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Correct behaviour and improves selaltloc (#136)
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* Add new tests

* add tests for the new scenario
* add vu7.pdb for tests that went missing on previous version

* correct implementation and add tests
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@joaomcteixeira
joaomcteixeira committed Jun 18, 2022
1 parent e9fe50e commit 575db16
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Showing 3 changed files with 247 additions and 26 deletions.
1 change: 1 addition & 0 deletions pdbtools/pdb_selaltloc.py
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Original file line number Diff line number Diff line change
Expand Up @@ -265,6 +265,7 @@ def is_another_altloc_group(
is_another = (
all((a0, ra0, ru0)) and (
(a0 != a1 and a1 == ' ' and ru1 > ru0)
or (a0 == ' ' and a1 != ' ' and ru1 > ru0)
or (a0 == ' ' and a1 == ' ' and (ru1 != ru0 or ra1 != ra0))
or (
a0 == a1
Expand Down
35 changes: 35 additions & 0 deletions tests/data/dummy_altloc3.pdb
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Original file line number Diff line number Diff line change
@@ -0,0 +1,35 @@
ATOM 153 N VAL A 18 -0.264 -17.574 22.788 0.00 0.00 N
ATOM 154 CA VAL A 18 -0.201 -17.901 24.209 0.00 0.00 C
ATOM 155 C VAL A 18 -1.047 -19.150 24.437 0.00 0.00 C
ATOM 156 O VAL A 18 -2.260 -19.144 24.214 0.00 0.00 O
ATOM 157 CB VAL A 18 -0.689 -16.724 25.084 0.00 0.00 C
ATOM 161 N TRP A 19 -0.408 -20.230 24.882 0.00 0.00 N
ATOM 162 CA TRP A 19 -1.091 -21.490 25.161 0.00 0.00 C
ATOM 163 C TRP A 19 -1.303 -21.563 26.667 0.00 0.00 C
ATOM 164 O TRP A 19 -0.357 -21.920 27.375 0.00 0.00 O
ATOM 165 CB TRP A 19 -0.272 -22.670 24.635 0.00 0.00 C
ATOM 176 N TYR A 20 -2.522 -21.226 27.083 0.00 0.00 N
ATOM 177 CA TYR A 20 -2.898 -21.178 28.493 0.00 0.00 C
ATOM 178 C TYR A 20 -3.718 -22.410 28.851 0.00 0.00 C
ATOM 179 O TYR A 20 -4.629 -22.780 28.105 0.00 0.00 O
ATOM 180 CB TYR A 20 -3.681 -19.898 28.795 0.00 0.00 C
ATOM 189 N AVAL A 21 -3.396 -23.034 29.982 0.40 0.00 N
ATOM 197 N BALA A 21 -5.676 -24.647 32.284 0.60 0.00 N
ATOM 190 CA AVAL A 21 -4.121 -24.205 30.467 0.40 0.00 C
ATOM 198 CA BALA A 21 -6.012 -24.814 33.696 0.60 0.00 C
ATOM 191 C AVAL A 21 -4.530 -24.072 31.930 0.40 0.00 C
ATOM 199 C BALA A 21 -4.990 -25.677 34.426 0.60 0.00 C
ATOM 192 O AVAL A 21 -3.835 -23.461 32.747 0.40 0.00 O
ATOM 200 O BALA A 21 -4.494 -26.675 33.897 0.60 0.00 O
ATOM 193 CB AVAL A 21 -3.289 -25.497 30.298 0.40 0.00 C
ATOM 201 CB BALA A 21 -7.405 -25.428 33.847 0.60 0.00 C
ATOM 189 N APRO A 22 -3.396 -23.034 29.982 0.40 0.00 N
ATOM 190 CA APRO A 22 -4.121 -24.205 30.467 0.40 0.00 C
ATOM 191 C APRO A 22 -4.530 -24.072 31.930 0.40 0.00 C
ATOM 192 O APRO A 22 -3.835 -23.461 32.747 0.40 0.00 O
ATOM 193 CB APRO A 22 -3.289 -25.497 30.298 0.40 0.00 C
ATOM 197 N BGLY A 22 -5.676 -24.647 32.284 0.60 0.00 N
ATOM 198 CA BGLY A 22 -6.012 -24.814 33.696 0.60 0.00 C
ATOM 199 C BGLY A 22 -4.990 -25.677 34.426 0.60 0.00 C
ATOM 200 O BGLY A 22 -4.494 -26.675 33.897 0.60 0.00 O
ATOM 201 CB BGLY A 22 -7.405 -25.428 33.847 0.60 0.00 C
237 changes: 211 additions & 26 deletions tests/test_pdb_selaltloc.py
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Original file line number Diff line number Diff line change
Expand Up @@ -54,9 +54,14 @@ def exec_module(self):

def test_is_same_group_1(self):
"""
Test if from the same group.
Test function to identify we entered another altloc group.
Exemple of a starting line with empty strings.
This indicates we are in the SAME altloc group.
previous line: "" # first line of the PDB file
current line: " ALA 1"
The result of `is_another_altloc_group` should be False.
"""
result = self.module.is_another_altloc_group(
' ', '', '1', '', 'ALA', '', {}, {})
Expand All @@ -65,9 +70,13 @@ def test_is_same_group_1(self):

def test_is_same_group_2(self):
"""
Test if from the same group.
Test function to identify we entered another altloc group.
This indicates we are in the SAME altloc group.
Example of a starting line with Nones.
All `None` case.
The result of `is_another_altloc_group` should be False.
"""
result = self.module.is_another_altloc_group(
' ', None, None, None, None, None, {}, {})
Expand All @@ -76,9 +85,16 @@ def test_is_same_group_2(self):

def test_is_same_group_3(self):
"""
Test if from the same group.
Test function to identify we entered another altloc group.
This indicates we are in the SAME altloc group.
Example of all parameters are the same as previous line.
Example: all parameters are the same as the previous line.
previous line: "BALA 12"
current line: "BALA 12"
The result of `is_another_altloc_group` should be False.
"""
result = self.module.is_another_altloc_group(
'B', 'B', '12', '12', 'ALA', 'ALA', {'B': None},
Expand All @@ -89,12 +105,19 @@ def test_is_same_group_3(self):

def test_is_same_group_4(self):
"""
Test if line is from another group.
Test function to identify we entered another altloc group.
This indicates we are in the SAME altloc group.
Example: Multiple residue altloc. This considers altloc spanning
several residues. See example dummy_altloc2.pdb.
previous line: "AGLU 25"
current line: "ALEU 26"
Multiple residue altloc.
It is important to note also the dictionary input.
This considers altloc spanning several residues. See example
dummy_altloc2.pdb.
The result of `is_another_altloc_group` should be False.
"""
result = self.module.is_another_altloc_group(
'A', 'A', '26', '25', 'LEU', 'GLU', {'A': ['lines']},
Expand All @@ -104,27 +127,19 @@ def test_is_same_group_4(self):

def test_is_same_group_5(self):
"""
Test if line is from another group.
Test function to identify we entered another altloc group.
Multiple residue altloc.
This indicates we are in the SAME altloc group.
This considers altloc spanning several residues. See example
dummy_altloc2.pdb.
"""
result = self.module.is_another_altloc_group(
'A', ' ', '26', '25', 'GLU', 'GLU', {' ': ['lines']},
{' ': {('GLU', '25')}}
)
self.assertFalse(result)
Example: Multiple residue altloc. This considers altloc spanning
several residues. See example dummy_altloc2.pdb.
def test_is_same_group_6(self):
"""
Test if line is from another group.
previous line: " GLU 25"
current line: "AALA 25"
Multiple residue altloc.
It is important to note also the dictionary input.
This considers altloc spanning several residues. See example
dummy_altloc2.pdb.
The result of `is_another_altloc_group` should be False.
"""
result = self.module.is_another_altloc_group(
'A', ' ', '25', '25', 'ALA', 'GLU', {' ': ['lines']},
Expand All @@ -133,27 +148,67 @@ def test_is_same_group_6(self):
self.assertFalse(result)

def test_is_another_group_1(self):
"""
Test function to identify we entered another altloc group.
This indicates we entered another altloc group.
previous line: "BPRO 1"
current line: " ALA 2"
The result of `is_another_altloc_group` should be True.
"""
result = self.module.is_another_altloc_group(
' ', 'B', '2', '1', 'ALA', 'PRO', {'B': ['lines']},
{'B': {('PRO', '1')}}
)
self.assertTrue(result)

def test_is_another_group_2(self):
"""
Test function to identify we entered another altloc group.
This indicates we entered another altloc group.
previous line: " ALA 1"
current line: " ALA 2"
The result of `is_another_altloc_group` should be True.
"""
result = self.module.is_another_altloc_group(
' ', ' ', '2', '1', 'ALA', 'ALA', {' ': ['lines']},
{' ': {('ALA', '1')}}
)
self.assertTrue(result)

def test_is_another_group_3(self):
"""
Test function to identify we entered another altloc group.
This indicates we entered another altloc group.
previous line: " GLU 1"
current line: " ALA 1"
The result of `is_another_altloc_group` should be True.
"""
result = self.module.is_another_altloc_group(
' ', ' ', '1', '1', 'ALA', 'GLU', {' ': ['lines']},
{' ': {('GLU', '1')}}
)
self.assertTrue(result)

def test_is_another_group_4(self):
"""
Test function to identify we entered another altloc group.
This indicates we entered another altloc group.
previous line: "AGLU 25"
current line: "ALEU 26"
The result of `is_another_altloc_group` should be True.
"""
result = self.module.is_another_altloc_group(
'A', 'A', '26', '25', 'LEU', 'GLU', {' ': ['lines'], 'A': ['lines']},
{' ': {('LEU', '25')}, 'A': {('GLU', '26')}}
Expand Down Expand Up @@ -686,6 +741,136 @@ def test_anisou_missing(self):
self.exec_module()
self.assertEqual(self.retcode, 0)

def test_captures_previous_residue_maxocc_A(self):
"""
Test the previous residue is not lost.
In version 2.4.5 we realised that the residue previous to the
residues having alternative locations was missing. See dummy_altloc3.pdb.
"""
sys.argv = ['', '-A', os.path.join(data_dir, 'dummy_altloc3.pdb')]
self.exec_module()
self.assertEqual(self.retcode, 0)
self.assertEqual(len(self.stdout), 25)
self.assertEqual(len(self.stderr), 0)
self.assertEqual(
self.stdout,
[
"ATOM 153 N VAL A 18 -0.264 -17.574 22.788 0.00 0.00 N ",
"ATOM 154 CA VAL A 18 -0.201 -17.901 24.209 0.00 0.00 C ",
"ATOM 155 C VAL A 18 -1.047 -19.150 24.437 0.00 0.00 C ",
"ATOM 156 O VAL A 18 -2.260 -19.144 24.214 0.00 0.00 O ",
"ATOM 157 CB VAL A 18 -0.689 -16.724 25.084 0.00 0.00 C ",
"ATOM 161 N TRP A 19 -0.408 -20.230 24.882 0.00 0.00 N ",
"ATOM 162 CA TRP A 19 -1.091 -21.490 25.161 0.00 0.00 C ",
"ATOM 163 C TRP A 19 -1.303 -21.563 26.667 0.00 0.00 C ",
"ATOM 164 O TRP A 19 -0.357 -21.920 27.375 0.00 0.00 O ",
"ATOM 165 CB TRP A 19 -0.272 -22.670 24.635 0.00 0.00 C ",
"ATOM 176 N TYR A 20 -2.522 -21.226 27.083 0.00 0.00 N ",
"ATOM 177 CA TYR A 20 -2.898 -21.178 28.493 0.00 0.00 C ",
"ATOM 178 C TYR A 20 -3.718 -22.410 28.851 0.00 0.00 C ",
"ATOM 179 O TYR A 20 -4.629 -22.780 28.105 0.00 0.00 O ",
"ATOM 180 CB TYR A 20 -3.681 -19.898 28.795 0.00 0.00 C ",
"ATOM 189 N VAL A 21 -3.396 -23.034 29.982 0.40 0.00 N ",
"ATOM 190 CA VAL A 21 -4.121 -24.205 30.467 0.40 0.00 C ",
"ATOM 191 C VAL A 21 -4.530 -24.072 31.930 0.40 0.00 C ",
"ATOM 192 O VAL A 21 -3.835 -23.461 32.747 0.40 0.00 O ",
"ATOM 193 CB VAL A 21 -3.289 -25.497 30.298 0.40 0.00 C ",
"ATOM 189 N PRO A 22 -3.396 -23.034 29.982 0.40 0.00 N ",
"ATOM 190 CA PRO A 22 -4.121 -24.205 30.467 0.40 0.00 C ",
"ATOM 191 C PRO A 22 -4.530 -24.072 31.930 0.40 0.00 C ",
"ATOM 192 O PRO A 22 -3.835 -23.461 32.747 0.40 0.00 O ",
"ATOM 193 CB PRO A 22 -3.289 -25.497 30.298 0.40 0.00 C ",
]
)

def test_captures_previous_residue_maxocc(self):
"""
Test the previous residue is not lost.
In version 2.4.5 we realised that the residue previous to the
residues having alternative locations was missing. See dummy_altloc3.pdb.
"""
sys.argv = ['', os.path.join(data_dir, 'dummy_altloc3.pdb')]
self.exec_module()
self.assertEqual(self.retcode, 0)
self.assertEqual(len(self.stdout), 25)
self.assertEqual(len(self.stderr), 0)
self.assertEqual(
self.stdout,
[
"ATOM 153 N VAL A 18 -0.264 -17.574 22.788 0.00 0.00 N ",
"ATOM 154 CA VAL A 18 -0.201 -17.901 24.209 0.00 0.00 C ",
"ATOM 155 C VAL A 18 -1.047 -19.150 24.437 0.00 0.00 C ",
"ATOM 156 O VAL A 18 -2.260 -19.144 24.214 0.00 0.00 O ",
"ATOM 157 CB VAL A 18 -0.689 -16.724 25.084 0.00 0.00 C ",
"ATOM 161 N TRP A 19 -0.408 -20.230 24.882 0.00 0.00 N ",
"ATOM 162 CA TRP A 19 -1.091 -21.490 25.161 0.00 0.00 C ",
"ATOM 163 C TRP A 19 -1.303 -21.563 26.667 0.00 0.00 C ",
"ATOM 164 O TRP A 19 -0.357 -21.920 27.375 0.00 0.00 O ",
"ATOM 165 CB TRP A 19 -0.272 -22.670 24.635 0.00 0.00 C ",
"ATOM 176 N TYR A 20 -2.522 -21.226 27.083 0.00 0.00 N ",
"ATOM 177 CA TYR A 20 -2.898 -21.178 28.493 0.00 0.00 C ",
"ATOM 178 C TYR A 20 -3.718 -22.410 28.851 0.00 0.00 C ",
"ATOM 179 O TYR A 20 -4.629 -22.780 28.105 0.00 0.00 O ",
"ATOM 180 CB TYR A 20 -3.681 -19.898 28.795 0.00 0.00 C ",
"ATOM 197 N ALA A 21 -5.676 -24.647 32.284 0.60 0.00 N ",
"ATOM 198 CA ALA A 21 -6.012 -24.814 33.696 0.60 0.00 C ",
"ATOM 199 C ALA A 21 -4.990 -25.677 34.426 0.60 0.00 C ",
"ATOM 200 O ALA A 21 -4.494 -26.675 33.897 0.60 0.00 O ",
"ATOM 201 CB ALA A 21 -7.405 -25.428 33.847 0.60 0.00 C ",
"ATOM 197 N GLY A 22 -5.676 -24.647 32.284 0.60 0.00 N ",
"ATOM 198 CA GLY A 22 -6.012 -24.814 33.696 0.60 0.00 C ",
"ATOM 199 C GLY A 22 -4.990 -25.677 34.426 0.60 0.00 C ",
"ATOM 200 O GLY A 22 -4.494 -26.675 33.897 0.60 0.00 O ",
"ATOM 201 CB GLY A 22 -7.405 -25.428 33.847 0.60 0.00 C ",
]
)

def test_captures_previous_residue_maxocc_B(self):
"""
Test the previous residue is not lost.
In version 2.4.5 we realised that the residue previous to the
residues having alternative locations was missing. See dummy_altloc3.pdb.
"""
sys.argv = ['', '-B', os.path.join(data_dir, 'dummy_altloc3.pdb')]
self.exec_module()
self.assertEqual(self.retcode, 0)
self.assertEqual(len(self.stdout), 25)
self.assertEqual(len(self.stderr), 0)
self.assertEqual(
self.stdout,
[
"ATOM 153 N VAL A 18 -0.264 -17.574 22.788 0.00 0.00 N ",
"ATOM 154 CA VAL A 18 -0.201 -17.901 24.209 0.00 0.00 C ",
"ATOM 155 C VAL A 18 -1.047 -19.150 24.437 0.00 0.00 C ",
"ATOM 156 O VAL A 18 -2.260 -19.144 24.214 0.00 0.00 O ",
"ATOM 157 CB VAL A 18 -0.689 -16.724 25.084 0.00 0.00 C ",
"ATOM 161 N TRP A 19 -0.408 -20.230 24.882 0.00 0.00 N ",
"ATOM 162 CA TRP A 19 -1.091 -21.490 25.161 0.00 0.00 C ",
"ATOM 163 C TRP A 19 -1.303 -21.563 26.667 0.00 0.00 C ",
"ATOM 164 O TRP A 19 -0.357 -21.920 27.375 0.00 0.00 O ",
"ATOM 165 CB TRP A 19 -0.272 -22.670 24.635 0.00 0.00 C ",
"ATOM 176 N TYR A 20 -2.522 -21.226 27.083 0.00 0.00 N ",
"ATOM 177 CA TYR A 20 -2.898 -21.178 28.493 0.00 0.00 C ",
"ATOM 178 C TYR A 20 -3.718 -22.410 28.851 0.00 0.00 C ",
"ATOM 179 O TYR A 20 -4.629 -22.780 28.105 0.00 0.00 O ",
"ATOM 180 CB TYR A 20 -3.681 -19.898 28.795 0.00 0.00 C ",
"ATOM 197 N ALA A 21 -5.676 -24.647 32.284 0.60 0.00 N ",
"ATOM 198 CA ALA A 21 -6.012 -24.814 33.696 0.60 0.00 C ",
"ATOM 199 C ALA A 21 -4.990 -25.677 34.426 0.60 0.00 C ",
"ATOM 200 O ALA A 21 -4.494 -26.675 33.897 0.60 0.00 O ",
"ATOM 201 CB ALA A 21 -7.405 -25.428 33.847 0.60 0.00 C ",
"ATOM 197 N GLY A 22 -5.676 -24.647 32.284 0.60 0.00 N ",
"ATOM 198 CA GLY A 22 -6.012 -24.814 33.696 0.60 0.00 C ",
"ATOM 199 C GLY A 22 -4.990 -25.677 34.426 0.60 0.00 C ",
"ATOM 200 O GLY A 22 -4.494 -26.675 33.897 0.60 0.00 O ",
"ATOM 201 CB GLY A 22 -7.405 -25.428 33.847 0.60 0.00 C ",
]
)


def test_file_not_found(self):
"""$ pdb_selaltloc not_existing.pdb"""

Expand Down

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