len(mol.chains[0].secondarystructureset)==11
def test_simplefile():
from MolKit import Read
mol = Read("./Data/1crn.pdb")[0]
mol.secondaryStructureFromFile()
assert hasattr(mol.chains[0], 'secondarystructureset') and \
len(mol.chains[0].secondarystructureset)==10
def test_getsecondarystructureChain():
if haveStride:
from MolKit import Read
mol = Read("./Data/fxnohtatm.pdb")[0]
from MolKit.getsecondarystructure import GetSecondaryStructureFromStride
ssb = GetSecondaryStructureFromStride(mol)
mol.secondaryStructure(ssb)
harness = testplus.TestHarness(
__name__,
#funs = testplus.testcollect( globals()),
funs=[
test_getsecondarystructureChain,
])
if __name__ == '__main__':
print harness
sys.exit(len(harness))
assert len(forms[2].select.keys()) == 2
assert len(forms[2].input.keys()) == 2
# testing comboboxes:
assert len(forms[2].select['what-to-do']['options']) == 5
assert forms[2].select['what-to-do']['options'][0] == 'Drink Coffee'
assert len(forms[2].select['who-to-do-it-with']['options']) == 6
assert forms[2].select['who-to-do-it-with']['options'][-1] == 'Chouck'
##########################################################################
# FORM 3
# form[3] has 3 textareas (TEXTAREA) and 2 buttons (INPUT)
print forms[3].textarea
assert len(forms[3].textarea.items()) == 3
assert len(forms[3].input) == 2
# testing textareas:
assert forms[3].textarea['positive']['cols'] == '60'
assert forms[3].textarea['positive']['rows'] == '20'
assert forms[3].textarea['username']['text'][0] == 'Your Name Here'
harness = testplus.TestHarness(
__name__,
funs=testplus.testcollect(globals()),
)
if __name__ == '__main__':
print harness
sys.exit(len(harness))
print mol.chains.name
# Protein with No TER records at all and 2 chains
print "Testing 1crn2Chains.pdb: protein with only 1 TER record at the end of the ATOM"
mol = Read("Data/1crn2ChainsNOTER.pdb")[0]
assert len(mol.chains) == 2, "Expecting 1 chain got %s" % len(mol.chains)
assert mol.chains.name == [
'A', 'B'
], "Expecting chain name ' ', got %s" % mol.chains.name
print mol.chains.name
def test_parsePQR():
from MolKit.pdbParser import PQRParser
parser = PQRParser("./Data/mead.pqr")
mols = parser.parse()
assert len(mols) == 1, "Expecting 1 molecule mead got %s" % mols.name
mol = mols[0]
assert len(mol.chains) == 1, "Expecting 1 chain got %s" % len(mol.chains)
harness = testplus.TestHarness(
__name__,
funs=testplus.testcollect(globals()),
#funs=[test_parsegetRecords],
)
if __name__ == '__main__':
print harness
sys.exit(len(harness))
'orient':'horizontal',
'buttontype':'radiobutton'},
'gridcfg':{'sticky':'w'} })
descr.append({'name':'radioselect',
'widgetType':Pmw.RadioSelect,
'parent':'Page3',
'defaultValue':'rb5',
'listtext':['rb1', 'rb2', 'rb3','rb4', 'rb5', 'rb6',
'rb7', 'rb8', 'rb9','rb10', 'rb11', 'rb12'],
'wcfg':{'labelpos':'n',
'label_text':'Radiobuttons: ',
'orient':'vertical',
'buttontype':'radiobutton'},
'gridcfg':{'sticky':'w'} })
form = InputForm(master, root, descr, modal=0, blocking=0)
values = form.testForm(container='Page3')
assert values['radioselect']=='rb5'
form.destroy()
harness = testplus.TestHarness( __name__,
connect = setUp,
funs = testplus.testcollect( globals()),
#funs = [test_inputform_4,] ,
disconnect = tearDown
)
if __name__ == '__main__':
print harness
sys.exit( len( harness))
print(m.sesr.fst.n_buried_sas_area)
vfloat, vint, tri = m.getBuriedSurfaceTriangles(selnum=1)
print(
"getBuriedSurfaceTriangles(selnum=1): len(vfloat): %d, len(vint): %d, len(tri): %d"
% (len(vfloat), len(vint), len(tri)))
vfloat, vint, tri = m.getBuriedSurfaceTriangles(selnum=2)
print(
"getBuriedSurfaceTriangles(selnum=2): len(vfloat): %d, len(vint): %d, len(tri): %d"
% (len(vfloat), len(vint), len(tri)))
vfloat, vint, tri = m.getBuriedSurfaceTriangles(selnum=3)
print(
"getBuriedSurfaceTriangles(selnum=3): len(vfloat): %d, len(vint): %d, len(tri): %d"
% (len(vfloat), len(vint), len(tri)))
## harness = testplus.TestHarness( __name__,
## connect = importLib,
## funs = testplus.testcollect( globals()),
## )
if __name__ == '__main__':
testplus.chdir()
args = ()
harness = testplus.TestHarness(__name__,
connect=(setUpSuite, args, {}),
funs=testplus.testcollect(globals()),
disconnect=tearDownSuite)
print(harness)
sys.exit(len(harness))
import sys
from mglutil.regression import testplus
import test_htmlparser
harness = testplus.TestHarness(
__name__,
funs=[],
dependents=[
test_htmlparser.harness,
],
)
if __name__ == '__main__':
print harness
sys.exit(len(harness))
assert rings.ringCount == 6
def test_findCycles2():
# test cycle detection on modified taxol to have 5 membered ring
atoms, bonds = getGraphFromFile('Data/fuzedRings2.graph')
from PyBabel.cycle import RingFinder
rings = RingFinder()
rings.findRings2(atoms, bonds)
assert rings.ringCount == 4
def test_findCycles3():
# test cycle detection on taxol merged rings only
atoms, bonds = getGraphFromFile('Data/fuzedRings1.graph')
from PyBabel.cycle import RingFinder
rings = RingFinder()
rings.findRings2(atoms, bonds)
assert rings.ringCount == 4
harness = testplus.TestHarness(
"PyBabel_cycles",
funs=testplus.testcollect(globals()),
)
if __name__ == '__main__':
testplus.chdir()
print harness
sys.exit(len(harness))