", ["B"]], # C becomes the ligand ["A", ["B", "E"]], # S is ignored (B,E are present) ["A", ["S", "E", "P"]], # B is not there, S-E-P become the ligands ["C", ["D"]], ] # B is not there, D becomes the ligand for n in range(len(obs_ch)): obs_r_chain, obs_l_chain = check_chains( obs_ch[n], inp_receptor_chains[n], inp_ligand_chains[n] ) exp_r_chain, exp_l_chain = exp_ch[n][0], exp_ch[n][1] assert obs_r_chain == exp_r_chain assert obs_l_chain == exp_l_chain