Please disregard this "bad hair day" message. I am, allegedly, a computer scientist, and I should know that counting starts from 0.
Bleh, Sorry, - Jean-Paul Ebejer Early Stage Researcher On 8 November 2012 15:33, JP <[email protected]> wrote: > 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) ------------------------------------------------------------------------------ Everyone hates slow websites. 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