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oe2fps
oe2fps - generate fingerprints using OpenEye tools
Featured IntroductionOpenEye sells the OEChem toolkit for cheminformatics and the OEGraphSim add-on toolkit for fingerprint generation. oe2fps uses both of them to generate the OpenEye path and MACCS fingerprints, and uses just the OEChem toolkit to generate the RDMACCS and Substruct fingerprints based on the chemfp patterns. More information can be found in the chemfp documentation. DetailsOEGraphSim's --path fingerprint (which is the chemfp default) is 4096 bits long, so I've folded the fingerprint so it fits better in this web page. The fingerprint lines should have the entire fingerprint on one line, in the first column, with the record identifier in the second column. % oe2fps $PUBCHEM/Compound_005050001_005075000.sdf.gz | head -9 #type=OpenEye-Path/1 numbits=4096 minbonds=0 maxbonds=5 atype=DefaultAtom btype=DefaultBond #software=OEGraphSim/1.0.0 (20100809) #aromaticity=openeye #source=/Users/dalke/databases/pubchem/Compound_005050001_005075000.sdf.gz #date=2011-09-20T16:35:07 9084018000104400c0844200500400028000804a01200500011110000010200001100e20000042 08000020180008080003004230100000010010001006010100420f0402c0000040008e00010014 000080002010002110014120010010080080410040000010080000000000050011062020008000 424000210040000000504150080048012048064000001000c80460810800008100004000040002 040c5000000400040000000181000080000080000008000002015000080080000800004a002100 000001000020000001000002080000000318000101024840010140104000248408004080008800 000000008400182100041220001000a800000000002400088000000c8400044000003000012500 000000000100140480844800000008000002000080240028800000020001000100124220401032 10c0000300400000250000002e004001841000004850000280021a081000020000004440880180 0044040000000008120100100010005a2110404020004225000880002100804050016800089010 800000082003a02400028000000404080495c84844084000200046100000280d00040102100001 12220008000200800410004010004004140400411000c200000000042000021810000000400404 000200002000003000c08a00000100800080420090080038040000000830206000001000009020 8400c00000 5050001 908480000090440040844240100000028000000001028400001100000050200005000a20000042 000000201800000840030042300000000000100208064004204202140200000044008000010010 000480000010002100000120090010090000400040000202080000000000040001022020000000 000000032040010000c00100000050002000104000001600000060810800400010404000040002 041c0000000c840400000001804000000030800000000008020010000800000000800148000100 0000010001000000a1000002000000000200000005004810000540004000200000004180000800 01004000240018010004a280005000880000000000201000000000088400040001003200012000 00000000012004040084400000200c000000410080240020800000000100800000904020411036 0000000200710200240000000e0041018010000008500002c44212401000000020044040880080 4448000000000008100100040010001a2100000020024205000080002200004200016800009018 08000200208160000000a008000404080005c840050040000020020000001801000c2120100001 000000000002000000140000180040008204005010005000010400002008021010000000400400 004001002000001000c08100000100800000020090001078040000400030206000001404000020 8400d00000 5050002 You can change the fingerprint parameters % oe2fps --numbits 220 --minbonds 3 $PUBCHEM/Compound_005050001_005075000.sdf.gz | head -13 #FPS1 #num_bits=220 #type=OpenEye-Path/1 numbits=220 minbonds=3 maxbonds=5 atype=DefaultAtom btype=DefaultBond #software=OEGraphSim/1.0.0 (20100809) #aromaticity=openeye #source=/Users/dalke/databases/pubchem/Compound_005050001_005075000.sdf.gz #date=2011-09-20T16:37:00 ef7bd3ffff77fb9fffefbf77d3ffb7fff6fbbdffcffbfdfbfb4f0600 5050001 7f7bf29c3f7fff3f7f3bbe6fdfbd2ffffcb9edfd5ed3eee9fbe40600 5050002 cf69ebf5d9dffffc97efb78fbfff7dfdfff7ddfbbfdaefff5fd70500 5050003 8b33080d42b3d60fc3dee7c6e9c30528504a50948cf62830fd590000 5050004 4e29cff59dc65fa8a6f7bfbc9fed777d3f777dfa0ff26bf71fee0500 5050005 aabb4e1c7ab5d517d5dae7d6f95b247f8a4f46948ed2aab6fd5f0300 5050006 OEGraphSim can generate MACCS keys. % oe2fps --maccs $PUBCHEM/Compound_005050001_005075000.sdf.gz | head -10 #FPS1 #num_bits=166 #type=OpenEye-MACCS166/1 #software=OEGraphSim/1.0.0 (20100809) #aromaticity=openeye #source=/Users/dalke/databases/pubchem/Compound_005050001_005075000.sdf.gz #date=2011-09-20T16:38:40 000000880100448f04e7f5e83af3f073dbaa3b7a3b 5050001 000000080000000001e654c81aa1d453d0a0392e3b 5050002 00000000000002008008000914810150809833523a 5050003 Even if you don't have an OEGraphSim license, you can still generate the RDMACCS variant of the MACCS keys: % oe2fps --rdmaccs $PUBCHEM/Compound_005050001_005075000.sdf.gz | head -12 #FPS1 #num_bits=166 #type=RDMACCS-OpenEye/1 #software=OEChem/1.7.4 (20100809) #aromaticity=openeye #source=/Users/dalke/databases/pubchem/Compound_005050001_005075000.sdf.gz #date=2011-09-20T16:39:49 000000800100449f04e7b5e83af3f0dbdbeb3ffb1f 5050001 000000000000000001e614c81a21d45350e139af1f 5050002 0000000000000200800800111401217000d8b7d21e 5050003 00000000000201018000248000940024280b82571a 5050004 0000000000000221000c30401e51a0d359c3ad7b1f 5050005 and the PubChem-influenced 881 bit Substruct keys. % oe2fps --substruct $PUBCHEM/Compound_005050001_005075000.sdf.gz | head -12 #FPS1 #num_bits=881 #type=ChemFP-Substruct-OpenEye/1 #software=OEChem/1.7.4 (20100809) #aromaticity=openeye #source=/Users/dalke/databases/pubchem/Compound_005050001_005075000.sdf.gz #date=2011-09-20T16:42:19 000000800100449f04e7b5e83af3f0dbdbeb3ffb1f 5050001 000000000000000001e614c81a21d45350e139af1f 5050002 0000000000000200800800111401217000d8b7d21e 5050003 00000000000201018000248000940024280b82571a 5050004 0000000000000221000c30401e51a0d359c3ad7b1f 5050005 oe2fps --helpusage: oe2fps [-h] [--path] [--numbits INT] [--minbonds INT] [--maxbonds INT]
[--atype ATYPE] [--btype BTYPE] [--maccs166] [--substruct]
[--rdmaccs] [--aromaticity NAME] [--id-tag NAME] [--in FORMAT]
[-o FILENAME] [--errors {strict,report,ignore}]
[filenames [filenames ...]]
Generate FPS fingerprints from a structure file using OEChem
positional arguments:
filenames input structure files (default is stdin)
optional arguments:
-h, --help show this help message and exit
--aromaticity NAME use the named aromaticity model
--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)
path fingerprints:
--path generate path fingerprints (default)
--numbits INT number of bits in the path fingerprint (default=4096)
--minbonds INT minimum number of bonds in path (default=0)
--maxbonds INT maximum number of bonds in path (default=5)
--atype ATYPE atom type (default=DefaultAtom)
--btype BTYPE bond type (default=DefaultBond)
166 bit MACCS substructure keys:
--maccs166 generate MACCS fingerprints
881 bit ChemFP substructure keys:
--substruct generate ChemFP substructure fingerprints
ChemFP version of the 166 bit RDKit/MACCS keys:
--rdmaccs generate 166 bit RDKit/MACCS fingerprints
ATYPE is one or more of the following, separated by commas
Aromaticity AtomicNumber Chiral DefaultAtom EqAromatic EqHalogen
FormalCharge HvyDegree Hybridization InRing
Examples:
--atype DefaultAtom
--atype AtomicNumber,HvyDegree
BTYPE is one or more of the following, separated by commas
BondOrder Chiral DefaultBond InRing
Examples:
--btype DefaultBond,Chiral
--btype BondOrder
OEChem guesses the input structure format based on the filename
extension and assumes SMILES for structures read from stdin.
Use "--in FORMAT" to select an alternative, where FORMAT is one of:
File Type Valid FORMATs (use gz if compressed)
--------- ------------------------------------
SMILES smi, ism, can, smi.gz, ism.gz, can.gz
SDF sdf, mol, sdf.gz, mol.gz
SKC skc, skc.gz
CDK cdk, cdk.gz
MOL2 mol2, mol2.gz
PDB pdb, ent, pdb.gz, ent.gz
MacroModel mmod, mmod.gz
OEBinary v2 oeb, oeb.gz
old OEBinary bin
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