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Mishima-syk / psikit

psi4+RDKit
BSD 3-Clause "New" or "Revised" License
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cube file doesn't work #13

Closed kzfm closed 5 years ago

kzfm commented 5 years ago

The orbitals of these molecules from PDB cannot be drawn correctly.

PDBCODE:2W26

 OpenBabel05131911243D

 47 50  0  0  0  0  0  0  0  0999 V2000
    9.6430    1.7770   18.4330 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.3030    2.3770   18.1090 N   0  0  0  0  0  0  0  0  0  0  0  0
   10.0530    0.6670   17.4410 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.6710    2.1220   16.8810 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.7680    1.1240   16.1110 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.3550    1.2230   15.8530 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4870    4.9590   20.9810 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.3330    5.4680   19.9840 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2370    3.5510   21.0130 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.9180    4.6190   19.0480 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.8370    2.6900   20.0700 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.6820    3.2220   19.0780 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5830    2.6130   16.6300 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.9060    5.8630   21.9470 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.0400    5.5430   22.9950 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1460    7.3260   22.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6900    6.6140   23.7570 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.2130    7.7870   23.1340 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.6340    4.4190   23.2280 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.9240    8.7210   24.1550 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0780    8.1360   24.9320 N   0  0  0  0  0  0  0  0  0  0  0  0
    8.4020    8.5580   24.6720 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.1310    8.2640   25.0630 S   0  0  0  0  0  0  0  0  0  0  0  0
   11.8050    7.5030   26.2880 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.5670    8.0440   25.4660 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.7940    7.0110   27.1300 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.5090    7.3240   26.6590 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.6110    9.3790   23.7970 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.5440    7.3020   26.5310 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    9.6022    1.3590   19.4171 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.3720    2.5573   18.3651 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.4964   -0.2239   17.6446 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.0960    0.4500   17.5408 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.2059    1.6328   14.8759 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.9277    0.2443   15.9190 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.5235    6.4815   19.9440 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6106    3.1604   21.7341 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.5339    5.0139   18.3201 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.6571    1.6745   20.1074 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8850    7.7927   21.0732 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.1718    7.5800   22.1674 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4198    8.3800   22.7288 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1893    9.0440   24.8627 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.3551    9.5015   23.5635 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.9078    7.4566   25.6239 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.9752    6.4800   27.9961 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.6334    7.0556   27.1348 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  1 30  1  0  0  0  0
  1 31  1  0  0  0  0
  2  4  1  0  0  0  0
  2 12  1  0  0  0  0
  3  5  1  0  0  0  0
  3 32  1  0  0  0  0
  3 33  1  0  0  0  0
  4  6  1  0  0  0  0
  4 13  2  0  0  0  0
  5  6  1  0  0  0  0
  6 34  1  0  0  0  0
  6 35  1  0  0  0  0
  7  8  1  0  0  0  0
  7  9  2  0  0  0  0
  7 14  1  0  0  0  0
  8 10  2  0  0  0  0
  8 36  1  0  0  0  0
  9 11  1  0  0  0  0
  9 37  1  0  0  0  0
 10 12  1  0  0  0  0
 10 38  1  0  0  0  0
 11 12  2  0  0  0  0
 11 39  1  0  0  0  0
 14 15  1  0  0  0  0
 14 16  1  0  0  0  0
 15 17  1  0  0  0  0
 15 19  2  0  0  0  0
 16 18  1  0  0  0  0
 16 40  1  0  0  0  0
 16 41  1  0  0  0  0
 17 18  1  0  0  0  0
 18 20  1  0  0  0  0
 18 42  1  6  0  0  0
 20 21  1  0  0  0  0
 20 43  1  0  0  0  0
 20 44  1  0  0  0  0
 21 22  1  0  0  0  0
 21 45  1  0  0  0  0
 22 25  1  0  0  0  0
 22 28  2  0  0  0  0
 23 24  1  0  0  0  0
 23 25  1  0  0  0  0
 24 26  2  0  0  0  0
 24 29  1  0  0  0  0
 25 27  2  0  0  0  0
 26 27  1  0  0  0  0
 26 46  1  0  0  0  0
 27 47  1  0  0  0  0
M  END
iwatobipen commented 5 years ago

I added 'no_reorient and no_com' options to mol2xyz. The option keeps original orientation of molecule.