General Molecule Tools

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PyMol Screen Layout
What information is displayed in each area on PyMol Screen? Once PyMol is started, you should see two windows displayed: External GUI - A Graphical User Interface window with the following areas: 1. Output message area - An area where output messages are displayed. Initially, the output area display... 2020-08-03, 146👍, 1💬

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JSME Molecule Editor User Interface
Where to find FAQ (Frequently Asked Questions) on JSME Molecule Editor User Interface? Here is a list of tutorials to answer many frequently asked questions compiled by FYIcenter.com team on JSME Molecule Editor User Interface. JSME User Interface Menu Icons Show InChi and InChi Key on JSME Build Mo... 2020-08-03, 143👍, 1💬

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Scaling SVG Images using "viewBox" Attribute
What is the meaning of the <svg viewBox="..." ...> attribute? I want to understand how it is used to scale up the image. The <svg viewBox="..." ...> attribute defines view box properties which work together to scale and translate a SVG image. View Port Properties - Specif... 2020-08-03, 190👍, 1💬

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"babel ... -o svg -xX" - Hide Implicit H in SVG
How to hide those H symbols (Hydrogen symbols) implicitly added to non-carbon terminal atoms in SVG with the "babel" command? If you want to hide those Hydrogen symbols implicitly added to non-carbon terminal atoms in SVG format, you can use the "-o svg -xX" option with the "babel" command. Here is ... 2020-07-22, 190👍, 0💬

"babel ... -o svg -xP300" Bug - width="px" height="px"
Why "babel ... -o svg -xP300" command is not able scale a molecule SVG image? The "babel ... -o svg -xP300" command has a code bug that results incorrect attributes, width="px" height="px", in the top level "svg" element. in both Open 2.3 and 2.4 releases. However, "obabel ... -o svg -xP300" command... 2020-07-22, 174👍, 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, 172👍, 0💬

"babel ... -o svg -xC" - Hide Terminal C in SVG
How to hide those C symbols for terminal carbon atoms in SVG with the "babel" command? If you want to hide those C symbols for terminal carbon atoms in SVG format, you can use the "-o svg -xC" option with the "babel" command. Here is how the "-xC" option is described in Open Babel help documebnt: "C... 2020-07-22, 172👍, 0💬

"obabel ... -o svg -xP300" - Scale SVG Image
How to scale and center a molecule SVG image in a given squar area? The default behavior of Open Babel 2.4 is different than 2.3 reguarding scalling and centering SVG images. With Open Babel 2.4, the molecule SVG image is defaulted in the center of 200x200 square. With Open Babel 2.3, the molecule S... 2020-07-22, 171👍, 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, 174👍, 0💬

"babel ... -o svg -xS" - Ball/Stick Depiction in SVG
How to generate a ball and stick depiction of a molecule in SVG with the "babel" command? If you want to a ball and stick depiction of a molecule in SVG format, you can use the "-o svg -xS" option with the "babel" command. For example, the following command generate a ball and stick depiction of of ... 2020-07-15, 183👍, 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, 164👍, 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, 159👍, 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, 139👍, 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, 137👍, 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, 135👍, 0💬

Substructure Search with Open Babel
Where to find FAQ (Frequently Asked Questions) on Substructure Search with Open Babel? Here is a list of tutorials to answer many frequently asked questions compiled by FYIcenter.com team on Substructure Search with Open Babel. "babel -s ..." Command - Substructure Search Substructure Search with Wi... 2020-06-08, 185👍, 0💬

Substructure Search with Wildcard Bond "~"
How to use Wildcard Bond in a substructure search using "babel" commands? You can use "~" in a SMARTS string as a wildcard bond to represent "ANY" bond in a substructure search using "babel" commands. Here are some examples of substructure matching with a wildcard bond "~" in the molecule pattern: f... 2020-06-08, 184👍, 0💬

Substructure Search with Wildcard Atom "*"
How to use Wildcard Atom in a substructure search using "babel" commands? You can use "*" in a SMARTS string as a wildcard atom to represent "ANY" atom in a substructure search using "babel" commands. Here are some examples of substructure matching with a wildcard atom "*" in the molecule pattern: f... 2020-06-08, 171👍, 0💬

"babel -s ..." Command - Substructure Search
How to use "babel -s ..." command to do substructure search? You can do substructure search using the "-s ..." option of the "babel" command with the following syntax: babel input_section output_section -s smarts_string The smarts_string specifies a SMARTS string that represents a molecule pattern. ... 2020-06-08, 165👍, 0💬

What Are SMARTS Expressions
What are SMARTS expressions? SMARTS expressions are divided into 3 types: 1. Atom Expressions - An expression that can be evaluated to an atom pattern using atom operations on atoms and atom expressions. An atom expression must be enclosed in square bracktes, if it is not a single simple atom symbol... 2020-06-08, 160👍, 0💬

"babel -i fs ... -s query_file" - Exact Match Search
How to perform exact match in fastsearch index file using a "babel" command? If you want to perform an exact match search using the fastsearch index file, you can use the following "babel" command syntax: babel -i fs index_file output_section -s query_file In the above command: "-i fs index_file" - ... 2020-05-25, 170👍, 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, 170👍, 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, 170👍, 0💬

Install Open Babel Binary Package on macOS
How to Install Open Babel binary package on macOS computers? The easiest option to install Open Babel on macOS computers is to install the Open Babel pre-compiled binary package as shown in this tutorial. 1. Go to Open Babel download Website at SourceForge.net. 2. Click to open "Files > openb... 2020-05-24, 181👍, 0💬

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General Molecule Tools