biotite 1.5.0__cp313-cp313-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl

biotite/sequence/graphics/color_schemes/3di_flower.json

@@ -0,0 +1,48 @@
+{
+    "comment": "Generated with 'gecos --matrix 3Di --name flower --lmin 60 --lmax 80 -f 3di_flower.json'",
+    "name": "flower",
+    "alphabet": [
+        "a",
+        "c",
+        "d",
+        "e",
+        "f",
+        "g",
+        "h",
+        "i",
+        "k",
+        "l",
+        "m",
+        "n",
+        "p",
+        "q",
+        "r",
+        "s",
+        "t",
+        "v",
+        "w",
+        "y"
+    ],
+    "colors": {
+        "a": "#a189a1",
+        "c": "#ff5806",
+        "d": "#ab9a93",
+        "e": "#e754d5",
+        "f": "#8191b5",
+        "g": "#cbc7ae",
+        "h": "#dac1bc",
+        "i": "#5eaf6e",
+        "k": "#04c1fd",
+        "l": "#ff544b",
+        "m": "#07e560",
+        "n": "#f28d05",
+        "p": "#b68767",
+        "q": "#bc8277",
+        "r": "#eebe86",
+        "s": "#ffa103",
+        "t": "#a4c49a",
+        "v": "#ed6903",
+        "w": "#3a97d8",
+        "y": "#f7adfd"
+    }
+}

biotite/sequence/graphics/color_schemes/autumn.json

@@ -0,0 +1,51 @@
+{
+    "name": "autumn",
+    "alphabet": [
+        "A",
+        "C",
+        "D",
+        "E",
+        "F",
+        "G",
+        "H",
+        "I",
+        "K",
+        "L",
+        "M",
+        "N",
+        "P",
+        "Q",
+        "R",
+        "S",
+        "T",
+        "V",
+        "W",
+        "Y",
+        "B",
+	"Z",
+	"X",
+	"*"
+    ],
+    "colors": {
+        "A": "#6a6a6a",
+        "C": "#01885a",
+        "D": "#a8060d",
+        "E": "#d33860",
+        "F": "#2876d9",
+        "G": "#bc5d04",
+        "H": "#de05a7",
+        "I": "#1c7897",
+        "K": "#982649",
+        "L": "#437bad",
+        "M": "#484f7d",
+        "N": "#df3245",
+        "P": "#8a7305",
+        "Q": "#c54b7e",
+        "R": "#a1035f",
+        "S": "#a9645d",
+        "T": "#674d39",
+        "V": "#26586a",
+        "W": "#1834e9",
+        "Y": "#8361d9"
+    }
+}

biotite/sequence/graphics/color_schemes/blossom.json

@@ -0,0 +1,51 @@
+{
+    "name": "blossom",
+    "alphabet": [
+        "A",
+        "C",
+        "D",
+        "E",
+        "F",
+        "G",
+        "H",
+        "I",
+        "K",
+        "L",
+        "M",
+        "N",
+        "P",
+        "Q",
+        "R",
+        "S",
+        "T",
+        "V",
+        "W",
+        "Y",
+        "B",
+	"Z",
+	"X",
+	"*"
+    ],
+    "colors": {
+        "A": "#8bc4b4",
+        "C": "#0893fe",
+        "D": "#5fa505",
+        "E": "#dbb501",
+        "F": "#f74fa8",
+        "G": "#00d382",
+        "H": "#ff5701",
+        "I": "#9abaf3",
+        "K": "#fea527",
+        "L": "#cda5dc",
+        "M": "#f5a1b8",
+        "N": "#b5c206",
+        "P": "#10d631",
+        "Q": "#bf8527",
+        "R": "#fc9502",
+        "S": "#7e9d59",
+        "T": "#00a29c",
+        "V": "#87c0e4",
+        "W": "#fe08fb",
+        "Y": "#ff4e7a"
+    }
+}

biotite/sequence/graphics/color_schemes/clustalx_dna.json

@@ -0,0 +1,11 @@
+{
+    "name" : "clustalx",
+    "alphabet" : ["A","C","G","T",
+                  "R","Y","W","S","M","K","H","B","V","D","N"],
+    "colors" : {
+        "A" : "#e53319",
+        "C" : "#197fe5",
+        "G" : "#e5994c",
+        "T" : "#19cc19"
+    }
+}

biotite/sequence/graphics/color_schemes/clustalx_protein.json

@@ -0,0 +1,28 @@
+{
+    "name" : "clustalx",
+    "alphabet" : ["A","C","D","E","F","G","H","I","K","L",
+                  "M","N","P","Q","R","S","T","V","W","Y",
+                  "B","Z","X","*"],
+    "colors" : {
+        "A" : "#197fe5",
+        "C" : "#e57f7f",
+        "D" : "#cc4ccc",
+        "E" : "#cc4ccc",
+        "F" : "#197fe5",
+        "G" : "#e5994c",
+        "H" : "#19b2b2",
+        "I" : "#197fe5",
+        "K" : "#e53319",
+        "L" : "#197fe5",
+        "M" : "#197fe5",
+        "N" : "#19cc19",
+        "P" : "#cccc00",
+        "Q" : "#19cc19",
+        "R" : "#e53319",
+        "S" : "#19cc19",
+        "T" : "#19cc19",
+        "V" : "#197fe5",
+        "W" : "#197fe5",
+        "Y" : "#19b2b2"
+    }
+}

biotite/sequence/graphics/color_schemes/flower.json

@@ -0,0 +1,51 @@
+{
+    "name": "flower",
+    "alphabet": [
+        "A",
+        "C",
+        "D",
+        "E",
+        "F",
+        "G",
+        "H",
+        "I",
+        "K",
+        "L",
+        "M",
+        "N",
+        "P",
+        "Q",
+        "R",
+        "S",
+        "T",
+        "V",
+        "W",
+        "Y",
+        "B",
+	"Z",
+	"X",
+	"*"
+    ],
+    "colors": {
+        "A": "#b18a51",
+        "C": "#ff5701",
+        "D": "#01a578",
+        "E": "#2da0a1",
+        "F": "#fa559d",
+        "G": "#b1c23c",
+        "H": "#0194f9",
+        "I": "#f27663",
+        "K": "#7fc3d7",
+        "L": "#df6e75",
+        "M": "#fe9daf",
+        "N": "#0bcec6",
+        "P": "#4fa32a",
+        "Q": "#7295ae",
+        "R": "#83bff1",
+        "S": "#b4bd9b",
+        "T": "#d2b576",
+        "V": "#fd997b",
+        "W": "#ff2ded",
+        "Y": "#c96ecf"
+    }
+}

biotite/sequence/graphics/color_schemes/jalview_buried.json

@@ -0,0 +1,31 @@
+{
+    "name" : "buried",
+    "alphabet" : ["A","C","D","E","F","G","H","I","K","L",
+                  "M","N","P","Q","R","S","T","V","W","Y",
+                  "B","Z","X","*"],
+    "colors" : {
+        "A" : "#00a35c",
+        "R" : "#00fc03",
+        "N" : "#00eb14",
+        "D" : "#00eb14",
+        "C" : "#0000ff",
+        "Q" : "#00f10e",
+        "E" : "#00f10e",
+        "G" : "#009d62",
+        "H" : "#00d52a",
+        "I" : "#0054ab",
+        "L" : "#007b84",
+        "K" : "#00ff00",
+        "M" : "#009768",
+        "F" : "#008778",
+        "P" : "#00e01f",
+        "S" : "#00d52a",
+        "T" : "#00db24",
+        "W" : "#00a857",
+        "Y" : "#00e619",
+        "V" : "#005fa0",
+        "B" : "#00eb14",
+        "X" : "#00b649",
+        "Z" : "#00f10e"
+    }
+}

biotite/sequence/graphics/color_schemes/jalview_hydrophobicity.json

@@ -0,0 +1,31 @@
+{
+    "name" : "hydrophobicity",
+    "alphabet" : ["A","C","D","E","F","G","H","I","K","L",
+                  "M","N","P","Q","R","S","T","V","W","Y",
+                  "B","Z","X","*"],
+    "colors" : {
+        "A" : "#ad0052",
+        "R" : "#0000ff",
+        "N" : "#0c00f3",
+        "D" : "#0c00f3",
+        "C" : "#c2003d",
+        "Q" : "#0c00f3",
+        "E" : "#0c00f3",
+        "G" : "#6a0095",
+        "H" : "#1500ea",
+        "I" : "#ff0000",
+        "L" : "#ea0015",
+        "K" : "#0000ff",
+        "M" : "#b0004f",
+        "F" : "#cb0034",
+        "P" : "#4600b9",
+        "S" : "#5e00a1",
+        "T" : "#61009e",
+        "W" : "#5b00a4",
+        "Y" : "#4f00b0",
+        "V" : "#f60009",
+        "B" : "#0c00f3",
+        "X" : "#680097",
+        "Z" : "#0c00f3"
+    }
+}

biotite/sequence/graphics/color_schemes/jalview_prop_helix.json

@@ -0,0 +1,31 @@
+{
+    "name" : "prophelix",
+    "alphabet" : ["A","C","D","E","F","G","H","I","K","L",
+                  "M","N","P","Q","R","S","T","V","W","Y",
+                  "B","Z","X","*"],
+    "colors" : {
+        "A" : "#e718e7",
+        "R" : "#6f906f",
+        "N" : "#1be41b",
+        "D" : "#778877",
+        "C" : "#23dc23",
+        "Q" : "#926d92",
+        "E" : "#ff00ff",
+        "G" : "#00ff00",
+        "H" : "#758a75",
+        "I" : "#8a758a",
+        "L" : "#ae51ae",
+        "K" : "#a05fa0",
+        "M" : "#ef10ef",
+        "F" : "#986798",
+        "P" : "#00ff00",
+        "S" : "#36c936",
+        "T" : "#47b847",
+        "W" : "#8a758a",
+        "Y" : "#21de21",
+        "V" : "#857a85",
+        "B" : "#49b649",
+        "X" : "#758a75",
+        "Z" : "#c936c9"
+    }
+}

biotite/sequence/graphics/color_schemes/jalview_prop_strand.json

@@ -0,0 +1,31 @@
+{
+    "name" : "propstrand",
+    "alphabet" : ["A","C","D","E","F","G","H","I","K","L",
+                  "M","N","P","Q","R","S","T","V","W","Y",
+                  "B","Z","X","*"],
+    "colors" : {
+        "A" : "#5858a7",
+        "R" : "#6b6b94",
+        "N" : "#64649b",
+        "D" : "#2121de",
+        "C" : "#9d9d62",
+        "Q" : "#8c8c73",
+        "E" : "#0000ff",
+        "G" : "#4949b6",
+        "H" : "#60609f",
+        "I" : "#ecec13",
+        "L" : "#b2b24d",
+        "K" : "#4747b8",
+        "M" : "#82827d",
+        "F" : "#c2c23d",
+        "P" : "#2323dc",
+        "S" : "#4949b6",
+        "T" : "#9d9d62",
+        "W" : "#c0c03f",
+        "Y" : "#d3d32c",
+        "V" : "#ffff00",
+        "B" : "#4343bc",
+        "X" : "#797986",
+        "Z" : "#4747b8"
+    }
+}

biotite/sequence/graphics/color_schemes/jalview_prop_turn.json

@@ -0,0 +1,31 @@
+{
+    "name" : "propturn",
+    "alphabet" : ["A","C","D","E","F","G","H","I","K","L",
+                  "M","N","P","Q","R","S","T","V","W","Y",
+                  "B","Z","X","*"],
+    "colors" : {
+        "A" : "#2cd3d3",
+        "R" : "#708f8f",
+        "N" : "#ff0000",
+        "D" : "#e81717",
+        "C" : "#a85757",
+        "Q" : "#3fc0c0",
+        "E" : "#778888",
+        "G" : "#ff0000",
+        "H" : "#708f8f",
+        "I" : "#00ffff",
+        "L" : "#1ce3e3",
+        "K" : "#7e8181",
+        "M" : "#1ee1e1",
+        "F" : "#1ee1e1",
+        "P" : "#f60909",
+        "S" : "#e11e1e",
+        "T" : "#738c8c",
+        "W" : "#738c8c",
+        "Y" : "#9d6262",
+        "V" : "#07f8f8",
+        "B" : "#f30c0c",
+        "X" : "#7c8383",
+        "Z" : "#5ba4a4"
+    }
+}

biotite/sequence/graphics/color_schemes/jalview_taylor.json

@@ -0,0 +1,28 @@
+{
+    "name" : "taylor",
+    "alphabet" : ["A","C","D","E","F","G","H","I","K","L",
+                  "M","N","P","Q","R","S","T","V","W","Y",
+                  "B","Z","X","*"],
+    "colors" : {
+        "A" : "#ccff00",
+        "R" : "#0000ff",
+        "N" : "#cc00ff",
+        "D" : "#ff0000",
+        "C" : "#ffff00",
+        "Q" : "#ff00cc",
+        "E" : "#ff0066",
+        "G" : "#ff9900",
+        "H" : "#0066ff",
+        "I" : "#66ff00",
+        "L" : "#33ff00",
+        "K" : "#6600ff",
+        "M" : "#00ff00",
+        "F" : "#00ff66",
+        "P" : "#ffcc00",
+        "S" : "#ff3300",
+        "T" : "#ff6600",
+        "W" : "#00ccff",
+        "Y" : "#00ffcc",
+        "V" : "#99ff00"
+    }
+}

biotite/sequence/graphics/color_schemes/jalview_zappo.json

@@ -0,0 +1,28 @@
+{
+    "name" : "zappo",
+    "alphabet" : ["A","C","D","E","F","G","H","I","K","L",
+                  "M","N","P","Q","R","S","T","V","W","Y",
+                  "B","Z","X","*"],
+    "colors" : {
+        "A" : "#ffafaf",
+        "R" : "#6464ff",
+        "N" : "#00ff00",
+        "D" : "#ff0000",
+        "C" : "#ffff00",
+        "Q" : "#00ff00",
+        "E" : "#ff0000",
+        "G" : "#ff00ff",
+        "H" : "#6464ff",
+        "I" : "#ffafaf",
+        "L" : "#ffafaf",
+        "K" : "#6464ff",
+        "M" : "#ffafaf",
+        "F" : "#ffc800",
+        "P" : "#ff00ff",
+        "S" : "#00ff00",
+        "T" : "#00ff00",
+        "W" : "#ffc800",
+        "Y" : "#ffc800",
+        "V" : "#ffafaf"
+    }
+}

biotite/sequence/graphics/color_schemes/ocean.json

@@ -0,0 +1,51 @@
+{
+    "name": "ocean",
+    "alphabet": [
+        "A",
+        "C",
+        "D",
+        "E",
+        "F",
+        "G",
+        "H",
+        "I",
+        "K",
+        "L",
+        "M",
+        "N",
+        "P",
+        "Q",
+        "R",
+        "S",
+        "T",
+        "V",
+        "W",
+        "Y",
+        "B",
+	"Z",
+	"X",
+	"*"
+    ],
+    "colors": {
+        "A": "#c6ca9b",
+        "C": "#c68136",
+        "D": "#4cdfa1",
+        "E": "#60dac9",
+        "F": "#ab88ae",
+        "G": "#33a551",
+        "H": "#00cffe",
+        "I": "#f2baaa",
+        "K": "#40a090",
+        "L": "#bb8a83",
+        "M": "#a48b88",
+        "N": "#0adfc3",
+        "P": "#afd365",
+        "Q": "#8bd3d1",
+        "R": "#0ca0a8",
+        "S": "#6d9b74",
+        "T": "#8d9566",
+        "V": "#e9bea4",
+        "W": "#758aee",
+        "Y": "#bac3fc"
+    }
+}

biotite/sequence/graphics/color_schemes/pb_flower.json

@@ -0,0 +1,40 @@
+{
+    "name": "flower",
+    "alphabet": [
+        "a",
+        "b",
+        "c",
+        "d",
+        "e",
+        "f",
+        "g",
+        "h",
+        "i",
+        "j",
+        "k",
+        "l",
+        "m",
+        "n",
+        "o",
+        "p",
+        "z"
+    ],
+    "colors": {
+        "a": "#31b5fc",
+        "b": "#c6a2ac",
+        "c": "#36a4f9",
+        "d": "#c981ff",
+        "e": "#fe60ce",
+        "f": "#fb69b5",
+        "g": "#4fabb2",
+        "h": "#ff7076",
+        "i": "#c8a677",
+        "j": "#fb7559",
+        "k": "#fc7710",
+        "l": "#c1a41a",
+        "m": "#56c205",
+        "n": "#01bd40",
+        "o": "#07c387",
+        "p": "#08c0ad"
+    }
+}

biotite/sequence/graphics/color_schemes/rainbow_dna.json

@@ -0,0 +1,11 @@
+{
+    "name" : "rainbow",
+    "alphabet" : ["A","C","G","T",
+                  "R","Y","W","S","M","K","H","B","V","D","N"],
+    "colors" : {
+        "A" : "#3737f5",
+        "C" : "#37f537",
+        "G" : "#f5f537",
+        "T" : "#f53737"
+    }
+}

biotite/sequence/graphics/color_schemes/rainbow_protein.json

@@ -0,0 +1,30 @@
+{
+    "name" : "rainbow",
+    "alphabet" : ["A","C","D","E","F","G","H","I","K","L",
+                  "M","N","P","Q","R","S","T","V","W","Y",
+                  "B","Z","X","*"],
+    "colors" : {
+        "A" : "#cbf537",
+        "C" : "#f537a5",
+        "D" : "#377af5",
+        "E" : "#3739f5",
+        "F" : "#37f57a",
+        "G" : "#eaf537",
+        "H" : "#f53737",
+        "I" : "#8cf537",
+        "K" : "#f53755",
+        "L" : "#6df537",
+        "M" : "#4df537",
+        "N" : "#bd37f5",
+        "P" : "#f5bf37",
+        "Q" : "#9037f5",
+        "R" : "#f56437",
+        "S" : "#f537d3",
+        "T" : "#ea37f5",
+        "V" : "#abf537",
+        "W" : "#37f5b9",
+        "Y" : "#37f599",
+        "B" : "#377af5",
+        "Z" : "#3739f5"
+    }
+}

biotite/sequence/graphics/color_schemes/spring.json

@@ -0,0 +1,51 @@
+{
+    "name": "spring",
+    "alphabet": [
+        "A",
+        "C",
+        "D",
+        "E",
+        "F",
+        "G",
+        "H",
+        "I",
+        "K",
+        "L",
+        "M",
+        "N",
+        "P",
+        "Q",
+        "R",
+        "S",
+        "T",
+        "V",
+        "W",
+        "Y",
+        "B",
+	"Z",
+	"X",
+	"*"
+    ],
+    "colors": {
+        "A": "#ababab",
+        "C": "#0893fe",
+        "D": "#fc5977",
+        "E": "#ff9c83",
+        "F": "#02d29b",
+        "G": "#f66c17",
+        "H": "#d2b907",
+        "I": "#3fc9e0",
+        "K": "#b7874f",
+        "L": "#4ecacf",
+        "M": "#4b9e93",
+        "N": "#eb684b",
+        "P": "#fd75cf",
+        "Q": "#deb16f",
+        "R": "#b38b2b",
+        "S": "#bb8187",
+        "T": "#d3add1",
+        "V": "#519db9",
+        "W": "#00d619",
+        "Y": "#38a549"
+    }
+}