sdf2fps(1) [debian man page]

SDF2FPS(1)							   User Commands							SDF2FPS(1)

NAME

       sdf2fps - sdf2fps

DESCRIPTION

       usage: sdf2fps [-h] [--id-tag TAG] [--fp-tag TAG] [--num-bits INT]

	      [--errors  {strict,report,ignore}]  [-o  FILENAME]  [--software  TEXT] [--type TEXT] [--decompress METHOD] [--binary] [--binary-msb]
	      [--hex] [--hex-lsb] [--hex-msb] [--base64] [--cactvs] [--decoder DECODER] [--pubchem] [filenames [filenames ...]]

       Extract a fingerprint tag from an SD file and generate FPS fingerprints

   positional arguments:
       filenames
	      input SD files (default is stdin)

   optional arguments:
       -h, --help
	      show this help message and exit

       --id-tag TAG
	      get the record id from TAG instead of the first line of the record

       --fp-tag TAG
	      get the fingerprint from tag TAG (required)

       --num-bits INT
	      use the first INT bits of the input. Use only when the last 1-7 bits of the last byte are not part of  the  fingerprint.	Unexpected
	      errors will occur if these bits are not all zero.

       --errors {strict,report,ignore}
	      how should structure parse errors be handled?  (default=strict)

       -o FILENAME, --output FILENAME
	      save the fingerprints to FILENAME (default=stdout)

       --software TEXT
	      use TEXT as the software description

       --type TEXT
	      use TEXT as the fingerprint type description

       --decompress METHOD
	      use METHOD to decompress the input (default='auto', 'none', 'gzip', 'bzip2')

   Fingerprint decoding options:
       --binary
	      Encoded with the characters '0' and '1'. Bit #0 comes first. Example: 00100000 encodes the value 4

       --binary-msb
	      Encoded with the characters '0' and '1'. Bit #0 comes last. Example: 00000100 encodes the value 4

       --hex  Hex encoded. Bit #0 is the first bit (1<<0) of the first byte. Example: 01f2 encodes the value x01xf2 = 498

       --hex-lsb
	      Hex encoded. Bit #0 is the eigth bit (1<<7) of the first byte. Example: 804f encodes the value x01xf2 = 498

       --hex-msb
	      Hex encoded. Bit #0 is the first bit (1<<0) of the last byte. Example: f201 encodes the value x01xf2 = 498

       --base64
	      Base-64 encoded. Bit #0 is first bit (1<<0) of first byte. Example: AfI= encodes value x01xf2 = 498

       --cactvs
	      CACTVS encoding, based on base64 and includes a version and bit length

       --decoder DECODER
	      import and use the DECODER function to decode the fingerprint

   shortcuts:
       --pubchem
	      decode  CACTVS  substructure  keys  used	in  PubChem.  Same  as	--software=CACTVS/unknown  --type  'CACTVSE_SCREEN/1.0 extended=2'
	      --fptag=PUBCHEM_CACTVS_SUBSKEYS --cactvs

sdf2fps 1.0							     June 2012								SDF2FPS(1)

Check Out this Related Man Page

RDKIT2FPS(1)							   User Commands						      RDKIT2FPS(1)

NAME

       rdkit2fps - rdkit2fps

DESCRIPTION

       usage: rdkit2fps [-h] [--RDK] [--fpSize INT] [--minPath INT] [--maxPath INT]

	      [--nBitsPerHash  INT]  [--useHs  USEHS] [--maccs166] [--substruct] [--rdmaccs] [--id-tag NAME] [--in FORMAT] [-o FILENAME] [--errors
	      {strict,report,ignore}] [filenames [filenames ...]]

       Generate FPS fingerprints from a structure file using RDKit

   positional arguments:
       filenames
	      input structure files (default is stdin)

   optional arguments:
       -h, --help
	      show this help message and exit

       --id-tag NAME
	      tag name containing the record id (SD files only)

       --in FORMAT
	      input structure format (default guesses from filename)

       -o FILENAME, --output FILENAME
	      save the fingerprints to FILENAME (default=stdout)

       --errors {strict,report,ignore}
	      how should structure parse errors be handled?  (default=strict)

   RDKit topological fingerprints:
       --RDK  generate RDK fingerprints (default)

       --fpSize INT
	      number of bits in the fingerprint (default=2048)

       --minPath INT
	      minimum number of bonds to include in the subgraphs (default=1)

       --maxPath INT
	      maximum number of bonds to include in the subgraphs (default=7)

       --nBitsPerHash INT
	      number of bits to set per path (default=4)

       --useHs USEHS
	      information about the number of hydrogens on each atom

   166 bit MACCS substructure keys:
       --maccs166
	      generate MACCS fingerprints

   881 bit substructure keys:
       --substruct
	      generate ChemFP substructure fingerprints

   ChemFP version of the 166 bit RDKit/MACCS keys:
       --rdmaccs
	      generate 166 bit RDKit/MACCS fingerprints

       This program guesses the input structure format based on the filename extension. If the data comes from stdin, or  the  extension  name	us
       unknown, then use "--in" to change the default input format. The supported format extensions are:

       File Type
	      Valid FORMATs (use gz if compressed)

       ---------      ------------------------------------

       SMILES
	      smi, ism, can, smi.gz, ism.gz, can.gz

       SDF    sdf, mol, sd, mdl, sdf.gz, mol.gz, sd.gz, mdl.gz

rdkit2fps 1.0							     June 2012							      RDKIT2FPS(1)

Linux and UNIX Man Pages

sdf2fps(1) [debian man page]

Check Out this Related Man Page