What this tool does
Read an input SD file, extract the fingerprints and store them in a FPS-file.
Input
SD-Format, storing the atom types, together with the Cartesian coordinates.
Example:
28434379
-OEChem-02031205132D
37 39 0 0 0 0 0 0 0999 V2000
8.1648 -1.8842 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
6.0812 -0.2134 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
6.0812 -1.8229 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
2.5369 -2.0182 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
6.3919 0.7371 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.3704 0.9433 0.0000 C 0 0 0 0
......
1 15 1 0 0 0 0
1 35 1 0 0 0 0
2 5 1 0 0 0 0
2 11 1 0 0 0 0
2 12 1 0 0 0 0
3 12 2 0 0 0 0
3 13 1 0 0 0 0
4 18 1 0 0 0 0
......
>PUBCHEM_COMPOUND_CID<
28434379
> <PUBCHEM_COMPOUND_CANONICALIZED>
1
> <PUBCHEM_CACTVS_COMPLEXITY>
280
> <PUBCHEM_CACTVS_HBOND_ACCEPTOR>
2
> <PUBCHEM_CACTVS_HBOND_DONOR>
2
> <PUBCHEM_CACTVS_ROTATABLE_BOND>
2
> <PUBCHEM_CACTVS_SUBSKEYS>
AAADceBzIAAAAAAAAAAAAAAAAAAAAWAAAAAwYAAAAAAAAFgB8AAAHgAQCAAACCjhlwYx0LdMEgCgASZiZASCgC0hEqAJ2CA4dJiKeKLA2dGUJAhokALYyCcQAAAAAACAAAQAACAAAQAACAAAQAAAAAAAAA==
>
Output
After the first few lines, starting with a hash symbol, which contain generic information, the fingerprints are listed as hexadecimal strings.
Example:
#FPS1 #num_bits=881 #type=CACTVS-E_SCREEN/1.0 extended=2 #software=CACTVS/unknown #source=/home/mohammed/galaxy-central/database/files/000/dataset_409.dat #date=2012-02-03T10:44:12 07ce04000000000000000000000000000080060000000c0600 00000000001a800f0000780008100000101487e9608c0bed32 48000580644626204101b4844805901b041c2e19511e45039b 8b2924101609401b13e4080000000000010020000004008000 0010000002000000000000 28434379