Atom Biology General Molecule Reaction Tools Trial Virus

<< < 1 2 3 4 5 6 7 8 9 10 … > >>   ∑:309  Sort:Date

Wedge/Hash Bond Changed by Open Babel
Why some Wedge/Hash Bonds are Changed by Open Babel? Sometimes, you may have an Wedge/Hash bond in the input data to specify a stereo center. When you convert the input data with Open Babel, you will see that the stereo center is identified with a different Wedge/Hash bond. For example, the followin... 2023-08-17, 788🔥, 0💬

"obrotate" - Rotate Dihedral Angles with SMARTS
What Is "obrotate" command? How to use it to batch-rotate dihedral angles matching SMARTS patterns? "obrotate" command is a command line tool provided in the Open Babel package that allows you to batch-rotate dihedral angles matching SMARTS patterns. Here is the user manual of the "obrotamer" comman... 2020-10-26, 784🔥, 0💬

Search Open Babel RPM Packages for CentOS
How to search for Open Babel RPM binary packages for CentOS computers? You can follow this tutorial to search for Open Babel RPM binary packages for CentOS computers. 1. Before searching the Internet for any RPM binary packages, you need to know the architecture type of your computer. This can be do... 2020-10-20, 784🔥, 0💬

"babel -i fs ... -s SMILES" - Substructure Search with Index
How to perform a substructure search using the fastsearch index file with the "babel" command? If you want to perform a substructure search using the fastsearch index file, you can use the following "babel" command syntax: babel -i fs index_file output_section -s SMILES In the above command: "-i fs ... 2020-05-25, 781🔥, 0💬

"obgrep" - Search Molecules using SMARTS
What Is "obgrep" command? How to use it to Search Molecules using SMARTS strings? "obgrep" command is a command line tool provided in the Open Babel package that allows you to Search Molecules using SMARTS strings. "obgrep" command does the same job as the "babel ... -s ..." with more options. Here ... 2020-11-11, 779🔥, 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, 773🔥, 0💬

"babel ... -o svg" - Generating SVG Pictures
Where to find FAQ (Frequently Asked Questions) on using Open Babel to generate SVG Pictures from molecule input data? Here is a list of tutorials to answer many frequently asked questions compiled by FYIcenter.com team on using Open Babel to generate SVG Pictures from molecule input data. "babel -o ... 2021-07-19, 767🔥, 0💬

"obrotamer" - Generate Random Rotational Isomers
What Is "obrotamer" command? How to use it to Generate Random Rotational Isomers for a given molecule? "obrotamer" command is a command line tool provided in the Open Babel package that allows you to Generate Random Rotational Isomers for a given molecule. Here is the user manual of the "obrotamer" ... 2020-10-26, 767🔥, 0💬

"babel -i fs ..." - Fingerprint Index Based Search
How to perform a Fingerprint Index Based Search with the "babel" command? You can perform a Fingerprint Index Based Search with the "babel" command using the "-i fs" option to specify the fingerprint index file as the input. For more information, read the help document on fastsearch index file forma... 2020-08-25, 764🔥, 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, 763🔥, 0💬

"babel ... -o svg" - Two "svg" Tag Levels
Why am getting two "svg" tag levels in SVG source code generated by the "babel" command? If you are using Open Babel 2.4.1 or higher, you will notice that there are two "svg" tag levels in SVG source code generated by the "babel" command. The main reason for using two "svg" tag levels for including ... 2020-07-22, 763🔥, 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, 748🔥, 0💬

Using Fastsearch Fingerprint Index
Where to find FAQ (Frequently Asked Questions) on Using Fastsearch Fingerprint Index with Open Babel? Here is a list of tutorials to answer many frequently asked questions compiled by FYIcenter.com team on Using Fastsearch Fingerprint Index with Open Babel. "babel ... -o fs" - Generate Fastsearch In... 2020-09-30, 745🔥, 0💬

"babel ... -o svg -xd -xP300" Bug - Option -d takes a parameter
Why "babel ... -o svg -xd -xP300" command is giving the "Option -d takes a parameter" error in Open Babel 2.4? It seems to be another code bug in the "babel" command in Open Babel 2.4 release. "-xd" option for "svg" output format should not require any parameters according the help document: "d - do... 2020-07-15, 745🔥, 0💬

"babel -d" Command - Delete Hydrogens from Molecule Data
How to delete hydrogen atoms from molecule data during data conversion? If hydrogen atoms of a molecule are included in the input data source, you can use the "babel" generic option "-d" remove those hydrogen atoms during the molecule data conversion process. Here is an example of using the "-d" opt... 2020-07-15, 743🔥, 0💬

"mvn dependency:build-classpath" - Generate Class Pass
How to generate class path for dependences with Maven? If you run your application JAR file generated from Maven, you need to include JAR files of all dependences in the class path. One way to build this class path is to use the "mvn dependency:build-classpath" command. 1. Generate class path of all... 2023-04-17, 742🔥, 0💬

"babel -i fs ... -s query_file" - Substructure Search
Why am I getting no results with "babel -i fs ... -s query_file" command? It should perform a substructure search in a fastsearch index file. According to the "babel -H fs" help document, you can perform a substructure search in a fastsearch index file with the query molecule stored in a file in any... 2020-05-25, 739🔥, 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, 735🔥, 0💬

Hash Bond with Solid Line
Why Hash Bond with a Solid Line used by Open Babel? Sometimes, when a hash bond is located on a ring structure, Open Babel adds a solid line to the hash bond. Here is an example SDF/Mol file, Hash-with-Solid-Line.sdf, that has 4 stereo centers on a ring structure. Hash-with-Solid-Line FYICenter.com ... 2022-07-26, 733🔥, 0💬

Read Stereoinformation from Input
How stereoinformation is being read from input data by Open Babel? Most molecule data files store stereoinformation in 3 ways: 0D, 2D, and 3D. 0D: Stereoinformation in 0 dimension is defined by parity (or chirality) at atom level. 2D: Stereoinformation in 2 dimension is defined by bond style as wedg... 2022-11-16, 729🔥, 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, 724🔥, 0💬

Stereo Perception Performed by Open Babel
What is stereo perception performed by Open Babel? Stereo perception performed by Open Babel is the process of constructing stereo centers with stereoinformation received from input data. Stereo perception is performed in the following order of precedence: 1. Constructing stereo centers with 3D ster... 2022-11-16, 720🔥, 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, 719🔥, 0💬

"babel -a..." Command - Extra Input Reading Options
How to pass extra options for "babel" to read input data of a specific format? If you want to pass extra options for "babel" to read input data of a specific format, you need to use one or more "-a..." options in the "babel" command line as shown in the following syntax: babel input_section output_s... 2020-07-15, 719🔥, 0💬

<< < 1 2 3 4 5 6 7 8 9 10 … > >>   ∑:309  Sort:Date

Atom Biology General Molecule Reaction Tools Trial Virus