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Color functional groups in chemfig syntax

Chemfig: colour entire atom or section of atomFill the background of functional groups in chemfigFill the background of functional groups in chemfigIn chemfig, grouping with color ineffective, unlike textcolorUsing the mhchem and chemfig packages in conjunctionScale chemfig molecule in beamer with tikzchemfig double bond gap at jointHow to apply colour options to the contents of TikZ nodes when the content includes sbox{}usebox{}?Conflict in chemfig between cap=round and cram bondsChemfig: color doesn't workchemfig: NAD+ chemical structurechemfig: molecule vibration

9

0

I want to color simple functional groups in organic molecules using the chemfig package. I've come up with a solution that achieves what I want (MWE), but I find it very cumbersome. I thought it could be possible to wrap an entire group in one single color-statement. This question about colouring the background of a group of atoms in chemfig also gives a neat graphical emphasis of a group of atoms.

Is my solution, and the solution to the question above, the easiest way to colour or mark groups of atoms (including bonds) in chemfig? Just now, I don't have a need to easily reproduce loads of coloured functional groups, but I would like to know if there are easier ways to solve this problem without predefining macros for each group.

I believe I understand that the underlying problem is the way chemfig uses TikZ nodes to draw the structures, but I can't help to think that there should be a way to define some color environment that applies to all the TikZ nodes made by chemfig.

MWE:

documentclass{article}



usepackage{chemfig}



begin{document}

    chemfig{H-C(-[2]H)(-[6]H)-C(-[2]H)(-[6]H)-{color{blue}C}(=[1,,,,blue] {color{blue}O})(-[7,,,,blue] {color{blue}OH})}

end{document}

Producing

color best-practices chemfig

share|improve this question

edited Apr 13 '17 at 12:36

Community♦

1

asked Feb 21 '15 at 10:20

HoleneHolene

3,93322858

• 
  
  
  

  
  

  
  
  
  
  
  

  
  
  I don't really have an answer but I'd probably really define macros or submols (depending on the wanted functionality)
  
  – clemens
  Feb 21 '15 at 18:50
  

  
  
  
  


• 
  
  
  

  
  

  
  
  
  
  
  

  
  
  I believe that what you did is the best you can do in chemfig at the moment.
  
  – pisoir
  Feb 25 '15 at 6:59
  

  
  
  
  

add a comment | 

9

0

I want to color simple functional groups in organic molecules using the chemfig package. I've come up with a solution that achieves what I want (MWE), but I find it very cumbersome. I thought it could be possible to wrap an entire group in one single color-statement. This question about colouring the background of a group of atoms in chemfig also gives a neat graphical emphasis of a group of atoms.

Is my solution, and the solution to the question above, the easiest way to colour or mark groups of atoms (including bonds) in chemfig? Just now, I don't have a need to easily reproduce loads of coloured functional groups, but I would like to know if there are easier ways to solve this problem without predefining macros for each group.

I believe I understand that the underlying problem is the way chemfig uses TikZ nodes to draw the structures, but I can't help to think that there should be a way to define some color environment that applies to all the TikZ nodes made by chemfig.

MWE:

documentclass{article}



usepackage{chemfig}



begin{document}

    chemfig{H-C(-[2]H)(-[6]H)-C(-[2]H)(-[6]H)-{color{blue}C}(=[1,,,,blue] {color{blue}O})(-[7,,,,blue] {color{blue}OH})}

end{document}

Producing

color best-practices chemfig

share|improve this question

edited Apr 13 '17 at 12:36

Community♦

1

asked Feb 21 '15 at 10:20

HoleneHolene

3,93322858

• 
  
  
  

  
  

  
  
  
  
  
  

  
  
  I don't really have an answer but I'd probably really define macros or submols (depending on the wanted functionality)
  
  – clemens
  Feb 21 '15 at 18:50
  

  
  
  
  


• 
  
  
  

  
  

  
  
  
  
  
  

  
  
  I believe that what you did is the best you can do in chemfig at the moment.
  
  – pisoir
  Feb 25 '15 at 6:59
  

  
  
  
  

add a comment | 

I want to color simple functional groups in organic molecules using the chemfig package. I've come up with a solution that achieves what I want (MWE), but I find it very cumbersome. I thought it could be possible to wrap an entire group in one single color-statement. This question about colouring the background of a group of atoms in chemfig also gives a neat graphical emphasis of a group of atoms.

Is my solution, and the solution to the question above, the easiest way to colour or mark groups of atoms (including bonds) in chemfig? Just now, I don't have a need to easily reproduce loads of coloured functional groups, but I would like to know if there are easier ways to solve this problem without predefining macros for each group.

I believe I understand that the underlying problem is the way chemfig uses TikZ nodes to draw the structures, but I can't help to think that there should be a way to define some color environment that applies to all the TikZ nodes made by chemfig.

MWE:

documentclass{article}



usepackage{chemfig}



begin{document}

    chemfig{H-C(-[2]H)(-[6]H)-C(-[2]H)(-[6]H)-{color{blue}C}(=[1,,,,blue] {color{blue}O})(-[7,,,,blue] {color{blue}OH})}

end{document}

Producing

color best-practices chemfig

share|improve this question

edited Apr 13 '17 at 12:36

Community♦

1

asked Feb 21 '15 at 10:20

HoleneHolene

3,93322858

documentclass{article}



usepackage{chemfig}



begin{document}

    chemfig{H-C(-[2]H)(-[6]H)-C(-[2]H)(-[6]H)-{color{blue}C}(=[1,,,,blue] {color{blue}O})(-[7,,,,blue] {color{blue}OH})}

end{document}

share|improve this question

edited Apr 13 '17 at 12:36

Community♦

1

asked Feb 21 '15 at 10:20

HoleneHolene

3,93322858

share|improve this question

edited Apr 13 '17 at 12:36

Community♦

1

asked Feb 21 '15 at 10:20

HoleneHolene

3,93322858

edited Apr 13 '17 at 12:36

Community♦

1

edited Apr 13 '17 at 12:36

Community♦

1

asked Feb 21 '15 at 10:20

HoleneHolene

3,93322858

asked Feb 21 '15 at 10:20

HoleneHolene

3,93322858

1 Answer
1

active

oldest

votes

7

Relate to this post.

documentclass{article}

usepackage{chemfig}

begin{document}

    defRED{gdefprintatom##1{color{red}ensuremath{mathrm{##1}}}}

    defBLACK{gdefprintatom##1{color{black}ensuremath{mathrm{##1}}}}

    noindent

    chemfig{H-C(-[2]H)(-[6]H)-C(-[2]H)(-[6]H)(-[,,,,draw=none]RED)([,,,,,red]-[,,,,black]C(=[1]O)(-[7]OH))}BLACK \[1cm]

    chemfig{H-C(-[2]H)(-[6]H)-C(-[2]H)(-[6]H)(-C(=[1]O)(-[7]OH))}

end{document}

Where

• 
  [,,,,red] is to set the color of bonds within COOH.


• 
  [,,,,black] is to set the color of bond between C2H5 and COOH.


• 
  (-[,,,,draw=none]RED) is to create an ad hoc atom to change the color.
  
  
  
  
  • you can change the color anywhere, but sometimes it may cause bad spacing/positioning.
  
  
  • (e.g. chemfig reads RED COOH as five atoms, with the first atom having zero width.)
  
  
  
  

share|improve this answer

edited Apr 13 '17 at 12:35

Community♦

1

answered Mar 3 '15 at 12:57

Symbol 1Symbol 1

25.3k240122

add a comment | 

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7

Relate to this post.

documentclass{article}

usepackage{chemfig}

begin{document}

    defRED{gdefprintatom##1{color{red}ensuremath{mathrm{##1}}}}

    defBLACK{gdefprintatom##1{color{black}ensuremath{mathrm{##1}}}}

    noindent

    chemfig{H-C(-[2]H)(-[6]H)-C(-[2]H)(-[6]H)(-[,,,,draw=none]RED)([,,,,,red]-[,,,,black]C(=[1]O)(-[7]OH))}BLACK \[1cm]

    chemfig{H-C(-[2]H)(-[6]H)-C(-[2]H)(-[6]H)(-C(=[1]O)(-[7]OH))}

end{document}

Where

• 
  [,,,,red] is to set the color of bonds within COOH.


• 
  [,,,,black] is to set the color of bond between C2H5 and COOH.


• 
  (-[,,,,draw=none]RED) is to create an ad hoc atom to change the color.
  
  
  
  
  • you can change the color anywhere, but sometimes it may cause bad spacing/positioning.
  
  
  • (e.g. chemfig reads RED COOH as five atoms, with the first atom having zero width.)
  
  
  
  

share|improve this answer

edited Apr 13 '17 at 12:35

Community♦

1

answered Mar 3 '15 at 12:57

Symbol 1Symbol 1

25.3k240122

add a comment | 

7

Relate to this post.

documentclass{article}

usepackage{chemfig}

begin{document}

    defRED{gdefprintatom##1{color{red}ensuremath{mathrm{##1}}}}

    defBLACK{gdefprintatom##1{color{black}ensuremath{mathrm{##1}}}}

    noindent

    chemfig{H-C(-[2]H)(-[6]H)-C(-[2]H)(-[6]H)(-[,,,,draw=none]RED)([,,,,,red]-[,,,,black]C(=[1]O)(-[7]OH))}BLACK \[1cm]

    chemfig{H-C(-[2]H)(-[6]H)-C(-[2]H)(-[6]H)(-C(=[1]O)(-[7]OH))}

end{document}

Where

• 
  [,,,,red] is to set the color of bonds within COOH.


• 
  [,,,,black] is to set the color of bond between C2H5 and COOH.


• 
  (-[,,,,draw=none]RED) is to create an ad hoc atom to change the color.
  
  
  
  
  • you can change the color anywhere, but sometimes it may cause bad spacing/positioning.
  
  
  • (e.g. chemfig reads RED COOH as five atoms, with the first atom having zero width.)
  
  
  
  

share|improve this answer

edited Apr 13 '17 at 12:35

Community♦

1

answered Mar 3 '15 at 12:57

Symbol 1Symbol 1

25.3k240122

add a comment | 

Relate to this post.

documentclass{article}

usepackage{chemfig}

begin{document}

    defRED{gdefprintatom##1{color{red}ensuremath{mathrm{##1}}}}

    defBLACK{gdefprintatom##1{color{black}ensuremath{mathrm{##1}}}}

    noindent

    chemfig{H-C(-[2]H)(-[6]H)-C(-[2]H)(-[6]H)(-[,,,,draw=none]RED)([,,,,,red]-[,,,,black]C(=[1]O)(-[7]OH))}BLACK \[1cm]

    chemfig{H-C(-[2]H)(-[6]H)-C(-[2]H)(-[6]H)(-C(=[1]O)(-[7]OH))}

end{document}

Where

• 
  [,,,,red] is to set the color of bonds within COOH.


• 
  [,,,,black] is to set the color of bond between C2H5 and COOH.


• 
  (-[,,,,draw=none]RED) is to create an ad hoc atom to change the color.
  
  
  
  
  • you can change the color anywhere, but sometimes it may cause bad spacing/positioning.
  
  
  • (e.g. chemfig reads RED COOH as five atoms, with the first atom having zero width.)
  
  
  
  

share|improve this answer

edited Apr 13 '17 at 12:35

Community♦

1

answered Mar 3 '15 at 12:57

Symbol 1Symbol 1

25.3k240122

documentclass{article}

usepackage{chemfig}

begin{document}

    defRED{gdefprintatom##1{color{red}ensuremath{mathrm{##1}}}}

    defBLACK{gdefprintatom##1{color{black}ensuremath{mathrm{##1}}}}

    noindent

    chemfig{H-C(-[2]H)(-[6]H)-C(-[2]H)(-[6]H)(-[,,,,draw=none]RED)([,,,,,red]-[,,,,black]C(=[1]O)(-[7]OH))}BLACK \[1cm]

    chemfig{H-C(-[2]H)(-[6]H)-C(-[2]H)(-[6]H)(-C(=[1]O)(-[7]OH))}

end{document}

share|improve this answer

edited Apr 13 '17 at 12:35

Community♦

1

answered Mar 3 '15 at 12:57

Symbol 1Symbol 1

25.3k240122

edited Apr 13 '17 at 12:35

Community♦

1

edited Apr 13 '17 at 12:35

Community♦

1

answered Mar 3 '15 at 12:57

Symbol 1Symbol 1

25.3k240122

answered Mar 3 '15 at 12:57

Symbol 1Symbol 1

25.3k240122