I imported the CDK package into Java, and converted a base64 string into binary. The length of the CDK generated string was 896 (I noticed that this question was already posted), and the actual length is 881. I took the first 15 bits off, and I got 881.
I also used the chemfp package to generate the binary string for the same compund. I got the FPS output (in Hex), and I did the binary conversion. The string length was 888 (and after chopping off the last 7 bits, I got 881).
The two strings don't match, and they are very different. Aren't they supposed to match? Nelfinavir is the compund.
Could someone please tell me what I am doing wrong? Which string is correct?
P.S. If this is not clear, I can post the two binary string outputs.