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"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, 451👍, 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, 450👍, 0💬

Molecule FYI-1000175
Molecule Summary: ID: FYI-1000175 SMILES: C#Cc1ccc(C(=O)CCCC(C)(C)N)cc1 Received at FYIcenter.com on: 2020-10-13
2020-10-26, 446👍, 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, 445👍, 0💬

Molecule FYI-1000279
Molecule Summary: ID: FYI-1000279 SMILES: C[C@H](CCl)F Received at FYIcenter.com on: 2021-03-03
2021-04-17, 444👍, 0💬

What Is Molecule Structure
What Is Molecule Structure? Molecule Structure is a graphical model of a molecule on how its atoms are bonded together, with information about atom types/sizes/locations and bound types. Molecule Structures are 3-dimensional structures which can be visualized in different models. Two examples are li...
2020-04-16, 444👍, 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, 443👍, 0💬

What Is PKNCA R Package
What Is the PKNCA R Package? The PKNCA R Package is designed to perform all Non-Compartmental Analysis (NCA) calculations for Pharmacokinetic (PK) data. The primary and secondary goals of the PKNCA package are to 1) only give correct answers to the specific questions being asked and 2) automate as m...
2021-06-20, 442👍, 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, 442👍, 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, 441👍, 0💬

"DNF/YUM search" - No Open Babel Binary Package
Is there any Open Babel binary package ready to be installed with DNF/YUM on CentOS systems? The answer is no. "dnf search" command returns no matches: fyicenter$ yum search babel ============================== =====================Name Exactly Matched: babel babel.noarch : Tools for internationaliz...
2020-10-20, 439👍, 0💬

Stereoinformation Presentation in SDF/Mol File
How Stereoinformation Is Presented in SDF/Mol and SDF/Mol V3000 Files? Ideally stereoinformation should be stored in atom's coordinates, since SDF/Mol files support x, y, and z, 3-dimensional coordinates. However, not all software supports 3-dimensional coordinates. So SDF/Mol file uses 3 types of p...
2021-03-21, 436👍, 0💬

Molecule FYI-1000187
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, 430👍, 0💬

Molecule FYI-1000262
Molecule Summary: ID: FYI-1000262 SMILES: [CH+]=C1CC=C(N2N=CC=N2)C=N1 Received at FYIcenter.com on: 2021-02-12
2021-03-21, 427👍, 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, 426👍, 0💬

Molecule FYI-1000178
Molecule Summary: ID: FYI-1000178 SMILES: CNC[C@H](O)c1ccc(O)c(O)c1 Received at FYIcenter.com on: 2020-10-16
2020-11-11, 425👍, 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, 419👍, 0💬

Molecule FYI-1000277
Molecule Summary: ID: FYI-1000277 SMILES: C(S)O Received at FYIcenter.com on: 2021-03-02
2021-04-17, 416👍, 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, 413👍, 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, 412👍, 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, 412👍, 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, 405👍, 0💬

"babel" Command - Use "-o ..." as Output Delimiter
How to use "-o ..." flag as a delimiter to separate output file from input files in a "babel" command? The "-o ..." flag is optional, since "babel" command can implicitly determine the output data format from the file extension of output file name. However, it is important to use the "-o ..." flag a...
2021-07-19, 404👍, 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, 403👍, 0💬

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