def test_input_PDBcount( self ):
"""
Check how selection works when a PDB count string
is provided
"""
arr = [2, 3, 4, 5, 15, 21, 22, 23, 24, 68, 72]
shw = "2A-5A,15A,21A-24A,68A,72A"
s = rc.Selection(shw)
assert s.to_list() == arr
assert s.to_string() == shw
assert s.seqID() == "A"
assert s.is_empty() == False
assert s.is_shifted() == True
s = rc.Selection("5A")
assert s.to_list() == [5]
assert s.to_string() == "5A"
assert s.is_empty() == False
assert s.is_shifted() == True
with pytest.raises(AttributeError):
shw = "2A-5A,15B,21A-24A,68A,72A"
s = rc.Selection(shw)
shw = "2A-5A,15,21A-24A,68A,72A"
s = rc.Selection(shw)
def _add_sequences(manager, data, chains):
"""
Fix and load requested sequence/structure into the data.
Also takes labels into account.
:return: data
"""
# Correct by non polymer residues
nonPoly = [x for x, v in enumerate(chains["seq"]) if v == 'Z']
ochaini = chains["id"]
for index in sorted(nonPoly, reverse=True):
del chains["id"][index]
del chains["seq"][index]
if len(chains["dssp"]) > 0:
del chains["dssp"][index]
for seqname, seq in manager.get_expected_sequences(chains):
data.setdefault(seqname, []).append(seq)
if len(chains["dssp"]) > 0:
for ssename, str3d in manager.get_expected_structures(chains):
data.setdefault(ssename, []).append(str3d)
if len(chains["psipred"]) > 0:
for ssename, str3d in manager.get_expected_psipred(chains):
data.setdefault(ssename, []).append(str3d)
if len(chains["phi"]) > 0:
for ssename, str3d in manager.get_expected_dihedrals(chains, "phi"):
data.setdefault(ssename, []).append(str3d)
if len(chains["psi"]) > 0:
for ssename, str3d in manager.get_expected_dihedrals(chains, "psi"):
data.setdefault(ssename, []).append(str3d)
for x in [i for i in data if i.startswith("lbl_")]:
data[x][-1] = rc.Selection(data[x][-1]).map_to_sequences(ochaini)
return data
def test_input_empty( self ):
"""
Check how Selection works when nothing is given
"""
arr = []
shw = ""
s = rc.Selection(arr)
assert s.to_list() == arr
assert s.to_string() == shw
assert s.is_empty() == True
assert s.is_shifted() == False
s = rc.Selection(shw)
assert s.to_list() == arr
assert s.to_string() == shw
assert s.is_empty() == True
assert s.is_shifted() == False
def test_input_string( self ):
"""
Check how Selection works when a string is given
"""
arr = [2, 3, 4, 5, 15, 21, 22, 23, 24, 68, 72]
shw = "2-5,15,21-24,68,72"
s = rc.Selection(shw)
assert s.to_list() == arr
assert s.to_string() == shw
assert s.seqID() is None
assert s.is_empty() == False
assert s.is_shifted() == False
s = rc.Selection("5")
assert s.to_list() == [5]
assert s.to_string() == "5"
assert s.is_empty() == False
assert s.is_shifted() == False
def test_input_array( self ):
"""
Check how Selection works when an array is given
"""
arr = [2, 3, 4, 5, 15, 21, 22, 23, 24, 68, 72]
shw = "2-5,15,21-24,68,72"
s = rc.Selection(arr)
assert s.to_list() == arr
assert s.to_string() == shw
assert s.is_empty() == False
assert s.is_shifted() == False
def test_map_to_sequences( self ):
a1 = [2, 3, 4, 5, 15, 21, 22, 23, 24, 50, 51, 68, 72, 110, 111, 112, 113]
a2 = [2, 3, 210]
_1 = [2, 3, 4, 5, 15, 21, 22, 23, 24, 50]
_2 = list(np.array([51, 68, 72]) - 50)
_3 = list(np.array([110, 111, 112, 113]) - 100)
t1 = "2A-5A,15A,21A-24A,68A,72A, 110A-113A"
s1 = rc.Selection(a1)
s2 = rc.Selection(t1)
s3 = rc.Selection(a2)
smap = ["A", ] * 50
smap.extend(["B", ] * 50)
smap.extend(["C", ] * 50)
smap.extend(["D", ] * 50)
cntr1 = "A:#(10),B:#(3),C:#(4),D:#(0)"
cntr2 = "A:@(10),B:@(3),C:#(4),D:#(0)"
s1a = s1.map_to_sequences(smap)
assert s1a["A"] == _1
assert s1a["B"] == _2
assert s1a["C"] == _3
assert str(s1a) == cntr1
# shift assumes first position is 1, not 0
s1a.shift("A", 5)
s1a.shift("B", 2)
assert s1a["A"].to_list() == list(np.array(_1) + (5 - 1))
assert s1a["B"].to_list() == list(np.array(_2) + (2 - 1))
assert s1a["C"] == _3
assert str(s1a) == cntr2
# Selection w/ seqID should raise an error
with pytest.raises(KeyError):
s2.map_to_sequences(smap)
# Going out of range raises error
with pytest.raises(IndexError):
s3.map_to_sequences(smap)
def test_operations( self ):
a1 = [2, 3, 4, 5, 15, 21, 22, 23, 24, 68, 72]
_12 = [2, 3, 4, 5, 6, 15, 21, 22, 23, 24, 68, 72]
_13 = [2, 3, 4, 5, 21, 22, 23, 24, 68, 72]
_14 = [1, 2, 3, 4, 14, 20, 21, 22, 23, 67, 71]
_15 = [3, 4, 5, 6, 16, 22, 23, 24, 25, 69, 73]
a2 = [2, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27]
_21 = [2, 3, 4, 5, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 68, 72]
_22 = [3, 4, 5, 68, 72]
_23 = [2, 15, 21, 22, 23, 24]
t1 = "2A-5A,15A,21A-24A,68A,72A"
t2 = "2A,15A-18A,21A-27A"
s1 = rc.Selection(a1)
s2 = rc.Selection(a2)
s3 = rc.Selection(t1)
s4 = rc.Selection(t2)
# equal
assert s1 == a1
assert s1 != a2
# invert
sn1 = ~s1
picks = sn1.to_list(100)
assert len(set(picks).intersection(s1.to_list())) == 0
assert len(set(picks).union(s1.to_list())) == 100
assert sn1 != s1
# add, sub
s1a = s1 + 6 # operate w/ integer
assert s1a == _12
s1a = s1 - 15 # operate w/ integer
assert s1a == _13
s2a = s1 + s2 # operate w/ Selection
assert s2a == _21
s2a = s1 - s2 # operate w/ Selection
assert s2a == _22
s2a = s1a + a2 # operate w/ list
assert s2a == _21
s2a = s1a - a2 # operate w/ list
assert s2a == _22
s3a = s3 + s4 # operate w/ Selection w/ seqID
assert s3a.to_list() == _21
s3a = s3 - s4 # operate w/ Selection w/ seqID
assert s3a.to_list() == _22
with pytest.raises(KeyError):
s3a = s3 + 6 # operate w/ in to Select w/ seqID
with pytest.raises(KeyError):
s3a = s3 + a2 # operate w/ in to Select w/ seqID
s3a = s3 + "6A" # opearte w/ string
assert s3a.to_list() == _12
s3a = s3 - "15A" # opearte w/ string
assert s3a.to_list() == _13
# operate w/ invert (does not have the working length)
with pytest.raises(AttributeError):
assert (s1 + s2) == (s1 - ~s2)
with pytest.raises(AttributeError):
assert (s1 - s2) == (s1 + ~s2)
# shift
s4a = s1 << 1
assert s4a == _14
s4a = s1 >> 1
assert s4a == _15
# logical operations
s5a = s1 & s2
assert s5a == _23
s5a = s1 | s2
assert s5a == _21
def test_input_selection_or_None( self ):
s = rc.Selection()
assert len(s) == 0
s2 = rc.Selection(s)
assert len(s) == len(s2)