Atom Biology General Molecule Tools Trial Virus

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"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, 579👍, 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, 574👍, 0💬

"babel -i fs ... -s ... -at n" - Top n Similarity Search
How to perform a top 10 similarity search using the fastsearch index file with the "babel" command? If you want to perform a top n similarity search using the fastsearch index file, you can use the following "babel" command syntax: babel -i fs index_file output_section -s query_molecule -at n -aa In... 2020-08-25, 574👍, 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, 570👍, 0💬

"babel -i fs ... -s ... -at score_range" - Similarity Search
How to perform a similarity search in a given score range using the fastsearch index file with the "babel" command? If you want to perform a similarity search in a specific score range using the fastsearch index file, you can use the following "babel" command syntax: babel -i fs index_file output_se... 2020-08-25, 565👍, 0💬

Molecule FYI-1000939
Molecule Summary: ID: FYI-1000939 SMILES: N#CN1CCC(C(=O)Nc2ncc(-c3ccccc3 )s2)C1Received at FYIcenter.com on: 2021-07-20 2021-08-13, 563👍, 0💬

"babel -... --..." Command - Generic Conversion Options
What are generic conversion options that I can use on "babel" commands for all input and output formats? "babel" commands supports a number of generic conversion options that applies all input and output formats as listed below: --addtotitle Append text to the current molecule title --addformula App... 2021-07-19, 563👍, 0💬

"babel" Command - Input Data Source and Format
How to specify Input Data Source and Format for a "babel" command? "babel" command arguments and options are organized into 3 sections as shown in the following syntax to convert chemical data from input to output with specified options. babel input_section output_section option_section You use inpu... 2021-07-19, 560👍, 0💬

"babel" Command - From STDIN To STDOUT
Can I use "babel" to convert chemical data from "stdin" to "stdout" without input and output files? Yes, you can use "babel" to convert chemical data from "stdin" to "stdout" without input and output files. Just use "-i ..." and "-o" flags to specify input data format and output data format. For exa... 2021-07-19, 556👍, 0💬

Simple Pharmacokinetics Script in Python
What Is the Simple Pharmacokinetics Script in Python? Simple Pharmacokinetics Script in Python is developed by Alex Dickson and available at https://github.com/alexrd/pk . Features supported are: can implement an arbitrary sequence of doses; can specify absorption, elimination, distribution and bind... 2021-06-20, 552👍, 0💬

"obfit" - Superimpose Two Molecules
What Is "obfit" command? How to use it to Superimpose Two Molecules? "obfit" command is a command line tool provided in the Open Babel package that allows you to Superimpose Two Molecules. Here is the user manual of the "obfit" command. NAME obfit -- superimpose two molecules based on a pattern SYNO... 2020-11-11, 550👍, 0💬

What Is Drug ADME
What Is drug ADME (Absorption, Distribution, Metabolism, and Excretion)? Drug ADME (Absorption, Distribution, Metabolism, and Excretion) are primary steps the human body handles a drug in the body. Step 1. Drug absorption: This is how the drug enters the blood -- usually from tablets or capsules in ... 2021-11-01, 548👍, 1💬

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, 548👍, 0💬

Molecule FYI-1000209
Molecule Summary: ID: FYI-1000209 SMILES: CC1=NC(NC2=NC=C(S2)C(=O)NC3=C( Cl)C=CC=C3C)=CC(=N1)N4CCN(CCO) CC4Received at FYIcenter.com on: 2020-12-22 2021-08-01, 545👍, 0💬

"babel" Command - Output Data Destination and Format
How to specify Output Data Destination and Format for a "babel" command? "babel" command arguments and options are organized into 3 sections as shown in the following syntax to convert chemical data from input to output with specified options. babel input_section output_section option_section You us... 2021-07-19, 539👍, 0💬

"babel -o svg" Command - SVG Generation Options
What options can I use when generating SVG pictures from molecule input data? You can see a list of options supported by Open Babel when generating SVG pictures from molecule input data by running the "babel -H svg" command: fyicenter$ babel -V Open Babel 2.4.1 fyicenter$ babel -H svg svg SVG 2D dep... 2021-07-19, 537👍, 0💬

Search Molecule by Name
Can I search for a molecule by its name? Yes. You can search for a molecule by its name using the search tool prepared by FYIcenter.com. All you need to do is to enter a name, and click the "Submit" button below. If a molecule is found for the given name, it will be displayed below: Molecule found b... 2023-01-24, 536👍, 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, 536👍, 0💬

Molecule FYI-1000942
Molecule Summary: ID: FYI-1000942 SMILES: O=C4N=C(NC23CC1CC(CC(C1)C2)C3) SC45CCC5Received at FYIcenter.com on: 2021-07-23 2021-09-09, 535👍, 0💬

What Is Stereochemistry
What Is Stereochemistry? Stereochemistry is the study of stereoisomers, which are molecules having same atoms and same connectivities, but with different spatial arrangements. Here are some stereoisomers listed in the picture below: Example of Stereoisomers   ⇒ Stereoinformation Presentation in SDF/... 2021-03-21, 533👍, 0💬

Molecule FYI-1000215
Molecule Summary: ID: FYI-1000215 SMILES: C(CC[C@@H](C(=O)O)NC(=O)C1=CC= C(NCC2=CN=C3N=C(N)NC(=O)C3=N2) C=C1)(=O)OReceived at FYIcenter.com on: 2020-12-29 2021-08-01, 530👍, 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, 530👍, 0💬

Molecule FYI-1000183
Molecule Summary: ID: FYI-1000183 SMILES: C[C@H]1CCO[C@H](C1)C=C(C)C Received at FYIcenter.com on: 2020-11-09 2020-11-22, 528👍, 0💬

Molecule FYI-1000206
Molecule Summary: ID: FYI-1000206 SMILES: CC(C)(C)C1=CC(=C(C(=C1)N2N=C3C =CC=CC3=N2)O)C(C)(C)CReceived at FYIcenter.com on: 2020-12-12 2021-07-19, 527👍, 0💬

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Atom Biology General Molecule Tools Trial Virus