我想制作一个python脚本，加载xyz文件。根据xyz参数，我需要找到原子之间的距离，原子之间的角度和二面角。我有一个矩阵形式的xyz坐标：
60 Buckminsterfullerene (C60 Bucky Ball)
1 C 0.56182991 1.03720708 -3.34153745 2 2 6 16
2 C -0.02867841 -0.20922332 -3.53733326 2 1 3 15
3 C 0.68868170 -1.41687735 -3.17419275 2 2 4 7
4 C 1.96798784 -1.33001731 -2.62971513 2 3 5 8
5 C 2.58298268 -0.03190141 -2.42580025 2 4 6 12
6 C 1.89418484 1.12766893 -2.77448204 2 1 5 11
7 C -0.26911535 -2.36054907 -2.62920302 2 3 9 21
8 C 2.34254586 -2.18322716 -1.51766993 2 4 10 19
9 C 0.09052931 -3.17978756 -1.56143494 2 7 10 43
10 C 1.42288437 -3.08932569 -0.99437947 2 8 9 36
11 C 1.93147043 2.28439304 -1.89955106 2 6 14 20
12 C 3.33762840 -0.08283139 -1.18772874 2 5 13 19
13 C 3.37342937 1.02783673 -0.34763393 2 12 14 32
14 C 2.65606922 2.23549084 -0.71077448 2 11 13 26
15 C -1.42982841 -0.40652370 -3.21677674 2 2 17 21
16 C -0.22432522 2.13802273 -2.81706602 2 1 18 20
17 C -2.18468203 0.65046195 -2.71318765 2 15 18 27
18 C -1.56968716 1.94857800 -2.50927274 2 16 17 22
19 C 3.18903027 -1.41242386 -0.62647337 2 8 12 34
20 C 0.62215914 2.90882602 -1.92586946 2 11 16 23
21 C -1.57842655 -1.73611615 -2.65552140 2 7 15 29
22 C -2.12435266 2.52208091 -1.29751971 2 18 24 28
23 C 0.08957811 3.45949446 -0.76236333 2 20 24 25
24 C -1.31157175 3.26219407 -0.44180686 2 22 23 37
25 C 0.84422386 3.40856444 0.47570821 2 23 26 42
26 C 2.10140370 2.80899380 0.50097868 2 14 25 31
27 C -3.11943529 0.42168510 -1.62746090 2 17 28 30
28 C -3.08214969 1.57840920 -0.75252997 2 22 27 39
29 C -2.47596183 -1.95578408 -1.61302381 2 21 30 44
30 C -3.26211692 -0.85496848 -1.08855240 2 27 29 40
31 C 2.47596171 1.95578403 1.61302382 2 26 32 46
32 C 3.26211681 0.85496841 1.08855240 2 13 31 33
33 C 3.11943527 -0.42168513 1.62746090 2 32 34 57
34 C 3.08214970 -1.57840928 0.75252996 2 19 33 35
35 C 2.12435273 -2.52208091 1.29751964 2 34 36 56
36 C 1.31157182 -3.26219401 0.44180679 2 10 35 47
37 C -1.42288432 3.08932572 0.99437953 2 24 38 42
38 C -2.34254574 2.18322716 1.51766996 2 37 39 52
39 C -3.18903022 1.41242378 0.62647331 2 28 38 41
40 C -3.37342947 -1.02783679 0.34763388 2 30 41 48
41 C -3.33762837 0.08283136 1.18772868 2 39 40 49
42 C -0.09052935 3.17978761 1.56143497 2 25 37 45
43 C -0.84422391 -3.40856443 -0.47570819 2 9 44 47
44 C -2.10140382 -2.80899386 -0.50097868 2 29 43 48
45 C 0.26911532 2.36054910 2.62920311 2 42 46 54
46 C 1.57842653 1.73611617 2.65552148 2 31 45 60
47 C -0.08957818 -3.45949441 0.76236329 2 36 43 53
48 C -2.65606930 -2.23549092 0.71077442 2 40 44 50
49 C -2.58298263 0.03190137 2.42580019 2 41 51 52
50 C -1.93147042 -2.28439306 1.89955101 2 48 51 53
51 C -1.89418482 -1.12766893 2.77448197 2 49 50 58
52 C -1.96798776 1.33001737 2.62971509 2 38 49 54
53 C -0.62215921 -2.90882598 1.92586939 2 47 50 55
54 C -0.68868164 1.41687744 3.17419279 2 45 52 59
55 C 0.22432525 -2.13802261 2.81706605 2 53 56 58
56 C 1.56968719 -1.94857793 2.50927279 2 35 55 57
57 C 2.18468202 -0.65046198 2.71318771 2 33 56 60
58 C -0.56182981 -1.03720706 3.34153744 2 51 55 59
59 C 0.02867849 0.20922332 3.53733334 2 54 58 60
60 C 1.42982839 0.40652370 3.21677684 2 46 57 59
我尝试过使用pyGSM，但它给出了一个错误'NoneType' object has no attribute 'group'，我不知道如何更正，因为我从未在python中使用过组。
from pygsm.utilities.manage_xyz import read_xyz,xyz_to_np
from pygsm.coordinate_systems.slots import Distance,Angle,Dihedral
bond = Distance(0,1)
angle = Angle(0,1,2)
dihedral=Dihedral(0,1,2,3)
geom = read_xyz('bucky.xyz')
xyz = xyz_to_np(geom)
bond_value = bond.value(xyz)
angle_value = angle.value(xyz)
dihedral_value = dihedral.value(xyz)
print(bond_value,angle_value,dihedral_value)
import numpy as np
try:
from . import units
except:
import units
import re
#import openbabel as ob
# => XYZ File Utility <= #
def read_xyz(
filename,
scale=1.):
lines = open(filename).readlines()
lines = lines[2:]
geom = []
for line in lines:
mobj = re.match(r'^s*(S+)s+(S+)s+(S+)s+(S+)s*$', line)
geom.append((
scale*float(mobj.group(1),
scale*float(mobj.group(2)),
scale*float(mobj.group(3)),
scale*float(mobj.group(4)),
)))
return geom
有人能帮我做这个吗？
我对python的了解不多，但我认为你可以做这样的事情：
filename = "filename.xyz"
xyz = open(filename, "r")
line = xyz.readline()
atom, x, y, z = line.split()
# Calculate what you need here
xyz.close()
或者使用for循环：
xyz = open(filename, "r")
for line in xyz:
print(line)
# Calculate what you need here
xyz.close()
按照@MateusJunges的建议手动解析文件可能是个好主意，因为这些xyz文件没有公认的格式。然而，一个常见的问题可能是，许多程序都期望这样的东西：
60
Buckminsterfullerene (C60 Bucky Ball)
C 0.56182991 1.03720708 -3.34153745 2 2 6 16
C -0.02867841 -0.20922332 -3.53733326 2 1 3 15
C 0.68868170 -1.41687735 -3.17419275 2 2 4 7
...
因此，第一行中的原子数，后面是注释行，后面是原子条目(第一列中没有索引(。
我不熟悉PyGSM，但有很多包可以读取xyz文件。以MDAnalysis为例。
import MDAnalysis
u = MDAnalysis.Universe("structure.xyz")
atom_positions = u.coord.positions
这将为您提供atom_positions作为形状(n_atoms，3(的NumPy数组，您可以使用它进行计算。
我相信还没有人回答这里的距离。
xyz文件中有1000个可供读取的库。我最喜欢的是asehttps://databases.fysik.dtu.dk/ase/index.html然后在numpy中构建一个邻居矩阵，如下所示：
import numpy as np
from ase.io import read
atoms = read(<your file>)
natoms = len(atoms)
# First pull out the atom positions arranged like an N x 3 array
positions = atoms.positions
positions = np.array(positions, ndmin=3) # This makes it a 3d array
# Here we make the actual neighbor matrix
distances = positions.repeat(natoms, axis=0)
- positions.repeat(natoms, axis=1)
.reshape((natoms, natoms, 3))
neigh = np.linalg.norm(distances, axis=2)
# Now if you know a charecteristic bond length, you can get an
# average coordination number
bond_length = <some number>
ave_coordination = np.count_nonzero(neigh < bond_length) / natoms