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Inverts -strict behaviour in pdb_tidy #151

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Inverts -strict behaviour in pdb_tidy #151

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7 changes: 3 additions & 4 deletions pdbtools/pdb_tidy.py
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Original file line number Diff line number Diff line change
Expand Up @@ -33,7 +33,7 @@

Example:
python pdb_tidy.py 1CTF.pdb
python pdb_tidy.py -strict 1CTF.pdb # does not add TER on chain breaks
python pdb_tidy.py -strict 1CTF.pdb # also adds TER on chain breaks

This program is part of the `pdb-tools` suite of utilities and should not be
distributed isolatedly. The `pdb-tools` were created to quickly manipulate PDB
Expand Down Expand Up @@ -117,14 +117,13 @@ def run(fhandle, strict=False):
fhandle : a line-by-line iterator of the original PDB file.

strict : bool
If True, does not add TER statements at intra-chain breaks.
If True, adds TER statements at intra-chain breaks.

Yields
------
str (line-by-line)
The modified (or not) PDB line.
"""
not_strict = not strict
fhandle = iter(fhandle)

def make_TER(prev_line):
Expand Down Expand Up @@ -185,7 +184,7 @@ def make_TER(prev_line):
if line.startswith('ATOM'):

is_gap = (int(line[22:26]) - int(prev_line[22:26])) > 1
if atom_section and (line[21] != prev_line[21] or (not_strict and is_gap)):
if atom_section and (line[21] != prev_line[21] or (strict and is_gap)):
serial_offset += 1 # account for TER statement
yield make_TER(prev_line)

Expand Down
20 changes: 10 additions & 10 deletions tests/test_pdb_tidy.py
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Original file line number Diff line number Diff line change
Expand Up @@ -75,12 +75,12 @@ def test_default(self):
# Validate results
self.assertEqual(self.retcode, 0) # ensure the program exited OK.
# CONECTs are ignored by issue #72, expected only 205 lines
self.assertEqual(len(self.stdout), 205)
self.assertEqual(len(self.stdout), 204)
self.assertEqual(len(self.stderr), 0) # no errors

# Check if we added TER statements correctly
n_ter = len([r for r in self.stdout if r.startswith('TER')])
self.assertEqual(n_ter, 5)
self.assertEqual(n_ter, 4)

# Check no CONECT in output
c_conect = sum(1 for i in self.stdout if i.startswith('CONECT'))
Expand Down Expand Up @@ -112,10 +112,10 @@ def test_default_in_lib(self):
fin.close()
lines = list(self.module.run(original_lines))

self.assertEqual(len(lines), 205)
self.assertEqual(len(lines), 204)
# Check if we added TER statements correctly
n_ter = len([r for r in lines if r.startswith('TER')])
self.assertEqual(n_ter, 5)
self.assertEqual(n_ter, 4)

# Check no CONECT in output
c_conect = sum(1 for i in lines if i.startswith('CONECT'))
Expand Down Expand Up @@ -151,12 +151,12 @@ def test_default_stdin(self):
# Validate results
self.assertEqual(self.retcode, 0) # ensure the program exited OK.
# CONECTs are ignored by issue #72, expected only 205 lines
self.assertEqual(len(self.stdout), 205)
self.assertEqual(len(self.stdout), 204)
self.assertEqual(len(self.stderr), 0) # no errors

# Check if we added TER statements correctly
n_ter = len([r for r in self.stdout if r.startswith('TER')])
self.assertEqual(n_ter, 5)
self.assertEqual(n_ter, 4)

# Check no CONECT in output
c_conect = sum(1 for i in self.stdout if i.startswith('CONECT'))
Expand All @@ -177,12 +177,12 @@ def test_default_strict(self):
# Validate results
self.assertEqual(self.retcode, 0) # ensure the program exited OK.
# CONECTs are ignored by issue #72, expected only 204 lines
self.assertEqual(len(self.stdout), 204)
self.assertEqual(len(self.stdout), 205)
self.assertEqual(len(self.stderr), 0) # no errors

# Check if we added TER statements correctly
n_ter = len([r for r in self.stdout if r.startswith('TER')])
self.assertEqual(n_ter, 4)
self.assertEqual(n_ter, 5)

# Check no CONECT in output
c_conect = sum(1 for i in self.stdout if i.startswith('CONECT'))
Expand All @@ -204,12 +204,12 @@ def test_default_strict_stdin(self):
# Validate results
self.assertEqual(self.retcode, 0) # ensure the program exited OK.
# CONECTs are ignored by issue #72, expected only 204 lines
self.assertEqual(len(self.stdout), 204)
self.assertEqual(len(self.stdout), 205)
self.assertEqual(len(self.stderr), 0) # no errors

# Check if we added TER statements correctly
n_ter = len([r for r in self.stdout if r.startswith('TER')])
self.assertEqual(n_ter, 4)
self.assertEqual(n_ter, 5)

# Check no CONECT in output
c_conect = sum(1 for i in self.stdout if i.startswith('CONECT'))
Expand Down