def seperate_with(self, targetItem, type, value):
""" [Bioperate] to seperate two items in opposite direction: (rel)ative distance is move EACH item in a distance under system unit; (abs)olute distance is the time of current distance of two items, e.g.: item+=unit_orientation_vector*rel; item+=orientation_vector*abs.
Args:
targetItem (Item): Atom|Molecule
type (str): rel|abs
value (Float): distance
"""
# orientation vector
if all(self.position == targetItem.position):
raise ValueError(_("两个atom完全重叠, 无法计算方向矢量"))
oriVec = targetItem.position - self.position
distance = np.linalg.norm(oriVec)
uniVec = oriVec / distance
if type == 'relative' or type == 'rel':
distance = distance * (value - 1) / 2
self.move(*-uniVec * distance)
targetItem.move(*+uniVec * distance)
if type == 'abusolute' or type == 'abs':
self.move(*-uniVec * value)
targetItem.move(*+uniVec * value)
return self
def rotate_orth(self, theta, x, y, z, xAxis, yAxis, zAxis):
"""围绕在(x,y,z)点的x/y/z轴旋转theta
Args:
theta (deg): 旋转角
x (float): 旋转参考点
y (float): 旋转参考点
z (float): 旋转参考点
xAxis (bool): 旋转轴指向
yAxis (bool): 旋转轴指向
zAxis (bool): 旋转轴指向
Raises:
SyntaxError: 只能有一个方向被设置成True来代表旋转轴指向
"""
if (xAxis, yAxis, zAxis) == (1, 0, 0) or\
(xAxis, yAxis, zAxis) == (0, 1, 0) or\
(xAxis, yAxis, zAxis) == (0, 0, 1):
self.rotate(theta, xAxis, yAxis, zAxis, x, y, z)
else:
raise SyntaxError(
_('为了指定空间中(x,y,z)的旋转轴的朝向, 需要将方向设定为1. 如: 旋转轴指向x方向则xAxis=1, yAxis=zAxis=0'
))
return self
def __getitem__(self, label):
if isinstance(label, str):
for item in self:
if item.label == label:
return item
elif isinstance(label, int):
return self.container[label]
elif isinstance(label, slice):
raise TypeError(_('暂不支持切片调用'))
def add_neighbors(self, *atoms):
"""添加键接的Atom. TODO: 将键接Atom和临近Atom区分开
Raises:
TypeError: 添加了错误种类的对象而不是Atom
"""
for atom in atoms:
if isinstance(atom, Atom):
if atom not in self:
self._neighbors.append(atom)
if self not in atom:
atom._neighbors.append(self)
else:
raise TypeError(_('相邻的atom应该是 ATOM类 而不是 %s' % (type(atom))))
def add_items(self, *items):
"""向Molecule中添加item
Raises:
TypeError: 如果不是Atom或者Molecule则报错
"""
for item in items:
if item.itemType == 'Molecule' or item.itemType == 'Atom':
item.parent = self.label
self.container.append(item)
else:
raise TypeError(_('传入的类型错误'))
self.update()
def rotate_orth(self, theta, x, y, z, xAxis, yAxis, zAxis):
""" 围绕(x,y,z)点的x/y/z轴旋转theta角
Raises: self.x = pos[0]
self.y = pos[1]
self.z = pos[2]
SyntaxError: [description]
"""
if (xAxis, yAxis, zAxis) == (1, 0, 0) or\
(xAxis, yAxis, zAxis) == (0, 1, 0) or\
(xAxis, yAxis, zAxis) == (0, 0, 1):
self.rotate(theta, xAxis, yAxis, zAxis, x, y, z)
else:
raise SyntaxError(
_('为了指定空间中(x,y,z)的旋转轴的朝向, 需要将方向设定为1. 如: 旋转轴指向x方向则xAxis=1, yAxis=zAxis=0'
))
def seperate_with(self, targetItem, type, value):
if all(self.position == targetItem.position):
raise ValueError(_("两个atom完全重叠, 无法计算方向矢量"))
oriVec = targetItem.position - self.position
distance = np.linalg.norm(oriVec)
uniVec = oriVec / distance
if type == 'relative' or type == 'rel':
distance = distance * (value - 1) / 2
self.move(*-uniVec * distance)
targetItem.move(*+uniVec * distance)
if type == 'abusolute' or type == 'abs':
self.move(*-uniVec * value)
targetItem.move(*+uniVec * value)
return self