本文整理汇总了Python中MolKit.Read.secondaryStructureFromFile方法的典型用法代码示例。如果您正苦于以下问题：Python Read.secondaryStructureFromFile方法的具体用法？Python Read.secondaryStructureFromFile怎么用？Python Read.secondaryStructureFromFile使用的例子？那么恭喜您, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类MolKit.Read的用法示例。
在下文中一共展示了Read.secondaryStructureFromFile方法的3个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的Python代码示例。
示例1: test_Write_6
# 需要导入模块: from MolKit import Read [as 别名]
# 或者: from MolKit.Read import secondaryStructureFromFile [as 别名]
def test_Write_6(self):
if not haveStride: return
from MolKit import Read
self.mol = Read("Data/1crn.pdb")[0]
self.mol.secondaryStructureFromStride()
from MolKit.pdbWriter import PdbWriter
writer = PdbWriter()
writer.write('Data/1crn_writer.pdb', self.mol,
records=['ATOM', 'HETATM', 'CONECT',
'TURN','HELIX', 'SHEET'],
bondOrigin='all', ssOrigin='Stride')
# Make sure that the ss information has been written out
# properly.
nmol = Read("Data/1crn_writer.pdb")[0]
nmol.secondaryStructureFromFile()
nsset = nmol.chains[0].secondarystructureset
osset = self.mol.chains[0].secondarystructureset
self.assertEqual(len(nsset), len(osset))
for nss, oss in map(None, nsset, osset):
self.assertEqual(nss.name, oss.name)
self.assertEqual(nss.start.name,oss.start.name)
self.assertEqual(nss.end.name, oss.end.name)
self.assertEqual(len(nss.residues), len(oss.residues))
os.system("rm Data/1crn_writer.pdb")示例2: PDBWriterTests
# 需要导入模块: from MolKit import Read [as 别名]
# 或者: from MolKit.Read import secondaryStructureFromFile [as 别名]
#.........这里部分代码省略.........
# default arguments
from MolKit.pdbWriter import PdbWriter
writer = PdbWriter()
writer.write('Data/1crn_writer.pdb', self.mol)
from MolKit.pdbParser import PdbParser
nmol = Read("Data/1crn_writer.pdb")[0]
os.system("rm Data/1crn_writer.pdb")
def test_Write_4(self):
"""
Test writing out the ATOM records and the CONECT records
without the HETATM
"""
from MolKit import Read
self.mol = Read("Data/1bsr.pdb")[0]
# instanciate a PdbWriter and call the write method with the
# default arguments
from MolKit.pdbWriter import PdbWriter
writer = PdbWriter()
writer.write('Data/1bsr_writer.pdb', self.mol,
records=['ATOM', 'CONECT'], bondOrigin=('File',))
nmol = Read("Data/1bsr_writer.pdb")[0]
nhoh = nmol.chains.residues.get(lambda x: x.type=="HOH")
ohoh = self.mol.chains.residues.get(lambda x: x.type=="HOH")
self.failUnless(len(nhoh)==0)
os.system("rm Data/1bsr_writer.pdb")
def test_Write_5(self):
from MolKit import Read
self.mol = Read("Data/1crn.pdb")[0]
self.mol.secondaryStructureFromFile()
from MolKit.pdbWriter import PdbWriter
writer = PdbWriter()
writer.write('Data/1crn_writer.pdb', self.mol,
records=['ATOM', 'HETATM', 'CONECT',
'TURN','HELIX', 'SHEET'],
bondOrigin='all', ssOrigin='File')
# Make sure that the ss information has been written out
# properly.
nmol = Read("Data/1crn_writer.pdb")[0]
nmol.secondaryStructureFromFile()
nsset = nmol.chains[0].secondarystructureset
osset = self.mol.chains[0].secondarystructureset
self.assertEqual(len(nsset), len(osset))
for nss, oss in map(None, nsset, osset):
self.assertEqual(nss.name, oss.name)
self.assertEqual(nss.start.name,oss.start.name)
self.assertEqual(nss.end.name, oss.end.name)
self.assertEqual(len(nss.residues), len(oss.residues))
os.system("rm Data/1crn_writer.pdb")
def test_Write_6(self):
if not haveStride: return
from MolKit import Read
self.mol = Read("Data/1crn.pdb")[0]
self.mol.secondaryStructureFromStride()
from MolKit.pdbWriter import PdbWriter
writer = PdbWriter()
writer.write('Data/1crn_writer.pdb', self.mol,
records=['ATOM', 'HETATM', 'CONECT',
'TURN','HELIX', 'SHEET'],
bondOrigin='all', ssOrigin='Stride')示例3: test_simplefile
# 需要导入模块: from MolKit import Read [as 别名]
# 或者: from MolKit.Read import secondaryStructureFromFile [as 别名]
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