Note
For an unknown reason, GitHub is no longer displaying the molecule printed ascii within the Jupyter Notebook, use the Jupyter nbviewer interface instead: rdkit_print_mol_ascii on nbviewer
This is a work in-progress and mostly for fun because I like to print molecules in the terminal. Below are two very basic methods that have worked for me.
While the below methods achieved my initial goals of printing a molecule as ascii characters, I haven't yet been able to figure out how to make the printing of the molecules more compact with either method, while maintaining a reasonable aspect ratio (i.e., molecule printing gets distorted if a lot smaller). If you have any feedback on how to 'shrink' the molecules, it would be greatly appreciated.
RDKit includes the Schroedinger 2D coordinate generation library (CoordGen) and this can be used to get the x,y coordinates of atoms and bonds for plotting.
The rdkit_print_mol_ascii notebook in this repository demonstrates one way of printing molecules as ascii characters using RDKit.
The print_mol_ascii function is likely most useful in an ipython console to quickly view molecules (i.e., not in a full Jupyter Notebook).
Here is an example of how molecules look. Atoms are printed with their standard symbols, and bonds are denoted with a *:
Br
*
C
* *
C C
* *
C N C C
* * * * * * * *
C C C C Br
* * *
C C N
* * *
O C
There is also a simple command line script included that is written with python argparse, print_mols.py, for use in a terminal window:
$ python3 print_mols.py -h
usage: print_mols.py [-h] [-m N] [-x N] SMILES_INPUT
print_mols is a command line interface that uses RDKit to draw molecules as ascii characters from input SMILES.
Atoms are printed with their standard symbols, and bonds are denoted with a '*' symbol. Written by Vincent Scalfani
positional arguments:
SMILES_INPUT input SMILES file; use '-' for stdin. The SMILES input file must contain one SMILES per line. Additional columns are not accepted.
optional arguments:
-h, --help show this help message and exit
-m N max number of molecules to draw, default: 10
-x N scale molecule size, default: 16Here are a couple of examples with the print_mols.py script:
$ python3 print_mols.py examples.smi -m2
C * C
*
*
N
F C *
* * *
C C
* *
F F
Br
*
C
* *
C C
* *
C N C C
* * * * * * * *
C C C C Br
* * *
C C N
* * *
O C
$ echo 'Cn1c(n[nH]c1=O)Cn2ccc(c(c2=O)Oc3cc(cc(c3)Cl)C#N)C(F)(F)F' | python3 print_mols.py - -x14
O
*
N * C
* *
N N
* * *
C C
*
C C
* * *
C N
* *
F C C
* * * * *
C C O
* * * N
*
F F O C C
* * * *
C C
* *
C C
* *
C
*
Cl
gnuplot can plot as ascii characters in a terminal window. So if you have atom/bond xy coordinates either from RDKit or some other toolkit, it's fairly straightforward to plot them using gnuplot. The bond coordinates below are the center xy positions of the bond. Note that the y direction is flipped from the example above:
$ cat mol2_atoms
156.596602856445 262.888402526855 C
125.485403515625 281.00359967041 C
94.2446039550782 263.118802307129 C
94.1150092285156 227.118799560547 C
125.226203076172 209.003601043701 C
156.474204174805 226.888399780273 C
187.578201977539 208.780400054932 N
218.819004284668 226.67240032959 C
249.930203625488 208.557200439453 C
281.178204724121 226.44919934082 C
312.282205273438 208.334000823975 C
312.159806591797 172.334000823975 C
280.911802746582 154.442000549316 C
249.807804257202 172.557200439453 C
280.782205273437 118.449202087402 Br
343.530200878906 226.218799560547 Br
281.307804943848 262.442000549316 N
63.1333991210938 281.226797912598 O
$ cat mol2_bonds
141.041003186035 271.946001098633
109.865003735352 272.06120098877
94.1798065917969 245.118800933838
109.670606152344 218.061200302124
140.850203625488 217.946000411987
172.026203076172 217.834399917603
203.198603131104 217.726400192261
234.374603955078 217.614800384522
265.554204174805 217.503199890137
296.730204998779 217.391600082397
312.221005932617 190.334000823975
296.535804669189 163.388000686646
265.359803501892 163.499600494385
280.84700401001 136.445601318359
327.906203076172 217.276400192261
281.243004833984 244.445599945068
78.6890015380859 272.172800109863
156.535403515625 244.888401153564
249.869003941345 190.557200439453
$ gnuplot -e "set term dumb; \
> unset xtics; unset ytics; unset border; \
> plot 'mol2_atoms' using 1:2:3 with labels notitle, \
> 'mol2_bonds' using 1:2 with points pt '*' notitle"
O C
* * *
C C N
* *
*
C C C C Br
* * * * * * * *
C N C C
* *
C C
* *
C
*
Br
- Noel O'Boyle's ascii format in Open Babel
- drewberryants asciiMOL - curses based ascii molecule viewer
- Carhart, R. E. A Model-Based Approach to the Teletype Printing of Chemical Structures. J. Chem. Inf. Model. 1976, 16 (2), 82–88. https://doi.org/10.1021/ci60006a011.
- Feldmann, R. J.; Koniver, D. A. Interactive Searching of Chemical Files and Structural Diagram Generation from Wiswesser Line Notation. J. Chem. Doc. 1971, 11 (3), 154–159. https://doi.org/10.1021/c160042a008.
- Thomson, L. H.; Hyde, E.; Matthews, F. W. Organic Search and Display Using a Connectivity Matrix Derived from Wiswesser Notation. J. Chem. Doc. 1967, 7 (4), 204–209. https://doi.org/10.1021/c160027a005.