biochemistry-colors (21apr17)

git-svn-id: svn://tug.org/texlive/trunk@43960 c570f23f-e606-0410-a88d-b1316a301751

7 files changed, 241 insertions, 1 deletions

diff --git a/Master/texmf-dist/doc/latex/biochemistry-colors/Biochemistry-colors.pdf b/Master/texmf-dist/doc/latex/biochemistry-colors/Biochemistry-colors.pdf
new file mode 100644
index 00000000000..ea12e0663cb
--- /dev/null
+++ b/Master/texmf-dist/doc/latex/biochemistry-colors/Biochemistry-colors.pdf
diff --git a/Master/texmf-dist/doc/latex/biochemistry-colors/Biochemistry-colors.xls b/Master/texmf-dist/doc/latex/biochemistry-colors/Biochemistry-colors.xls
new file mode 100644
index 00000000000..717791ffa9c
--- /dev/null
+++ b/Master/texmf-dist/doc/latex/biochemistry-colors/Biochemistry-colors.xls
diff --git a/Master/texmf-dist/doc/latex/biochemistry-colors/README.txt b/Master/texmf-dist/doc/latex/biochemistry-colors/README.txt
new file mode 100644
index 00000000000..3b6fcc4c092
--- /dev/null
+++ b/Master/texmf-dist/doc/latex/biochemistry-colors/README.txt
@@ -0,0 +1,26 @@
+Biochemistry-colors is copyright 2017 by Dr Engelbert Buxbaum
+<engelbert_buxbaum@web.de>
+
+This file may be distributed and/or modified
+
+1. under the LaTeX Project Public License and/or
+2. under the GNU Public License.
+
+Biochemistry-colors.sty defines the standard colors of biochemistry
+colors for use with D.P. Carlisle's color-package and U. Kern's
+xcolor (xcolor is loaded by Biochemistry-colors). They may be used
+by authors (with \usepackage) or by package writers (with
+\RequirePackage, e.g. to create Beamer color themes).
+
+Colors include:
+  - Shapely-colors for amino acids and nucleotides
+  - CPK-Colors (Corey, Pauling and Koltun) of elements 		
+  - Jmol-colors of elements, important isotopes and structures	
+  - Glycopedia colors for sugars		
+
+Biochemistry-colors.pdf provides a list of these colors with
+components in rgb (hex, word, decimal) and hsl-format. The source
+for this file is the spreadsheat Biochemistry-colors.xls
+
+These files are provided in the hope that they may be useful, but
+without any warranties.
diff --git a/Master/texmf-dist/tex/latex/biochemistry-colors/Biochemistry-colors.sty b/Master/texmf-dist/tex/latex/biochemistry-colors/Biochemistry-colors.sty
new file mode 100644
index 00000000000..7bba3d70e74
--- /dev/null
+++ b/Master/texmf-dist/tex/latex/biochemistry-colors/Biochemistry-colors.sty
@@ -0,0 +1,213 @@
+% Copyright 2017 by Dr Engelbert Buxbaum <engelbert_buxbaum@web.de>
+%
+% This file may be distributed and/or modified
+%
+% 1. under the LaTeX Project Public License and/or
+% 2. under the GNU Public License.
+%
+% Literature:
+%   http://jmol.sourceforge.net/jscolors/#Residues:%20amino%20acids,%20nucleotides
+%   http://www.glycopedia.eu/IMG/pdf/the_symbolic_representation_of_monosaccharides_2014.pdf														
+%	https://en.wikipedia.org/wiki/CPK_coloring												
+
+\ProvidesPackage{biochemistry-colors}[2017/04/20 v1.00 named standard colors for biochemistry]
+\NeedsTeXFormat{LaTeX2e}
+\RequirePackage{xcolor}
+
+% Shapely-colors for amino acids (with Pyl and Sec added)	
+\definecolor{Alanine}{rgb}{0.549,1.000,0.549}
+\definecolor{Arginine}{rgb}{0.000,0.000,0.486}
+\definecolor{Asparagine}{rgb}{1.000,0.486,0.439}
+\definecolor{Aspartate}{rgb}{0.628,0.000,0.259}
+\definecolor{Cysteine}{rgb}{1.000,1.000,0.439}
+\definecolor{Glutamine}{rgb}{1.000,0.298,0.298}
+\definecolor{Glutamate}{rgb}{0.400,0.000,0.000}
+\definecolor{Glycine}{rgb}{1.000,1.000,1.000}
+\definecolor{Histidine}{rgb}{0.439,0.439,1.000}
+\definecolor{Isoleucine}{rgb}{0.000,0.298,0.000}
+\definecolor{Leucine}{rgb}{0.271,0.369,0.271}
+\definecolor{Lysine}{rgb}{0.278,0.278,0.722}
+\definecolor{Methionine}{rgb}{0.722,0.628,0.259}
+\definecolor{Phenylalanine}{rgb}{0.326,0.298,0.322}
+\definecolor{Proline}{rgb}{0.322,0.322,0.322}
+\definecolor{Pyrrolysine}{rgb}{0.137,0.333,0.078}
+\definecolor{Selenocysteine}{rgb}{0.400,0.231,0.000}
+\definecolor{Serine}{rgb}{1.000,0.439,0.259}
+\definecolor{Threonine}{rgb}{0.722,0.298,0.000}
+\definecolor{Tryptophan}{rgb}{0.310,0.275,0.000}
+\definecolor{Tyrosine}{rgb}{0.549,0.439,0.298}
+\definecolor{Valine}{rgb}{1.000,0.549,1.000}
+\definecolor{other}{rgb}{1.000,0.000,1.000}
+
+% Shapely-colors of nucleotides		
+\definecolor{Adenosine}{rgb}{0.628,0.628,1.000}
+\definecolor{Cytosin}{rgb}{1.000,0.549,0.294}
+\definecolor{Guanosine}{rgb}{1.000,0.439,0.439}
+\definecolor{Tymidine}{rgb}{0.628,1.000,0.628}
+\definecolor{Uridine}{rgb}{0.722,0.722,0.722}
+
+% CPK-Colors of elements 		
+\definecolor{CPK-Carbon}{rgb}{0.126,0.126,0.126}
+\definecolor{CPK-Oxygen}{rgb}{0.933,0.126,0.063}
+\definecolor{CPK-Hydrogen}{rgb}{1.000,1.000,1.000}
+\definecolor{CPK-Nitrogen}{rgb}{0.126,0.377,1.000}
+\definecolor{CPK-Sulfur}{rgb}{1.000,1.000,0.000}
+\definecolor{CPK-Phosphorus}{rgb}{0.502,0.126,1.000}
+\definecolor{CPK-Chlorine}{rgb}{0.000,0.733,0.000}
+\definecolor{CPK-Bromine}{rgb}{0.000,0.533,0.000}
+\definecolor{CPK-Iodine}{rgb}{0.000,0.333,0.000}
+\definecolor{CPK-Metall}{rgb}{0.816,0.816,0.816}
+
+% Jmol-colors of elements		
+\definecolor{hydrogen}{rgb}{1.000,1.000,1.000}
+\definecolor{helium}{rgb}{0.851,1.000,1.000}
+\definecolor{lithium}{rgb}{0.800,0.502,1.000}
+\definecolor{beryllium}{rgb}{0.761,1.000,0.000}
+\definecolor{boron}{rgb}{1.000,0.710,0.710}
+\definecolor{carbon}{rgb}{0.565,0.565,0.565}
+\definecolor{nitrogen}{rgb}{0.188,0.314,0.973}
+\definecolor{oxygen}{rgb}{1.000,0.051,0.051}
+\definecolor{fluorine}{rgb}{0.565,0.878,0.314}
+\definecolor{neon}{rgb}{0.702,0.890,0.961}
+\definecolor{sodium}{rgb}{0.671,0.361,0.949}
+\definecolor{magnesium}{rgb}{0.541,1.000,0.000}
+\definecolor{aluminium}{rgb}{0.749,0.651,0.651}
+\definecolor{silicon}{rgb}{0.941,0.784,0.628}
+\definecolor{phosphorus}{rgb}{1.000,0.502,0.000}
+\definecolor{sulfur}{rgb}{1.000,1.000,0.188}
+\definecolor{chlorine}{rgb}{0.122,0.941,0.122}
+\definecolor{argon}{rgb}{0.502,0.820,0.890}
+\definecolor{potassium}{rgb}{0.561,0.251,0.831}
+\definecolor{calcium}{rgb}{0.239,1.000,0.000}
+\definecolor{scandium}{rgb}{0.902,0.902,0.902}
+\definecolor{titanium}{rgb}{0.749,0.761,0.780}
+\definecolor{vanadium}{rgb}{0.651,0.651,0.671}
+\definecolor{chromium}{rgb}{0.541,0.600,0.780}
+\definecolor{manganese}{rgb}{0.612,0.478,0.780}
+\definecolor{iron}{rgb}{0.878,0.400,0.200}
+\definecolor{cobalt}{rgb}{0.941,0.565,0.628}
+\definecolor{nickel}{rgb}{0.314,0.816,0.314}
+\definecolor{copper}{rgb}{0.784,0.502,0.200}
+\definecolor{zinc}{rgb}{0.490,0.502,0.690}
+\definecolor{gallium}{rgb}{0.761,0.561,0.561}
+\definecolor{germanium}{rgb}{0.400,0.561,0.561}
+\definecolor{arsenic}{rgb}{0.741,0.502,0.890}
+\definecolor{selenium}{rgb}{1.000,0.631,0.000}
+\definecolor{bromine}{rgb}{0.651,0.161,0.161}
+\definecolor{krypton}{rgb}{0.361,0.722,0.820}
+\definecolor{rubidium}{rgb}{0.439,0.180,0.690}
+\definecolor{strontium}{rgb}{0.000,1.000,0.000}
+\definecolor{yttrium}{rgb}{0.580,1.000,1.000}
+\definecolor{zirconium}{rgb}{0.580,0.878,0.878}
+\definecolor{niobium}{rgb}{0.451,0.761,0.788}
+\definecolor{molybdenum}{rgb}{0.329,0.710,0.710}
+\definecolor{technetium}{rgb}{0.231,0.620,0.620}
+\definecolor{ruthenium}{rgb}{0.141,0.561,0.561}
+\definecolor{rhodium}{rgb}{0.039,0.490,0.549}
+\definecolor{palladium}{rgb}{0.000,0.412,0.522}
+\definecolor{silver}{rgb}{0.753,0.753,0.753}
+\definecolor{cadmium}{rgb}{1.000,0.851,0.561}
+\definecolor{indium}{rgb}{0.651,0.459,0.451}
+\definecolor{tin}{rgb}{0.400,0.502,0.502}
+\definecolor{antimony}{rgb}{0.620,0.388,0.710}
+\definecolor{tellurium}{rgb}{0.831,0.478,0.000}
+\definecolor{iodine}{rgb}{0.580,0.000,0.580}
+\definecolor{xenon}{rgb}{0.259,0.620,0.690}
+\definecolor{caesium}{rgb}{0.341,0.090,0.561}
+\definecolor{barium}{rgb}{0.000,0.788,0.000}
+\definecolor{lanthanum}{rgb}{0.439,0.831,1.000}
+\definecolor{cerium}{rgb}{1.000,1.000,0.780}
+\definecolor{praseodymium}{rgb}{0.851,1.000,0.780}
+\definecolor{neodymium}{rgb}{0.780,1.000,0.780}
+\definecolor{promethium}{rgb}{0.639,1.000,0.780}
+\definecolor{samarium}{rgb}{0.561,1.000,0.780}
+\definecolor{europium}{rgb}{0.380,1.000,0.780}
+\definecolor{gadolinium}{rgb}{0.271,1.000,0.780}
+\definecolor{terbium}{rgb}{0.188,1.000,0.780}
+\definecolor{dysprosium}{rgb}{0.122,1.000,0.780}
+\definecolor{holmium}{rgb}{0.000,1.000,0.612}
+\definecolor{erbium}{rgb}{0.000,0.902,0.459}
+\definecolor{thulium}{rgb}{0.000,0.831,0.322}
+\definecolor{ytterbium}{rgb}{0.000,0.749,0.220}
+\definecolor{lutetium}{rgb}{0.000,0.671,0.141}
+\definecolor{hafnium}{rgb}{0.302,0.761,1.000}
+\definecolor{tantalum}{rgb}{0.302,0.651,1.000}
+\definecolor{tungsten}{rgb}{0.129,0.580,0.839}
+\definecolor{rhenium}{rgb}{0.149,0.490,0.671}
+\definecolor{osmium}{rgb}{0.149,0.400,0.588}
+\definecolor{iridium}{rgb}{0.090,0.329,0.529}
+\definecolor{platinum}{rgb}{0.816,0.816,0.878}
+\definecolor{gold}{rgb}{1.000,0.820,0.137}
+\definecolor{mercury}{rgb}{0.722,0.722,0.816}
+\definecolor{thallium}{rgb}{0.651,0.329,0.302}
+\definecolor{lead}{rgb}{0.341,0.349,0.380}
+\definecolor{bismuth}{rgb}{0.620,0.310,0.710}
+\definecolor{polonium}{rgb}{0.671,0.361,0.000}
+\definecolor{astatine}{rgb}{0.459,0.310,0.271}
+\definecolor{radon}{rgb}{0.259,0.510,0.588}
+\definecolor{francium}{rgb}{0.259,0.000,0.400}
+\definecolor{radium}{rgb}{0.000,0.490,0.000}
+\definecolor{actinium}{rgb}{0.439,0.671,0.980}
+\definecolor{thorium}{rgb}{0.000,0.729,1.000}
+\definecolor{protactinium}{rgb}{0.000,0.631,1.000}
+\definecolor{uranium}{rgb}{0.000,0.561,1.000}
+\definecolor{neptunium}{rgb}{0.000,0.502,1.000}
+\definecolor{plutonium}{rgb}{0.000,0.420,1.000}
+\definecolor{americium}{rgb}{0.329,0.361,0.949}
+\definecolor{curium}{rgb}{0.471,0.361,0.890}
+\definecolor{berkelium}{rgb}{0.541,0.310,0.890}
+\definecolor{californium}{rgb}{0.631,0.212,0.831}
+\definecolor{einsteinium}{rgb}{0.702,0.122,0.831}
+\definecolor{fermium}{rgb}{0.702,0.122,0.729}
+\definecolor{mendelevium}{rgb}{0.702,0.051,0.651}
+\definecolor{nobelium}{rgb}{0.741,0.051,0.529}
+\definecolor{lawrencium}{rgb}{0.780,0.000,0.400}
+\definecolor{rutherfordium }{rgb}{0.800,0.000,0.349}
+\definecolor{dubnium}{rgb}{0.820,0.000,0.310}
+\definecolor{seaborgium}{rgb}{0.851,0.000,0.271}
+\definecolor{bohrium}{rgb}{0.878,0.000,0.220}
+\definecolor{hassium}{rgb}{0.902,0.000,0.180}
+\definecolor{meitnerium}{rgb}{0.922,0.000,0.149}
+\definecolor{darmstadtium}{rgb}{1.000,0.078,0.577}
+\definecolor{roentgenium}{rgb}{1.000,0.078,0.577}
+\definecolor{copernicium}{rgb}{1.000,0.078,0.577}
+\definecolor{nihonium}{rgb}{1.000,0.078,0.577}
+\definecolor{flerovium}{rgb}{1.000,0.078,0.577}
+\definecolor{moscovium}{rgb}{1.000,0.078,0.577}
+\definecolor{livermorium}{rgb}{1.000,0.078,0.577}
+\definecolor{tennessine}{rgb}{1.000,0.078,0.577}
+\definecolor{oganesson}{rgb}{1.000,0.078,0.577}
+
+% Isotopes		
+\definecolor{Deuterium}{rgb}{1.000,1.000,0.753}
+\definecolor{Tritium}{rgb}{1.000,1.000,0.628}
+\definecolor{carbon-13}{rgb}{0.314,0.314,0.314}
+\definecolor{carbon-14}{rgb}{0.251,0.251,0.251}
+\definecolor{nitrogen-15}{rgb}{0.063,0.314,0.314}
+
+% Structures		
+\definecolor{alpha-helix}{rgb}{1.000,0.000,0.502}
+\definecolor{310-helix}{rgb}{0.628,0.000,0.502}
+\definecolor{pi-helix}{rgb}{0.377,0.000,0.502}
+\definecolor{beta-strand}{rgb}{1.000,0.784,0.000}
+\definecolor{beta-turn}{rgb}{0.377,0.502,1.000}
+\definecolor{DNA}{rgb}{0.682,0.000,0.996}
+\definecolor{RNA}{rgb}{0.992,0.004,0.384}
+\definecolor{carbohydrate}{rgb}{0.651,0.651,0.980}
+\definecolor{other-struc}{rgb}{0.502,0.502,0.502}
+
+% Sugars
+\definecolor{Ribose}{rgb}{0.310,0.506,0.741}
+\definecolor{Xylose}{rgb}{0.980,0.392,0.000}
+\definecolor{Glucose}{rgb}{0.000,0.000,0.980}
+\definecolor{Mannose}{rgb}{0.000,0.784,0.196}
+\definecolor{Gulose}{rgb}{1.000,0.600,1.000}
+\definecolor{Idose}{rgb}{0.588,0.392,0.196}
+\definecolor{Galactose}{rgb}{1.000,1.000,0.000}
+\definecolor{KDO}{rgb}{0.557,0.706,0.890}
+\definecolor{Fucose}{rgb}{0.980,0.000,0.000}
+\definecolor{Nana}{rgb}{0.490,0.000,0.490}
+\definecolor{Fructose}{rgb}{0.753,0.000,0.000}
+\definecolor{Sorbose}{rgb}{0.894,0.424,0.039}
+\definecolor{Rhamnose}{rgb}{0.498,0.498,0.498}
+\definecolor{Quinovose}{rgb}{0.000,0.125,0.376}
diff --git a/Master/tlpkg/bin/tlpkg-ctan-check b/Master/tlpkg/bin/tlpkg-ctan-check
index 6b0cc841ec7..3ac4445e1fd 100755
--- a/Master/tlpkg/bin/tlpkg-ctan-check
+++ b/Master/tlpkg/bin/tlpkg-ctan-check
@@ -109,7 +109,7 @@ my @TLP_working = qw(
     bibtopicprefix bibexport bibunits
     bidi bidi-atbegshi bidicontour bidihl
     bidipagegrid bidipresentation bidishadowtext
-    bigfoot bigints binarytree binomexp biocon biolett-bst
+    bigfoot bigints binarytree binomexp biochemistry-colors biocon biolett-bst
     bitelist bitpattern bizcard
     blacklettert1 blindtext blkarray
     blochsphere block blockdraw_mp bloques blox
diff --git a/Master/tlpkg/tlpsrc/biochemistry-colors.tlpsrc b/Master/tlpkg/tlpsrc/biochemistry-colors.tlpsrc
new file mode 100644
index 00000000000..e69de29bb2d
--- /dev/null
+++ b/Master/tlpkg/tlpsrc/biochemistry-colors.tlpsrc
diff --git a/Master/tlpkg/tlpsrc/collection-latexextra.tlpsrc b/Master/tlpkg/tlpsrc/collection-latexextra.tlpsrc
index a1ebe24fd9c..0f27d92d792 100644
--- a/Master/tlpkg/tlpsrc/collection-latexextra.tlpsrc
+++ b/Master/tlpkg/tlpsrc/collection-latexextra.tlpsrc
@@ -82,6 +82,7 @@ depend bhcexam
 depend bibletext
 depend bigfoot
 depend bigints
+depend biochemistry-colors
 depend bizcard
 depend blindtext
 depend blkarray