Esempio n. 1
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def test_common_contacts_featurizer_1():
    trajectories = MetEnkephalin().get_cached().trajectories
    top = trajectories[0].topology
    met_seq = top.to_fasta(0)
    #fake sequence has an insertion
    fake_met_eq ='YGGFMF'
    alignment={}
    #do "alignment "
    alignment["actual"] = met_seq+"-"
    alignment["fake"] = fake_met_eq

    feat = CommonContactFeaturizer(alignment=alignment, contacts='all',
                                   same_residue=True)
    rnd_traj = np.random.randint(len(trajectories))
    df = pd.DataFrame(feat.describe_features(trajectories[rnd_traj]))
    features = feat.transform([trajectories[rnd_traj]])
Esempio n. 2
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def test_common_contacts_featurizer_1():
    trajectories = MetEnkephalin().get_cached().trajectories
    top = trajectories[0].topology
    met_seq = top.to_fasta(0)
    # fake sequence has an insertion
    fake_met_eq = 'YGGFMF'
    alignment = {}
    # do "alignment "
    alignment["actual"] = met_seq + "-"
    alignment["fake"] = fake_met_eq
    max_len = max([len(alignment[i]) for i in alignment.keys()])
    contacts = [i for i in itertools.combinations(np.arange(max_len), 2)]
    feat = CommonContactFeaturizer(alignment=alignment, contacts=contacts,
                                   same_residue=True)
    rnd_traj = np.random.randint(len(trajectories))
    df = pd.DataFrame(feat.describe_features(trajectories[rnd_traj]))
    features = feat.transform([trajectories[rnd_traj]])
Esempio n. 3
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def test_common_contacts_featurizer_2():
    trajectories = MetEnkephalin().get_cached().trajectories
    top = trajectories[0].topology
    met_seq = top.to_fasta(0)
    #fake sequence
    fake_met_eq ='FGGFM'
    alignment={}
    #do "alignment "
    alignment["actual"] = met_seq
    alignment["fake"] = fake_met_eq

    feat = CommonContactFeaturizer(alignment=alignment, contacts='all',
                                   same_residue=True)

    rnd_traj = np.random.randint(len(trajectories))
    df = pd.DataFrame(feat.describe_features(trajectories[rnd_traj]))
    assert(np.all([j!=0 for i in df.resids for j in i]))
Esempio n. 4
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def test_common_contacts_featurizer_2():
    #test randomly mutates one of the residues to make sure that residues contacts are not
    #included
    trajectories = MetEnkephalin().get_cached().trajectories
    top = trajectories[0].topology
    met_seq = top.to_fasta(0)
    #randomly "mutate one of the residues to alanine
    rnd_loc = np.random.randint(len(met_seq))
    fake_met_eq=met_seq[:rnd_loc]+"A"+met_seq[rnd_loc+1:]
    alignment={}
    #do "alignment "
    alignment["actual"] = met_seq
    alignment["fake"] = fake_met_eq

    feat = CommonContactFeaturizer(alignment=alignment, contacts='all',
                                   same_residue=True)

    rnd_traj = np.random.randint(len(trajectories))
    df = pd.DataFrame(feat.describe_features(trajectories[rnd_traj]))
    assert(np.all([j!=rnd_loc for i in df.resids for j in i]))