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💬
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, 305👍, 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, 322👍, 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, 311👍, 0💬
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, 298👍, 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, 322👍, 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, 307👍, 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, 307👍, 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, 300👍, 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, 289👍, 0💬
"obconformer" - Generate Best Conformer
What Is "obconformer" command? How to use it to generate the best conformer from a base molecule? "obconformer" command is a command line tool provided in the Open Babel package that allows you to generate the best conformer from a base molecule. Here is the user manual of the "obconformer" command.... 2020-11-22, 346👍, 0💬
"obchiral" - Print Chirality Information
What Is "obchiral" command? How to use it to Print Chirality Information? "obchiral" command is a command line tool provided in the Open Babel package that allows you to calculate and print molecule chirality information. Here is the user manual of the "obchiral" command. NAME obchiral -- print mole... 2020-11-22, 323👍, 0💬
"babel -H fpt" - Fingerprint Help Information
How to get help information on Open Babel Fingerprints? You can use the "babel -H fpt" command to get help information on Open Babel Fingerprints: fyicenter$ babel -H fpt fpt Fingerprint format Generate or display molecular fingerprints. This format constructs and displays fingerprints and (for mult... 2020-11-22, 313👍, 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, 311👍, 0💬
Other Open Babel Commands
Where to find FAQ (Frequently Asked Questions) on Open Babel Commands other than the format converter? Here is a list of tutorials to answer many frequently asked questions compiled by FYIcenter.com team on Open Babel Commands other than the format converter. List of Open Babel Commands "obchiral" -... 2020-11-22, 307👍, 0💬
Collections: Atoms and Elements Molecule FAQ SDF/Mol File FAQ Open Babel Tutorials PyMol Tutorials J...
What are SDF (Structural Data File) format specifications? Here is summary of SDF (Structural Data F...
What is Isomer? An Isomer is molecule that has the same the same chemical formula as another molecul...
How to convert SMILES to SDF/Mol file and view the molecule structure? To help you to SMILES to SDF/...