"-o svg -xd -d" Bug in Open Babel 3.1.1

Q

Why "obabel ... -o svg -xd -d" is not able to remove hydrogens?

✍: FYIcenter.com

A

It seems to be code bug in the "obabel" command in Open Babel 3.1.1 release.

In Open Babel 3.1.1 release, options -xd and -d are not respected together for SVG output in the "obabel -i sdf -o svg -xC -xt -xP400 -xd -d" command.

For example, the following commands shows you that hydrogens and molecule name are included in the SVG output:

fyicenter$ obabel -V
Open Babel 3.1.1 -- Sep 27 2022 -- 18:26:52

fyicenter$ obabel -:C -O carbon.sdf -h --gen2D --title Carbon

fyicenter$ cat carbon.sdf | obabel -i sdf -o svg -xC -xt -xP400
<?xml version="1.0"?>
<svg version="1.1" id="topsvg"
xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink"
xmlns:cml="http://www.xml-cml.org/schema" x="0" y="0" width="200px" height="200px" viewBox="0 0 100 100">
<title>Carbon - Open Babel Depiction</title>
<rect x="0" y="0" width="100" height="100" fill="white"/>
<g transform="translate(0,0)">
<svg width="100" height="100" x="0" y="0" viewBox="0 0 160.002 149.28"
font-family="sans-serif" stroke="rgb(0,0,0)" stroke-width="2"  stroke-linecap="round">
<line x1="80.0" y1="74.6" x2="107.0" y2="74.6" opacity="1.0" stroke="rgb(0,0,0)"  stroke-width="2.0"/>
<line x1="80.0" y1="74.6" x2="66.5" y2="51.3" opacity="1.0" stroke="rgb(0,0,0)"  stroke-width="2.0"/>
<line x1="80.0" y1="74.6" x2="66.5" y2="98.0" opacity="1.0" stroke="rgb(0,0,0)"  stroke-width="2.0"/>
<line x1="80.0" y1="74.6" x2="53.0" y2="74.6" opacity="1.0" stroke="rgb(0,0,0)"  stroke-width="2.0"/>
<text x="114.001528" y="82.639914" fill="rgb(191,191,191)" stroke-width="0" font-weight="bold" font-size="16" >H</text>
<text x="54.000382" y="48.000000" fill="rgb(191,191,191)" stroke-width="0" font-weight="bold" font-size="16" >H</text>
<text x="54.000382" y="117.279827" fill="rgb(191,191,191)" stroke-width="0" font-weight="bold" font-size="16" >H</text>
<text x="34.000000" y="82.639914" fill="rgb(191,191,191)" stroke-width="0" font-weight="bold" font-size="16" >H</text>
</svg>
</g>
<text font-size="18.000000" fill ="black" font-family="sans-serif"
x="10.000000" y="20.000000" >Carbon</text>
</svg>

If you add -xd and -d options to remove molecule name and hydrogens, only -xd is respected. Only molecule name is removed.

fyicenter$ cat carbon.sdf | obabel -i sdf -o svg -xC -xt -xP400 -xd -d 

<?xml version="1.0"?>
<svg version="1.1" id="topsvg"
xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink"
xmlns:cml="http://www.xml-cml.org/schema" x="0" y="0" width="400px" height="400px" viewBox="0 0 100 100">
<title>Carbon - Open Babel Depiction</title>
<rect x="0" y="0" width="100" height="100" fill="white"/>
<g transform="translate(0,0)">
<svg width="100" height="100" x="0" y="0" viewBox="0 0 160.002 149.28"
font-family="sans-serif" stroke="rgb(0,0,0)" stroke-width="4"  stroke-linecap="round">
<line x1="80.0" y1="74.6" x2="107.0" y2="74.6" opacity="1.0" stroke="rgb(0,0,0)"  stroke-width="4.0"/>
<line x1="80.0" y1="74.6" x2="66.5" y2="51.3" opacity="1.0" stroke="rgb(0,0,0)"  stroke-width="4.0"/>
<line x1="80.0" y1="74.6" x2="66.5" y2="98.0" opacity="1.0" stroke="rgb(0,0,0)"  stroke-width="4.0"/>
<line x1="80.0" y1="74.6" x2="53.0" y2="74.6" opacity="1.0" stroke="rgb(0,0,0)"  stroke-width="4.0"/>
<text x="114.001528" y="82.639914" fill="rgb(191,191,191)" stroke-width="0" font-weight="bold" font-size="16" >H</text>
<text x="54.000382" y="48.000000" fill="rgb(191,191,191)" stroke-width="0" font-weight="bold" font-size="16" >H</text>
<text x="54.000382" y="117.279827" fill="rgb(191,191,191)" stroke-width="0" font-weight="bold" font-size="16" >H</text>
<text x="34.000000" y="82.639914" fill="rgb(191,191,191)" stroke-width="0" font-weight="bold" font-size="16" >H</text>
</svg>
</g>
</svg>

If you add -d and -xd options to remove hydrogens and molecule name, only -d is respected. Only hydrogens are removed.

fyicenter$ cat carbon.sdf | obabel -i sdf -o svg -xC -xt -xP400 -d -xd 

<?xml version="1.0"?>
<svg version="1.1" id="topsvg"
xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink"
xmlns:cml="http://www.xml-cml.org/schema" x="0" y="0" width="400px" height="400px" viewBox="0 0 100 100">
<title>Carbon - Open Babel Depiction</title>
<rect x="0" y="0" width="100" height="100" fill="white"/>
<g transform="translate(0,0)">
<svg width="100" height="100" x="0" y="0" viewBox="0 0 80 80"
font-family="sans-serif" stroke="rgb(0,0,0)" stroke-width="4"  stroke-linecap="round">
<text x="36" y="48" fill="rgb(102,102,102)" stroke-width="0" font-weight="bold" font-size="16" >CH</text>
<text x="60" y="51.68" fill="rgb(102,102,102)" stroke-width="0" font-weight="bold" font-size="13" >4</text>
</svg>
</g>
<text font-size="18" fill ="black" font-family="sans-serif"
x="10" y="20" >Carbon</text>
</svg>

However, in Open Babel 3.1.0, both "obabel -i sdf -o svg -xC -xt -xP400 -d -xd" and "obabel -i sdf -o svg -xC -xt -xP400 -xd -d" commands works as expected. Molecule name and hydrogens are all removed.

fyicenter$ obabel -V
Open Babel 3.1.0 -- Jul 19 2021 -- 10:30:02

fyicenter$ obabel -:C -O carbon.sdf -h --gen2D --title Carbon

fyicenter$ cat carbon.sdf | obabel -i sdf -o svg -xC -xt -xP400
<?xml version="1.0"?>
<svg version="1.1" id="topsvg"
xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink"
xmlns:cml="http://www.xml-cml.org/schema" x="0" y="0" width="400px" height="400px" viewBox="0 0 100 100">
<title>Carbon - Open Babel Depiction</title>
<rect x="0" y="0" width="100" height="100" fill="white"/>
<g transform="translate(0,0)">
<svg width="100" height="100" x="0" y="0" viewBox="0 0 160.002 149.28"
font-family="sans-serif" stroke="rgb(0,0,0)" stroke-width="4"  stroke-linecap="round">
<line x1="80.0" y1="74.6" x2="107.0" y2="74.6" opacity="1.0" stroke="rgb(0,0,0)"  stroke-width="4.0"/>
<line x1="80.0" y1="74.6" x2="66.5" y2="51.3" opacity="1.0" stroke="rgb(0,0,0)"  stroke-width="4.0"/>
<line x1="80.0" y1="74.6" x2="66.5" y2="98.0" opacity="1.0" stroke="rgb(0,0,0)"  stroke-width="4.0"/>
<line x1="80.0" y1="74.6" x2="53.0" y2="74.6" opacity="1.0" stroke="rgb(0,0,0)"  stroke-width="4.0"/>
<text x="114.001528" y="82.639914" fill="rgb(191,191,191)" stroke-width="0" font-weight="bold" font-size="16" >H</text>
<text x="54.000382" y="48.000000" fill="rgb(191,191,191)" stroke-width="0" font-weight="bold" font-size="16" >H</text>
<text x="54.000382" y="117.279827" fill="rgb(191,191,191)" stroke-width="0" font-weight="bold" font-size="16" >H</text>
<text x="34.000000" y="82.639914" fill="rgb(191,191,191)" stroke-width="0" font-weight="bold" font-size="16" >H</text>
</svg>
</g>
<text font-size="18.000000" fill ="black" font-family="sans-serif"
x="10.000000" y="20.000000" >Carbon</text>
</svg>

fyicenter$ cat carbon.sdf | obabel -i sdf -o svg -xC -xt -xP400 -xd -d 
<?xml version="1.0"?>
<svg version="1.1" id="topsvg"
xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink"
xmlns:cml="http://www.xml-cml.org/schema" x="0" y="0" width="400px" height="400px" viewBox="0 0 100 100">
<title>Carbon - Open Babel Depiction</title>
<rect x="0" y="0" width="100" height="100" fill="white"/>
<g transform="translate(0,0)">
<svg width="100" height="100" x="0" y="0" viewBox="0 0 80 80"
font-family="sans-serif" stroke="rgb(0,0,0)" stroke-width="4"  stroke-linecap="round">
<text x="36" y="48" fill="rgb(102,102,102)" stroke-width="0" font-weight="bold" font-size="16" >CH</text>
<text x="60" y="51.68" fill="rgb(102,102,102)" stroke-width="0" font-weight="bold" font-size="13" >4</text>
</svg>
</g>
</svg>

fyicenter$ cat carbon.sdf | obabel -i sdf -o svg -xC -xt -xP400 -d -xd 
<?xml version="1.0"?>
<svg version="1.1" id="topsvg"
xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink"
xmlns:cml="http://www.xml-cml.org/schema" x="0" y="0" width="400px" height="400px" viewBox="0 0 100 100">
<title>Carbon - Open Babel Depiction</title>
<rect x="0" y="0" width="100" height="100" fill="white"/>
<g transform="translate(0,0)">
<svg width="100" height="100" x="0" y="0" viewBox="0 0 80 80"
font-family="sans-serif" stroke="rgb(0,0,0)" stroke-width="4"  stroke-linecap="round">
<text x="36" y="48" fill="rgb(102,102,102)" stroke-width="0" font-weight="bold" font-size="16" >CH</text>
<text x="60" y="51.68" fill="rgb(102,102,102)" stroke-width="0" font-weight="bold" font-size="13" >4</text>
</svg>
</g>
</svg>

 

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2023-01-24, 284🔥, 0💬