Hi there RDkitters,
Poll season: Does anyone else feel the need for more informative error messages?
For example the below code gives me:
[15:25:17] non-ring atom 22 marked aromatic
But which is atom 22 ? Any ideas?
Is it possible to have the equivalent atom rank/index in the file?
I tried the
m = Chem.MolFromMol2Block(mol_block, sanitize=False)
m.Debug()
trick -- but I am none wiser.
Thanks for your attention,
JP
#!/usr/bin/env python
import rdkit
from rdkit import Chem
mol_block="""@<TRIPOS>MOLECULE
2oc2_RX3
78 82 1
SMALL
NO_CHARGES
@<TRIPOS>ATOM
1 O1 -19.515 24.565 -8.011 O.co2 1 <1> 0.0000
2 C2 -19.776 25.440 -8.864 C.2 1 <1> 0.0000
3 O3 -20.246 26.552 -8.531 O.co2 1 <1> 0.0000
4 C4 -19.512 25.155 -10.329 C.3 1 <1> 0.0000
5 C5 -20.814 24.987 -11.129 C.3 1 <1> 0.0000
6 C6 -21.642 23.767 -10.778 C.2 1 <1> 0.0000
7 C7 -22.682 23.712 -9.857 C.2 1 <1> 0.0000
8 N8 -23.191 22.452 -9.833 N.pl3 1 <1> 0.0000
9 C10 -22.513 21.684 -10.723 C.ar 1 <1> 0.0000
10 C11 -22.614 20.330 -11.100 C.ar 1 <1> 0.0000
11 C12 -21.750 19.816 -12.075 C.ar 1 <1> 0.0000
12 C13 -20.790 20.638 -12.669 C.ar 1 <1> 0.0000
13 C14 -20.679 21.982 -12.302 C.ar 1 <1> 0.0000
14 C15 -21.544 22.491 -11.327 C.ar 1 <1> 0.0000
15 N16 -18.743 23.936 -10.541 N.am 1 <1> 0.0000
16 C17 -17.459 23.796 -10.209 C.2 1 <1> 0.0000
17 O18 -16.768 24.685 -9.703 O.2 1 <1> 0.0000
18 C19 -16.909 22.423 -10.508 C.3 1 <1> 0.0000
19 C20 -17.524 21.376 -9.584 C.3 1 <1> 0.0000
20 C21 -16.456 20.972 -8.565 C.3 1 <1> 0.0000
21 C22 -15.123 21.615 -8.959 C.3 1 <1> 0.0000
22 C23 -15.434 22.259 -10.280 C.3 1 <1> 0.0000
23 P24 -14.271 22.624 -11.492 P.3 1 <1> 0.0000
24 O25 -13.833 21.276 -11.986 O.2 1 <1> 0.0000
25 O26 -14.970 23.450 -12.557 O.2 1 <1> 0.0000
26 C27 -12.886 23.592 -11.095 C.3 1 <1> 0.0000
27 C28 -12.793 24.508 -9.881 C.3 1 <1> 0.0000
28 C29 -11.480 25.268 -9.723 C.ar 1 <1> 0.0000
29 C30 -10.703 25.075 -8.574 C.ar 1 <1> 0.0000
30 C31 -9.491 25.757 -8.403 C.ar 1 <1> 0.0000
31 C32 -9.042 26.649 -9.384 C.ar 1 <1> 0.0000
32 C33 -9.810 26.851 -10.535 C.ar 1 <1> 0.0000
33 C34 -11.022 26.171 -10.695 C.ar 1 <1> 0.0000
34 N35 -11.911 23.631 -12.008 N.am 1 <1> 0.0000
35 C36 -11.052 22.673 -12.362 C.2 1 <1> 0.0000
36 O37 -10.990 21.566 -11.861 O.2 1 <1> 0.0000
37 O38 -10.113 22.980 -13.418 O.3 1 <1> 0.0000
38 C39 -9.792 22.030 -14.432 C.3 1 <1> 0.0000
39 C40 -9.122 22.726 -15.601 C.ar 1 <1> 0.0000
40 C41 -9.888 23.248 -16.644 C.ar 1 <1> 0.0000
41 C42 -9.259 23.881 -17.718 C.ar 1 <1> 0.0000
42 C43 -7.865 24.003 -17.757 C.ar 1 <1> 0.0000
43 C44 -7.099 23.484 -16.717 C.ar 1 <1> 0.0000
44 C45 -7.727 22.849 -15.642 C.ar 1 <1> 0.0000
45 H1 -18.948 26.006 -10.739 H 1 <1> 0.0000
46 H2 -20.552 24.923 -12.195 H 1 <1> 0.0000
47 H3 -21.435 25.878 -10.957 H 1 <1> 0.0000
48 H4 -23.033 24.546 -9.251 H 1 <1> 0.0000
49 H5 -23.967 22.132 -9.235 H 1 <1> 0.0000
50 H6 -23.356 19.690 -10.637 H 1 <1> 0.0000
51 H7 -21.826 18.775 -12.369 H 1 <1> 0.0000
52 H8 -20.126 20.230 -13.423 H 1 <1> 0.0000
53 H9 -19.934 22.619 -12.764 H 1 <1> 0.0000
54 H10 -19.206 23.155 -10.961 H 1 <1> 0.0000
55 H11 -17.143 22.188 -11.557 H 1 <1> 0.0000
56 H12 -17.836 20.498 -10.167 H 1 <1> 0.0000
57 H13 -18.395 21.801 -9.064 H 1 <1> 0.0000
58 H14 -16.349 19.878 -8.558 H 1 <1> 0.0000
59 H15 -16.751 21.319 -7.564 H 1 <1> 0.0000
60 H16 -14.334 20.856 -9.065 H 1 <1> 0.0000
61 H17 -14.812 22.366 -8.217 H 1 <1> 0.0000
62 H18 -15.330 23.271 -9.862 H 1 <1> 0.0000
63 H19 -12.418 22.764 -10.543 H 1 <1> 0.0000
64 H20 -12.936 23.892 -8.981 H 1 <1> 0.0000
65 H21 -13.605 25.247 -9.952 H 1 <1> 0.0000
66 H22 -11.044 24.389 -7.807 H 1 <1> 0.0000
67 H23 -8.900 25.592 -7.510 H 1 <1> 0.0000
68 H24 -8.107 27.180 -9.252 H 1 <1> 0.0000
69 H25 -9.466 27.534 -11.303 H 1 <1> 0.0000
70 H26 -11.618 26.344 -11.584 H 1 <1> 0.0000
71 H27 -11.810 24.500 -12.493 H 1 <1> 0.0000
72 H28 -10.714 21.542 -14.779 H 1 <1> 0.0000
73 H29 -9.109 21.273 -14.019 H 1 <1> 0.0000
74 H30 -10.968 23.161 -16.620 H 1 <1> 0.0000
75 H31 -9.856 24.282 -18.530 H 1 <1> 0.0000
76 H32 -7.384 24.500 -18.592 H 1 <1> 0.0000
77 H33 -6.019 23.572 -16.742 H 1 <1> 0.0000
78 H34 -7.129 22.448 -14.831 H 1 <1> 0.0000
@<TRIPOS>BOND
1 1 2 ar
2 2 3 ar
3 2 4 1
4 4 5 1
5 4 15 1
6 5 6 1
7 6 14 1
8 6 7 2
9 7 8 1
10 8 9 1
11 9 14 ar
12 9 10 ar
13 10 11 ar
14 11 12 ar
15 12 13 ar
16 13 14 ar
17 15 16 am
18 16 17 2
19 16 18 1
20 18 22 1
21 18 19 1
22 19 20 1
23 20 21 1
24 21 22 1
25 22 23 1
26 23 24 ar
27 23 25 ar
28 23 26 1
29 26 27 1
30 26 34 1
31 27 28 1
32 28 33 ar
33 28 29 ar
34 29 30 ar
35 30 31 ar
36 31 32 ar
37 32 33 ar
38 34 35 am
39 35 36 2
40 35 37 1
41 37 38 1
42 38 39 1
43 39 44 ar
44 39 40 ar
45 40 41 ar
46 41 42 ar
47 42 43 ar
48 43 44 ar
49 4 45 1
50 5 46 1
51 5 47 1
52 7 48 1
53 8 49 1
54 10 50 1
55 11 51 1
56 12 52 1
57 13 53 1
58 15 54 1
59 18 55 1
60 19 56 1
61 19 57 1
62 20 58 1
63 20 59 1
64 21 60 1
65 21 61 1
66 22 62 1
67 26 63 1
68 27 64 1
69 27 65 1
70 29 66 1
71 30 67 1
72 31 68 1
73 32 69 1
74 33 70 1
75 34 71 1
76 38 72 1
77 38 73 1
78 40 74 1
79 41 75 1
80 42 76 1
81 43 77 1
82 44 78 1
@<TRIPOS>SUBSTRUCTURE
1 **** 1
@<TRIPOS>SET
DONOR_HYDROGENS STATIC ATOMS <user> **** ""
3 49 54 71
ATOM$RED STATIC ATOMS COLORGROUP SYSTEM
3 49 54 71"""
m = Chem.MolFromMol2Block(mol_block)
------------------------------------------------------------------------------
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