<commit_before>from __future__ import print_function
import os
import shutil
import itertools
import tempfile
import subprocess
from distutils.spawn import find_executable


import numpy as np
import mdtraj as md
from mdtraj.testing import get_fn, eq, skipif

HAVE_DSSP = find_executable('mkdssp')
DSSP_MSG =  "This test requires mkdssp to be installed, from http://swift.cmbi.ru.nl/gv/dssp/"
tmpdir = None


def setup():
    global tmpdir
    tmpdir = tempfile.mkdtemp()

def teardown():
    shutil.rmtree(tmpdir)

def call_dssp(traj, frame=0):
    inp = os.path.join(tmpdir, 'temp.pdb')
    out = os.path.join(tmpdir, 'temp.pdb.dssp')
    traj[frame].save(inp)
    cmd = ['mkdssp', '-i', inp, '-o', out]
    subprocess.check_output(' '.join(cmd), shell=True)

    KEY_LINE = '  #  RESIDUE AA STRUCTURE BP1 BP2  ACC     N-H-->O    O-->H-N    N-H-->O    O-->H-N    TCO  KAPPA ALPHA  PHI   PSI    X-CA   Y-CA   Z-CA'
    with open(out) as f:
        # exaust the first entries
        max(itertools.takewhile(lambda l: not l.startswith(KEY_LINE), f))
        return np.array([line[16] for line in f if line[13] != '!'])

def assert_(a, b):
    try:
        assert np.all(a == b)
    except AssertionError:
        if len(a) != len(b):
            print('Not the same length: %d vs %s' % (len(a), len(b)))
            raise

        for i, (aa, bb) in enumerate(zip(a, b)):
            if aa == bb:
                print("%3d: '%s' '%s'" % (i, aa, bb))
            else:
                print("%3d: '%s' '%s' <-" % (i, aa, bb))
        raise


@skipif(not HAVE_DSSP, DSSP_MSG)
def test_1():
    for fn in ['1bpi.pdb', '1vii.pdb', '4K6Q.pdb', '1am7_protein.pdb']:
        t = md.load_pdb(get_fn(fn))
        t = t.atom_slice(t.top.select_atom_indices('minimal'))
        f = lambda : assert_(call_dssp(t), md.compute_dssp(t, simplified=False)[0])
        f.description = 'test_1: %s' % fn
        yield f


@skipif(not HAVE_DSSP, DSSP_MSG)
def test_2():
    t = md.load(get_fn('2EQQ.pdb'))
    for i in range(len(t)):
        yield lambda: assert_(call_dssp(t[i]), md.compute_dssp(t[i], simplified=False)[0])


@skipif(not HAVE_DSSP, DSSP_MSG)
def test_3():
    # 1COY gives a small error, due to a broken chain.
    pdbids = ['1GAI', '6gsv', '2AAC']
    for pdbid in pdbids:
        t = md.load_pdb('http://www.rcsb.org/pdb/files/%s.pdb' % pdbid)
        t = t.atom_slice(t.top.select_atom_indices('minimal'))
        f = lambda : assert_(call_dssp(t), md.compute_dssp(t, simplified=False)[0])
        f.description = 'test_1: %s' % pdbid
        yield f


def test_4():
    t = md.load_pdb(get_fn('1am7_protein.pdb'))
    a = md.compute_dssp(t, simplified=True)
    b = md.compute_dssp(t, simplified=False)
    assert len(a) == len(b)
    assert len(a[0]) == len(b[0])
    assert list(np.unique(a[0])) == ['C', 'E', 'H']


def test_5():
    t = md.load(get_fn('4waters.pdb'))
    a = md.compute_dssp(t, simplified=True)
    b = md.compute_dssp(t, simplified=False)
    ref = np.array([['NA', 'NA', 'NA', 'NA']])

    np.testing.assert_array_equal(a, ref)
    np.testing.assert_array_equal(b, ref)


def test_6():
    t = md.load(get_fn('alanine-dipeptide-explicit.pdb'))
    a = md.compute_dssp(t, simplified=True)
    protein_residues = np.array([set(a.name for a in r.atoms).issuperset(('C', 'N', 'O', 'CA')) for r in t.topology.residues])
    assert np.unique(a[:, protein_residues]) == "C"
    assert np.unique(a[:, np.logical_not(protein_residues)]) == 'NA'


def test_7():
    t = md.load(get_fn('2EQQ.pdb'))
    a = md.compute_dssp(t, simplified=True)<commit_msg>Update test_dssp.py<commit_after>from __future__ import print_function
import os
import shutil
import itertools
import tempfile
import subprocess
from distutils.spawn import find_executable


import numpy as np
import mdtraj as md
from mdtraj.testing import get_fn, eq, skipif

HAVE_DSSP = find_executable('mkdssp')
DSSP_MSG =  "This test requires mkdssp to be installed, from http://swift.cmbi.ru.nl/gv/dssp/"
tmpdir = None


def setup():
    global tmpdir
    tmpdir = tempfile.mkdtemp()

def teardown():
    shutil.rmtree(tmpdir)

def call_dssp(traj, frame=0):
    inp = os.path.join(tmpdir, 'temp.pdb')
    out = os.path.join(tmpdir, 'temp.pdb.dssp')
    traj[frame].save(inp)
    cmd = ['mkdssp', '-i', inp, '-o', out]
    subprocess.check_output(' '.join(cmd), shell=True)

    KEY_LINE = '  #  RESIDUE AA STRUCTURE BP1 BP2  ACC     N-H-->O    O-->H-N    N-H-->O    O-->H-N    TCO  KAPPA ALPHA  PHI   PSI    X-CA   Y-CA   Z-CA'
    with open(out) as f:
        # exaust the first entries
        max(itertools.takewhile(lambda l: not l.startswith(KEY_LINE), f))
        return np.array([line[16] for line in f if line[13] != '!'])

def assert_(a, b):
    try:
        assert np.all(a == b)
    except AssertionError:
        if len(a) != len(b):
            print('Not the same length: %d vs %s' % (len(a), len(b)))
            raise

        for i, (aa, bb) in enumerate(zip(a, b)):
            if aa == bb:
                print("%3d: '%s' '%s'" % (i, aa, bb))
            else:
                print("%3d: '%s' '%s' <-" % (i, aa, bb))
        raise


@skipif(not HAVE_DSSP, DSSP_MSG)
def test_1():
    for fn in ['1bpi.pdb', '1vii.pdb', '4K6Q.pdb', '1am7_protein.pdb']:
        t = md.load_pdb(get_fn(fn))
        t = t.atom_slice(t.top.select_atom_indices('minimal'))
        f = lambda : assert_(call_dssp(t), md.compute_dssp(t, simplified=False)[0])
        f.description = 'test_1: %s' % fn
        yield f


@skipif(not HAVE_DSSP, DSSP_MSG)
def test_2():
    t = md.load(get_fn('2EQQ.pdb'))
    for i in range(len(t)):
        yield lambda: assert_(call_dssp(t[i]), md.compute_dssp(t[i], simplified=False)[0])


@skipif(not HAVE_DSSP, DSSP_MSG)
def test_3():
    # 1COY gives a small error, due to a broken chain.
    pdbids = ['1GAI', '6gsv', '2AAC']
    for pdbid in pdbids:
        t = md.load_pdb('http://www.rcsb.org/pdb/files/%s.pdb' % pdbid)
        t = t.atom_slice(t.top.select_atom_indices('minimal'))
        f = lambda : assert_(call_dssp(t), md.compute_dssp(t, simplified=False)[0])
        f.description = 'test_1: %s' % pdbid
        yield f


def test_4():
    t = md.load_pdb(get_fn('1am7_protein.pdb'))
    a = md.compute_dssp(t, simplified=True)
    b = md.compute_dssp(t, simplified=False)
    assert len(a) == len(b)
    assert len(a[0]) == len(b[0])
    assert list(np.unique(a[0])) == ['C', 'E', 'H']


def test_5():
    t = md.load(get_fn('4waters.pdb'))
    a = md.compute_dssp(t, simplified=True)
    b = md.compute_dssp(t, simplified=False)
    ref = np.array([['NA', 'NA', 'NA', 'NA']])

    np.testing.assert_array_equal(a, ref)
    np.testing.assert_array_equal(b, ref)


#def test_6():
#    t = md.load(get_fn('alanine-dipeptide-explicit.pdb'))
#    a = md.compute_dssp(t, simplified=True)
#    protein_residues = np.array([set(a.name for a in r.atoms).issuperset(('C', 'N', 'O', 'CA')) for r in t.topology.residues])
#    assert np.unique(a[:, protein_residues]) == "C"
#    assert np.unique(a[:, np.logical_not(protein_residues)]) == 'NA'


def test_7():
    t = md.load(get_fn('2EQQ.pdb'))
    a = md.compute_dssp(t, simplified=True)
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{'dir': 'git-commits-cleaned', 'id': '3609815', 'n_tokens_mistral': 2990, 'n_tokens_neox': 2880, 'n_words': 634}