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?