"babel -a..." Command - Extra Input Reading Options

Q

How to pass extra options for "babel" to read input data of a specific format?

✍: FYIcenter.com

A

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_section [-aX...] [-aY...] ...

# "X..." and "Y..." are extra options for reading input data.

For example, when "babel" is reading input data in "sdf" format, it supports an option called "T", which tells "babel" to read only the "title" part of each molecule. To specify this "T" option for reading data, you can enter it as "-aT" in the command line as shown below:

fyicenter$ babel molecule.sdf -o sdf -aT

20009
 OpenBabel05202015543D

  0  0  0  0  0  0  0  0  0  0999 V2000
M  END
$$$$
1 molecule converted
1 info messages 8 audit log messages

As you can see, the "-aT" option worked properly.

⇒ "babel -x..." Command - Extra Output Writing Options

⇐ List of File Formats Supported by Open Babel

⇑ Understanding "babel" Command Line Syntax

⇑⇑ Open Babel Tutorials

2020-07-15, 481👍, 0💬

"babel -h" Command - Add Hydrogens to Molecule Data
How to add hydrogen atoms to molecule data during data conversion? Most molecules contains many hydrogen atoms. When molecules are written in many data formats, those hydrogen atoms are removed. We normally can read molecule structure without hydrogen atoms. But if you want to add those removed hydr... 2020-07-15, 834👍, 0💬

List of File Formats Supported by Open Babel
How to get a list of File Formats Supported by Open Babel? You can use "babel -L formats" command to get a list of File Formats Supported by Open Babel: fyicenter$ babel -L formats abinit -- ABINIT Output Format [Read-only] acr -- ACR format [Read-only] adf -- ADF cartesian input format [Write-only]... 2020-07-15, 536👍, 0💬

"babel -x..." Command - Extra Output Writing Options
How to pass extra options for "babel" to write output data of a specific format? If you want to pass extra options for "babel" to write output data of a specific format, you need to use one or more "-x..." options in the "babel" command line as shown in the following syntax: babel input_section outp... 2020-07-15, 530👍, 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, 498👍, 0💬

"obabel ... -o svg" Command - Generate SVG from SMILES
How to generate a molecule SVG picture from a SMILES string? The easiest way to generate a molecule SVG picture from a SMILES string is to use the the "babel ... -o svg" command. For example, the following command generate a SVG picture of the tyrosine molecule from a SMILES string: fyicenter$ obabe... 2021-07-19, 485👍, 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, 482👍, 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, 482👍, 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, 455👍, 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, 443👍, 0💬

All rights in the contents of this web site are reserved by the individual author. fyicenter.com does not guarantee the truthfulness, accuracy, or reliability of any contents.