CS 264 final project:

finding symmetry in the universe of organic compounds


NOTES:

#Retrieval of chemical structures from PubChem:

2D Structures (to get all)
wget --mirror --accept "*.sdf.gz" ftp://ftp.ncbi.nlm.nih.gov/pubchem/Compound/CURRENT-Full/SDF/

3D structures can be retrieved from 
ftp://ftp.ncbi.nih.gov/pubchem/Compound_3D/01_conf_per_cmpd/

Images of structures can be downloaded as:
http://pubchem.ncbi.nlm.nih.gov/image/imgsrv.fcgi?t=l&cid=3794239


BENCHMARKING

91.8720929623 seconds elapsed (total)
2.00971269608 seconds sorting
78.4631748199 seconds calculating distances <--- GPU acceleration can really help, calculation of distances is what we spend 80% of the time doing

ACCURACY

Appear in 3D model, not in 2D, and is correct:

21397
22288
21971
20060
19221
15699
13915 (bad ass)
13914
11088
8970
359

Sometimes, hydrogen causes these problems, like on hydroxyls

Rotations? Resonance?