Convert xyz file with several structures in it (different molecules or same molecule, conformers)

[jensengroup]

Convert xyz file with several structures in it (different molecules or same molecule, conformers)

[jhjensen2]

No, that's not currently possible

[nbehrnd]

@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.