本文整理汇总了Python中MolKit.Read.hasBonds方法的典型用法代码示例。如果您正苦于以下问题：Python Read.hasBonds方法的具体用法？Python Read.hasBonds怎么用？Python Read.hasBonds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.hasBonds方法的1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: range
# 需要导入模块: from MolKit import Read [as 别名]
# 或者: from MolKit.Read import hasBonds [as 别名]
rot.append(random.uniform(-1,1)*xscale)
#for the rotation angle
rot.append(random.uniform(-1,1)*ascale)
if verbose: print 'axis=', rot[:3], ' and angle=', rot[-1]
#torsions:
dihe = []
for ind in range(ndihe):
dihe.append(dscale * random.uniform(-1,1))
if verbose: print 'dihe=', dihe
conf = Conformation(m, origin, TRANS, rot, dihe)
new_coords = conf.getCoords()
#verify that no new bonds would be formed for this conformation
m.allAtoms.updateCoords(new_coords, ind=coord_index)
#remove all original bonds and set hasBonds to 0 on all levels
del(m.allAtoms.bonds)
m.hasBonds=0
for c in m.chains: c.hasBonds=0
for r in m.chains.residues: r.hasBonds=0
for a in m.allAtoms:
a.bonds = BondSet([])
a.hasBonds = 0
m.buildBondsByDistance()
newLen = len(m.allAtoms.bonds[0])
if verbose: print "originally %d bonds form; after transformation %d bonds form" %(orig, newLen)
new_d = {}
for a in m.allAtoms: new_d[a]=set(a.bonds.getAtoms())
ok = True
for a in m.allAtoms:
if orig_d[a]!=new_d[a]:
ok = False
if verbose: