smi_to

Assembling off-the-shelf Components Into Useful Applications, TJ O'Donnell, MUG2004

smi_to_2d

Sample output of smi_to_2d after display using smitable

smi_to_2d is an command-line application - an extension of the original code in $DY_ROOT/contrib/src/c/depict/smi_to_2d.c

There is now an alignment option, for example:

smi_to_2d -a '$SMI<CC(=O)c1ccccc1>2D<-1.75,1.53,-1.25,2.40,-1.76,3.28,-0.24,2.41,0.24,1.53,1.25,1.53,1.76,2.40,1.26,3.28,0.26,3.28>|'
CC(=O)c1ccccc1
CC(=O)c1ccc(F)cc1
CC(=O)c1ccc(cc1)C(O)C(CO)NC(=O)C(Cl)Cl
CC(=O)c1ccc(cc1)S(=O)(=O)NC(=O)NC2CCCCC2
CC(NC(C)(C)C)C(=O)c1cccc(Cl)c1

which will output 2D coords (2D TDT tag) for all input SMILES after SMARTS-matching the SMILES in the $SMI tag above and setting the coords of the matched atoms to the corresponding atoms in the 2D tag above.

$SMI<CC(=O)c1ccccc1>2D<-1.75,1.52,-1.25,2.40,-1.75,3.27,-0.23,2.41,0.25,3.27,1.25,3.27,1.75,2.40,1.25,1.52,0.23,1.52>MATCH<111111111>ALAB<.1,.1,.1,.1,.1,.1,.1,.1,.1>|
$SMI<CC(=O)c1ccc(F)cc1>2D<-1.75,1.52,-1.25,2.40,-1.75,3.27,-0.23,2.41,0.25,3.27,1.25,3.27,1.75,2.40,2.26,3.28,1.25,1.52,0.23,1.52>MATCH<1111111011>ALAB<.1,.1,.1,.1,.1,.1,.1,.0,.1,.1>|
$SMI<CC(=O)c1ccc(cc1)C(O)C(CO)NC(=O)C(Cl)Cl>2D<-1.75,1.52,-1.25,2.40,-1.75,3.27,-0.23,2.41,0.25,3.27,1.25,3.27,1.75,2.40,1.25,1.52,0.23,1.52,2.26,3.28,3.28,3.28,1.75,4.16,2.26,5.04,3.28,5.04,0.73,4.16,0.22,5.04,0.73,5.92,-0.79,5.04,-1.29,5.92,-1.30,4.15>MATCH<11111111100000000000>ALAB<.1,.1,.1,.1,.1,.1,.1,.1,.1,.0,.0,.0,.0,.0,.0,.0,.0,.0,.0,.0>|
$SMI<CC(=O)c1ccc(cc1)S(=O)(=O)NC(=O)NC2CCCCC2>2D<-1.75,1.52,-1.25,2.40,-1.75,3.27,-0.23,2.41,0.25,3.27,1.25,3.27,1.75,2.40,1.25,1.52,0.23,1.52,2.77,2.40,2.76,1.38,2.77,3.41,3.65,2.90,4.53,2.38,5.04,3.26,5.03,1.49,6.05,1.49,6.02,0.47,6.90,-0.03,7.78,0.47,7.79,1.48,6.92,1.99>MATCH<1111111110000000000000>ALAB<.1,.1,.1,.1,.1,.1,.1,.1,.1,.0,.0,.0,.0,.0,.0,.0,.0,.0,.0,.0,.0,.0>|
$SMI<CC(NC(C)(C)C)C(=O)c1cccc(Cl)c1>2D<-2.63,2.03,-1.75,1.52,-1.75,0.50,-2.63,0.00,-2.12,-0.88,-3.51,0.51,-3.14,-0.88,-1.25,2.40,-1.75,3.27,-0.23,2.41,0.25,3.27,1.25,3.27,1.75,2.40,1.25,1.52,1.75,0.63,0.23,1.52>MATCH<0100000111111101>ALAB<.0,.1,.0,.0,.0,.0,.0,.1,.1,.1,.1,.1,.1,.1,.0,.1>|

Notes:

The output MATCH tag is an indication of which atoms matched the SMILES in the alignment target. It is used by the smitable utility.

The output ALAB tag is also an indication of which atoms matched and is used by smitable.

The input TDT (after the -a in the command line above) can come from smi_to_2d itself, or from '$DY_ROOT/contrib/bin/mol2smi -output_format TDT -write_2d'.