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"babel -H fpt" - Fingerprint Help Information
How to get help information on Open Babel Fingerprints?
✍: FYIcenter.com
You can use the "babel -H fpt" command to get help information on Open Babel Fingerprints:
fyicenter$ babel -H fpt fpt Fingerprint format Generate or display molecular fingerprints. This format constructs and displays fingerprints and (for multiple input objects) the Tanimoto coefficient and whether a superstructure of the first object. A list of available fingerprint types can be obtained by:: babel -L fingerprints The current default type FP2 is is of the Daylight type, indexing a molecule based on the occurrence of linear fragment up to 7 atoms in length. To use a fingerprint type other than the default, use the ``-xf`` option, for example:: babel infile.xxx -o fpt -xfFP3 For a single molecule the fingerprint is output in hexadecimal form (intended mainly for debugging). With multiple molecules the hexadecimal form is output only if the ``-xh`` option is specified. But in addition the Tanimoto coefficient between the first molecule and each of the subsequent ones is displayed. If the first molecule is a substructure of the object molecule a note saying this is also displayed. The Tanimoto coefficient is defined as:: Number of bits set in (patternFP & targetFP) / Number of bits in (patternFP | targetFP) where the boolean operations between the fingerprints are bitwise. The Tanimoto coefficient has no absolute meaning and depends on the design of the fingerprint. Use the ``-xs`` option to describe the bits that are set in the fingerprint. The output depends on the fingerprint type. For Fingerprint FP4, each bit corresponds to a particular chemical feature, which are specified as SMARTS patterns in :file:`SMARTS_InteLigand.txt`, and the output is a tab-separated list of the features of a molecule. For instance, a well-known molecule gives:: Primary_carbon: Carboxylic_acid: Carboxylic_ester: Carboxylic_acid_derivative: Vinylogous_carbonyl_or_carboxyl_derivative: Vinylogous_ester: Aromatic: Conjugated_double_bond: C_ONS_bond: 1,3-Tautomerizable: Rotatable_bond: CH-acidic: For the path-based fingerprint FP2, the output from the ``-xs`` option is instead a list of the chemical fragments used to set bits, e.g.:: $ obabel -:"CCC(=O)Cl" -o fpt -xs -xf FP2 > 0 6 1 6 <670> 0 6 1 6 1 6 <260> 0 8 2 6 <623> ...etc where the first digit is 0 for linear fragments but is a bond order for cyclic fragments. The remaining digits indicate the atomic number and bond order alternatively. Note that a bond order of 5 is used for aromatic bonds. For example, bit 623 above is the linear fragment O=C (8 for oxygen, 2 for double bond and 6 for carbon). Write Options e.g. -xfFP3 -xN128 f <id> fingerprint type N# fold to specified number of bits, 32, 64, 128, etc. h hex output when multiple molecules o hex output only s describe each set bit u describe each unset bit This format is Write-only
⇒ Using Fastsearch Fingerprint Index
⇐ "babel" - FP2 Fingerprint Fragment Ends at Ring
2020-11-22, 910🔥, 0💬
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