本文整理汇总了Python中MolKit.Read.addBond方法的典型用法代码示例。如果您正苦于以下问题：Python Read.addBond方法的具体用法？Python Read.addBond怎么用？Python Read.addBond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.addBond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: len
# 需要导入模块: from MolKit import Read [as 别名]
# 或者: from MolKit.Read import addBond [as 别名]
if verbose: print 'removed rat3 %s'%rat3.full_name()
rM.allAtoms = rM.chains.residues.atoms
if verbose: print 'after removing rat1,rat2 and rat3 but before adding ligand atoms, residue %s has %d atoms.' %( resP.name, len(resP.atoms))
if verbose: print 'and the receptor has %d atoms'%len(rM.allAtoms)
#keep handle to existing atoms for possible clashes
res_atoms_to_check = resP.atoms[:]
#(4) add the ligand atoms to the residue
#for h in atoms_to_adopt:
for h in lM.allAtoms:
resP.adopt(h)
if verbose: print "%s added to %s"%(h.full_name(), resP.full_name())
if verbose: print 'after adding %d ligand atoms, residue %s has %d atoms.' %( len(lM.allAtoms), resP.name, len(resP.atoms))
rM.allAtoms = rM.chains.residues.atoms
if verbose: print 'and the receptor has %d atoms'%len(rM.allAtoms)
#(5) add the bonds between at3 'CB' in the ligand and the attachment atom in the receptor
rM.addBond(at3, atom_to_attach)
if verbose:
print 'built bond between %s from ligand and atom %s in residue %s' %( at3.name,atom_to_attach.name, resP.name)
print "now the bonds of atom %s are:"%(at3.name)
for b in at3.bonds:
print " %s -%s"%(b.atom1.full_name(), b.atom2.full_name())
#(6) do some necessary updates of the protein data structure
rM.allAtoms = rM.chains.residues.atoms
num_ats = len(rM.allAtoms)
rM.allAtoms.number = range(1, num_ats+1)
# LOOK FOR CLOSE CONTACTS BETWEEN atoms_to_adopt and res_atoms_to_check
#if find close contacts, iterate rotation around bond
#in steps of 30degrees using setAngle stuff...
clashes = detect_clashes(res_atoms_to_check, atoms_to_adopt, verbose=verbose)
print "@@@ detected %d clashes! @@@"%len(clashes)