JSME Molecule Online Editor
How to create and edit a molecule structure with JSME molecule editor? To help you to create and edit a molecule structure, FYIcenter.com provides this JSME Molecule Online Editor tool. All you need to do is to click a menu icon and starts to draw a molecule by adding one part at a time. When you ar... 2020-11-11, 1024👍, 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, 260👍, 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, 391👍, 0💬
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[2 220.127.116.11,6.28,11.213,16.218,21 .223,26]dotetracon... 2021-02-04, 195👍, 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 Â For more information, visit cactus.nci.nih.gov/transla... 2021-02-02, 718👍, 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, 337👍, 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, 315👍, 0💬
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, 213👍, 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, 335👍, 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, 332👍, 0💬
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What is cactus.nci.nih.gov/trans lateSDF translator? pubcactus.nci.nih.gov/tr anslateSDF translator ...
How to convert Convert SDF to SVG (Scalable Vector Graphics) using "sdf2svg" PHP script? I want to s...
How to save molecules created in JSME editor to the Web server? If you want to save the molecule str...
Where to find FAQ (Frequently Asked Questions) on online tools for SDF/Mol files? I want to use them...