General Molecule Tools

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Running Open Babel on Windows
Where to find FAQ (Frequently Asked Questions) on running Open Babel on Windows? Here is a list of tutorials to answer many frequently asked questions compiled by FYIcenter.com team on running Open Babel on Windows. Install Open Babel Binary Package on Windows Run Open Babel GUI on Windows Structure... 2021-02-17, 289👍, 0💬

Install Open Babel Binary Package on Windows
How to Install Open Babel binary package on Windows computers? The easiest option to install Open Babel on Windows computers is to install the Open Babel pre-compiled binary package as shown in this tutorial.: 1. Go to GitHub Website for Open Babel 3.0.0. 2. Click to download "OpenBabel-3.0.0.exe" f... 2021-02-17, 282👍, 0💬

Molecule FYI-1000237
Molecule Summary: ID: FYI-1000237 SMILES: CCCCC Received at FYIcenter.com on: 2021-02-04 2021-02-17, 111👍, 0💬

Molecule FYI-1000234
Molecule Summary: ID: FYI-1000234 SMILES: O=Cc1ccc(cc1)C(=O)OC Received at FYIcenter.com on: 2021-01-25 2021-02-17, 107👍, 0💬

Molecule FYI-1000236
Molecule Summary: ID: FYI-1000236 SMILES: NCc5ccc4OC3(CCN(C(=O)c2cc(C#Cc 1ccccc1)co2)CC3)Cc4c5Received at FYIcenter.com on: 2021-01-30 2021-02-17, 106👍, 0💬

Molecule FYI-1000235
Molecule Summary: ID: FYI-1000235 SMILES: COC1=CC=C(C=C1)C=O Received at FYIcenter.com on: 2021-01-29 2021-02-17, 106👍, 0💬

Stereochemistry with JSME (Molecule Editor in JavaScript)
Can JSME (Molecule Editor in JavaScript) be used to do Stereochemistry? Yes. JSME (Molecule Editor in JavaScript) can be used to stereochemistry. You can create a molecule structure with wedges and hatches provide stereoinformation on bonds. Here is an example with 1 wedge and 1 hatch: Molecule with... 2021-02-06, 136👍, 0💬

Stereoinformation in SDF/Mol V3000 Files
How Stereoinformation is stored in in SDF/Mol V3000 files? Similar to SDF/Mol V2000, stereoinformation can be stored in SDF/Mol V3000 files in 3 ways: 0D, 2D, and 3D. 0D: Stereoinformation in 0 dimension is defined by parity at atom lines as "CFG=n" options. 2D: Stereoinformation in 2 dimension is d... 2021-02-06, 125👍, 0💬

"babel ... -o svg -xi" - Show Atom Indices in SVG
How to show atom indices in a molecule SVG picture? I want to see in what order each atom is listed in the SMILES string. The SMILES string list each atom a molecule is a specific sequence. You can use the "-xi" option when generating the SVG file to show the index of each atom corresponding to the ... 2021-02-04, 294👍, 0💬

Molecule FYI-1000201
Molecule Summary: ID: FYI-1000201 SMILES: CCCCCCOC(=O)CC(CC(=O)OCCCCCC)( OC(=O)CCC)C(=O)OCCCCCCReceived at FYIcenter.com on: 2020-12-12 2021-02-04, 125👍, 0💬

Molecule FYI-1000203
Molecule Summary: ID: FYI-1000203 SMILES: CCCCCCCCCCO.CCCCCCCCO.CCCCCCO. C1=CC=C(C(=C1)C(=O)O)C(=O)OReceived at FYIcenter.com on: 2020-12-12 2021-02-04, 123👍, 0💬

Molecule FYI-1000202
Molecule Summary: ID: FYI-1000202 SMILES: CCCCCCOC(=O)C1=CC=CC=C1C(=O)OC CCCCCReceived at FYIcenter.com on: 2020-12-12 2021-02-04, 122👍, 0💬

Molecule FYI-1000198
Molecule Summary: ID: FYI-1000198 SMILES: (1S,3R,5R,6S,8S,10S,11R,13S,15 S,16R,18S,20S,21R,23R,25R,26S, 28R,30R,31R,32R,33R,34R,35S,36 S,37S,38S,39S,40S,41R,42R)-5,1 0,15,20,25,30-Hexakis(hydroxym ethyl)-2,4,7,9,12,14,17,19,22, 24,27,29-dodecaoxaheptacyclo[2 6.2.2.23,6.28,11.213,16.218,21 .223,26]dotetracon... 2021-02-04, 122👍, 0💬

Molecule FYI-1000199
Molecule Summary: ID: FYI-1000199 SMILES: N[C@H]1CCN(Cc2ccn3ncncc23)C[C@ H]1OReceived at FYIcenter.com on: 2020-12-07 2021-02-04, 121👍, 0💬

Molecule FYI-1000204
Molecule Summary: ID: FYI-1000204 SMILES: CC1=CC(=C(C=C1)OP(=O)(OC2=C(C= C(C=C2)C)C)OC3=C(C=C(C=C3)C)C) CReceived at FYIcenter.com on: 2020-12-12 2021-02-04, 120👍, 0💬

Molecule FYI-1000200
Molecule Summary: ID: FYI-1000200 SMILES: COc1cccc(Nc2ncnn3ccc(CN4CC[C@@ H](N)[C@H](O)C4)c23)c1Received at FYIcenter.com on: 2020-12-07 2021-02-04, 118👍, 0💬

cactus.nci.nih.gov/translate - Convert to/from SDF
What is cactus.nci.nih.gov/translate SDF translator? pubcactus.nci.nih.gov/translat eSDF translator allows you to translate SDF files from and to other types of files, including SMILES, SD, MOL, etc. SDF Online Tool - pubchem.ncbi.nlm.nih.gov   For more information, visit cactus.nci.nih.gov/translat... 2021-02-02, 474👍, 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, 235👍, 0💬

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, 232👍, 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, 147👍, 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, 144👍, 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, 252👍, 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, 247👍, 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, 154👍, 0💬

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General Molecule Tools