本文整理汇总了Python中framework.Framework.reconstruct_cif方法的典型用法代码示例。如果您正苦于以下问题：Python Framework.reconstruct_cif方法的具体用法？Python Framework.reconstruct_cif怎么用？Python Framework.reconstruct_cif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framework.Framework的用法示例。
在下文中一共展示了Framework.reconstruct_cif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: Assembly
# 需要导入模块: from framework import Framework [as 别名]
# 或者: from framework.Framework import reconstruct_cif [as 别名]
#.........这里部分代码省略.........
to_fractional = np.linalg.inv(to_cartesian)
# get the current oriented and translated ligands
oriented = self.orient_molecule_and_translate(self.opt_vec)
#print(oriented)
# produce optimized orientation
for i in range(len(oriented)):
oriented[i] = np.dot(to_fractional, oriented[i][0:3,:])
oriented[i] = self.frame.modGroupUC(oriented[i][0:3,:])
# produced optimized rod shift
# for i in range(len(rods)):
# for j in range(len(rods[i])):
# self.rod_coords_abc[i][self.oned_direct,j] += self.opt_vec[1+i]
# self.rod_coords_abc[i] = self.frame.modGroupUC(self.rod_coords_abc[i])
final_rods_abc = []
for i in range(len(self.rods)):
this_new_abc = np.copy(self.rod_ref_abc[i])
# start of this cxn info in the optimization vec
conn_start_ind = 1 + len(self.rods) + i*6 + i*len(self.cxns[i])
for j in range(len(self.rods[i])):
# shift ref pt based on curr val of rod shift
# print(xuse[1 + self.connect_to_rod[i][j]])
this_new_abc[self.oned_direct,j] += self.opt_vec[1 + i]
# shift ref pt as well based on the periodic image indicated in the opt_Vec
periodic_image = round(self.opt_vec[conn_start_ind + 6 + j], 0)
this_new_abc[self.oned_direct,j] += periodic_image
# get the new xyz
this_new_xyz = np.dot(to_cartesian, this_new_abc)
# apply shift (this is the fixed relative positions in rod constraint)
# non-trivial if we have non perpendicular oned_direct, but we took care of this
# in self.get_rod_coords()
this_shifted_xyz = this_new_xyz + self.rod_disp_xyz[i]
# use modified UC matrix to get back abc coords
this_shifted_abc = np.dot(to_fractional, this_shifted_xyz)
# mod rods back into the UC if they left
this_modded_abc = self.frame.modGroupUC(this_shifted_abc)
#final_rods_abc.append(this_modded_abc)
self.rod_coords_abc[i] = this_modded_abc
# modify UC parameters
final_a = self.frame.a
final_b = self.frame.b
final_c = self.frame.c
for direct in self.twod_direct:
if(direct == 0):
final_a = self.frame.a * self.opt_vec[0]
elif(direct == 1):
final_b = self.frame.b * self.opt_vec[0]
elif(direct == 2):
final_c = self.frame.c * self.opt_vec[0]
# create lists for final atomic coords/labels
final_ra = []
final_rb = []
final_rc = []
final_atmtype = []
final_label = []
overall_ind = 0
# add oriented molecules
for i in range(len(oriented)):
for j in range(np.shape(oriented[i])[1]):
final_atmtype.append(self.mol.labels[j])
final_label.append(self.mol.labels[j]+str(overall_ind))
overall_ind += 1
final_ra.append(oriented[i][0,j])
final_rb.append(oriented[i][1,j])
final_rc.append(oriented[i][2,j])
# add shifted rods
for i in range(len(rods)):
for j in range(len(rods[i])):
final_atmtype.append(self.rod_atmtype[i][j])
final_label.append(self.rod_atmtype[i][j] + str(overall_ind))
overall_ind += 1
final_ra.append(self.rod_coords_abc[i][0,j])
final_rb.append(self.rod_coords_abc[i][1,j])
final_rc.append(self.rod_coords_abc[i][2,j])
self.frame.reconstruct_cif(final_a, final_b, final_c, final_ra, final_rb, final_rc,
final_label, final_atmtype, self.mol.molname)