本文整理汇总了Python中MolKit.molecule.AtomSet.sort方法的典型用法代码示例。如果您正苦于以下问题：Python AtomSet.sort方法的具体用法？Python AtomSet.sort怎么用？Python AtomSet.sort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.molecule.AtomSet的用法示例。
在下文中一共展示了AtomSet.sort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: detectPiInteractions
# 需要导入模块: from MolKit.molecule import AtomSet [as 别名]
# 或者: from MolKit.molecule.AtomSet import sort [as 别名]
def detectPiInteractions(self, tolerance=0.95, debug=False, use_all_cycles=False):
if debug: print "in detectPiInteractions"
self.results['pi_pi'] = [] #stacked rings...?
self.results['t_shaped'] = [] #one ring perpendicular to the other
self.results['cation_pi'] = [] #
self.results['pi_cation'] = [] #
self.results['macro_cations'] = []#
self.results['lig_cations'] = [] #
#at this point have self.results
if not len(self.results['lig_close_atoms']):
return
lig_atoms = self.results['lig_close_atoms'].parent.uniq().atoms
macro_res = self.results['macro_close_atoms'].parent.uniq()
if not len(macro_res):
return
macro_atoms = macro_res.atoms
l_rf = RingFinder()
#Ligand
l_rf.findRings2(lig_atoms, lig_atoms.bonds[0])
#rf.rings is list of dictionaries, one per ring, with keys 'bonds' and 'atoms'
if debug: print "LIG: len(l_rf.rings)=", len(l_rf.rings)
if not len(l_rf.rings):
if debug: print "no lig rings found by l_rf!"
return
acbs = self.aromatic_cycle_bond_selector
#acbs = AromaticCycleBondSelector()
lig_rings = []
for r in l_rf.rings:
ring_bnds = r['bonds']
if use_all_cycles:
lig_rings.append(ring_bnds)
else:
arom_bnds = acbs.select(ring_bnds)
if len(arom_bnds)>4:
lig_rings.append(arom_bnds)
if debug: print "LIG: len(lig_arom_rings)=", len(lig_rings)
self.results['lig_rings'] = lig_rings
self.results['lig_ring_atoms'] = AtomSet()
#only check for pi-cation if lig_rings exist
if len(lig_rings):
macro_cations = self.results['macro_cations'] = self.getCations(macro_atoms)
macro_cations = macro_cations.get(lambda x: x.element!='H')
lig_ring_atoms = AtomSet()
u = {}
for r in lig_rings:
for a in BondSet(r).getAtoms():
u[a] = 1
if len(u):
lig_ring_atoms = AtomSet(u.keys())
lig_ring_atoms.sort()
self.results['lig_ring_atoms'] = lig_ring_atoms
if len(macro_cations):
if debug: print "check distances from lig_rings to macro_cations here"
#macro cations->lig rings
pairDict2 = self.distanceSelector.select(lig_ring_atoms,macro_cations)
z = {}
for key,v in pairDict2.items():
val = v.tolist()[0]
if val in macro_cations:
z[val] = [key]
if len(z):
self.results['pi_cation'] = (z.items())
else:
self.results['pi_cation'] = []
#check the distance between the rings and the macro_cations
self.results['lig_cations'] = self.getCations(lig_atoms)
lig_cations = self.results['lig_cations']
#remove hydrogens
lig_cations = lig_cations.get(lambda x: x.element!='H')
#Macromolecule
m_rf = RingFinder()
m_rf.findRings2(macro_res.atoms, macro_res.atoms.bonds[0])
#rf.rings is list of dictionaries, one per ring, with keys 'bonds' and 'atoms'
if debug: print "MACRO: len(m_rf.rings)=", len(m_rf.rings)
if not len(m_rf.rings):
if debug: print "no macro rings found by m_rf!"
return
macro_rings = []
for r in m_rf.rings:
ring_bnds = r['bonds']
if use_all_cycles:
macro_rings.append(ring_bnds)
else:
arom_bnds = acbs.select(ring_bnds)
if len(arom_bnds)>4:
macro_rings.append(arom_bnds)
if debug: print "len(macro_arom_rings)=", len(macro_rings)
self.results['macro_rings'] = macro_rings
self.results['macro_ring_atoms'] = AtomSet()
#only check for pi-cation if macro_rings exist
if len(macro_rings):
macro_ring_atoms = AtomSet()
u = {}
for r in macro_rings:
for a in BondSet(r).getAtoms(): #new method of bondSets
u[a] = 1
if len(u):
macro_ring_atoms = AtomSet(u.keys())
macro_ring_atoms.sort()
self.results['macro_ring_atoms'] = macro_ring_atoms
#.........这里部分代码省略.........