xyz2mol
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jensengroup
Convert xyz file with several structures in it (different molecules or same molecule, conformers)
Is it possible to convert several molecules in xyz format that are in the same file to an sdf output? For the moment, It works for me but only with single molecule per file.
@stnrl It seems to depend on the input.
- An example where this works: Generation of a model including pyridine and diethyl ether in one data set with OpenBabel (3.1.1 -- Sep 8 2022 -- 12:29:09, Linux Debian 12/bookworm) by
obabel -:"c1ccncc1.CCOCC" -h --gen3d -O py_Et2O.xyz
yields a test data set similar to
26
C 0.66023 0.62902 -1.81071
C -0.16353 1.61570 -1.27828
C -1.41741 1.24497 -0.81939
N -1.88558 -0.02202 -0.85568
C -1.06234 -0.95946 -1.37401
C 0.20711 -0.68586 -1.85859
C 1.14077 -0.37698 1.79810
C 2.46962 -0.62285 1.11274
O 3.48114 -0.52854 2.10885
C 4.77258 -0.85279 1.60438
C 5.74302 -0.75889 2.76427
H 1.65370 0.88115 -2.17036
H 0.16494 2.64694 -1.21534
H -2.09635 1.97721 -0.39187
H -1.45720 -1.97127 -1.37534
H 0.83206 -1.48070 -2.24925
H 0.30852 -0.48442 1.10511
H 1.11444 0.62717 2.23061
H 1.00003 -1.08648 2.61918
H 2.64920 0.13030 0.33917
H 2.47898 -1.61692 0.65292
H 5.05736 -0.15356 0.81065
H 4.77092 -1.87231 1.20165
H 5.80440 0.27335 3.12474
H 6.74216 -1.09244 2.47453
H 5.39381 -1.36611 3.60588
The subsequent call
$ python xyz2mol.py ./examples/py_et2o.xyz -o sdf > recovery.sdf
yields
RDKit 3D
26 25 0 0 0 0 0 0 0 0999 V2000
0.6602 0.6290 -1.8107 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.1635 1.6157 -1.2783 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.4174 1.2450 -0.8194 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.8856 -0.0220 -0.8557 N 0 0 0 0 0 0 0 0 0 0 0 0
-1.0623 -0.9595 -1.3740 C 0 0 0 0 0 0 0 0 0 0 0 0
0.2071 -0.6859 -1.8586 C 0 0 0 0 0 0 0 0 0 0 0 0
1.1408 -0.3770 1.7981 C 0 0 0 0 0 0 0 0 0 0 0 0
2.4696 -0.6229 1.1127 C 0 0 0 0 0 0 0 0 0 0 0 0
3.4811 -0.5285 2.1088 O 0 0 0 0 0 0 0 0 0 0 0 0
4.7726 -0.8528 1.6044 C 0 0 0 0 0 0 0 0 0 0 0 0
5.7430 -0.7589 2.7643 C 0 0 0 0 0 0 0 0 0 0 0 0
1.6537 0.8811 -2.1704 H 0 0 0 0 0 0 0 0 0 0 0 0
0.1649 2.6469 -1.2153 H 0 0 0 0 0 0 0 0 0 0 0 0
-2.0964 1.9772 -0.3919 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.4572 -1.9713 -1.3753 H 0 0 0 0 0 0 0 0 0 0 0 0
0.8321 -1.4807 -2.2492 H 0 0 0 0 0 0 0 0 0 0 0 0
0.3085 -0.4844 1.1051 H 0 0 0 0 0 0 0 0 0 0 0 0
1.1144 0.6272 2.2306 H 0 0 0 0 0 0 0 0 0 0 0 0
1.0000 -1.0865 2.6192 H 0 0 0 0 0 0 0 0 0 0 0 0
2.6492 0.1303 0.3392 H 0 0 0 0 0 0 0 0 0 0 0 0
2.4790 -1.6169 0.6529 H 0 0 0 0 0 0 0 0 0 0 0 0
5.0574 -0.1536 0.8106 H 0 0 0 0 0 0 0 0 0 0 0 0
4.7709 -1.8723 1.2017 H 0 0 0 0 0 0 0 0 0 0 0 0
5.8044 0.2733 3.1247 H 0 0 0 0 0 0 0 0 0 0 0 0
6.7422 -1.0924 2.4745 H 0 0 0 0 0 0 0 0 0 0 0 0
5.3938 -1.3661 3.6059 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 2 0
1 6 1 0
1 12 1 0
2 3 1 0
2 13 1 0
3 4 2 0
3 14 1 0
4 5 1 0
5 6 2 0
5 15 1 0
6 16 1 0
7 8 1 0
7 17 1 0
7 18 1 0
7 19 1 0
8 9 1 0
8 20 1 0
8 21 1 0
9 10 1 0
10 11 1 0
10 22 1 0
10 23 1 0
11 24 1 0
11 25 1 0
11 26 1 0
M END
one may read again into obabel for a visualization, e.g.
obabel recovery.sdf -O recovery.svg
or Jmol
- And an example, where this does not work:
obabel -:"c1ccncc1.c1ccccc1" -h --gen3d -O py_benzene.xyz
python xyz2mol.py benz_py.xyz -o sdf > recovery2.sdf
because the OpenBabel's intermediate .xyz file describes a geometry of the two molecules as if they there intercalated:
23
C 1.09472 0.18388 0.62199
C 0.22445 -0.78231 -0.93482
C -1.53084 -0.58986 -1.16195
C -2.38027 0.44777 -0.05584
C -1.61232 1.31553 1.26254
C 0.07673 1.21771 1.63532
C 2.46037 -0.39474 -1.07462
C 1.41813 0.99491 -1.36746
C -0.13693 1.02962 -0.55139
N -0.60992 -0.44977 0.64771
C 0.51589 -1.80602 0.84480
C 2.03336 -1.76142 -0.01435
H 2.12876 0.18703 0.97545
H 0.64176 -1.48502 -1.67530
H -2.06532 -1.17270 -1.90369
H -3.45972 0.54416 -0.15900
H -2.22595 1.99641 1.84888
H 0.52390 1.81605 2.41714
H 3.46081 -0.37413 -1.50611
H 1.75944 1.86006 -1.92070
H -0.79524 1.88733 -0.69495
H 0.13597 -2.61848 1.45282
H 2.73482 -2.58428 0.08258
If you read the later .xyz file e.g., into Jmol (and use the optional Edit -> Preferences -> Bonds -> Compute Bonds Automatically, if not used by you by default, you have to confirm this by Apply in addition), there is a good reason xyz2mol does not provide a new record:
Because the example of pyridine and diethyl ether worked reasonably well, perhaps there is a way to introduce some «pertubation» into OpenBabel's action to report benzene and pyridine as two molecules more remote of each other than here. However, I do not recall if OpenBabel's documentation describes how to leave this local energetic minimum when running the --gen3d optimization.
