Python config.data_dir() Examples
The following are 30
code examples of config.data_dir().
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Example #1
| Source File: test_pdb_chkensemble.py From pdb-tools with Apache License 2.0 | 6 votes |
|
def test_ensemble_noendmdl2(self):
"""$ pdb_chkensemble data/ensemble_error_4.pdb"""
fpath = os.path.join(data_dir, 'ensemble_error_4.pdb')
sys.argv = ['', fpath]
# Execute the script
self.exec_module()
# Validate results
self.assertEqual(self.retcode, 1)
self.assertEqual(len(self.stdout), 0)
self.assertEqual(len(self.stderr), 1)
self.assertEqual(self.stderr[0],
"ERROR!! MODEL record found before ENDMDL at line '6'")
Example #2
| Source File: test_pdb_chkensemble.py From pdb-tools with Apache License 2.0 | 6 votes |
|
def test_ensemble_noendmdl(self):
"""$ pdb_chkensemble data/ensemble_error_3.pdb"""
fpath = os.path.join(data_dir, 'ensemble_error_3.pdb')
sys.argv = ['', fpath]
# Execute the script
self.exec_module()
# Validate results
self.assertEqual(self.retcode, 1)
self.assertEqual(len(self.stdout), 0)
self.assertEqual(len(self.stderr), 1)
self.assertEqual(self.stderr[0],
"ERROR!! ENDMDL record missing at line '10'")
Example #3
| Source File: test_pdb_chkensemble.py From pdb-tools with Apache License 2.0 | 6 votes |
|
def test_ensemble_nomodel(self):
"""$ pdb_chkensemble data/ensemble_error_2.pdb"""
fpath = os.path.join(data_dir, 'ensemble_error_2.pdb')
sys.argv = ['', fpath]
# Execute the script
self.exec_module()
# Validate results
self.assertEqual(self.retcode, 1)
self.assertEqual(len(self.stdout), 0)
self.assertEqual(len(self.stderr), 1)
self.assertEqual(self.stderr[0],
"ERROR!! MODEL record missing before ATOM at line '3'")
Example #4
| Source File: test_pdb_chkensemble.py From pdb-tools with Apache License 2.0 | 6 votes |
|
def test_ensemble_diffatom(self):
"""$ pdb_chkensemble data/ensemble_error_1.pdb"""
fpath = os.path.join(data_dir, 'ensemble_error_1.pdb')
sys.argv = ['', fpath]
# Execute the script
self.exec_module()
# Validate results
self.assertEqual(self.retcode, 1)
self.assertEqual(len(self.stdout), 0)
self.assertEqual(len(self.stderr), 3)
self.assertEqual(self.stderr,
["Models 1 and 2 differ:",
"Atoms in model 1 only:",
" 2 H ASN A 1 "])
Example #5
| Source File: test_pdb_occ.py From pdb-tools with Apache License 2.0 | 6 votes |
|
def test_default(self):
"""$ pdb_occ data/dummy.pdb"""
# Simulate input
# pdb_occ dummy.pdb
sys.argv = ['', os.path.join(data_dir, 'dummy.pdb')]
# Execute the script
self.exec_module()
# Validate results
self.assertEqual(self.retcode, 0) # ensure the program exited OK.
self.assertEqual(len(self.stdout), 204) # no lines deleted
self.assertEqual(len(self.stderr), 0) # no errors
records = (('ATOM', 'HETATM'))
occ_list = [l[54:60] for l in self.stdout if l.startswith(records)]
unique_occ = list(set(map(float, occ_list)))
self.assertEqual(unique_occ, [1.0]) # all occ values changed
Example #6
| Source File: test_pdb_chkensemble.py From pdb-tools with Apache License 2.0 | 6 votes |
|
def test_valid_ensemble(self):
"""$ pdb_chkensemble data/ensemble_OK.pdb"""
fpath = os.path.join(data_dir, 'ensemble_OK.pdb')
sys.argv = ['', fpath]
# Execute the script
self.exec_module()
# Validate results
self.assertEqual(self.retcode, 0) # ensure the program exited OK.
self.assertEqual(len(self.stdout), 1)
self.assertEqual(len(self.stderr), 0) # no errors
self.assertEqual(self.stdout[0],
"Ensemble of 2 models *seems* OK")
Example #7
| Source File: test_pdb_tidy.py From pdb-tools with Apache License 2.0 | 6 votes |
|
def test_default(self):
"""$ pdb_tidy data/dummy.pdb"""
fpath = os.path.join(data_dir, 'dummy.pdb')
sys.argv = ['', fpath]
# Execute the script
self.exec_module()
# Validate results
self.assertEqual(self.retcode, 0) # ensure the program exited OK.
self.assertEqual(len(self.stdout), 207)
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)
# Check if we added END statements correctly
self.assertTrue(self.stdout[-1].startswith('END'))
Example #8
| Source File: test_pdb_b.py From pdb-tools with Apache License 2.0 | 6 votes |
|
def test_default(self):
"""$ pdb_b data/dummy.pdb"""
# Simulate input
# pdb_b -20 dummy.pdb
sys.argv = ['', os.path.join(data_dir, 'dummy.pdb')]
# Execute the script
self.exec_module()
# Validate results
self.assertEqual(self.retcode, 0) # ensure the program exited OK.
self.assertEqual(len(self.stdout), 204) # no lines deleted
self.assertEqual(len(self.stderr), 0) # no errors
records = (('ATOM', 'HETATM'))
bfactors = [l[60:66] for l in self.stdout if l.startswith(records)]
unique_bfac = list(set(map(float, bfactors)))
self.assertEqual(unique_bfac, [10.00]) # all bfactors changed
Example #9
| Source File: test_pdb_gap.py From pdb-tools with Apache License 2.0 | 6 votes |
|
def test_default(self):
"""$ pdb_gap data/dummy.pdb"""
# Simulate input
sys.argv = ['', os.path.join(data_dir, 'dummy.pdb')]
# Execute the script
self.exec_module()
# Validate results
self.assertEqual(self.retcode, 0) # ensure the program exited OK.
self.assertEqual(len(self.stdout), 5) # no lines deleted
self.assertEqual(len(self.stderr), 0) # no errors
self.assertEqual(self.stdout,
["B:ARG4 < Seq. Gap > B:GLU6",
"A:ASN1 < 9.42A > A:ASN1",
"C:ARG5 < Seq. Gap > C:GLU2",
"C:GLU2 < 95.75A > C:MET-1",
"Found 4 gap(s) in the structure"])
Example #10
| Source File: test_pdb_selchain.py From pdb-tools with Apache License 2.0 | 5 votes |
|
def test_multiple(self):
"""
$ pdb_selchain -A,B data/dummy.pdb
"""
sys.argv = ['', '-A,B', os.path.join(data_dir, 'dummy.pdb')]
self.exec_module()
self.assertEqual(self.retcode, 0)
self.assertEqual(len(self.stdout), 129) # c.A + c.B
self.assertEqual(len(self.stderr), 0)
Example #11
| Source File: test_pdb_delresname.py From pdb-tools with Apache License 2.0 | 5 votes |
|
def test_file_not_found(self):
"""$ pdb_delresname not_existing.pdb"""
afile = os.path.join(data_dir, 'not_existing.pdb')
sys.argv = ['', afile]
self.exec_module()
self.assertEqual(self.retcode, 1) # exit code is 1 (error)
self.assertEqual(len(self.stdout), 0) # nothing written to stdout
self.assertEqual(self.stderr[0][:22],
"ERROR!! File not found") # proper error message
Example #12
| Source File: test_pdb_delresname.py From pdb-tools with Apache License 2.0 | 5 votes |
|
def test_not_an_option(self):
"""$ pdb_delresname 20 data/dummy.pdb"""
sys.argv = ['', '20', os.path.join(data_dir, 'dummy.pdb')]
self.exec_module()
self.assertEqual(self.retcode, 1)
self.assertEqual(len(self.stdout), 0)
self.assertEqual(self.stderr[0],
"ERROR! First argument is not an option: '20'")
Example #13
| Source File: test_pdb_tidy.py From pdb-tools with Apache License 2.0 | 5 votes |
|
def test_file_not_found(self):
"""$ pdb_tidy not_existing.pdb"""
# Error (file not found)
afile = os.path.join(data_dir, 'not_existing.pdb')
sys.argv = ['', afile]
# Execute the script
self.exec_module()
self.assertEqual(self.retcode, 1)
self.assertEqual(len(self.stdout), 0)
self.assertEqual(self.stderr[0][:22],
"ERROR!! File not found")
Example #14
| Source File: test_pdb_selchain.py From pdb-tools with Apache License 2.0 | 5 votes |
|
def test_invalid_option(self):
"""$ pdb_selchain data/dummy.pdb"""
sys.argv = ['', os.path.join(data_dir, 'dummy.pdb')]
self.exec_module()
self.assertEqual(self.retcode, 1)
self.assertEqual(len(self.stdout), 0)
self.assertEqual(self.stderr[0][:47],
"ERROR!! You must provide at least one chain ide")
Example #15
| Source File: test_pdb_selchain.py From pdb-tools with Apache License 2.0 | 5 votes |
|
def test_one_option_CAPS_lowercase(self):
"""$ pdb_selchain -A data/dummy_az09.pdb"""
# Simulate input
# pdb_selchain dummy_az09.pdb
sys.argv = ['', '-A', os.path.join(data_dir, 'dummy_az09.pdb')]
# Execute the script
self.exec_module()
# Validate results
self.assertEqual(self.retcode, 0) # ensure the program exited OK.
self.assertEqual(len(self.stdout), 76) # selected c.A
self.assertEqual(len(self.stderr), 0) # no errors
Example #16
| Source File: test_pdb_selchain.py From pdb-tools with Apache License 2.0 | 5 votes |
|
def test_one_option_digit(self):
"""$ pdb_selchain -1 data/dummy_az09.pdb"""
# Simulate input
# pdb_selchain dummy.pdb
sys.argv = ['', '-1', os.path.join(data_dir, 'dummy_az09.pdb')]
# Execute the script
self.exec_module()
# Validate results
self.assertEqual(self.retcode, 0) # ensure the program exited OK.
self.assertEqual(len(self.stdout), 71) # selected c.1
self.assertEqual(len(self.stderr), 0) # no errors
Example #17
| Source File: test_pdb_chkensemble.py From pdb-tools with Apache License 2.0 | 5 votes |
|
def test_invalid_option(self):
"""$ pdb_chkensemble -A data/dummy.pdb"""
sys.argv = ['', '-A', os.path.join(data_dir, 'dummy.pdb')]
# Execute the script
self.exec_module()
self.assertEqual(self.retcode, 1)
self.assertEqual(len(self.stdout), 0)
self.assertEqual(self.stderr[0][:36],
"ERROR!! Script takes 1 argument, not")
Example #18
| Source File: test_pdb_selchain.py From pdb-tools with Apache License 2.0 | 5 votes |
|
def test_file_not_found(self):
"""$ pdb_selchain not_existing.pdb"""
afile = os.path.join(data_dir, 'not_existing.pdb')
sys.argv = ['', afile]
self.exec_module()
self.assertEqual(self.retcode, 1) # exit code is 1 (error)
self.assertEqual(len(self.stdout), 0) # nothing written to stdout
self.assertEqual(self.stderr[0][:22],
"ERROR!! File not found") # proper error message
Example #19
| Source File: test_pdb_shiftres.py From pdb-tools with Apache License 2.0 | 5 votes |
|
def test_too_many_residues(self):
"""$ pdb_shiftres -9998 data/dummy.pdb"""
sys.argv = ['', '-9998', os.path.join(data_dir, 'dummy.pdb')]
self.exec_module()
self.assertEqual(self.retcode, 1)
self.assertEqual(len(self.stdout), 0)
self.assertEqual(len(self.stderr), 1)
self.assertEqual(self.stderr[0][:22],
"Cannot set residue num") # proper error message
Example #20
| Source File: test_pdb_delresname.py From pdb-tools with Apache License 2.0 | 5 votes |
|
def test_empty_sele(self):
"""$ pdb_delresname - data/dummy.pdb"""
# Simulate input
sys.argv = ['', '-', os.path.join(data_dir, 'dummy.pdb')]
# Execute the script
self.exec_module()
# Validate results
self.assertEqual(self.retcode, 1)
self.assertEqual(len(self.stdout), 0)
self.assertEqual(self.stderr[0][:22],
"ERROR!! Residue name s")
Example #21
| Source File: test_pdb_delresname.py From pdb-tools with Apache License 2.0 | 5 votes |
|
def test_multiple_sele(self):
"""$ pdb_delresname -ARG,CA data/dummy.pdb"""
# Simulate input
sys.argv = ['', '-ARG,CA', os.path.join(data_dir, 'dummy.pdb')]
# Execute the script
self.exec_module()
# Validate results
self.assertEqual(self.retcode, 0)
self.assertEqual(len(self.stdout), 127)
self.assertEqual(len(self.stderr), 0)
Example #22
| Source File: test_pdb_delresname.py From pdb-tools with Apache License 2.0 | 5 votes |
|
def test_single_sele(self):
"""$ pdb_delresname -ARG data/dummy.pdb"""
# Simulate input
sys.argv = ['', '-ARG', os.path.join(data_dir, 'dummy.pdb')]
# Execute the script
self.exec_module()
# Validate results
self.assertEqual(self.retcode, 0)
self.assertEqual(len(self.stdout), 128)
self.assertEqual(len(self.stderr), 0)
Example #23
| Source File: test_pdb_segxchain.py From pdb-tools with Apache License 2.0 | 5 votes |
|
def test_invalid_option(self):
"""$ pdb_segxchain -A data/dummy.pdb"""
sys.argv = ['', '-A', os.path.join(data_dir, 'dummy.pdb')]
# Execute the script
self.exec_module()
self.assertEqual(self.retcode, 1)
self.assertEqual(len(self.stdout), 0)
self.assertEqual(self.stderr[0][:36],
"ERROR!! Script takes 1 argument, not")
Example #24
| Source File: test_pdb_segxchain.py From pdb-tools with Apache License 2.0 | 5 votes |
|
def test_file_not_found(self):
"""$ pdb_segxchain not_existing.pdb"""
# Error (file not found)
afile = os.path.join(data_dir, 'not_existing.pdb')
sys.argv = ['', afile]
# Execute the script
self.exec_module()
self.assertEqual(self.retcode, 1) # exit code is 1 (error)
self.assertEqual(len(self.stdout), 0) # nothing written to stdout
self.assertEqual(self.stderr[0][:22],
"ERROR!! File not found") # proper error message
Example #25
| Source File: test_pdb_selelem.py From pdb-tools with Apache License 2.0 | 5 votes |
|
def test_not_an_option(self):
"""$ pdb_selelem 20 data/dummy.pdb"""
sys.argv = ['', '20', os.path.join(data_dir, 'dummy.pdb')]
self.exec_module()
self.assertEqual(self.retcode, 1)
self.assertEqual(len(self.stdout), 0)
self.assertEqual(self.stderr[0],
"ERROR! First argument is not an option: '20'")
Example #26
| Source File: test_pdb_selelem.py From pdb-tools with Apache License 2.0 | 5 votes |
|
def test_invalid_option_2(self):
"""$ pdb_selelem -ABC data/dummy.pdb"""
sys.argv = ['', '-ABC', os.path.join(data_dir, 'dummy.pdb')]
self.exec_module()
self.assertEqual(self.retcode, 1)
self.assertEqual(len(self.stdout), 0)
self.assertEqual(self.stderr[0][:38],
"ERROR!! Element name is invalid: 'ABC'")
Example #27
| Source File: test_pdb_selelem.py From pdb-tools with Apache License 2.0 | 5 votes |
|
def test_invalid_option(self):
"""$ pdb_selelem data/dummy.pdb"""
sys.argv = ['', os.path.join(data_dir, 'dummy.pdb')]
self.exec_module()
self.assertEqual(self.retcode, 1)
self.assertEqual(len(self.stdout), 0)
self.assertEqual(self.stderr[0][:37],
"ERROR!! Element set cannot be empty")
Example #28
| Source File: test_pdb_selelem.py From pdb-tools with Apache License 2.0 | 5 votes |
|
def test_file_not_found(self):
"""$ pdb_selelem not_existing.pdb"""
afile = os.path.join(data_dir, 'not_existing.pdb')
sys.argv = ['', afile]
self.exec_module()
self.assertEqual(self.retcode, 1) # exit code is 1 (error)
self.assertEqual(len(self.stdout), 0) # nothing written to stdout
self.assertEqual(self.stderr[0][:22],
"ERROR!! File not found") # proper error message
Example #29
| Source File: test_pdb_selelem.py From pdb-tools with Apache License 2.0 | 5 votes |
|
def test_multiple(self):
"""
$ pdb_selelem -C,O data/dummy.pdb
"""
sys.argv = ['', '-C,O', os.path.join(data_dir, 'dummy.pdb')]
self.exec_module()
self.assertEqual(self.retcode, 0)
self.assertEqual(len(self.stdout), 75)
self.assertEqual(len(self.stderr), 0)
Example #30
| Source File: test_pdb_b.py From pdb-tools with Apache License 2.0 | 5 votes |
|
def test_not_an_option(self):
"""$ pdb_b 20 data/dummy.pdb"""
sys.argv = ['', '20', os.path.join(data_dir, 'dummy.pdb')]
self.exec_module()
self.assertEqual(self.retcode, 1)
self.assertEqual(len(self.stdout), 0)
self.assertEqual(self.stderr[0],
"ERROR! First argument is not an option: '20'")
