Over the last few days I've developed a command-line tool that I call "smiview".
It's a SMILES viewer. It isn't a depiction tool where the input is in SMILES but rather a tool to highlight different aspects of the SMILES string. I'll put some examples at the end. If you want to try it out you can download it from https://bitbucket.org/dalke/smiview/downloads/smiview-1.1.tar.gz or see the README from the project page at https://bitbucket.org/dalke/smiview As the README says, this was mostly built for fun. I would like to know if you use it for serious work. I have no long terms plan for this project. I think it would be cool (perhaps for pedagogical reasons) to have a GUI version in an IPython notebook, tied to a graphical depiction so you can see the connection between the SMILES terms and the depiction. I don't have those skills, so if it's something you want to do, you might look to this code as a starting point. It was developed under Python 3 and it seems to work under Python 2.7. Enjoy! Andrew da...@dalkescientific.com The default view highlights the atom locations (and numbers them), shows the branches and the atom that the branches are attached to, shows the closures (highlighting the closure atom and the closure indicator for both side of the closure), and shows you which part of the SMILES string correspond to which fragments. % smiview 'C#CCC[N+](C)(C)CCCCCCCCCCCC[N+](C)(C)CCC#C.Cc1ccc(S(=O)(=O)[O-])cc1.Cc1ccc(S(=O)(=O)[O-])cc1' ┌ 1111111111 2 2 222 2 22 223 3 3 3 3 atoms│ 0 1234 5 6 7890123456789 0 1 234 5 67 890 1 2 3 4 └ | |||| | | ||||||||||||| | | ||| | || ||| | | | | SMILES[ C#CCC[N+](C)(C)CCCCCCCCCCCC[N+](C)(C)CCC#C.Cc1ccc(S(=O)(=O)[O branches┌ *---(.)(.) *---(.)(.) *(........... └ *(..)(..) closures┌ 1*↑-------- 1 ---- └ ┌ 000000000000000000000000000000000000000000 fragments│ 111111111111111111 └ ┌ 33 33 344 4 4 4 4 44 atoms│ 56 78 901 2 3 4 5 67 └ || || ||| | | | | || SMILES[ -])cc1.Cc1ccc(S(=O)(=O)[O-])cc1 branches┌ ..) *(.............) └ *(..)(..) closures┌ ----*↑1 └ 1*↑-------- 1 --------*↑1 ┌ fragments│ 111111 └ 222222222222222222222222 (Thanks to Greg for feedback on the 'branches' visualization, and for suggesting the 'fragments' track.) If you give it a SMARTS pattern it will show where the corresponding atoms are: % smiview 'CC1CC2C3CCC4=CC(=O)C=CC4(C)C3(F)C(O)CC2(C)C1(O)C(=O)CO' --smarts '*=O' ┌ 1 1 11 1 1 1 1 1 12 2 2 2 2 2 22 atoms│ 01 23 4 567 89 0 1 23 4 5 6 7 8 90 1 2 3 4 5 67 └ || || | ||| || | | || | | | | | || | | | | | || SMILES[ CC1CC2C3CCC4=CC(=O)C=CC4(C)C3(F)C(O)CC2(C)C1(O)C(=O)CO match 1[ * * match 2[ * * If you give it an atom index, it shows the neighbors around that index, along with a summary of how the atom is attached to those neighbors: % smiview 'NC(=O)c1nonc1CNC(c1c[nH]cn1)C1CCNCC1' --atom-index 10 ┌ 1 1 11 11 1 11122 atoms│ 01 2 3 4567 890 1 23 45 6 78901 └ || | | |||| ||| | || || | ||||| SMILES[ NC(=O)c1nonc1CNC(c1c[nH]cn1)C1CCNCC1 neighbors┌ ^X ^ ^ └ C(-N9)(-c11)(-C16) You can modify how things look. In the following I'll have it show the offset to each character in the SMILES string on the top, and the atom indices on the bottom. % smiview 'NC(=O)c1nonc1CNC(c1c[nH]cn1)C1CCNCC1' -a offsets -b atoms -b closures byte offsets┌ 1 1 2 2 3 3 └ 0 5 0 5 0 5 0 5 SMILES[ NC(=O)c1nonc1CNC(c1c[nH]cn1)C1CCNCC1 ┌ || | | |||| ||| | || || | ||||| atoms│ 01 2 3 4567 891 1 11 11 1 11122 └ 0 1 23 45 6 78901 Here's the output for buckminsterfullerene: % smiview 'c12c3c4c5c1c6c7c8c2c9c1c3c2c3c4c4c%10c5c5c6c6c7c7c%11c8c9c8c9c1c2c1c2c3c4c3c4c%10c5c5c6c6c7c7c%11c8c8c9c1c1c2c3c2c4c5c6c3c7c8c1c23' --legend once ┌ 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2 atoms│ 0 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 6 7 └ | | | | | | | | | | | | | | | | | | | | | | | | | | | | SMILES[ c12c3c4c5c1c6c7c8c2c9c1c3c2c3c4c4c%10c5c5c6c6c7c7c%11c8c9c8c branches[ ┌ 1*↑-------*↑1 8*↑------ 8 ------- 8 ------- 8 -------*↑8 9* │ 2*-↑----- 2 ------*↑2 2*↑------ 2 ------- 2 ------- 2 ---- │ 3*↑------- 3 --------*↑3 4*↑------- 4 ------- 4 ------- │ 4*↑--------- 4 ----------*↑4 5*↑------- 5 -------- │ 5*↑------- 5 ------- 5 --------*↑5 6*↑------- 6 ----- closures│ 6*↑------- 6 ------- 6 --------*↑6 7*↑------- 7 - │ 7*↑------- 7 --------- 7 --------*↑7 8*↑- │ 9*↑------ 9 ------ 9 ------- 9 ------*↑9 │ 1*↑------- 1 ------- 1 -------- 1 ------ │ 3*↑------- 3 -------- 3 -------- 3 │ 10*↑------- 10 -------- 10 -- └ 11*↑------- 1 fragments[ 000000000000000000000000000000000000000000000000000000000000 2 2 3 3 3 3 3 3 3 3 3 3 4 4 4 4 4 4 4 4 4 4 5 5 5 5 5 5 5 5 5 5 8 9 0 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 6 7 8 9 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 9c1c2c1c2c3c4c3c4c%10c5c5c6c6c7c7c%11c8c8c9c1c1c2c3c2c4c5c6c3c7c8c1c23 ↑------- 9 -------- 9 -------- 9 --------*↑9 2*↑----- 2 ------*↑2 ---*↑2 3*↑------ 3 ------ 3 ------- 3 ------*↑3 3*↑------*-↑3 - 4 -------*↑4 5*↑------- 5 --------- 5 --------*↑5 5 -------- 5 --------*↑5 6*↑------- 6 ------- 6 --------*↑6 --- 6 -------- 6 --------*↑6 7*↑------- 7 ------- 7 --------*↑7 ------- 7 -------- 7 --------*↑7 8*↑--------- 8 ----------*↑8 ------ 8 ------- 8 -------- 8 -------*↑8 1*↑------- 1 --------*↑1 1*↑------ 1 ------- 1 ------- 1 -------*↑1 -*↑1 2*↑------- 2 ------- 2 -------- 2 -------*↑2 --------*↑3 4*↑------ 4 ------- 4 ------- 4 -------*↑4 ----- 10 --------*↑10 1 -------- 11 ------- 11 --------*↑11 0000000000000000000000000000000000000000000000000000000000000000000000 ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
