diff options
Diffstat (limited to 'graphics/mol2chemfig/docs/examples')
95 files changed, 3116 insertions, 0 deletions
diff --git a/graphics/mol2chemfig/docs/examples/atcc.mol b/graphics/mol2chemfig/docs/examples/atcc.mol new file mode 100644 index 0000000000..f89a2c3c99 --- /dev/null +++ b/graphics/mol2chemfig/docs/examples/atcc.mol @@ -0,0 +1,49 @@ +43232 + Marvin 02171312492D + + 21 23 0 0 1 0 999 V2000 + 5.2962 -0.1515 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 6.7251 -0.1697 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 5.3278 2.3234 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 3.5008 2.4702 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.8930 1.6596 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 3.1066 0.6270 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.9120 1.1808 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.1255 0.3840 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.4955 1.0815 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 3.8280 -0.0746 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.5818 0.2610 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.0159 0.2519 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.0265 1.0768 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.3173 1.4984 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.7462 1.4802 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.7567 2.3051 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 7.4553 1.0586 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 7.4764 2.7085 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 8.1750 1.4620 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 8.1855 2.2869 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 3.8425 3.2211 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 11 1 0 0 0 0 + 1 12 1 0 0 0 0 + 2 12 2 0 0 0 0 + 3 14 1 0 0 0 0 + 5 4 1 0 0 0 0 + 5 7 1 0 0 0 0 + 5 9 1 0 0 0 0 + 6 8 1 0 0 0 0 + 6 10 1 0 0 0 0 + 7 8 1 0 0 0 0 + 9 11 1 0 0 0 0 + 10 11 1 0 0 0 0 + 12 13 1 0 0 0 0 + 13 14 1 0 0 0 0 + 13 15 1 0 0 0 0 + 15 16 2 0 0 0 0 + 15 17 1 0 0 0 0 + 16 18 1 0 0 0 0 + 17 19 2 0 0 0 0 + 18 20 2 0 0 0 0 + 19 20 1 0 0 0 0 + 4 21 1 0 0 0 0 + 6 4 2 0 0 0 0 +M END diff --git a/graphics/mol2chemfig/docs/examples/atcc.sh b/graphics/mol2chemfig/docs/examples/atcc.sh new file mode 100755 index 0000000000..12c6dbc3e0 --- /dev/null +++ b/graphics/mol2chemfig/docs/examples/atcc.sh @@ -0,0 +1 @@ +mol2chemfig -w atcc.mol > atcc.tex
\ No newline at end of file diff --git a/graphics/mol2chemfig/docs/examples/atcc.tex b/graphics/mol2chemfig/docs/examples/atcc.tex new file mode 100644 index 0000000000..9507eeacc9 --- /dev/null +++ b/graphics/mol2chemfig/docs/examples/atcc.tex @@ -0,0 +1,36 @@ +\chemfig{ + O% 2 + =[:149.3]% 12 + ( + -[:89.3]% 13 + ( + -[:29.3]% 15 + =_[:89.3]% 16 + -[:29.3]% 18 + =_[:329.3]% 20 + -[:269.3]% 19 + =_[:209.3]% 17 + -[:149.3]% -> 15 + ) + -[:149.3]% 14 + -[:89.3,,,1]OH% 3 + ) + -[:209.3]O% 1 + -[:150]% 11 + -[:96]% 9 + -[:160.2,2.065]% 5 + -[:53.1,1.228]% 4 + ( + -[:65.5]% 21 + ) + =^[:257.9,2.285]% 6 + ( + -[:315.8,1.22]% 10 + -[:24]% -> 11 + ) + -[:193.9,1.225]% 8 + -[:105]% 7 + ( + -[:26,1.323]% -> 5 + ) +} diff --git a/graphics/mol2chemfig/docs/examples/buildscripts.sh b/graphics/mol2chemfig/docs/examples/buildscripts.sh new file mode 100755 index 0000000000..a4ddb132ec --- /dev/null +++ b/graphics/mol2chemfig/docs/examples/buildscripts.sh @@ -0,0 +1,43 @@ +#!/bin/bash +chmod +x ./*.sh + +# ./twisted.sh + +# ./cubane.sh +# ./cubane-cross.sh +./cubane-n.sh +./cubane-cross-n.sh + +./caffeine-from-smiles.sh +./caffeine-from-smiles-rotated.sh + +./daptomycin1.sh +./daptomycin-u.sh + +./printoptions.sh + +./phenol-from-smiles.sh +./phenol-from-smiles-w.sh +./phenol-from-smiles-wz.sh +./phenol-as-submol.sh +./phenol-add-h.sh + +./doxo-from-sdf.sh +./doxo-strip-h.sh +./doxo-numbered.sh +./doxo-recalculated.sh +./doxo-recalculated-flopped.sh +./doxo-recalculated-rotated.sh + +./dichlorofluorescein1.sh +./dichlorofluorescein2.sh +./dichlorofluorescein3.sh + +./morphine.sh +./morphine-f.sh +./morphine-n.sh +./morphine-k.sh + +./plp.sh + +./mp.sh
\ No newline at end of file diff --git a/graphics/mol2chemfig/docs/examples/caffeine-from-smiles-rotated.sh b/graphics/mol2chemfig/docs/examples/caffeine-from-smiles-rotated.sh new file mode 100755 index 0000000000..328348612c --- /dev/null +++ b/graphics/mol2chemfig/docs/examples/caffeine-from-smiles-rotated.sh @@ -0,0 +1 @@ +mol2chemfig -zwom -a -30 caffeine.smi > caffeine-smi2.tex
\ No newline at end of file diff --git a/graphics/mol2chemfig/docs/examples/caffeine-from-smiles.sh b/graphics/mol2chemfig/docs/examples/caffeine-from-smiles.sh new file mode 100755 index 0000000000..33899ea052 --- /dev/null +++ b/graphics/mol2chemfig/docs/examples/caffeine-from-smiles.sh @@ -0,0 +1 @@ +mol2chemfig -zw caffeine.smi > caffeine-smi.tex
\ No newline at end of file diff --git a/graphics/mol2chemfig/docs/examples/caffeine-smi.tex b/graphics/mol2chemfig/docs/examples/caffeine-smi.tex new file mode 100644 index 0000000000..2aa7e08f8c --- /dev/null +++ b/graphics/mol2chemfig/docs/examples/caffeine-smi.tex @@ -0,0 +1,2 @@ +\chemfig{-[:138]N-[:84]=^[:156]N-[:228]=^[:300](-[:12]\phantom{N})-[:240](% +=[:300]O)-[:180]N(-[:240])-[:120](=[:180]O)-[:60]N(-)-[:120]} diff --git a/graphics/mol2chemfig/docs/examples/caffeine-smi2.tex b/graphics/mol2chemfig/docs/examples/caffeine-smi2.tex new file mode 100644 index 0000000000..25a670d931 --- /dev/null +++ b/graphics/mol2chemfig/docs/examples/caffeine-smi2.tex @@ -0,0 +1,3 @@ +\chemfig{CH_3-[:108,,1]N-[:54](-[:180,0.85,,,draw=none]\mcfcringle{1.03})% +-[:126]N-[:198]-[:270](-[:342]\phantom{N})-[:210](=[:270]O)-[:150]N(% +-[:210,,,2]H_3C)-[:90](=[:150]O)-[:30]N(-[:330])-[:90,,,1]CH_3} diff --git a/graphics/mol2chemfig/docs/examples/caffeine.mol b/graphics/mol2chemfig/docs/examples/caffeine.mol new file mode 100644 index 0000000000..b2d778e47e --- /dev/null +++ b/graphics/mol2chemfig/docs/examples/caffeine.mol @@ -0,0 +1,34 @@ + + Marvin 01220818012D + + 14 15 0 0 0 0 999 V2000 + 3.7321 2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 2.0000 -1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 3.7321 -1.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 5.5443 0.8047 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 2.8660 0.5000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 5.5443 -0.8047 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 4.5981 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.5981 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 3.7321 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.8660 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.1279 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 3.7321 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.8550 1.7553 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.0000 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 9 2 0 0 0 0 + 2 10 2 0 0 0 0 + 3 8 1 0 0 0 0 + 3 10 1 0 0 0 0 + 3 12 1 0 0 0 0 + 4 7 1 0 0 0 0 + 4 11 1 0 0 0 0 + 4 13 1 0 0 0 0 + 5 9 1 0 0 0 0 + 5 10 1 0 0 0 0 + 5 14 1 0 0 0 0 + 6 8 1 0 0 0 0 + 6 11 2 0 0 0 0 + 7 8 2 0 0 0 0 + 7 9 1 0 0 0 0 +M END
\ No newline at end of file diff --git a/graphics/mol2chemfig/docs/examples/caffeine.smi b/graphics/mol2chemfig/docs/examples/caffeine.smi new file mode 100644 index 0000000000..fd1cc5f151 --- /dev/null +++ b/graphics/mol2chemfig/docs/examples/caffeine.smi @@ -0,0 +1 @@ +CN1C=NC2=C1C(=O)N(C(=O)N2C)C diff --git a/graphics/mol2chemfig/docs/examples/ce-submol1.tex b/graphics/mol2chemfig/docs/examples/ce-submol1.tex new file mode 100644 index 0000000000..361453c98e --- /dev/null +++ b/graphics/mol2chemfig/docs/examples/ce-submol1.tex @@ -0,0 +1,56 @@ +\definesubmol{ce1}{ + % 9 + -[:180]O% 8 + -[:240]% 6 + =_[:300]% 5 + ( + -[:240]% 4 + =_[:180]% 3 + ( + -[:240]O% 10 + -[:180]% 11 + ) + -[:120]% 2 + ( + -[:180,,,2]H_2N% 12 + ) + =_[:60]% 1 + -% -> 6 + ) + -N% 7 + -[:240]% 13 + -[:315]% 14 + -[:15]O% 15 + -[:300]% 16 + -% 17 + -[:60]O% 18 + -[:345]% 19 + -[:45]% 20 + -[:120]N% 21 + ( + -[:120]% 24 + -[:180]% 37 + -[:231.5,1.089]O% 25 + -[:128.1,1.084]% 23 + -[:180]% 22 + -[:240]\phantom{N}% -> 7 + ) + -% 26 + =_[:60]% 27 + ( + -[:120]O% 33 + -[:180]% 34 + ) + -% 31 + =_[:300]% 30 + ( + -[,,,1]NH_2% 32 + ) + -[:240]% 29 + ( + =_[:180]% 28 + -[:120]% -> 26 + ) + -[:300]O% 35 + -% 36 +} diff --git a/graphics/mol2chemfig/docs/examples/ce-submol2.tex b/graphics/mol2chemfig/docs/examples/ce-submol2.tex new file mode 100644 index 0000000000..fa9d4f44d7 --- /dev/null +++ b/graphics/mol2chemfig/docs/examples/ce-submol2.tex @@ -0,0 +1,56 @@ +\definesubmol{ce2}{ + \mcfatomno{9}% 9 + -[:180]\mcfabove{O}{\mcfatomno{8}}% 8 + -[:240]\mcfatomno{6}% 6 + =_[:300]\mcfatomno{5}% 5 + ( + -[:240]\mcfatomno{4}% 4 + =_[:180]\mcfatomno{3}% 3 + ( + -[:240]\mcfbelow{O}{\mcfatomno{10}}% 10 + -[:180]\mcfatomno{11}% 11 + ) + -[:120]\mcfatomno{2}% 2 + ( + -[:180]\mcfleft{\mcfatomno{12}}{N}% 12 + ) + =_[:60]\mcfatomno{1}% 1 + -\phantom{6}% -> 6 + ) + -\mcfright{N}{\mcfatomno{7}}% 7 + -[:240]\mcfatomno{13}% 13 + -[:315]\mcfatomno{14}% 14 + -[:15]\mcfabove{O}{\mcfatomno{15}}% 15 + -[:300]\mcfatomno{16}% 16 + -\mcfatomno{17}% 17 + -[:60]\mcfabove{O}{\mcfatomno{18}}% 18 + -[:345]\mcfatomno{19}% 19 + -[:45]\mcfatomno{20}% 20 + -[:120]\mcfleft{\mcfatomno{21}}{N}% 21 + ( + -[:120]\mcfatomno{24}% 24 + -[:180]\mcfatomno{37}% 37 + -[:231.5,1.089]\mcfbelow{O}{\mcfatomno{25}}% 25 + -[:128.1,1.084]\mcfatomno{23}% 23 + -[:180]\mcfatomno{22}% 22 + -[:240]\phantom{N}% -> 7 + ) + -\mcfatomno{26}% 26 + =_[:60]\mcfatomno{27}% 27 + ( + -[:120]\mcfabove{O}{\mcfatomno{33}}% 33 + -[:180]\mcfatomno{34}% 34 + ) + -\mcfatomno{31}% 31 + =_[:300]\mcfatomno{30}% 30 + ( + -\mcfright{N}{\mcfatomno{32}}% 32 + ) + -[:240]\mcfatomno{29}% 29 + ( + =_[:180]\mcfatomno{28}% 28 + -[:120]\phantom{26}% -> 26 + ) + -[:300]\mcfbelow{O}{\mcfatomno{35}}% 35 + -\mcfatomno{36}% 36 +} diff --git a/graphics/mol2chemfig/docs/examples/ce-submol3.tex b/graphics/mol2chemfig/docs/examples/ce-submol3.tex new file mode 100644 index 0000000000..1821d496c5 --- /dev/null +++ b/graphics/mol2chemfig/docs/examples/ce-submol3.tex @@ -0,0 +1,56 @@ +\definesubmol{ce3}{ + H_2N% 12 + -[,,2]% 2 + =_[:60]% 1 + -% 6 + ( + -[:60]O% 8 + -% 9 + ) + =_[:300]% 5 + ( + -[:240]% 4 + =_[:180]% 3 + ( + -[:240]O% 10 + -[:180]% 11 + ) + -[:120]% -> 2 + ) + -N% 7 + -[:240]% 13 + -[:315]% 14 + -[:15]O% 15 + -[:300]% 16 + -% 17 + -[:60]O% 18 + -[:345]% 19 + -[:45]% 20 + -[:120]N% 21 + ( + -[:120]% 24 + -[:180]% 37 + -[:231.5,1.089]O% 25 + -[:128.1,1.084]% 23 + -[:180]% 22 + -[:240]\phantom{N}% -> 7 + ) + -% 26 + =_[:60]% 27 + ( + -[:120]O% 33 + -[:180]% 34 + ) + -% 31 + =_[:300]% 30 + ( + -[:240]% 29 + ( + -[:300]O% 35 + -% 36 + ) + =_[:180]% 28 + -[:120]% -> 26 + ) + -[,,,1]NH_2% 32 +} diff --git a/graphics/mol2chemfig/docs/examples/crown-ether.mol b/graphics/mol2chemfig/docs/examples/crown-ether.mol new file mode 100644 index 0000000000..f7cf5a32e8 --- /dev/null +++ b/graphics/mol2chemfig/docs/examples/crown-ether.mol @@ -0,0 +1,81 @@ + + Marvin 05211219442D + + 37 39 0 0 0 0 999 V2000 + -2.8249 2.1308 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -3.2373 1.4163 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.8248 0.7018 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.9998 0.7018 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.5873 1.4163 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.9999 2.1308 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.7623 1.4163 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + -1.5873 2.8452 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + -0.7623 2.8452 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -3.2373 -0.0127 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + -4.0623 -0.0127 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -4.0623 1.4163 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + -1.1748 0.7018 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.5914 0.1185 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.2055 0.3320 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 0.6180 -0.3825 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.4430 -0.3825 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.8555 0.3320 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 2.6523 0.1185 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 3.2357 0.7018 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.8232 1.4163 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + -0.3498 2.1308 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.4752 2.1308 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.4107 2.1308 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.0266 1.4272 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 3.6482 1.4163 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.0607 2.1308 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.0607 0.7018 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.8857 0.7018 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.2982 1.4163 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.8857 2.1308 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.1232 1.4163 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 3.6482 2.8452 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 2.8232 2.8452 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.2982 -0.0127 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 6.1232 -0.0127 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.5857 2.1308 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 2 0 0 0 0 + 2 3 1 0 0 0 0 + 3 4 2 0 0 0 0 + 4 5 1 0 0 0 0 + 5 6 2 0 0 0 0 + 1 6 1 0 0 0 0 + 5 7 1 0 0 0 0 + 6 8 1 0 0 0 0 + 8 9 1 0 0 0 0 + 3 10 1 0 0 0 0 + 10 11 1 0 0 0 0 + 2 12 1 0 0 0 0 + 7 13 1 0 0 0 0 + 13 14 1 0 0 0 0 + 14 15 1 0 0 0 0 + 15 16 1 0 0 0 0 + 16 17 1 0 0 0 0 + 17 18 1 0 0 0 0 + 18 19 1 0 0 0 0 + 19 20 1 0 0 0 0 + 20 21 1 0 0 0 0 + 7 22 1 0 0 0 0 + 22 23 1 0 0 0 0 + 21 24 1 0 0 0 0 + 23 25 1 0 0 0 0 + 21 26 1 0 0 0 0 + 27 26 2 0 0 0 0 + 26 28 1 0 0 0 0 + 28 29 2 0 0 0 0 + 29 30 1 0 0 0 0 + 30 31 2 0 0 0 0 + 27 31 1 0 0 0 0 + 30 32 1 0 0 0 0 + 27 33 1 0 0 0 0 + 33 34 1 0 0 0 0 + 29 35 1 0 0 0 0 + 35 36 1 0 0 0 0 + 24 37 1 0 0 0 0 + 37 25 1 0 0 0 0 +M END diff --git a/graphics/mol2chemfig/docs/examples/cubane-cross-n.sh b/graphics/mol2chemfig/docs/examples/cubane-cross-n.sh new file mode 100755 index 0000000000..02902da4ac --- /dev/null +++ b/graphics/mol2chemfig/docs/examples/cubane-cross-n.sh @@ -0,0 +1 @@ +mol2chemfig -t 2 -wn -k 2-5,4-7 cubane.mol > eschers-cubane.tex
\ No newline at end of file diff --git a/graphics/mol2chemfig/docs/examples/cubane-cross.sh b/graphics/mol2chemfig/docs/examples/cubane-cross.sh new file mode 100755 index 0000000000..6f6d8671ce --- /dev/null +++ b/graphics/mol2chemfig/docs/examples/cubane-cross.sh @@ -0,0 +1 @@ +mol2chemfig -t 2 -w -k 2-5,4-7 cubane.mol > cubane-cross.tex
\ No newline at end of file diff --git a/graphics/mol2chemfig/docs/examples/cubane-n.sh b/graphics/mol2chemfig/docs/examples/cubane-n.sh new file mode 100755 index 0000000000..1756709010 --- /dev/null +++ b/graphics/mol2chemfig/docs/examples/cubane-n.sh @@ -0,0 +1 @@ +mol2chemfig -t 2 -wn cubane.mol > cubane-n.tex
\ No newline at end of file diff --git a/graphics/mol2chemfig/docs/examples/cubane-n.tex b/graphics/mol2chemfig/docs/examples/cubane-n.tex new file mode 100644 index 0000000000..a63dadb9b1 --- /dev/null +++ b/graphics/mol2chemfig/docs/examples/cubane-n.tex @@ -0,0 +1,25 @@ +\chemfig{ + \mcfatomno{1}% 1 + -[:90,2]\mcfatomno{2}% 2 + -[,2]\mcfatomno{5}% 5 + -[:270,2]\mcfatomno{3}% 3 + ( + -[:180,2]\phantom{1}% -> 1 + ) + -[:45,1.131]\mcfatomno{7}% 7 + -[:180,2]\mcfatomno{4}% 4 + ( + -[:225,1.131]\phantom{1}% -> 1 + ) + -[:90,2]\mcfatomno{6}% 6 + ( + -[:225,1.131]\phantom{2}% -> 2 + ) + -[,2]\mcfatomno{8}% 8 + ( + -[:225,1.131]\phantom{5}% -> 5 + ) + ( + -[:270,2]\phantom{7}% -> 7 + ) +} diff --git a/graphics/mol2chemfig/docs/examples/cubane.mol b/graphics/mol2chemfig/docs/examples/cubane.mol new file mode 100644 index 0000000000..cd329e0eff --- /dev/null +++ b/graphics/mol2chemfig/docs/examples/cubane.mol @@ -0,0 +1,25 @@ +136090 + OpenBabel01111309492D + + 8 12 0 0 1 0 0 0 0 0999 V2000 + 2.0000 -0.7000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 + 2.0000 0.3000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 + 3.0000 -0.7000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 + 2.4000 -0.3000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 + 3.0000 0.3000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 + 2.4000 0.7000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 + 3.4000 -0.3000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 + 3.4000 0.7000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 1 3 1 0 0 0 0 + 1 4 1 0 0 0 0 + 2 5 1 0 0 0 0 + 2 6 1 0 0 0 0 + 3 5 1 0 0 0 0 + 3 7 1 0 0 0 0 + 4 6 1 0 0 0 0 + 4 7 1 0 0 0 0 + 5 8 1 0 0 0 0 + 6 8 1 0 0 0 0 + 7 8 1 0 0 0 0 +M END diff --git a/graphics/mol2chemfig/docs/examples/cubane.sdf b/graphics/mol2chemfig/docs/examples/cubane.sdf new file mode 100644 index 0000000000..17032e80c8 --- /dev/null +++ b/graphics/mol2chemfig/docs/examples/cubane.sdf @@ -0,0 +1,140 @@ +136090 + -OEChem-01111309252D + + 16 20 0 0 0 0 0 0 0999 V2000 + 2.0000 -0.7000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.0000 0.3000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 3.0000 -0.7000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.4000 -0.3000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 3.0000 0.3000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.4000 0.7000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 3.4000 -0.3000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 3.4000 0.7000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.5616 -1.1384 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1.4272 0.5373 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 3.2373 -1.2728 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 2.6373 -0.8728 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 2.7627 0.8728 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 2.1627 1.2728 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 3.9728 -0.5373 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 3.8384 1.1384 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 1 3 1 0 0 0 0 + 1 4 1 0 0 0 0 + 1 9 1 0 0 0 0 + 2 5 1 0 0 0 0 + 2 6 1 0 0 0 0 + 2 10 1 0 0 0 0 + 3 5 1 0 0 0 0 + 3 7 1 0 0 0 0 + 3 11 1 0 0 0 0 + 4 6 1 0 0 0 0 + 4 7 1 0 0 0 0 + 4 12 1 0 0 0 0 + 5 8 1 0 0 0 0 + 5 13 1 0 0 0 0 + 6 8 1 0 0 0 0 + 6 14 1 0 0 0 0 + 7 8 1 0 0 0 0 + 7 15 1 0 0 0 0 + 8 16 1 0 0 0 0 +M END +> <PUBCHEM_COMPOUND_CID> +136090 + +> <PUBCHEM_COMPOUND_CANONICALIZED> +1 + +> <PUBCHEM_CACTVS_COMPLEXITY> +110 + +> <PUBCHEM_CACTVS_HBOND_ACCEPTOR> +0 + +> <PUBCHEM_CACTVS_HBOND_DONOR> +0 + +> <PUBCHEM_CACTVS_ROTATABLE_BOND> +0 + +> <PUBCHEM_CACTVS_SUBSKEYS> +AAADccBwAAAAAAAAAAAAAAAAAABgwAAAAAAAAAAAAAAAAAAAAAAAGAAAAAAADQCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAIAAAAAAAAAAAAAAAEAgIAOgAAAAAAAAACAAAAAACAAAAAAAAAAAA== + +> <PUBCHEM_IUPAC_OPENEYE_NAME> +cubane + +> <PUBCHEM_IUPAC_CAS_NAME> +cubane + +> <PUBCHEM_IUPAC_NAME> +cubane + +> <PUBCHEM_IUPAC_SYSTEMATIC_NAME> +cubane + +> <PUBCHEM_IUPAC_TRADITIONAL_NAME> +cubane + +> <PUBCHEM_IUPAC_INCHI> +InChI=1S/C8H8/c1-2-5-3(1)7-4(1)6(2)8(5)7/h1-8H + +> <PUBCHEM_IUPAC_INCHIKEY> +TXWRERCHRDBNLG-UHFFFAOYSA-N + +> <PUBCHEM_XLOGP3_AA> +1.2 + +> <PUBCHEM_EXACT_MASS> +104.0626 + +> <PUBCHEM_MOLECULAR_FORMULA> +C8H8 + +> <PUBCHEM_MOLECULAR_WEIGHT> +104.14912 + +> <PUBCHEM_OPENEYE_CAN_SMILES> +C12C3C4C1C5C2C3C45 + +> <PUBCHEM_OPENEYE_ISO_SMILES> +C12C3C4C1C5C2C3C45 + +> <PUBCHEM_CACTVS_TPSA> +0 + +> <PUBCHEM_MONOISOTOPIC_WEIGHT> +104.0626 + +> <PUBCHEM_TOTAL_CHARGE> +0 + +> <PUBCHEM_HEAVY_ATOM_COUNT> +8 + +> <PUBCHEM_ATOM_DEF_STEREO_COUNT> +0 + +> <PUBCHEM_ATOM_UDEF_STEREO_COUNT> +0 + +> <PUBCHEM_BOND_DEF_STEREO_COUNT> +0 + +> <PUBCHEM_BOND_UDEF_STEREO_COUNT> +0 + +> <PUBCHEM_ISOTOPIC_ATOM_COUNT> +0 + +> <PUBCHEM_COMPONENT_COUNT> +1 + +> <PUBCHEM_CACTVS_TAUTO_COUNT> +1 + +> <PUBCHEM_COORDINATE_TYPE> +1 +5 +255 + +$$$$ diff --git a/graphics/mol2chemfig/docs/examples/cubane.sh b/graphics/mol2chemfig/docs/examples/cubane.sh new file mode 100755 index 0000000000..fc2973d3a5 --- /dev/null +++ b/graphics/mol2chemfig/docs/examples/cubane.sh @@ -0,0 +1 @@ +mol2chemfig -t 2 -w cubane.mol > cubane.tex
\ No newline at end of file diff --git a/graphics/mol2chemfig/docs/examples/daptomycin-u.sh b/graphics/mol2chemfig/docs/examples/daptomycin-u.sh new file mode 100755 index 0000000000..bd26c321ea --- /dev/null +++ b/graphics/mol2chemfig/docs/examples/daptomycin-u.sh @@ -0,0 +1 @@ +mol2chemfig -u -wf daptomycin.mol > daptomycin-u.tex
\ No newline at end of file diff --git a/graphics/mol2chemfig/docs/examples/daptomycin-u.tex b/graphics/mol2chemfig/docs/examples/daptomycin-u.tex new file mode 100644 index 0000000000..7bd845b685 --- /dev/null +++ b/graphics/mol2chemfig/docs/examples/daptomycin-u.tex @@ -0,0 +1,191 @@ +\chemfig{ + O% 5 + =[:305.8]% 3 + ( + >:[:5.8]% 2 + ( + -[:65.8]% 4 + -[:5.8]% 115 + -[:59.8]% 109 + -[:107.8]% 110 + -[:47.8,,,,drh]% 111 + -[:347.8]% 112 + -[:287.8,,,,drh]% 107 + -[:227.8]% 108 + ( + -[:275.8,,,1]NH% 113 + -[:203.8,,1]% 114 + -[:131.8,,,,dbr={73}{73}]% -> 115 + ) + -[:167.8,,,,drh]% -> 109 + ) + -[:305.8,,,1]NH% 1 + -[:245.8,,1]% 93 + ( + -[:305.8]% 95 + -[:5.8]% 96 + -[:305.8]% 97 + -[:5.8]% 98 + -[:305.8]% 99 + -[:5.8]% 100 + -[:305.8]% 101 + -[:5.8]% 102 + -[:305.8]% 103 + ) + =[:185.8]O% 94 + ) + -[:245.8]\mcfbelow{N}{H}% 6 + -[:185.8]% 7 + ( + <:[:245.8]% 9 + -[:305.8]% 10 + ( + -[:245.8,,,2]H_2N% 12 + ) + =[:5.8]O% 11 + ) + -[:125.8]% 8 + ( + =[:65.8]O% 15 + ) + -[:185.8]\mcfbelow{N}{H}% 13 + -[:125.8]% 14 + ( + -[:65.8]% 16 + -[:125.8]% 19 + ( + =[:65.8]O% 21 + ) + -[:185.8,,,2]HO% 20 + ) + <:[:185.8]% 17 + ( + -[:265.8,,,,dbl={84}{0}]O% 22 + ) + -[:125.8]\mcfabove{N}{H}% 18 + >:[:185.8]% 23 + -[:270]% 24 + ( + =[:354.2]O% 26 + ) + -[:258.4,,,1]NH% 25 + -[:246.8,,1]% 27 + -[:235.2]% 28 + ( + =[:319.4]O% 29 + ) + -[:223.5]\mcfbelow{N}{H}% 30 + -[:211.9]% 31 + ( + -[:296.1]% 33 + -[:356.1]% 34 + -[:296.1]% 35 + -[:356.1,,,1]NH_2% 36 + ) + -[:200.3]% 32 + ( + =[:284.5]O% 37 + ) + -[:188.7]\mcfbelow{N}{H}% 38 + -[:177.1]% 39 + ( + <[:261.3]% 43 + -[:321.3]% 44 + ( + -[:261.3,,,1]OH% 46 + ) + =[:21.3]O% 45 + ) + -[:165.5]% 40 + ( + =[:249.7]O% 42 + ) + -[:153.9]\mcfbelow{N}{H}% 41 + -[:142.3]% 47 + ( + <:[:226.5]% 49 + ) + -[:130.6]% 48 + ( + =[:214.8]O% 51 + ) + -[:119,,,2]HN% 50 + -[:107.4,,2]% 52 + ( + <[:191.6]% 54 + -[:251.6]% 55 + ( + -[:191.6,,,2]HO% 57 + ) + =[:311.6]O% 56 + ) + -[:95.8]% 53 + ( + =[:180]O% 58 + ) + -[:84.2,,,2]HN% 59 + -[:72.6,,2]% 60 + -[:61]% 61 + ( + =[:145.2]O% 62 + ) + -[:49.4]\mcfabove{N}{H}% 63 + -[:37.7]% 64 + ( + <:[:121.9]% 104 + -[:181.9,,,2]HO% 105 + ) + -[:26.1]% 91 + ( + =[:110.3]O% 92 + ) + -[:14.5]\mcfabove{N}{H}% 90 + -[:2.9]% 82 + ( + <[:87.1]% 84 + ( + -[:147.1]% 86 + -[:87.1]% 87 + ( + -[:147.1,,,2]HO% 89 + ) + =[:27.1]O% 88 + ) + -[:27.1]% 85 + ) + -[:351.3]% 81 + ( + =[:75.5]O% 83 + ) + -[:339.7]\mcfabove{N}{H}% 71 + -[:328.1]% 69 + ( + -[:316.5]% 68 + ( + =[:40.6]O% 70 + ) + -[:304.8]O% 67 + -[:293.2]% 65 + ( + <:[:17.4]% 66 + ) + -[:281.6]% -> 23 + ) + <[:52.3]% 72 + -[:112.3]% 73 + ( + =[:172.3]O% 75 + ) + -[:52.3]% 74 + -[:112.3,,,,drh]% 80 + ( + -[:172.3,,,2]H_2N% 106 + ) + -[:52.3]% 79 + -[:352.3,,,,drh]% 78 + -[:292.3]% 77 + -[:232.3,,,,drh]% 76 + ( + -[:172.3]% -> 74 + ) +} diff --git a/graphics/mol2chemfig/docs/examples/daptomycin.mol b/graphics/mol2chemfig/docs/examples/daptomycin.mol new file mode 100644 index 0000000000..7db489f00b --- /dev/null +++ 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1 0 0 0 0 + 10 11 2 0 0 0 0 + 10 12 1 0 0 0 0 + 8 13 1 0 0 0 0 + 13 14 1 0 0 0 0 + 8 15 2 0 0 0 0 + 14 16 1 6 0 0 0 + 14 17 1 0 0 0 0 + 17 18 1 0 0 0 0 + 16 19 1 0 0 0 0 + 19 20 1 0 0 0 0 + 19 21 2 0 0 0 0 + 17 22 2 0 0 0 0 + 18 23 1 0 0 0 0 + 23 24 1 6 0 0 0 + 24 25 1 0 0 0 0 + 24 26 2 0 0 0 0 + 25 27 1 0 0 0 0 + 27 28 1 0 0 0 0 + 28 29 2 0 0 0 0 + 28 30 1 0 0 0 0 + 30 31 1 0 0 0 0 + 31 32 1 0 0 0 0 + 31 33 1 0 0 0 0 + 33 34 1 0 0 0 0 + 34 35 1 0 0 0 0 + 35 36 1 0 0 0 0 + 32 37 2 0 0 0 0 + 32 38 1 0 0 0 0 + 38 39 1 0 0 0 0 + 39 40 1 0 0 0 0 + 40 41 1 0 0 0 0 + 40 42 2 0 0 0 0 + 39 43 1 6 0 0 0 + 43 44 1 0 0 0 0 + 44 45 2 0 0 0 0 + 44 46 1 0 0 0 0 + 41 47 1 0 0 0 0 + 47 48 1 0 0 0 0 + 47 49 1 6 0 0 0 + 48 50 1 0 0 0 0 + 48 51 2 0 0 0 0 + 50 52 1 0 0 0 0 + 52 53 1 0 0 0 0 + 52 54 1 1 0 0 0 + 54 55 1 0 0 0 0 + 55 56 2 0 0 0 0 + 55 57 1 0 0 0 0 + 53 58 2 0 0 0 0 + 53 59 1 0 0 0 0 + 59 60 1 0 0 0 0 + 60 61 1 0 0 0 0 + 61 62 2 0 0 0 0 + 61 63 1 0 0 0 0 + 63 64 1 0 0 0 0 + 23 65 1 0 0 0 0 + 65 66 1 1 0 0 0 + 65 67 1 0 0 0 0 + 67 68 1 0 0 0 0 + 68 69 1 0 0 0 0 + 68 70 2 0 0 0 0 + 69 71 1 0 0 0 0 + 69 72 1 1 0 0 0 + 72 73 1 0 0 0 0 + 73 74 1 0 0 0 0 + 73 75 2 0 0 0 0 + 80 74 2 0 0 0 0 + 76 74 1 0 0 0 0 + 76 77 2 0 0 0 0 + 77 78 1 0 0 0 0 + 78 79 2 0 0 0 0 + 79 80 1 0 0 0 0 + 71 81 1 0 0 0 0 + 81 82 1 0 0 0 0 + 81 83 2 0 0 0 0 + 82 84 1 1 0 0 0 + 84 85 1 0 0 0 0 + 84 86 1 0 0 0 0 + 86 87 1 0 0 0 0 + 87 88 2 0 0 0 0 + 87 89 1 0 0 0 0 + 82 90 1 0 0 0 0 + 90 91 1 0 0 0 0 + 91 92 2 0 0 0 0 + 1 93 1 0 0 0 0 + 93 94 2 0 0 0 0 + 93 95 1 0 0 0 0 + 95 96 1 0 0 0 0 + 96 97 1 0 0 0 0 + 97 98 1 0 0 0 0 + 98 99 1 0 0 0 0 + 99100 1 0 0 0 0 +100101 1 0 0 0 0 +101102 1 0 0 0 0 +102103 1 0 0 0 0 + 64104 1 6 0 0 0 +104105 1 0 0 0 0 + 64 91 1 0 0 0 0 + 80106 1 0 0 0 0 +107108 1 0 0 0 0 +109110 1 0 0 0 0 +110111 2 0 0 0 0 +111112 1 0 0 0 0 +107112 2 0 0 0 0 +115109 1 0 0 0 0 +108109 2 0 0 0 0 +113108 1 0 0 0 0 +113114 1 0 0 0 0 +114115 2 0 0 0 0 +M END diff --git a/graphics/mol2chemfig/docs/examples/daptomycin.tex b/graphics/mol2chemfig/docs/examples/daptomycin.tex new file mode 100644 index 0000000000..2ccf1e736f --- /dev/null +++ b/graphics/mol2chemfig/docs/examples/daptomycin.tex @@ -0,0 +1,191 @@ +\chemfig{ + O% 5 + =[:270]% 3 + ( + -[:210]% 2 + ( + <[:150]% 4 + -[:90.4,2.094]% 115 + -[:18]% 109 + -[:330]% 110 + -[:30,,,,dlh]% 111 + -[:90]% 112 + -[:150,,,,dlh]% 107 + -[:210]% 108 + ( + -[:162]\mcfabove{N}{H}% 113 + -[:234]% 114 + -[:306,,,,dbl={73}{73}]% -> 115 + ) + -[:270,,,,dlh]% -> 109 + ) + -[:270,,,2]HN% 1 + -[:330,,2]% 93 + ( + -[:270]% 95 + -[:210]% 96 + -[:270]% 97 + -[:330]% 98 + -[:30]% 99 + -[:330]% 100 + -[:270]% 101 + -[:210]% 102 + -[:270]% 103 + ) + =[:30]O% 94 + ) + -[:330]\mcfbelow{N}{H}% 6 + -[:30]% 7 + ( + <:[:90]% 9 + -[:30]% 10 + ( + -[:330,,,1]NH_2% 12 + ) + =[:90]O% 11 + ) + -[:330]% 8 + ( + =[:270]O% 15 + ) + -[:30]\mcfabove{N}{H}% 13 + -[:330]% 14 + ( + <:[:270]% 16 + -[:330]% 19 + ( + =[:270]O% 21 + ) + -[:30,,,1]OH% 20 + ) + -[:30]% 17 + ( + =[:90]O% 22 + ) + -[:330]\mcfbelow{N}{H}% 18 + -[:30]% 23 + <:[:90]% 24 + ( + =[:150]O% 26 + ) + -[:30,,,1]NH% 25 + -[:90,,1]% 27 + -[:30]% 28 + ( + =[:90]O% 29 + ) + -[:330]\mcfbelow{N}{H}% 30 + -[:30]% 31 + ( + -[:90]% 33 + -[:30]% 34 + -[:90]% 35 + -[:30,,,1]NH_2% 36 + ) + -[:330]% 32 + ( + =[:270]O% 37 + ) + -[:30]\mcfabove{N}{H}% 38 + -[:330]% 39 + ( + <:[:270]% 43 + -[:330]% 44 + ( + -[:30,,,1]OH% 46 + ) + =[:270]O% 45 + ) + -[:30]% 40 + ( + =[:90]O% 42 + ) + -[:330]\mcfbelow{N}{H}% 41 + -[:30]% 47 + ( + <:[:90]% 49 + ) + -[:330]% 48 + ( + =[:30]O% 51 + ) + -[:270,,,2]HN% 50 + -[:330,,2]% 52 + ( + <[:30]% 54 + -[:330]% 55 + ( + -[:270,,,1]OH% 57 + ) + =[:30]O% 56 + ) + -[:270]% 53 + ( + =[:330]O% 58 + ) + -[:210,,,2]HN% 59 + -[:270,,2]% 60 + -[:210]% 61 + ( + =[:270]O% 62 + ) + -[:150]\mcfabove{N}{H}% 63 + -[:210]% 64 + ( + <:[:270]% 104 + -[:330,,,1]OH% 105 + ) + -[:180,1.732]% 91 + ( + -[:150,,,,dlhs]O% 92 + ) + -[:270,,,1]NH% 90 + -[:210,,1]% 82 + ( + <[:270]% 84 + ( + -[:330]% 86 + -[:270]% 87 + ( + -[:210,,,2]HO% 89 + ) + =[:330]O% 88 + ) + -[:210]% 85 + ) + -[:150]% 81 + ( + =[:90]O% 83 + ) + -[:210]\mcfbelow{N}{H}% 71 + -[:150]% 69 + ( + -[:90]% 68 + ( + =[:30]O% 70 + ) + -[:150]O% 67 + -[:90]% 65 + ( + <[:30]% 66 + ) + -[:150]% -> 23 + ) + <[:210]% 72 + -[:270]% 73 + ( + =[:330]O% 75 + ) + -[:210]% 74 + -[:270,,,,drh]% 80 + ( + -[:330,,,1]NH_2% 106 + ) + -[:210]% 79 + -[:150,,,,drh]% 78 + -[:90]% 77 + -[:30,,,,drh]% 76 + ( + -[:330]% -> 74 + ) +} diff --git a/graphics/mol2chemfig/docs/examples/daptomycin1.sh b/graphics/mol2chemfig/docs/examples/daptomycin1.sh new file mode 100755 index 0000000000..12314a3aec --- /dev/null +++ b/graphics/mol2chemfig/docs/examples/daptomycin1.sh @@ -0,0 +1 @@ +mol2chemfig -wf daptomycin.mol > daptomycin.tex
\ No newline at end of file diff --git a/graphics/mol2chemfig/docs/examples/dcf-submol1.tex b/graphics/mol2chemfig/docs/examples/dcf-submol1.tex new file mode 100644 index 0000000000..3787320606 --- /dev/null +++ b/graphics/mol2chemfig/docs/examples/dcf-submol1.tex @@ -0,0 +1,51 @@ +\definesubmol{dcf1}{ + O% 15 + =[:210]% 14 + -[:270]% 13 + ( + -[:330]% 18 + ) + =_[:210]% 12 + -[:150]% 9 + =_[:210]% 8 + ( + -[:270,1.755]% 16 + =^[:210]% 20 + -[:270]% 21 + =^[:330]% 22 + -[:30]% 23 + =^[:90]% 24 + ( + -[:30]% 25 + ( + -[:330]\mcfright{O}{^{\mcfminus}}% 27 + ) + =[:90]O% 26 + ) + -[:150]% -> 16 + ) + -[:150]% 5 + -[:210]% 4 + =_[:150]% 3 + ( + -[:210]% 17 + ) + -[:90]% 2 + ( + -[:150,,,2]^{\mcfminus}O% 19 + ) + =_[:30]% 1 + -[:330]% 6 + ( + =_[:270]% -> 5 + ) + -[:30]O% 7 + -[:330]% 10 + ( + -[:270]% -> 9 + ) + =_[:30]% 11 + ( + -[:330]% -> 14 + ) +} diff --git a/graphics/mol2chemfig/docs/examples/dcf-submol2.tex b/graphics/mol2chemfig/docs/examples/dcf-submol2.tex new file mode 100644 index 0000000000..e7a95777fe --- /dev/null +++ b/graphics/mol2chemfig/docs/examples/dcf-submol2.tex @@ -0,0 +1,51 @@ +\definesubmol{dcf2}{ + \mcfright{O}{\mcfatomno{15}}% 15 + =[:210]\mcfatomno{14}% 14 + -[:270]\mcfatomno{13}% 13 + ( + -[:330]\mcfatomno{18}% 18 + ) + =_[:210]\mcfatomno{12}% 12 + -[:150]\mcfatomno{9}% 9 + =_[:210]\mcfatomno{8}% 8 + ( + -[:270,1.755]\mcfatomno{16}% 16 + =^[:210]\mcfatomno{20}% 20 + -[:270]\mcfatomno{21}% 21 + =^[:330]\mcfatomno{22}% 22 + -[:30]\mcfatomno{23}% 23 + =^[:90]\mcfatomno{24}% 24 + ( + -[:30]\mcfatomno{25}% 25 + ( + -[:330]\mcfright{O}{\mcfatomno{27}}% 27 + ) + =[:90]\mcfright{O}{\mcfatomno{26}}% 26 + ) + -[:150]\phantom{16}% -> 16 + ) + -[:150]\mcfatomno{5}% 5 + -[:210]\mcfatomno{4}% 4 + =_[:150]\mcfatomno{3}% 3 + ( + -[:210]\mcfatomno{17}% 17 + ) + -[:90]\mcfatomno{2}% 2 + ( + -[:150]\mcfleft{\mcfatomno{19}}{O}% 19 + ) + =_[:30]\mcfatomno{1}% 1 + -[:330]\mcfatomno{6}% 6 + ( + =_[:270]\phantom{5}% -> 5 + ) + -[:30]\mcfabove{O}{\mcfatomno{7}}% 7 + -[:330]\mcfatomno{10}% 10 + ( + -[:270]\phantom{9}% -> 9 + ) + =_[:30]\mcfatomno{11}% 11 + ( + -[:330]\phantom{14}% -> 14 + ) +} diff --git a/graphics/mol2chemfig/docs/examples/dcf-submol3.tex b/graphics/mol2chemfig/docs/examples/dcf-submol3.tex new file mode 100644 index 0000000000..33413d9eb5 --- /dev/null +++ b/graphics/mol2chemfig/docs/examples/dcf-submol3.tex @@ -0,0 +1,53 @@ +\definesubmol{dcf3}{ + % 22 + =_[:150]% 21 + -[:90]% 20 + =_[:30]% 16 + ( + -[:330]% 24 + ( + -[:30]% 25 + ( + -[:330]\mcfright{O}{^{\mcfminus}}% 27 + ) + =[:90]O% 26 + ) + =_[:270]% 23 + -[:210]% -> 22 + ) + -[:90,1.755]% 8 + -[:150]% 5 + -[:210]% 4 + =_[:150]% 3 + ( + -[:210]% 17 + ) + -[:90]% 2 + ( + -[:150,,,2]^{\mcfminus}O% 19 + ) + =_[:30]% 1 + -[:330]% 6 + ( + =_[:270]% -> 5 + ) + -[:30]O% 7 + -[:330]% 10 + =_[:30]% 11 + -[:330]% 14 + ( + =[:30]O% 15 + ) + -[:270]% 13 + ( + -[:330]% 18 + ) + =_[:210]% 12 + -[:150]% 9 + ( + =_[:210]% -> 8 + ) + ( + -[:90]% -> 10 + ) +} diff --git a/graphics/mol2chemfig/docs/examples/dichlorofluorescein.mol b/graphics/mol2chemfig/docs/examples/dichlorofluorescein.mol new file mode 100644 index 0000000000..620c1683c8 --- /dev/null +++ b/graphics/mol2chemfig/docs/examples/dichlorofluorescein.mol @@ -0,0 +1,63 @@ + + Marvin 05191217082D + + 27 30 0 0 0 0 999 V2000 + -2.8481 3.3463 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -3.5626 2.9338 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -3.5626 2.1088 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.8481 1.6963 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.1337 2.1088 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.1337 2.9338 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.4192 3.3463 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + -1.4192 1.6963 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.7047 2.1088 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.7047 2.9338 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0097 3.3463 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0097 1.6963 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.7242 2.1088 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.7242 2.9338 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.4387 3.3463 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + -1.4192 0.2487 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -4.2771 1.6963 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.4387 1.6963 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -4.2771 3.3463 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0 + -2.1337 -0.1638 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.1337 -0.9888 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.4192 -1.4013 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.7047 -0.9888 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.7047 -0.1638 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0098 0.2487 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0098 1.0737 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 0.7242 -0.1638 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0 + 1 2 2 0 0 0 0 + 2 3 1 0 0 0 0 + 3 4 2 0 0 0 0 + 4 5 1 0 0 0 0 + 1 6 1 0 0 0 0 + 7 6 1 0 0 0 0 + 6 5 2 0 0 0 0 + 5 8 1 0 0 0 0 + 8 9 2 0 0 0 0 + 7 10 1 0 0 0 0 + 11 10 2 0 0 0 0 + 10 9 1 0 0 0 0 + 9 12 1 0 0 0 0 + 12 13 2 0 0 0 0 + 13 14 1 0 0 0 0 + 11 14 1 0 0 0 0 + 14 15 2 0 0 0 0 + 8 16 1 0 0 0 0 + 3 17 1 0 0 0 0 + 13 18 1 0 0 0 0 + 2 19 1 0 0 0 0 + 16 20 2 0 0 0 0 + 16 24 1 0 0 0 0 + 20 21 1 0 0 0 0 + 21 22 2 0 0 0 0 + 22 23 1 0 0 0 0 + 23 24 2 0 0 0 0 + 24 25 1 0 0 0 0 + 25 26 2 0 0 0 0 + 25 27 1 0 0 0 0 +M CHG 2 19 -1 27 -1 +M END diff --git a/graphics/mol2chemfig/docs/examples/dichlorofluorescein1.sh b/graphics/mol2chemfig/docs/examples/dichlorofluorescein1.sh new file mode 100755 index 0000000000..51d2b28545 --- /dev/null +++ b/graphics/mol2chemfig/docs/examples/dichlorofluorescein1.sh @@ -0,0 +1,2 @@ +mol2chemfig -l dcf1 dichlorofluorescein.mol > dcf-submol1.tex +mol2chemfig -l ce1 crown-ether.mol > ce-submol1.tex diff --git a/graphics/mol2chemfig/docs/examples/dichlorofluorescein2.sh b/graphics/mol2chemfig/docs/examples/dichlorofluorescein2.sh new file mode 100755 index 0000000000..ef10d00ea3 --- /dev/null +++ b/graphics/mol2chemfig/docs/examples/dichlorofluorescein2.sh @@ -0,0 +1,3 @@ +# numbered versions +mol2chemfig -n -l dcf2 dichlorofluorescein.mol > dcf-submol2.tex +mol2chemfig -n -l ce2 crown-ether.mol > ce-submol2.tex diff --git a/graphics/mol2chemfig/docs/examples/dichlorofluorescein3.sh b/graphics/mol2chemfig/docs/examples/dichlorofluorescein3.sh new file mode 100755 index 0000000000..2d7c788b20 --- /dev/null +++ b/graphics/mol2chemfig/docs/examples/dichlorofluorescein3.sh @@ -0,0 +1,3 @@ +# correctly ordered versions +mol2chemfig -e 22 -l dcf3 dichlorofluorescein.mol > dcf-submol3.tex +mol2chemfig -e 12 -x 32 -l ce3 crown-ether.mol > ce-submol3.tex diff --git a/graphics/mol2chemfig/docs/examples/doxo-from-sdf.sh b/graphics/mol2chemfig/docs/examples/doxo-from-sdf.sh new file mode 100755 index 0000000000..b948344b9a --- /dev/null +++ b/graphics/mol2chemfig/docs/examples/doxo-from-sdf.sh @@ -0,0 +1 @@ +mol2chemfig -w doxorubicin.sdf > doxo-raw.tex
\ No newline at end of file diff --git a/graphics/mol2chemfig/docs/examples/doxo-hand-rotated.sh b/graphics/mol2chemfig/docs/examples/doxo-hand-rotated.sh new file mode 100755 index 0000000000..ea509cfd42 --- /dev/null +++ b/graphics/mol2chemfig/docs/examples/doxo-hand-rotated.sh @@ -0,0 +1 @@ +mol2chemfig -a 20 -u -w -y delete doxorubicin.sdf > doxo-hand-rotated.tex
\ No newline at end of file diff --git a/graphics/mol2chemfig/docs/examples/doxo-numbered.sh b/graphics/mol2chemfig/docs/examples/doxo-numbered.sh new file mode 100755 index 0000000000..72af2b46be --- /dev/null +++ b/graphics/mol2chemfig/docs/examples/doxo-numbered.sh @@ -0,0 +1 @@ +mol2chemfig -n -w -y delete doxorubicin.sdf > doxo-numbered.tex
\ No newline at end of file diff --git a/graphics/mol2chemfig/docs/examples/doxo-numbered.tex b/graphics/mol2chemfig/docs/examples/doxo-numbered.tex new file mode 100644 index 0000000000..80fcfdd637 --- /dev/null +++ b/graphics/mol2chemfig/docs/examples/doxo-numbered.tex @@ -0,0 +1,74 @@ +\chemfig{ + \mcfleft{\mcfatomno{3}}{O}% 3 + >:[:60.2]\mcfatomno{14}% 14 + ( + -[:180.2]\mcfatomno{25}% 25 + ( + -[:240.2]\mcfatomno{30}% 30 + -[:180.2]\mcfleft{\mcfatomno{8}}{O}% 8 + ) + =[:120.2]\mcfleft{\mcfatomno{7}}{O}% 7 + ) + -[:90,1.042]\mcfatomno{15}% 15 + -[:29.6,1.042]\mcfatomno{13}% 13 + ( + <:[:89.3]\mcfright{O}{\mcfatomno{1}}% 1 + >:[:149.3]\mcfatomno{19}% 19 + -[:209.3]\mcfbelow{O}{\mcfatomno{2}}% 2 + -[:149.3]\mcfatomno{23}% 23 + ( + <[:209.3]\mcfatomno{29}% 29 + ) + -[:89.3]\mcfatomno{22}% 22 + ( + -[:29.3]\mcfatomno{21}% 21 + ( + -[:329.3]\mcfatomno{20}% 20 + -[:269.3]\phantom{19}% -> 19 + ) + <[:89.3]\mcfright{N}{\mcfatomno{12}}% 12 + ) + <[:149.3]\mcfleft{\mcfatomno{4}}{O}% 4 + ) + -[:329.1,1.042]\mcfatomno{17}% 17 + -[:270]\mcfatomno{18}% 18 + ( + -[:210.9,1.042]\mcfatomno{16}% 16 + -[:150.4,1.042]\phantom{14}% -> 14 + ) + =^[:330]\mcfatomno{26}% 26 + ( + -[:270]\mcfright{O}{\mcfatomno{6}}% 6 + ) + -[:30]\mcfatomno{28}% 28 + =^[:90]\mcfatomno{27}% 27 + ( + -[:150]\mcfatomno{24}% 24 + ( + =^[:210]\phantom{17}% -> 17 + ) + -[:90]\mcfright{O}{\mcfatomno{5}}% 5 + ) + -[:30.9,1.042]\mcfatomno{31}% 31 + ( + =[:90.7]\mcfright{O}{\mcfatomno{9}}% 9 + ) + -[:330.4,1.042]\mcfatomno{33}% 33 + =^[:270,1.042]\mcfatomno{34}% 34 + ( + -[:209.6,1.042]\mcfatomno{32}% 32 + ( + -[:149.1,1.042]\phantom{28}% -> 28 + ) + =[:269.3]\mcfright{O}{\mcfatomno{10}}% 10 + ) + -[:329.1,1.085]\mcfatomno{36}% 36 + =^[:29.6,1.085]\mcfatomno{38}% 38 + -[:90,1.085]\mcfatomno{37}% 37 + =^[:150.4,1.085]\mcfatomno{35}% 35 + ( + -[:210.9,1.085]\phantom{33}% -> 33 + ) + -[:90.7]\mcfleft{\mcfatomno{11}}{O}% 11 + -[:30.7]\mcfatomno{39}% 39 +} diff --git a/graphics/mol2chemfig/docs/examples/doxo-ratcheted-rotated.sh b/graphics/mol2chemfig/docs/examples/doxo-ratcheted-rotated.sh new file mode 100755 index 0000000000..4bad92b51f --- /dev/null +++ b/graphics/mol2chemfig/docs/examples/doxo-ratcheted-rotated.sh @@ -0,0 +1 @@ +mol2chemfig -r 30 -a 180 -u -w -y delete doxorubicin.sdf > doxo-rat-rot.tex
\ No newline at end of file diff --git a/graphics/mol2chemfig/docs/examples/doxo-ratcheted.sh b/graphics/mol2chemfig/docs/examples/doxo-ratcheted.sh new file mode 100755 index 0000000000..07810a9a01 --- /dev/null +++ b/graphics/mol2chemfig/docs/examples/doxo-ratcheted.sh @@ -0,0 +1 @@ +mol2chemfig -r 30 -u -w -y delete doxorubicin.sdf > doxo-ratcheted.tex
\ No newline at end of file diff --git a/graphics/mol2chemfig/docs/examples/doxo-raw.tex b/graphics/mol2chemfig/docs/examples/doxo-raw.tex new file mode 100644 index 0000000000..1af8856904 --- /dev/null +++ b/graphics/mol2chemfig/docs/examples/doxo-raw.tex @@ -0,0 +1,145 @@ +\chemfig{ + O% 7 + =[:300.2,1.613]% 25 + ( + -[:240.2,1.613]% 30 + ( + -[:260.2]H% 57 + ) + ( + -[:340.2]H% 58 + ) + -[:180.2,1.613]O% 8 + -[:240.2]H% 63 + ) + -[:0.2,1.613]% 14 + ( + <:[:240.2,1.613]O% 3 + -[:300.2]H% 51 + ) + -[:90,1.68]% 15 + ( + -[:109.7]H% 41 + ) + ( + -[:189.9]H% 42 + ) + -[:29.6,1.68]% 13 + ( + <:[:89.3,1.613]O% 1 + >:[:149.3,1.613]% 19 + ( + -[:29.3]H% 45 + ) + -[:209.3,1.613]O% 2 + -[:149.3,1.613]% 23 + ( + <[:209.3,1.613]% 29 + ( + -[:209.3]H% 53 + ) + ( + -[:299.3]H% 54 + ) + -[:119.3]H% 52 + ) + ( + -[:269.3]H% 50 + ) + -[:89.3,1.613]% 22 + ( + -[:29.3,1.613]% 21 + ( + -[:329.3,1.613]% 20 + ( + -[:349.3]H% 46 + ) + ( + -[:69.3]H% 47 + ) + -[:269.3,1.613]% -> 19 + ) + ( + -[:149.3]H% 48 + ) + <[:89.3,1.613]N% 12 + ( + -[:149.3]H% 56 + ) + -[:29.3]H% 55 + ) + ( + -[:209.3]H% 49 + ) + <[:149.3,1.613]O% 4 + -[:209.3]H% 59 + ) + ( + -[:149.5]H% 40 + ) + -[:329.1,1.68]% 17 + -[:270,1.613]% 18 + ( + -[:210.9,1.68]% 16 + ( + -[:230.6]H% 43 + ) + ( + -[:310.7]H% 44 + ) + -[:150.4,1.68]% -> 14 + ) + =^[:330,1.613]% 26 + ( + -[:270,1.613]O% 6 + -[:210]H% 61 + ) + -[:30,1.613]% 28 + =^[:90,1.613]% 27 + ( + -[:150,1.613]% 24 + ( + =^[:210,1.613]% -> 17 + ) + -[:90,1.613]O% 5 + -[:30]H% 60 + ) + -[:30.9,1.68]% 31 + ( + =[:90.7,1.613]O% 9 + ) + -[:330.4,1.68]% 33 + =^[:270,1.68]% 34 + ( + -[:209.6,1.68]% 32 + ( + -[:149.1,1.68]% -> 28 + ) + =[:269.3,1.613]O% 10 + ) + -[:329.1,1.75]% 36 + ( + -[:269.3]H% 62 + ) + =^[:29.6,1.75]% 38 + ( + -[:329.8]H% 65 + ) + -[:90,1.75]% 37 + ( + -[:30.2]H% 64 + ) + =^[:150.4,1.75]% 35 + ( + -[:210.9,1.75]% -> 33 + ) + -[:90.7,1.613]O% 11 + -[:30.7,1.613]% 39 + ( + -[:300.7]H% 66 + ) + ( + -[:30.7]H% 67 + ) + -[:120.7]H% 68 +} diff --git a/graphics/mol2chemfig/docs/examples/doxo-recalculated-flopped.sh b/graphics/mol2chemfig/docs/examples/doxo-recalculated-flopped.sh new file mode 100755 index 0000000000..9f03e17faf --- /dev/null +++ b/graphics/mol2chemfig/docs/examples/doxo-recalculated-flopped.sh @@ -0,0 +1 @@ +mol2chemfig -qwu -y delete doxorubicin.sdf > doxo-recalculated-flopped.tex
\ No newline at end of file diff --git a/graphics/mol2chemfig/docs/examples/doxo-recalculated-flopped.tex b/graphics/mol2chemfig/docs/examples/doxo-recalculated-flopped.tex new file mode 100644 index 0000000000..7b3407a792 --- /dev/null +++ b/graphics/mol2chemfig/docs/examples/doxo-recalculated-flopped.tex @@ -0,0 +1,74 @@ +\chemfig{ + HO% 3 + >[:290,,2]% 14 + ( + -[:190]% 25 + ( + -[:130]% 30 + -[:190,,,2]HO% 8 + ) + =[:250]O% 7 + ) + -[:270]% 15 + -[:330]% 13 + ( + <[:270]O% 1 + >:[:210]% 19 + -[:270]O% 2 + -[:210]% 23 + ( + <[:270]% 29 + ) + -[:150]% 22 + ( + -[:90]% 21 + ( + -[:30]% 20 + -[:330]% -> 19 + ) + <[:150,,,2]H_2N% 12 + ) + <[:210,,,2]HO% 4 + ) + -[:30]% 17 + -[:90]% 18 + ( + -[:150]% 16 + -[:210]% -> 14 + ) + =_[:30]% 26 + ( + -[:90,,,1]OH% 6 + ) + -[:330]% 28 + =_[:270]% 27 + ( + -[:210]% 24 + ( + =_[:150]% -> 17 + ) + -[:270,,,1]OH% 5 + ) + -[:330]% 31 + ( + =[:270]O% 9 + ) + -[:30]% 33 + =_[:90]% 34 + ( + -[:150]% 32 + ( + -[:210]% -> 28 + ) + =[:90]O% 10 + ) + -[:30]% 36 + =_[:330]% 38 + -[:270]% 37 + =_[:210]% 35 + ( + -[:150]% -> 33 + ) + -[:270]O% 11 + -[:330]% 39 +} diff --git a/graphics/mol2chemfig/docs/examples/doxo-recalculated-rotated.sh b/graphics/mol2chemfig/docs/examples/doxo-recalculated-rotated.sh new file mode 100755 index 0000000000..22c0a8ffdd --- /dev/null +++ b/graphics/mol2chemfig/docs/examples/doxo-recalculated-rotated.sh @@ -0,0 +1 @@ +mol2chemfig -wu -y delete -a 30 doxorubicin.sdf > doxo-recalculated-rotated.tex
\ No newline at end of file diff --git a/graphics/mol2chemfig/docs/examples/doxo-recalculated-rotated.tex b/graphics/mol2chemfig/docs/examples/doxo-recalculated-rotated.tex new file mode 100644 index 0000000000..4be5361799 --- /dev/null +++ b/graphics/mol2chemfig/docs/examples/doxo-recalculated-rotated.tex @@ -0,0 +1,74 @@ +\chemfig{ + OH% 3 + >:[:100,,1]% 14 + ( + -[:200]% 25 + ( + -[:260]% 30 + -[:200,,,2]HO% 8 + ) + =[:140]O% 7 + ) + -[:120]% 15 + -[:60]% 13 + ( + <:[:120]O% 1 + >[:180]% 19 + -[:120]O% 2 + -[:180]% 23 + ( + <:[:120]% 29 + ) + -[:240]% 22 + ( + -[:300]% 21 + ( + -% 20 + -[:60]% -> 19 + ) + <:[:240,,,2]H_2N% 12 + ) + <:[:180,,,2]HO% 4 + ) + -% 17 + -[:300]% 18 + ( + -[:240]% 16 + -[:180]% -> 14 + ) + =^% 26 + ( + -[:300,,,1]OH% 6 + ) + -[:60]% 28 + =^[:120]% 27 + ( + -[:180]% 24 + ( + =^[:240]% -> 17 + ) + -[:120,,,2]HO% 5 + ) + -[:60]% 31 + ( + =[:120]O% 9 + ) + -% 33 + =^[:300]% 34 + ( + -[:240]% 32 + ( + -[:180]% -> 28 + ) + =[:300]O% 10 + ) + -% 36 + =^[:60]% 38 + -[:120]% 37 + =^[:180]% 35 + ( + -[:240]% -> 33 + ) + -[:120]O% 11 + -[:60]% 39 +} diff --git a/graphics/mol2chemfig/docs/examples/doxo-recalculated.sh b/graphics/mol2chemfig/docs/examples/doxo-recalculated.sh new file mode 100755 index 0000000000..de4e694226 --- /dev/null +++ b/graphics/mol2chemfig/docs/examples/doxo-recalculated.sh @@ -0,0 +1 @@ +mol2chemfig -u -w -y delete doxorubicin.sdf > doxo-recalculated.tex
\ No newline at end of file diff --git a/graphics/mol2chemfig/docs/examples/doxo-recalculated.tex b/graphics/mol2chemfig/docs/examples/doxo-recalculated.tex new file mode 100644 index 0000000000..a4029d35c1 --- /dev/null +++ b/graphics/mol2chemfig/docs/examples/doxo-recalculated.tex @@ -0,0 +1,74 @@ +\chemfig{ + HO% 3 + >:[:70,,2]% 14 + ( + -[:170]% 25 + ( + -[:230]% 30 + -[:170,,,2]HO% 8 + ) + =[:110]O% 7 + ) + -[:90]% 15 + -[:30]% 13 + ( + <:[:90]O% 1 + >[:150]% 19 + -[:90]O% 2 + -[:150]% 23 + ( + <:[:90]% 29 + ) + -[:210]% 22 + ( + -[:270]% 21 + ( + -[:330]% 20 + -[:30]% -> 19 + ) + <:[:210,,,2]H_2N% 12 + ) + <:[:150,,,2]HO% 4 + ) + -[:330]% 17 + -[:270]% 18 + ( + -[:210]% 16 + -[:150]% -> 14 + ) + =^[:330]% 26 + ( + -[:270,,,1]OH% 6 + ) + -[:30]% 28 + =^[:90]% 27 + ( + -[:150]% 24 + ( + =^[:210]% -> 17 + ) + -[:90,,,1]OH% 5 + ) + -[:30]% 31 + ( + =[:90]O% 9 + ) + -[:330]% 33 + =^[:270]% 34 + ( + -[:210]% 32 + ( + -[:150]% -> 28 + ) + =[:270]O% 10 + ) + -[:330]% 36 + =^[:30]% 38 + -[:90]% 37 + =^[:150]% 35 + ( + -[:210]% -> 33 + ) + -[:90]O% 11 + -[:30]% 39 +} diff --git a/graphics/mol2chemfig/docs/examples/doxo-strip-h.sh b/graphics/mol2chemfig/docs/examples/doxo-strip-h.sh new file mode 100755 index 0000000000..411ecf8d89 --- /dev/null +++ b/graphics/mol2chemfig/docs/examples/doxo-strip-h.sh @@ -0,0 +1 @@ +mol2chemfig -w -y delete doxorubicin.sdf > doxo-stripped.tex
\ No newline at end of file diff --git a/graphics/mol2chemfig/docs/examples/doxo-stripped.tex b/graphics/mol2chemfig/docs/examples/doxo-stripped.tex new file mode 100644 index 0000000000..c177de0873 --- /dev/null +++ b/graphics/mol2chemfig/docs/examples/doxo-stripped.tex @@ -0,0 +1,74 @@ +\chemfig{ + HO% 3 + >:[:60.2,,2]% 14 + ( + -[:180.2]% 25 + ( + -[:240.2]% 30 + -[:180.2,,,2]HO% 8 + ) + =[:120.2]O% 7 + ) + -[:90,1.042]% 15 + -[:29.6,1.042]% 13 + ( + <:[:89.3]O% 1 + >:[:149.3]% 19 + -[:209.3]O% 2 + -[:149.3]% 23 + ( + <[:209.3]% 29 + ) + -[:89.3]% 22 + ( + -[:29.3]% 21 + ( + -[:329.3]% 20 + -[:269.3]% -> 19 + ) + <[:89.3,,,1]NH_2% 12 + ) + <[:149.3,,,2]HO% 4 + ) + -[:329.1,1.042]% 17 + -[:270]% 18 + ( + -[:210.9,1.042]% 16 + -[:150.4,1.042]% -> 14 + ) + =^[:330]% 26 + ( + -[:270,,,1]OH% 6 + ) + -[:30]% 28 + =^[:90]% 27 + ( + -[:150]% 24 + ( + =^[:210]% -> 17 + ) + -[:90,,,1]OH% 5 + ) + -[:30.9,1.042]% 31 + ( + =[:90.7]O% 9 + ) + -[:330.4,1.042]% 33 + =^[:270,1.042]% 34 + ( + -[:209.6,1.042]% 32 + ( + -[:149.1,1.042]% -> 28 + ) + =[:269.3]O% 10 + ) + -[:329.1,1.085]% 36 + =^[:29.6,1.085]% 38 + -[:90,1.085]% 37 + =^[:150.4,1.085]% 35 + ( + -[:210.9,1.085]% -> 33 + ) + -[:90.7]O% 11 + -[:30.7]% 39 +} diff --git a/graphics/mol2chemfig/docs/examples/doxorubicin.sdf b/graphics/mol2chemfig/docs/examples/doxorubicin.sdf new file mode 100644 index 0000000000..01b7ceeaa2 --- /dev/null +++ b/graphics/mol2chemfig/docs/examples/doxorubicin.sdf @@ -0,0 +1,264 @@ +31703 + -OEChem-05091217182D + + 68 72 0 1 0 0 0 0 0999 V2000 + 5.9812 0.5043 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 4.2493 0.5243 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 4.5669 -2.9191 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 2.5405 2.5442 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 7.7296 0.4697 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 7.7296 -3.5303 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 3.5603 -1.1909 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 2.5670 -2.9268 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 9.4780 0.5043 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 9.4780 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+C[C@H]1[C@H]([C@H](C[C@@H](O1)O[C@H]2C[C@@](CC3=C(C4=C(C(=C23)O)C(=O)C5=C(C4=O)C=CC=C5OC)O)(C(=O)CO)O)N)O + +> <PUBCHEM_IUPAC_NAME> +(7S,9S)-7-[(2R,4S,5S,6S)-4-amino-5-hydroxy-6-methyloxan-2-yl]oxy-6,9,11-trihydroxy-9-(2-hydroxyacetyl)-4-methoxy-8,10-dihydro-7H-tetracene-5,12-dione + +> <PUBCHEM_IUPAC_OPENEYE_NAME> +(7S,9S)-7-[(2R,4S,5S,6S)-4-amino-5-hydroxy-6-methyl-tetrahydropyran-2-yl]oxy-6,9,11-trihydroxy-9-(2-hydroxyacetyl)-4-methoxy-8,10-dihydro-7H-tetracene-5,12-dione + +> <PUBCHEM_IUPAC_CAS_NAME> +(7S,9S)-7-[[(2R,4S,5S,6S)-4-amino-5-hydroxy-6-methyl-2-oxanyl]oxy]-6,9,11-trihydroxy-9-(2-hydroxy-1-oxoethyl)-4-methoxy-8,10-dihydro-7H-tetracene-5,12-dione + +> <PUBCHEM_IUPAC_TRADITIONAL_NAME> +(7S,9S)-7-[(2R,4S,5S,6S)-4-amino-5-hydroxy-6-methyl-tetrahydropyran-2-yl]oxy-9-glycoloyl-6,9,11-trihydroxy-4-methoxy-8,10-dihydro-7H-tetracene-5,12-quinone + +> <PUBCHEM_IUPAC_SYSTEMATIC_NAME> +(7S,9S)-7-[(2R,4S,5S,6S)-4-azanyl-6-methyl-5-oxidanyl-oxan-2-yl]oxy-4-methoxy-6,9,11-tris(oxidanyl)-9-(2-oxidanylethanoyl)-8,10-dihydro-7H-tetracene-5,12-dione + +> <PUBCHEM_CACTVS_HBOND_DONOR> +6 + +> <PUBCHEM_CACTVS_HBOND_ACCEPTOR> +12 + +> <PUBCHEM_CACTVS_ROTATABLE_BOND> +5 + +> <PUBCHEM_CACTVS_COMPLEXITY> +977 + +> <PUBCHEM_CACTVS_TPSA> +206 + +> <PUBCHEM_CACTVS_SUBSKEYS> +AAADceB6PAAAAAAAAAAAAAAAAAAAAAAAAAA0YMGCAAAAAADBQAAAHgAQCAAADHzxmAcyDoBABgCIAqBSAAICCAAkIAAIiIFGCMgfNzaGtRqicWAn8BEPuYfL7PzOwQADAAAYAADCAAYQADAAAAAAAAAAAA== + +> <PUBCHEM_TOTAL_CHARGE> +0 + +> <PUBCHEM_HEAVY_ATOM_COUNT> +39 + +> <PUBCHEM_ATOM_DEF_STEREO_COUNT> +6 + +> <PUBCHEM_ATOM_UDEF_STEREO_COUNT> +0 + +> <PUBCHEM_BOND_DEF_STEREO_COUNT> +0 + +> <PUBCHEM_BOND_UDEF_STEREO_COUNT> +0 + +> <PUBCHEM_ISOTOPIC_ATOM_COUNT> +0 + +> <PUBCHEM_COMPONENT_COUNT> +1 + +> <PUBCHEM_CACTVS_TAUTO_COUNT> +81 + +> <PUBCHEM_COORDINATE_TYPE> +1 +3 + +> <PUBCHEM_BONDANNOTATIONS> +13 1 6 +19 1 6 +21 12 5 +17 18 8 +17 24 8 +18 26 8 +23 29 5 +24 27 8 +26 28 8 +27 28 8 +14 3 6 +33 34 8 +33 35 8 +34 36 8 +35 37 8 +36 38 8 +37 38 8 +22 4 5 + +$$$$ + diff --git a/graphics/mol2chemfig/docs/examples/eschers-cubane.tex b/graphics/mol2chemfig/docs/examples/eschers-cubane.tex new file mode 100644 index 0000000000..cd7711eb5c --- /dev/null +++ b/graphics/mol2chemfig/docs/examples/eschers-cubane.tex @@ -0,0 +1,33 @@ +\chemfig{ + \mcfatomno{1}% 1 + -[:90,2]\mcfatomno{2}% 2 + -[,2,,,draw=none]\mcfatomno{5}% 5 + -[:270,2]\mcfatomno{3}% 3 + ( + -[:180,2]\phantom{1}% -> 1 + ) + -[:45,1.131]\mcfatomno{7}% 7 + -[:180,2,,,draw=none]\mcfatomno{4}% 4 + ( + -[:225,1.131]\phantom{1}% -> 1 + ) + -[:90,2]\mcfatomno{6}% 6 + ( + -[:225,1.131]\phantom{2}% -> 2 + ) + -[,2]\mcfatomno{8}% 8 + ( + -[:225,1.131]\phantom{5}% -> 5 + ) + ( + -[:270,2]\phantom{7}% -> 7 + ) + ( + -[:195.9,2.912,,,draw=none]\phantom{2}% -> 2 + -[,2,,,mcfx={100}{10}]\phantom{5}% -> 5 + ) + ( + -[:270,2,,,draw=none]\phantom{7}% -> 7 + -[:180,2,,,mcfx={100}{10}]\phantom{4}% -> 4 + ) +} diff --git a/graphics/mol2chemfig/docs/examples/fmnh.mol b/graphics/mol2chemfig/docs/examples/fmnh.mol new file mode 100644 index 0000000000..048bc84d05 --- /dev/null +++ b/graphics/mol2chemfig/docs/examples/fmnh.mol @@ -0,0 +1,71 @@ + + Marvin 09131216222D + + 31 33 0 0 0 0 999 V2000 + -0.8545 -2.2393 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.5689 -2.6518 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.5689 -3.4768 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.8545 -3.8893 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.1400 -3.4768 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.1400 -2.6518 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.5745 -2.2393 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 0.5745 -3.8893 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 1.2889 -3.4768 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.2889 -2.6518 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.0034 -2.2393 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 2.0034 -3.8893 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.7179 -3.4768 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 2.7179 -2.6518 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.5745 -1.4143 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.1620 -0.6998 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.5745 0.0147 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.1620 0.7291 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.5745 1.4436 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.6630 -0.6998 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 1.3995 0.0147 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + -0.6630 0.7291 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 1.3995 1.4436 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 2.2245 1.4436 0.0000 P 0 0 0 0 0 0 0 0 0 0 0 0 + 3.0495 1.4436 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 2.2245 0.6186 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0 + 2.2245 2.2686 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0 + -2.2834 -2.2393 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.2834 -3.8893 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.0034 -4.7143 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 3.4323 -2.2393 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 1 6 2 0 0 0 0 + 2 3 2 0 0 0 0 + 3 4 1 0 0 0 0 + 4 5 2 0 0 0 0 + 7 6 1 0 0 0 0 + 6 5 1 0 0 0 0 + 5 8 1 0 0 0 0 + 7 10 1 0 0 0 0 + 8 9 1 0 0 0 0 + 11 10 2 0 0 0 0 + 10 9 1 0 0 0 0 + 9 12 1 0 0 0 0 + 11 14 1 0 0 0 0 + 12 13 1 0 0 0 0 + 13 14 1 0 0 0 0 + 7 15 1 0 0 0 0 + 15 16 1 0 0 0 0 + 16 17 1 0 0 0 0 + 17 18 1 0 0 0 0 + 18 19 1 0 0 0 0 + 16 20 1 0 0 0 0 + 17 21 1 0 0 0 0 + 18 22 1 0 0 0 0 + 19 23 1 0 0 0 0 + 23 24 1 0 0 0 0 + 24 25 2 0 0 0 0 + 24 26 1 0 0 0 0 + 24 27 1 0 0 0 0 + 2 28 1 0 0 0 0 + 3 29 1 0 0 0 0 + 12 30 2 0 0 0 0 + 14 31 2 0 0 0 0 +M CHG 2 26 -1 27 -1 +M RAD 1 9 2 +M END diff --git a/graphics/mol2chemfig/docs/examples/hand-coded-tex/aspirin.tex b/graphics/mol2chemfig/docs/examples/hand-coded-tex/aspirin.tex new file mode 100644 index 0000000000..576c9d8a43 --- /dev/null +++ b/graphics/mol2chemfig/docs/examples/hand-coded-tex/aspirin.tex @@ -0,0 +1,8 @@ +\definesubmol{acetyl}{(=[::60]O)-[::-60]H_3C} +\definesubmol{benzoate}{*6(-=-=-(-(=[::60]O)-[::-60]OH)=)}% + +\chemfig{ + {\color{red}O} % the oxygen in the middle + (-[:210]!{acetyl}) % treat one submol as a branch, + -[:-30]!{benzoate} % the other one as the main chain +} diff --git a/graphics/mol2chemfig/docs/examples/hand-coded-tex/caffeine.tex b/graphics/mol2chemfig/docs/examples/hand-coded-tex/caffeine.tex new file mode 100644 index 0000000000..8b49661938 --- /dev/null +++ b/graphics/mol2chemfig/docs/examples/hand-coded-tex/caffeine.tex @@ -0,0 +1 @@ +\chemfig{H_3C-[:30]N**6(-(=O)-(**5(-N(-CH_3)--N-))--N(-CH_3)-(=O)-)} diff --git a/graphics/mol2chemfig/docs/examples/hand-coded-tex/chemfig-settings.tex b/graphics/mol2chemfig/docs/examples/hand-coded-tex/chemfig-settings.tex new file mode 100644 index 0000000000..df543546d0 --- /dev/null +++ b/graphics/mol2chemfig/docs/examples/hand-coded-tex/chemfig-settings.tex @@ -0,0 +1,15 @@ +% reduce font size and use sans-serif for atoms +\renewcommand{\printatom}[1]{% +\fontsize{8pt}{10pt}\selectfont{\ensuremath{\mathsf{#1}}}} + +% reduce bond dimensions to match smaller fonts +\setchemfig{ + cram rectangle=false, + cram width=2.5pt, + cram dash width=0.4pt, + cram dash sep=1pt, + atom sep=16pt, + bond offset=1pt, + double bond sep=2pt +} + diff --git a/graphics/mol2chemfig/docs/examples/hand-coded-tex/sodium-green.png b/graphics/mol2chemfig/docs/examples/hand-coded-tex/sodium-green.png Binary files differnew file mode 100644 index 0000000000..0d8b8c9275 --- /dev/null +++ b/graphics/mol2chemfig/docs/examples/hand-coded-tex/sodium-green.png diff --git a/graphics/mol2chemfig/docs/examples/hand-coded-tex/sodium-green1.tex b/graphics/mol2chemfig/docs/examples/hand-coded-tex/sodium-green1.tex new file mode 100644 index 0000000000..84da34dd2c --- /dev/null +++ b/graphics/mol2chemfig/docs/examples/hand-coded-tex/sodium-green1.tex @@ -0,0 +1,9 @@ +\input{dcf-submol1} % load generated submolecules ... +\input{ce-submol1} + +\chemfig{ % and stitch them together + {\color{red}C} + (=[:45]O) + (-[:180,6]!{dcf1}) + -[:-90]!{ce1} +} diff --git a/graphics/mol2chemfig/docs/examples/hand-coded-tex/sodium-green2.tex b/graphics/mol2chemfig/docs/examples/hand-coded-tex/sodium-green2.tex new file mode 100644 index 0000000000..7cea9f0df7 --- /dev/null +++ b/graphics/mol2chemfig/docs/examples/hand-coded-tex/sodium-green2.tex @@ -0,0 +1,14 @@ +\input{dcf-submol2} +\input{ce-submol2} +\begin{center} +\begin{tikzpicture} +\node at(0,0){\chemfig{!{dcf2}}}; +\node at(3.0in,0){\chemfig{!{ce2}}}; +\end{tikzpicture} +\end{center} +%\chemfig{ +% {\color{red}C} +% (=[:45]O) +% (-[:180,6]!{dcf2}) +% -[:-90]!{ce2} +%} diff --git a/graphics/mol2chemfig/docs/examples/hand-coded-tex/sodium-green3.tex b/graphics/mol2chemfig/docs/examples/hand-coded-tex/sodium-green3.tex new file mode 100644 index 0000000000..501995ab65 --- /dev/null +++ b/graphics/mol2chemfig/docs/examples/hand-coded-tex/sodium-green3.tex @@ -0,0 +1,12 @@ +\input{dcf-submol3} +\input{ce-submol3} + +\chemfig{ + {\color{red}C} + (=[:225]O) + (-[:90]!{dcf3}) + -!{ce3} + -{\color{blue}C} + (=[:-45]O) + -[:90]!{dcf3} +} diff --git a/graphics/mol2chemfig/docs/examples/hand-coded-tex/stuff.tex b/graphics/mol2chemfig/docs/examples/hand-coded-tex/stuff.tex new file mode 100644 index 0000000000..c22fbd3373 --- /dev/null +++ b/graphics/mol2chemfig/docs/examples/hand-coded-tex/stuff.tex @@ -0,0 +1,8 @@ +\definesubmol{acetyl}{(=[::60]O)-[::-60]H_3C} +\definesubmol{benzoate}{*6(-=-=-(-(=[::60]O)-[::-60]OH)=)}% + +\chemfig{ + {\color{red}O} % the oxygen in the middle + (-[:210]!{acetyl}) % treat one submol as a branch, + -[:-30]!{benzoate}% % the other one as the main chain +} diff --git a/graphics/mol2chemfig/docs/examples/hand-coded-tex/twisted-commented.tex b/graphics/mol2chemfig/docs/examples/hand-coded-tex/twisted-commented.tex new file mode 100644 index 0000000000..dfe0fdb3a7 --- /dev/null +++ b/graphics/mol2chemfig/docs/examples/hand-coded-tex/twisted-commented.tex @@ -0,0 +1,25 @@ +% used options: used options: -w -t 2 (no cross bond) +\chemfig{ + % 1 + -[,1.414]% 2 + -[:225,2]% 4 + -[,1.414]% 3 + ( + -[:135,2]% -> 1 + ) +} + +% added option: --cross-bond 2-4 +\chemfig{ + % 1 + -[,1.414]% 2 + -[:225,2,,,draw=none]% 4 bond 2 -> 4 is not rendered at first + -[,1.414]% 3 + ( + -[:135,2]% -> 1 + ) + (% append cross bond to end of molecule + -[:90,1.414,,,draw=none]% -> 2 - invisible bond moves the pen to atom 2 + -[:225,2,,,mcfcrossbond]% -> 4 - the cross bond is rendered, applying + )% the mcfcrossbond tikz key +} diff --git a/graphics/mol2chemfig/docs/examples/morphine-f.sh b/graphics/mol2chemfig/docs/examples/morphine-f.sh new file mode 100755 index 0000000000..bd4b560de5 --- /dev/null +++ b/graphics/mol2chemfig/docs/examples/morphine-f.sh @@ -0,0 +1 @@ +mol2chemfig -f -w morphine.mol > morphine-f.tex diff --git a/graphics/mol2chemfig/docs/examples/morphine-f.tex b/graphics/mol2chemfig/docs/examples/morphine-f.tex new file mode 100644 index 0000000000..3557709128 --- /dev/null +++ b/graphics/mol2chemfig/docs/examples/morphine-f.tex @@ -0,0 +1,40 @@ +\chemfig{ + HO% 16 + -[:60,,2]% 13 + -[:120,,,,drh]% 12 + -[:60]% 11 + -[,,,,drh]% 8 + -[:60]% 7 + -% 10 + -[:300]% 1 + -% 6 + -[:300,,,,drh]% 5 + -[:240]% 4 + ( + -[:300,,,1]OH% 17 + ) + -[:180]% 3 + -[:120]% 2 + ( + -[:60]% -> 1 + ) + ( + -[:180]% 9 + ( + -[:120]% -> 8 + ) + -[:240,,,,drh]% 14 + ( + -[:327.1,1.233]O% 15 + -[:34.8,1.174]% -> 3 + ) + -[:180]% -> 13 + ) + -[:123.3,0.928]% 19 + -[:89.9,1.239]% 20 + -[:30.1,1.163]N% 18 + ( + -[:240]% -> 10 + ) + -[:37.5]% 21 +} diff --git a/graphics/mol2chemfig/docs/examples/morphine-k.sh b/graphics/mol2chemfig/docs/examples/morphine-k.sh new file mode 100755 index 0000000000..a280f43747 --- /dev/null +++ b/graphics/mol2chemfig/docs/examples/morphine-k.sh @@ -0,0 +1 @@ +mol2chemfig -k 19-20 -wf morphine.mol > morphine-k.tex diff --git a/graphics/mol2chemfig/docs/examples/morphine-k.tex b/graphics/mol2chemfig/docs/examples/morphine-k.tex new file mode 100644 index 0000000000..bb75634e18 --- /dev/null +++ b/graphics/mol2chemfig/docs/examples/morphine-k.tex @@ -0,0 +1,44 @@ +\chemfig{ + HO% 16 + -[:60,,2]% 13 + -[:120,,,,drh]% 12 + -[:60]% 11 + -[,,,,drh]% 8 + -[:60]% 7 + -% 10 + -[:300]% 1 + -% 6 + -[:300,,,,drh]% 5 + -[:240]% 4 + ( + -[:300,,,1]OH% 17 + ) + -[:180]% 3 + -[:120]% 2 + ( + -[:60]% -> 1 + ) + ( + -[:180]% 9 + ( + -[:120]% -> 8 + ) + -[:240,,,,drh]% 14 + ( + -[:327.1,1.233]O% 15 + -[:34.8,1.174]% -> 3 + ) + -[:180]% -> 13 + ) + -[:123.3,0.928]% 19 + -[:89.9,1.239,,,draw=none]% 20 + -[:30.1,1.163]N% 18 + ( + -[:240]% -> 10 + ) + -[:37.5]% 21 + ( + -[:233.4,3.026,,,draw=none]% -> 19 + -[:89.9,1.239,,,mcfx={10}{10}]% -> 20 + ) +} diff --git a/graphics/mol2chemfig/docs/examples/morphine-n.sh b/graphics/mol2chemfig/docs/examples/morphine-n.sh new file mode 100755 index 0000000000..d2c76db071 --- /dev/null +++ b/graphics/mol2chemfig/docs/examples/morphine-n.sh @@ -0,0 +1 @@ +mol2chemfig -n -w morphine.mol > morphine-n.tex diff --git a/graphics/mol2chemfig/docs/examples/morphine-n.tex b/graphics/mol2chemfig/docs/examples/morphine-n.tex new file mode 100644 index 0000000000..3ad8cc6d48 --- /dev/null +++ b/graphics/mol2chemfig/docs/examples/morphine-n.tex @@ -0,0 +1,40 @@ +\chemfig{ + \mcfleft{\mcfatomno{16}}{O}% 16 + -[:60]\mcfatomno{13}% 13 + =_[:120]\mcfatomno{12}% 12 + -[:60]\mcfatomno{11}% 11 + =_\mcfatomno{8}% 8 + -[:60]\mcfatomno{7}% 7 + -\mcfatomno{10}% 10 + -[:300]\mcfatomno{1}% 1 + -\mcfatomno{6}% 6 + =_[:300]\mcfatomno{5}% 5 + -[:240]\mcfatomno{4}% 4 + ( + -[:300]\mcfright{O}{\mcfatomno{17}}% 17 + ) + -[:180]\mcfatomno{3}% 3 + -[:120]\mcfatomno{2}% 2 + ( + -[:60]\phantom{1}% -> 1 + ) + ( + -[:180]\mcfatomno{9}% 9 + ( + -[:120]\phantom{8}% -> 8 + ) + =_[:240]\mcfatomno{14}% 14 + ( + -[:327.1,1.233]\mcfbelow{O}{\mcfatomno{15}}% 15 + -[:34.8,1.174]\phantom{3}% -> 3 + ) + -[:180]\phantom{13}% -> 13 + ) + -[:123.3,0.928]\mcfatomno{19}% 19 + -[:89.9,1.239]\mcfatomno{20}% 20 + -[:30.1,1.163]\mcfabove{N}{\mcfatomno{18}}% 18 + ( + -[:240]\phantom{10}% -> 10 + ) + -[:37.5]\mcfatomno{21}% 21 +} diff --git a/graphics/mol2chemfig/docs/examples/morphine.mol b/graphics/mol2chemfig/docs/examples/morphine.mol new file mode 100644 index 0000000000..4d17710747 --- /dev/null +++ b/graphics/mol2chemfig/docs/examples/morphine.mol @@ -0,0 +1,51 @@ +5288826 + Marvin 05021316212D + + 21 25 0 0 1 0 999 V2000 + 11.4469 1.8931 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 11.0344 1.1786 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 11.4469 0.4641 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 12.2719 0.4641 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 12.6844 1.1786 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 12.2719 1.8930 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 10.2094 2.6076 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 9.7969 1.8931 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 10.2094 1.1786 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 11.0344 2.6075 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 8.9719 1.8930 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 8.5594 1.1786 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 8.9719 0.4641 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 9.7969 0.4641 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 10.6513 -0.0886 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 8.5594 -0.2504 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 12.6844 -0.2504 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 11.4469 3.3220 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 10.6145 1.8189 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 10.6166 2.8411 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 12.1014 3.8242 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2 3 1 0 0 0 0 + 3 4 1 0 0 0 0 + 4 5 1 0 0 0 0 + 5 6 2 0 0 0 0 + 1 6 1 0 0 0 0 + 1 10 1 0 0 0 0 + 2 1 1 0 0 0 0 + 9 2 1 0 0 0 0 + 7 8 1 0 0 0 0 + 7 10 1 0 0 0 0 + 14 9 2 0 0 0 0 + 8 9 1 0 0 0 0 + 8 11 2 0 0 0 0 + 11 12 1 0 0 0 0 + 12 13 2 0 0 0 0 + 13 14 1 0 0 0 0 + 14 15 1 0 0 0 0 + 3 15 1 0 0 0 0 + 13 16 1 0 0 0 0 + 4 17 1 0 0 0 0 + 10 18 1 0 0 0 0 + 2 19 1 0 0 0 0 + 18 20 1 0 0 0 0 + 20 19 1 0 0 0 0 + 18 21 1 0 0 0 0 +M END diff --git a/graphics/mol2chemfig/docs/examples/morphine.sh b/graphics/mol2chemfig/docs/examples/morphine.sh new file mode 100755 index 0000000000..e0b0319867 --- /dev/null +++ b/graphics/mol2chemfig/docs/examples/morphine.sh @@ -0,0 +1 @@ +mol2chemfig -w morphine.mol > morphine.tex diff --git a/graphics/mol2chemfig/docs/examples/morphine.tex b/graphics/mol2chemfig/docs/examples/morphine.tex new file mode 100644 index 0000000000..ba80f885ba --- /dev/null +++ b/graphics/mol2chemfig/docs/examples/morphine.tex @@ -0,0 +1,40 @@ +\chemfig{ + HO% 16 + -[:60,,2]% 13 + =_[:120]% 12 + -[:60]% 11 + =_% 8 + -[:60]% 7 + -% 10 + -[:300]% 1 + -% 6 + =_[:300]% 5 + -[:240]% 4 + ( + -[:300,,,1]OH% 17 + ) + -[:180]% 3 + -[:120]% 2 + ( + -[:60]% -> 1 + ) + ( + -[:180]% 9 + ( + -[:120]% -> 8 + ) + =_[:240]% 14 + ( + -[:327.1,1.233]O% 15 + -[:34.8,1.174]% -> 3 + ) + -[:180]% -> 13 + ) + -[:123.3,0.928]% 19 + -[:89.9,1.239]% 20 + -[:30.1,1.163]N% 18 + ( + -[:240]% -> 10 + ) + -[:37.5]% 21 +} diff --git a/graphics/mol2chemfig/docs/examples/mp.mol b/graphics/mol2chemfig/docs/examples/mp.mol new file mode 100644 index 0000000000..5dcb270ade --- /dev/null +++ b/graphics/mol2chemfig/docs/examples/mp.mol @@ -0,0 +1,42 @@ + + Marvin 10271217122D + + 17 20 0 0 0 0 999 V2000 + -1.2670 -1.7089 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.9814 -2.1214 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.9814 -2.9464 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.2670 -3.3589 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.5525 -2.9464 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.5525 -2.1214 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.5525 -0.4714 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.2670 -0.8839 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.1620 -1.7089 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.1620 -0.8839 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.9814 -0.4714 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.6959 -0.8839 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.6959 -1.7089 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.2670 0.7661 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.9814 0.3536 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.5525 0.3536 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.2670 1.5911 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2 3 2 0 0 0 0 + 3 4 1 0 0 0 0 + 4 5 2 0 0 0 0 + 5 6 1 0 0 0 0 + 6 9 1 0 0 0 0 + 1 6 2 0 0 0 0 + 7 10 1 0 0 0 0 + 9 10 2 0 0 0 0 + 8 1 1 0 0 0 0 + 1 2 1 0 0 0 0 + 13 2 1 0 0 0 0 + 11 12 1 0 0 0 0 + 12 13 2 0 0 0 0 + 15 11 1 0 0 0 0 + 11 8 2 0 0 0 0 + 8 7 1 0 0 0 0 + 7 16 2 0 0 0 0 + 14 15 2 0 0 0 0 + 14 16 1 0 0 0 0 + 14 17 1 0 0 0 0 +M END diff --git a/graphics/mol2chemfig/docs/examples/mp.sh b/graphics/mol2chemfig/docs/examples/mp.sh new file mode 100755 index 0000000000..4e9ab919ec --- /dev/null +++ b/graphics/mol2chemfig/docs/examples/mp.sh @@ -0,0 +1 @@ +mol2chemfig -f -l mp -g mp -a 270 mp.mol > mp.tex diff --git a/graphics/mol2chemfig/docs/examples/mp.tex b/graphics/mol2chemfig/docs/examples/mp.tex new file mode 100644 index 0000000000..9b94d693ef --- /dev/null +++ b/graphics/mol2chemfig/docs/examples/mp.tex @@ -0,0 +1,31 @@ +\definesubmol{mp}{ + @{mp17}% + -[@{mp14-17}:180]@{mp14}% + -[@{mp14-15}:120,,,,dlh]@{mp15}% + -[@{mp11-15}:180]@{mp11}% + -[@{mp11-12}:120]@{mp12}% + -[@{mp12-13}:180,,,,dlh]@{mp13}% + -[@{mp2-13}:240]@{mp2}% + -[@{mp2-3}:180,,,,dlh]@{mp3}% + -[@{mp3-4}:240]@{mp4}% + -[@{mp4-5}:300,,,,dlh]@{mp5}% + -[@{mp5-6}]@{mp6}% + -[@{mp6-9}:300]@{mp9}% + -[@{mp9-10},,,,dlh]@{mp10}% + -[@{mp7-10}:60]@{mp7}% + ( + -[@{mp7-16},,,,dlh]@{mp16}% + -[@{mp14-16}:60]% -> 14 + ) + -[@{mp7-8}:120]@{mp8}% + ( + -[@{mp8-11}:60,,,,dlh]% -> 11 + ) + -[@{mp1-8}:180]@{mp1}% + ( + -[@{mp1-6}:240,,,,dlh]% -> 6 + ) + ( + -[@{mp1-2}:120]% -> 2 + ) +} diff --git a/graphics/mol2chemfig/docs/examples/mp06900.pdf b/graphics/mol2chemfig/docs/examples/mp06900.pdf Binary files differnew file mode 100644 index 0000000000..687989258f --- /dev/null +++ b/graphics/mol2chemfig/docs/examples/mp06900.pdf diff --git a/graphics/mol2chemfig/docs/examples/optionlist.tex b/graphics/mol2chemfig/docs/examples/optionlist.tex new file mode 100644 index 0000000000..0b0d1b2a3b --- /dev/null +++ b/graphics/mol2chemfig/docs/examples/optionlist.tex @@ -0,0 +1,115 @@ +mol2chemfig v. 1.5, by Eric Brefo-Mensah and Michael Palmer +mol2chemfig generates chemfig code from molfiles. Usage example: + +mol2chemfig --angle=45 --aromatic-circles somefile.mol + +Options: +-h, --help Print help message and exit (Default: + False) + +-b, --version Print program version and exit (Default: + False) + +-i, --input How to interpret the argument. With 'file', + mol2chemfig expects a filename. With + 'direct', the argument is intrepreted + directly; don't forget to put quotes around + it. With 'pubchem', the argument is treated + as an identifier for the PubChem database. + (Default: file) + +-z, --terse Remove all whitespace and comments from the + output. If you can still read it + afterwards, Bill Gates wants your resume + (Default: False) + +-r, --strict Abide by Indigo's chemical structure + validation. If true, mol2chemfig will fail + if Indigo reports that something is wrong + with the molecule, like a carbon with five + bonds. If false, mol2chemfig will ignore + such errors (Default: True) + +-d, --indent Number of spaces to use for indenting + molecule branches in generated code. + Without effect when 'terse' option is + passed. Affects only the generated tex + code, not the rendered molecule (Default: + 4) + +-u, --recalculate-coordinates Discard existing coordinate and calculate + new ones from covalent structure. For + smiles input, this is performed implicitly + (Default: False) + +-a, --angle Rotate molecule counterclockwise by this + angle (Default: 0.0) + +-v, --relative-angles Use relative bond angles (Default: False) + +-p, --flip Flip the structure horizontally (Default: + False) + +-q, --flop Flip the structure vertically (Default: + False) + +-c, --show-carbons Show element symbol for carbon atoms + (Default: False) + +-m, --show-methyls Show element symbols for methyl groups + (implied if show-carbons is True) (Default: + False) + +-y, --hydrogens How to deal with explicit hydrogen atoms. + One of 'keep', 'add' or 'delete'. Note that + 'add' will also trigger calculation of new + coordinates for the entire molecule. Option + 'keep' does nothing (Default: keep) + +-o, --aromatic-circles Draw circles instead of double bonds inside + aromatic rings (Default: False) + +-f, --fancy-bonds Draw fancier double and triple bonds + (Default: False) + +-g, --markers Give each atom and each bond a unique + marker that can be used for attaching + electron movement arrows. With value 'a', + atom 2 will be labeled @{a2}, and its bond + to atom 5 @{a2-5}. (Default: None) + +-n, --atom-numbers Show the molfile number of each atom next + to it. When this option is set, charges and + implicit hydrogens will not be shown + (Default: False) + +-s, --bond-scale How to scale the lengths of bonds (one of + 'keep', 'scale', or 'normalize') (Default: + normalize) + +-t, --bond-stretch Used as scaling factor (with --bond- + scale=scale) or average (with --bond- + scale=normalize) for bond lengths (Default: + 1.0) + +-w, --wrap-chemfig Wrap generated code into \chemfig{...} + command (Default: False) + +-l, --submol-name If a name is given, wrap generated code + into chemfig \definesubmol{name}{...} + command (Default: None) + +-e, --entry-atom Number of first atom to be rendered. + Relevant only if generated code is to be + used as sub-molecule (Default: None) + +-x, --exit-atom Number of last atom to be rendered. + Relevant only if generated code is to be + used as sub-molecule (Default: None) + +-k, --cross-bond Specify bonds that should be drawn on top + of others they cross over. Give the start + and the end atoms. Example for one bond: + --cross-bond=5-6 Example for two bonds: + --crossbond=4-8,12-13 (Default: None) + diff --git a/graphics/mol2chemfig/docs/examples/packmoles.sh b/graphics/mol2chemfig/docs/examples/packmoles.sh new file mode 100755 index 0000000000..6aee669191 --- /dev/null +++ b/graphics/mol2chemfig/docs/examples/packmoles.sh @@ -0,0 +1 @@ +zip example-mol.zip *.mol *.smi *.sdf diff --git a/graphics/mol2chemfig/docs/examples/phenol-add-h.sh b/graphics/mol2chemfig/docs/examples/phenol-add-h.sh new file mode 100755 index 0000000000..5701daf90e --- /dev/null +++ b/graphics/mol2chemfig/docs/examples/phenol-add-h.sh @@ -0,0 +1 @@ +mol2chemfig -y add -w -i direct 'C1=CC=C(C=C1)O' > phenol-with-hydrogens.tex
\ No newline at end of file diff --git a/graphics/mol2chemfig/docs/examples/phenol-as-submol.sh b/graphics/mol2chemfig/docs/examples/phenol-as-submol.sh new file mode 100755 index 0000000000..59f11e2cf2 --- /dev/null +++ b/graphics/mol2chemfig/docs/examples/phenol-as-submol.sh @@ -0,0 +1 @@ +mol2chemfig -l phenol -i direct 'C1=CC=C(C=C1)O' > phenol-as-submol.tex
\ No newline at end of file diff --git a/graphics/mol2chemfig/docs/examples/phenol-as-submol.tex b/graphics/mol2chemfig/docs/examples/phenol-as-submol.tex new file mode 100644 index 0000000000..b51ef95581 --- /dev/null +++ b/graphics/mol2chemfig/docs/examples/phenol-as-submol.tex @@ -0,0 +1,12 @@ +\definesubmol{phenol}{ + HO% 7 + -[,,2]% 4 + =^[:300]% 3 + -% 2 + =^[:60]% 1 + -[:120]% 6 + =^[:180]% 5 + ( + -[:240]% -> 4 + ) +} diff --git a/graphics/mol2chemfig/docs/examples/phenol-from-smiles-w.sh b/graphics/mol2chemfig/docs/examples/phenol-from-smiles-w.sh new file mode 100755 index 0000000000..6f25cbdde4 --- /dev/null +++ b/graphics/mol2chemfig/docs/examples/phenol-from-smiles-w.sh @@ -0,0 +1 @@ +mol2chemfig -w -i direct 'C1=CC=C(C=C1)O' > phenol-smi-wrapped.tex
\ No newline at end of file diff --git a/graphics/mol2chemfig/docs/examples/phenol-from-smiles-wz.sh b/graphics/mol2chemfig/docs/examples/phenol-from-smiles-wz.sh new file mode 100755 index 0000000000..97c218a62f --- /dev/null +++ b/graphics/mol2chemfig/docs/examples/phenol-from-smiles-wz.sh @@ -0,0 +1 @@ +mol2chemfig -zw -i direct 'C1=CC=C(C=C1)O' > phenol-smi-terse.tex
\ No newline at end of file diff --git a/graphics/mol2chemfig/docs/examples/phenol-from-smiles.sh b/graphics/mol2chemfig/docs/examples/phenol-from-smiles.sh new file mode 100755 index 0000000000..5e1df1db25 --- /dev/null +++ b/graphics/mol2chemfig/docs/examples/phenol-from-smiles.sh @@ -0,0 +1 @@ +mol2chemfig -i direct 'C1=CC=C(C=C1)O' > phenol-smi.tex
\ No newline at end of file diff --git a/graphics/mol2chemfig/docs/examples/phenol-smi-terse.tex b/graphics/mol2chemfig/docs/examples/phenol-smi-terse.tex new file mode 100644 index 0000000000..3793a018c5 --- /dev/null +++ b/graphics/mol2chemfig/docs/examples/phenol-smi-terse.tex @@ -0,0 +1 @@ +\chemfig{HO-[,,2]=^[:300]-=^[:60]-[:120]=^[:180](-[:240])} diff --git a/graphics/mol2chemfig/docs/examples/phenol-smi-wrapped.tex b/graphics/mol2chemfig/docs/examples/phenol-smi-wrapped.tex new file mode 100644 index 0000000000..c6f70ef10e --- /dev/null +++ b/graphics/mol2chemfig/docs/examples/phenol-smi-wrapped.tex @@ -0,0 +1,12 @@ +\chemfig{ + HO% 7 + -[,,2]% 4 + =^[:300]% 3 + -% 2 + =^[:60]% 1 + -[:120]% 6 + =^[:180]% 5 + ( + -[:240]% -> 4 + ) +} diff --git a/graphics/mol2chemfig/docs/examples/phenol-smi.tex b/graphics/mol2chemfig/docs/examples/phenol-smi.tex new file mode 100644 index 0000000000..0bc164867d --- /dev/null +++ b/graphics/mol2chemfig/docs/examples/phenol-smi.tex @@ -0,0 +1,10 @@ + HO% 7 + -[,,2]% 4 + =^[:300]% 3 + -% 2 + =^[:60]% 1 + -[:120]% 6 + =^[:180]% 5 + ( + -[:240]% -> 4 + ) diff --git a/graphics/mol2chemfig/docs/examples/phenol-with-hydrogens.tex b/graphics/mol2chemfig/docs/examples/phenol-with-hydrogens.tex new file mode 100644 index 0000000000..c831a20d4b --- /dev/null +++ b/graphics/mol2chemfig/docs/examples/phenol-with-hydrogens.tex @@ -0,0 +1,26 @@ +\chemfig{ + H% 8 + -[:180]% 1 + =_[:240]% 2 + ( + -[:300]H% 9 + ) + -[:180]% 3 + ( + -[:240]H% 10 + ) + =_[:120]% 4 + ( + -[:180]O% 7 + -[:120]H% 13 + ) + -[:60]% 5 + ( + -[:120]H% 11 + ) + =_% 6 + ( + -[:300]% -> 1 + ) + -[:60]H% 12 +} diff --git a/graphics/mol2chemfig/docs/examples/plp-arrows.sh b/graphics/mol2chemfig/docs/examples/plp-arrows.sh new file mode 100755 index 0000000000..1095711b9f --- /dev/null +++ b/graphics/mol2chemfig/docs/examples/plp-arrows.sh @@ -0,0 +1,2 @@ +mol2chemfig -f -l plp plp.mol > plp.tex +mol2chemfig -f -l plp2 plp2.mol > plp2.tex
\ No newline at end of file diff --git a/graphics/mol2chemfig/docs/examples/plp.mol b/graphics/mol2chemfig/docs/examples/plp.mol new file mode 100644 index 0000000000..09f686e869 --- /dev/null +++ b/graphics/mol2chemfig/docs/examples/plp.mol @@ -0,0 +1,48 @@ + + Marvin 09131213202D + + 21 21 0 0 0 0 999 V2000 + -3.2411 0.2063 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -3.9555 -0.2062 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -3.9555 -1.0313 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -3.2411 -1.4438 0.0000 N 0 3 0 0 0 0 0 0 0 0 0 0 + -2.5266 -1.0313 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.5266 -0.2062 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.8121 -1.4438 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.8121 0.2063 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0 + -4.6700 0.2063 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -5.3845 -0.2062 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + -6.2095 -0.2062 0.0000 P 0 0 0 0 0 0 0 0 0 0 0 0 + -7.0345 -0.2062 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + -6.2095 -1.0312 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0 + -6.2095 0.6188 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0 + -3.2411 1.0313 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.5266 1.4438 0.0000 N 0 3 0 0 0 0 0 0 0 0 0 0 + -2.5266 2.2688 0.0000 C 0 5 0 0 0 0 0 0 0 0 0 0 + -1.8121 2.6813 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -3.2411 2.6813 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.8121 3.5063 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + -1.0977 2.2688 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 1 6 2 0 0 0 0 + 2 3 2 0 0 0 0 + 3 4 1 0 0 0 0 + 4 5 2 0 0 0 0 + 5 6 1 0 0 0 0 + 5 7 1 0 0 0 0 + 6 8 1 0 0 0 0 + 2 9 1 0 0 0 0 + 9 10 1 0 0 0 0 + 10 11 1 0 0 0 0 + 11 12 2 0 0 0 0 + 11 13 1 0 0 0 0 + 11 14 1 0 0 0 0 + 1 15 1 0 0 0 0 + 15 16 2 0 0 0 0 + 16 17 1 0 0 0 0 + 17 18 1 0 0 0 0 + 17 19 1 0 0 0 0 + 18 20 2 0 0 0 0 + 18 21 1 0 0 0 0 +M CHG 7 4 1 8 -1 13 -1 14 -1 16 1 17 -1 21 -1 +M END diff --git a/graphics/mol2chemfig/docs/examples/plp.sh b/graphics/mol2chemfig/docs/examples/plp.sh new file mode 100755 index 0000000000..a351f09bc3 --- /dev/null +++ b/graphics/mol2chemfig/docs/examples/plp.sh @@ -0,0 +1,2 @@ +mol2chemfig -f --submol-name plp plp.mol > plp.tex +mol2chemfig -f --submol-name plp2 plp2.mol > plp2.tex
\ No newline at end of file diff --git a/graphics/mol2chemfig/docs/examples/plp.tex b/graphics/mol2chemfig/docs/examples/plp.tex new file mode 100644 index 0000000000..6dd82a1146 --- /dev/null +++ b/graphics/mol2chemfig/docs/examples/plp.tex @@ -0,0 +1,38 @@ +\definesubmol{plp}{ + % 7 + -[:150]% 5 + -[:210,,,,drhs]\mcfbelowright{N}{H}{^{\mcfplus}}% 4 + -[:150]% 3 + -[:90,,,,drh]% 2 + ( + -[:150]% 9 + -[:210]O% 10 + -[:180]P% 11 + ( + -[:270]\mcfright{O}{^{\mcfminus}}% 13 + ) + ( + -[:90]\mcfright{O}{^{\mcfminus}}% 14 + ) + =[:180]O% 12 + ) + -[:30]% 1 + ( + -[:330,,,,drh]% 6 + ( + -[:30]\mcfright{O}{^{\mcfminus}}% 8 + ) + -[:270]% -> 5 + ) + -[:90]% 15 + -[:30,,,1,dlhs]NH^{\mcfplus}% 16 + -[:90,,1]\mcfabove{C}{_{\mcfminus}}% 17 + ( + -[:150]% 19 + ) + -[:30]% 18 + ( + =[:90]O% 20 + ) + -[:330]\mcfright{O}{^{\mcfminus}}% 21 +} diff --git a/graphics/mol2chemfig/docs/examples/plp2.mol b/graphics/mol2chemfig/docs/examples/plp2.mol new file mode 100644 index 0000000000..8d1459f4fd --- /dev/null +++ b/graphics/mol2chemfig/docs/examples/plp2.mol @@ -0,0 +1,48 @@ + + Marvin 09131213192D + + 21 21 0 0 0 0 999 V2000 + -3.2411 0.2063 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -3.9555 -0.2062 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -3.9555 -1.0313 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -3.2411 -1.4438 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + -2.5266 -1.0313 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.5266 -0.2062 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.8121 -1.4438 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.8121 0.2063 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0 + -4.6700 0.2063 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -5.3845 -0.2062 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + -6.2095 -0.2062 0.0000 P 0 0 0 0 0 0 0 0 0 0 0 0 + -7.0345 -0.2062 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + -6.2095 -1.0312 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0 + -6.2095 0.6188 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0 + -3.2411 1.0313 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.5266 1.4438 0.0000 N 0 3 0 0 0 0 0 0 0 0 0 0 + -2.5266 2.2688 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.8121 2.6813 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -3.2411 2.6813 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.8121 3.5063 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + -1.0977 2.2688 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 1 6 1 0 0 0 0 + 2 3 2 0 0 0 0 + 3 4 1 0 0 0 0 + 4 5 1 0 0 0 0 + 5 6 2 0 0 0 0 + 5 7 1 0 0 0 0 + 6 8 1 0 0 0 0 + 2 9 1 0 0 0 0 + 9 10 1 0 0 0 0 + 10 11 1 0 0 0 0 + 11 12 2 0 0 0 0 + 11 13 1 0 0 0 0 + 11 14 1 0 0 0 0 + 1 15 2 0 0 0 0 + 15 16 1 0 0 0 0 + 16 17 2 0 0 0 0 + 17 18 1 0 0 0 0 + 17 19 1 0 0 0 0 + 18 20 2 0 0 0 0 + 18 21 1 0 0 0 0 +M CHG 5 8 -1 13 -1 14 -1 16 1 21 -1 +M END diff --git a/graphics/mol2chemfig/docs/examples/plp2.tex b/graphics/mol2chemfig/docs/examples/plp2.tex new file mode 100644 index 0000000000..c0d352a655 --- /dev/null +++ b/graphics/mol2chemfig/docs/examples/plp2.tex @@ -0,0 +1,38 @@ +\definesubmol{plp2}{ + % 7 + -[:150]% 5 + -[:210]\mcfbelow{N}{H}% 4 + -[:150]% 3 + -[:90,,,,drh]% 2 + ( + -[:150]% 9 + -[:210]O% 10 + -[:180]P% 11 + ( + -[:270]\mcfright{O}{^{\mcfminus}}% 13 + ) + ( + -[:90]\mcfright{O}{^{\mcfminus}}% 14 + ) + =[:180]O% 12 + ) + -[:30]% 1 + ( + -[:330]% 6 + ( + -[:30]\mcfright{O}{^{\mcfminus}}% 8 + ) + -[:270,,,,drh]% -> 5 + ) + -[:90,,,,drh]% 15 + -[:30,,,1]NH^{\mcfplus}% 16 + =[:90,,1]% 17 + ( + -[:150]% 19 + ) + -[:30]% 18 + ( + =[:90]O% 20 + ) + -[:330]\mcfright{O}{^{\mcfminus}}% 21 +} diff --git a/graphics/mol2chemfig/docs/examples/printoptions.sh b/graphics/mol2chemfig/docs/examples/printoptions.sh new file mode 100755 index 0000000000..eade23b8f8 --- /dev/null +++ b/graphics/mol2chemfig/docs/examples/printoptions.sh @@ -0,0 +1 @@ +mol2chemfig 2> optionlist.tex
\ No newline at end of file diff --git a/graphics/mol2chemfig/docs/examples/setbondstyle.tex b/graphics/mol2chemfig/docs/examples/setbondstyle.tex new file mode 100644 index 0000000000..792ee3aae7 --- /dev/null +++ b/graphics/mol2chemfig/docs/examples/setbondstyle.tex @@ -0,0 +1,2 @@ +\setbondstyle[draw=magenta!50,-,line width=3pt,shorten <=2pt,shorten >=2pt]% + {draw=black,line width=0.5pt}
\ No newline at end of file diff --git a/graphics/mol2chemfig/docs/examples/twisted.mol b/graphics/mol2chemfig/docs/examples/twisted.mol new file mode 100644 index 0000000000..0dca2407ae --- /dev/null +++ b/graphics/mol2chemfig/docs/examples/twisted.mol @@ -0,0 +1,13 @@ + + Marvin 01131309442D + + 4 4 0 0 0 0 999 V2000 + -1.6058 0.4862 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.7808 0.4862 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.7808 -0.3388 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.6058 -0.3388 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 3 4 1 0 0 0 0 + 3 1 1 0 0 0 0 + 2 4 1 0 0 0 0 +M END diff --git a/graphics/mol2chemfig/docs/examples/twisted.sh b/graphics/mol2chemfig/docs/examples/twisted.sh new file mode 100755 index 0000000000..930bcb37e0 --- /dev/null +++ b/graphics/mol2chemfig/docs/examples/twisted.sh @@ -0,0 +1,3 @@ +mol2chemfig -t 2 -wn twisted.mol > twisted-n.tex +mol2chemfig -t 2 -w twisted.mol > twisted-simple.tex +mol2chemfig -t 2 -w -k 2-4 twisted.mol > twisted-k.tex |