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Molecule FYI-1000196
Molecule Summary: ID: FYI-1000196 SMILES: O=C(N(C(C(OC(=O)CCCCC(=O)OC)([ H])[H])([H])[H])[H])C2=C([N]1C (=NC(=C1C([H])([H])[H])C([H])( [H])[H])C(=C2[H])N(C(C3=C(C(=C (C(=C3C([H])([H])[H])[H])[H])[ H])C([H])([H])[H])([H])[H])[H] )[H].[H]Received at FYIcenter.com on: 2020-12-04
2021-01-09, 383👍, 0💬

"babel --append ..." Command - Calculate Molecule Properties
How to use "babel --append ..." command to calculate Molecule Properties? The "--append ..." option of the "babel" command can be used to copy existing molecule properties from the input data source, and append them to the "title" field of output molecules. But the "--append ..." option can also be ...
2020-12-26, 715👍, 0💬

"babel" Command Option Argument Syntax
How to write "babel" command option argument properly? What's the difference between "-isdf" and "-i sdf"? There is no difference between "-isdf" and "-i sdf". Both are valid "babel" option "-i" with an argument of "sdf". If a "babel" command option takes an argument, you can specify the argument in...
2020-12-26, 545👍, 0💬

Molecule FYI-1000193
Molecule Summary: ID: FYI-1000193 SMILES: CH3COOH Received at FYIcenter.com on: 2020-11-27
2020-12-26, 400👍, 0💬

Molecule FYI-1000190
Molecule Summary: ID: FYI-1000190 SMILES: Cc1cc(C)n2nc(C(=O)N/N=C/c3ccc4 c(c3)OCO4)nc2n1Received at FYIcenter.com on: 2020-11-11
2020-12-26, 398👍, 0💬

Molecule FYI-1000195
Molecule Summary: ID: FYI-1000195 SMILES: c1c(ccc(c1)CCC(CC(=O)CCc1ccc(c c1)O)OC)OReceived at FYIcenter.com on: 2020-12-02
2020-12-26, 388👍, 0💬

Molecule FYI-1000194
Molecule Summary: ID: FYI-1000194 SMILES: c3ccc2cc1ccccc1cc2c3 Received at FYIcenter.com on: 2020-12-01
2020-12-26, 383👍, 0💬

Similarity Search with Open Babel
Where to find FAQ (Frequently Asked Questions) on Similarity Search with Open Babel? Here is a list of tutorials to answer many frequently asked questions compiled by FYIcenter.com team on Similarity Search with Open Babel. "babel -o fpt ..." Command - Similarity Search Fingerprint Types Supported i...
2020-12-22, 761👍, 0💬

Molecule FYI-1000192
Molecule Summary: ID: FYI-1000192 SMILES: NS(=O)(=O)N Received at FYIcenter.com on: 2020-11-24
2020-12-22, 442👍, 0💬

Molecule FYI-1000191
Molecule Summary: ID: FYI-1000191 SMILES: C1CCCCCCCC1 Received at FYIcenter.com on: 2020-11-13
2020-12-22, 411👍, 0💬

"babel -o fpt ..." Command - Similarity Search
How to use "babel -o fpt ..." command to do similarity search? You can use the "fpt" output file format with the "babel" command to do similarity search using the following syntax: babel input_section -o fpt When you run the above commands, Open Babel will perform the following: Take the first molec...
2020-12-15, 882👍, 0💬

Fingerprint Types Supported in Open Babel
What Fingerprint Types are Supported in Open Babel? You can get a list of fingerprint types supported in Open Babel by running the "babel -L fingerprints" command: fyicenter$ babel -L fingerprints FP2 Indexes linear fragments up to 7 atoms. FP3 SMARTS patterns specified in the file patterns.txt FP4 ...
2020-12-15, 607👍, 0💬

Molecule FYI-1000187
Molecule Summary: ID: FYI-1000187 SMILES: CC1=C(C(C[C@@H](C1)O)(C)C)/C=C /C(=C/C=C/C(=C/C=C/C=C(\\C)/C= C/C=C(\\C)/C=C/[C@H]2C(=C[C@@H ](CC2(C)C)O)C)/C)/CReceived at FYIcenter.com on: 2020-11-09
2020-12-15, 505👍, 0💬

Molecule FYI-1000189
Molecule Summary: ID: FYI-1000189 SMILES: Cc1ccc(C(=O)OCC(=O)Nc2ccccc2)c c1CReceived at FYIcenter.com on: 2020-11-11
2020-12-15, 424👍, 0💬

Molecule FYI-1000188
Molecule Summary: ID: FYI-1000188 SMILES: Cl.CC1(C)N=C(N)N=C(N)N1OCCCc1c cccc1Received at FYIcenter.com on: 2020-11-09
2020-12-15, 402👍, 0💬

Molecule FYI-1000184
Molecule Summary: ID: FYI-1000184 SMILES: CC(C)CC1=NC=CN=C1OC Received at FYIcenter.com on: 2020-11-09
2020-12-02, 644👍, 0💬

"babel" - FP2 Exhaustive Fingerprint Fragments
How to exhaust all possible Open Babel FP2 Fingerprint Fragments in a molecule? The easiest way to exhaust all possible Open Babel FP2 Fingerprint Fragments in a molecule to following this algorithm: Loop through all atoms (except H) in the molecule. Set each atom as the root of a bond-atom tree. An...
2020-12-02, 632👍, 0💬

Molecule FYI-1000186
Molecule Summary: ID: FYI-1000186 SMILES: CCC/C=C/C=O Received at FYIcenter.com on: 2020-11-09
2020-12-02, 623👍, 0💬

"babel -ofpt -xs" - Display Fingerprint Fragments
How to Display Fingerprint Fragments using "babel" command? I want to know how many fragments are used when taking the fingerprint of a given molecule. You can using ""-ofpt -xs" options of the "babel" command to Display Fingerprint Fragment information. Here are some examples of molecule fingerprin...
2020-12-02, 605👍, 0💬

Generate Fingerprint of Single Molecule
How to generate the fingerprint of a single molecule? I want to see the fingerprint value. If you want see the fingerprint value of a single molecule, you can just specify the molecule as the only input molecule to the "babel ... -o fpt " command. Open Babel will output its fingerprint in hexadecima...
2020-12-02, 601👍, 0💬

Substructure Search with Fingerprints
Can I do Substructure Search with fingerprints using Open Babel? Yes, you can do Substructure Search with fingerprints using Open Babel. All you have to do is to take substructure as the query molecule and run a similarity search using the fingerprint output option "-o fpt ". When Open Babel calcula...
2020-12-02, 542👍, 0💬

"babel" - FP2 Fingerprint Fragment Ends at Ring
What happens if a ring is in the molecule FP2 fragment path? In the Open Babel FP2 fingerprint algorithm, if a ring is in the fragment path, the path will end when the atom meets the same atom again in the path. In other words, the same atom in a ring should not appear twice in the same fragment pat...
2020-12-02, 500👍, 0💬

Molecule FYI-1000185
Molecule Summary: ID: FYI-1000185 SMILES: CC/C=C\\CC/C=C/C=O Received at FYIcenter.com on: 2020-11-09
2020-12-02, 459👍, 0💬

List of Open Babel Commands
How many command line tools are provided in the Open Babel package? By default, Open Babel package provides the following command line tools: babel (obabel) - Convert chemistry and molecular modeling data files. obchiral - Print molecular chirality information. obconformer - Generate conformer coord...
2020-11-22, 876👍, 0💬

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