General Molecule Tools

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Open Babel Documentation and Resources
Where can I find Open Babel documentations and resources? Here is a list of links to Open Babel documentations and resources. Open Babel Command Manuals and Tutorials - http://openbabel.org/wiki/Cate gory:GuidesOpen Babel v2.3.1 Documentation - "Open Babel, or how I learned to love the chemistry fil... 2021-01-09, 202👍, 0💬

Substructure Search with SMARTS Expressions
How to use SMARTS expressions in a substructure search using "babel" commands? You can use SMARTS expressions in the "-s ..." option in "babel" commands to filter molecules that match given SMARTS expressions. Here are some examples: # C, C and O connected with single bonds fyicenter$ obabel "-:c1cc... 2021-01-09, 195👍, 0💬

Molecule FYI-1000197
Molecule Summary: ID: FYI-1000197 SMILES: CC(C)C1=CC=CC=C1.[CH-]1C=CC=C1 .F[Sb-](F)(F)(F)(F)F.[Fe+2]Received at FYIcenter.com on: 2020-12-07 2021-01-09, 112👍, 0💬

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, 111👍, 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, 209👍, 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, 202👍, 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, 120👍, 0💬

Molecule FYI-1000193
Molecule Summary: ID: FYI-1000193 SMILES: CH3COOH Received at FYIcenter.com on: 2020-11-27 2020-12-26, 117👍, 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, 114👍, 0💬

Molecule FYI-1000194
Molecule Summary: ID: FYI-1000194 SMILES: c3ccc2cc1ccccc1cc2c3 Received at FYIcenter.com on: 2020-12-01 2020-12-26, 114👍, 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, 194👍, 0💬

Molecule FYI-1000191
Molecule Summary: ID: FYI-1000191 SMILES: C1CCCCCCCC1 Received at FYIcenter.com on: 2020-11-13 2020-12-22, 123👍, 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, 117👍, 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, 214👍, 0💬

"babel -o fpt ..." Command - Similarity Search
How to use "babel -o fpt ..." command to do similarity search? You can do similarity search using the "-o fpt ..." option of the "babel" command with the following syntax: babel input_section -o fpt When you run the above commands, Open Babel will perform the following: Take the first molecule from ... 2020-12-15, 193👍, 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, 123👍, 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, 121👍, 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, 121👍, 0💬

"babel -ofpt -xs" - Display Fingerprint Fragments
How to Display Fingerprint Fragments usig "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 fingerprint... 2020-12-02, 206👍, 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, 202👍, 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, 196👍, 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, 190👍, 0💬

"babel" - FP2 Fingerprint Fragment Ends at Ring
What hyppens if a ring is in the molecule FP2 fragement 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 orther words, the same atom in a ring should not appear twice in the same fragment p... 2020-12-02, 187👍, 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, 146👍, 0💬

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General Molecule Tools