mirror of
https://github.com/rdk/p2rank.git
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add ChimeraX visualization
This commit is contained in:
rdk
@@ -1,5 +1,5 @@
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version: 2.5-dev.12
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git head: aae633f5
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git head: 0c543696
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Params[
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apoholo_use_for_eval = false
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@@ -183,6 +183,7 @@ Params[
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vis_copy_proteins = true
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vis_generate_proteins = true
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vis_highlight_ligands = false
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vis_renderers = [pymol, chimerax]
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visualizations = true
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weight_dist_param = 4.5
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weight_function = INV
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@@ -0,0 +1,36 @@
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open data/1fbl.pdb
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surf
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hide solvent
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color protein #d9d9ff
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color ligand magenta
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color name color_pocket1 #5c93e6
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color name color_pocket2 #7d47b3
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color name color_pocket3 #e65cae
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color name color_pocket4 #b36847
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name pocket1_atoms @@serial_number=991 @@serial_number=992 @@serial_number=993 @@serial_number=994 @@serial_number=1033 @@serial_number=1035 @@serial_number=1036 @@serial_number=1026 @@serial_number=664 @@serial_number=670 @@serial_number=676 @@serial_number=971 @@serial_number=679 @@serial_number=958 @@serial_number=959 @@serial_number=960 @@serial_number=961 @@serial_number=962 @@serial_number=963 @@serial_number=938 @@serial_number=942 @@serial_number=972 @@serial_number=934 @@serial_number=929 @@serial_number=943 @@serial_number=989 @@serial_number=1016 @@serial_number=32 @@serial_number=692 @@serial_number=700 @@serial_number=33 @@serial_number=1118 @@serial_number=1119 @@serial_number=658 @@serial_number=659 @@serial_number=1122 @@serial_number=1124 @@serial_number=651 @@serial_number=1112 @@serial_number=1106
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color pocket1_atoms color_pocket1
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name pocket2_atoms @@serial_number=2109 @@serial_number=2144 @@serial_number=2091 @@serial_number=2092 @@serial_number=1991 @@serial_number=2150 @@serial_number=2151 @@serial_number=2161 @@serial_number=2163 @@serial_number=2444 @@serial_number=1891 @@serial_number=2426 @@serial_number=2439 @@serial_number=1910 @@serial_number=2064 @@serial_number=1909 @@serial_number=1890 @@serial_number=1926
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color pocket2_atoms color_pocket2
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name pocket3_atoms @@serial_number=760 @@serial_number=761 @@serial_number=730 @@serial_number=728 @@serial_number=746 @@serial_number=173 @@serial_number=514 @@serial_number=515 @@serial_number=171 @@serial_number=172 @@serial_number=501 @@serial_number=472 @@serial_number=499 @@serial_number=532 @@serial_number=560
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color pocket3_atoms color_pocket3
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name pocket4_atoms @@serial_number=1488 @@serial_number=1497 @@serial_number=1513 @@serial_number=1619 @@serial_number=1620 @@serial_number=1769 @@serial_number=1490 @@serial_number=1756 @@serial_number=1757 @@serial_number=1489 @@serial_number=1766 @@serial_number=1917 @@serial_number=1499 @@serial_number=2030 @@serial_number=2031 @@serial_number=2034 @@serial_number=2035
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color pocket4_atoms color_pocket4
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open data/1fbl.pdb_points.pdb.gz
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color by bfactor #2 palette lime:red range 0,0.7
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set bgcolor #242455
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transparency 0
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graphics silhouettes false
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lighting soft
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@@ -0,0 +1,74 @@
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from pymol import cmd,stored
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set depth_cue, 1
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set fog_start, 0.4
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set_color b_col, [36,36,85]
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set_color t_col, [10,10,10]
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set bg_rgb_bottom, b_col
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set bg_rgb_top, t_col
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set bg_gradient
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set spec_power = 200
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set spec_refl = 0
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load "data/1fbl.pdb", protein
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create ligands, protein and organic
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select xlig, protein and organic
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delete xlig
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hide everything, all
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color white, elem c
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color bluewhite, protein
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#show_as cartoon, protein
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show surface, protein
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#set transparency, 0.15
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show sticks, ligands
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set stick_color, magenta
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# SAS points
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load "data/1fbl.pdb_points.pdb.gz", points
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hide nonbonded, points
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show nb_spheres, points
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set sphere_scale, 0.2, points
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cmd.spectrum("b", "green_red", selection="points", minimum=0, maximum=0.7)
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stored.list=[]
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cmd.iterate("(resn STP)","stored.list.append(resi)") # read info about residues STP
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lastSTP=stored.list[-1] # get the index of the last residue
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hide lines, resn STP
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cmd.select("rest", "resn STP and resi 0")
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for my_index in range(1,int(lastSTP)+1): cmd.select("pocket"+str(my_index), "resn STP and resi "+str(my_index))
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for my_index in range(1,int(lastSTP)+1): cmd.show("spheres","pocket"+str(my_index))
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for my_index in range(1,int(lastSTP)+1): cmd.set("sphere_scale","0.4","pocket"+str(my_index))
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for my_index in range(1,int(lastSTP)+1): cmd.set("sphere_transparency","0.1","pocket"+str(my_index))
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set_color pcol1 = [0.361,0.576,0.902]
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select surf_pocket1, protein and id [991,992,993,994,1033,1035,1036,1026,664,670,676,971,679,958,959,960,961,962,963,938,942,972,934,929,943,989,1016,32,692,700,33,1118,1119,658,659,1122,1124,651,1112,1106]
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set surface_color, pcol1, surf_pocket1
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set_color pcol2 = [0.490,0.278,0.702]
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select surf_pocket2, protein and id [2109,2144,2091,2092,1991,2150,2151,2161,2163,2444,1891,2426,2439,1910,2064,1909,1890,1926]
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set surface_color, pcol2, surf_pocket2
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set_color pcol3 = [0.902,0.361,0.682]
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select surf_pocket3, protein and id [760,761,730,728,746,173,514,515,171,172,501,472,499,532,560]
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set surface_color, pcol3, surf_pocket3
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set_color pcol4 = [0.702,0.408,0.278]
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select surf_pocket4, protein and id [1488,1497,1513,1619,1620,1769,1490,1756,1757,1489,1766,1917,1499,2030,2031,2034,2035]
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set surface_color, pcol4, surf_pocket4
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deselect
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orient
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@@ -1,5 +1,5 @@
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version: 2.5-dev.12
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git head: aae633f5
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git head: 0c543696
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Params[
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apoholo_use_for_eval = false
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@@ -183,6 +183,7 @@ Params[
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vis_copy_proteins = true
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vis_generate_proteins = true
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vis_highlight_ligands = false
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vis_renderers = [pymol, chimerax]
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visualizations = true
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weight_dist_param = 4.5
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weight_function = INV
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@@ -0,0 +1,48 @@
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open data/1fbl.pdb
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surf
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hide solvent
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color protein #d9d9ff
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color ligand magenta
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color name color_pocket1 #5c93e6
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color name color_pocket2 #5447b3
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color name color_pocket3 #b25ce6
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color name color_pocket4 #b347a3
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color name color_pocket5 #e65c8b
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color name color_pocket6 #b35a47
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color name color_pocket7 #e6ba5c
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name pocket1_atoms @@serial_number=963 @@serial_number=990 @@serial_number=991 @@serial_number=992 @@serial_number=993 @@serial_number=994 @@serial_number=1027 @@serial_number=1033 @@serial_number=1035 @@serial_number=1036 @@serial_number=1025 @@serial_number=1026 @@serial_number=664 @@serial_number=667 @@serial_number=670 @@serial_number=671 @@serial_number=676 @@serial_number=971 @@serial_number=679 @@serial_number=958 @@serial_number=959 @@serial_number=960 @@serial_number=961 @@serial_number=962 @@serial_number=938 @@serial_number=942 @@serial_number=943 @@serial_number=972 @@serial_number=661 @@serial_number=934 @@serial_number=929 @@serial_number=988 @@serial_number=989 @@serial_number=1016 @@serial_number=682 @@serial_number=700 @@serial_number=692 @@serial_number=693 @@serial_number=696 @@serial_number=32 @@serial_number=33 @@serial_number=1105 @@serial_number=1106 @@serial_number=1111 @@serial_number=1117 @@serial_number=651 @@serial_number=653 @@serial_number=644 @@serial_number=646 @@serial_number=1112 @@serial_number=1113 @@serial_number=1118 @@serial_number=1119 @@serial_number=658 @@serial_number=659 @@serial_number=1122 @@serial_number=1124 @@serial_number=657
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color pocket1_atoms color_pocket1
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name pocket2_atoms @@serial_number=758 @@serial_number=760 @@serial_number=173 @@serial_number=514 @@serial_number=515 @@serial_number=761 @@serial_number=730 @@serial_number=728 @@serial_number=746 @@serial_number=171 @@serial_number=172 @@serial_number=501 @@serial_number=472 @@serial_number=499 @@serial_number=498 @@serial_number=564 @@serial_number=582 @@serial_number=560 @@serial_number=570 @@serial_number=532 @@serial_number=561
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color pocket2_atoms color_pocket2
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name pocket3_atoms @@serial_number=2107 @@serial_number=2109 @@serial_number=2144 @@serial_number=2152 @@serial_number=2091 @@serial_number=2092 @@serial_number=1991 @@serial_number=2150 @@serial_number=2151 @@serial_number=2161 @@serial_number=2163 @@serial_number=2444 @@serial_number=1890 @@serial_number=1891 @@serial_number=2426 @@serial_number=2439 @@serial_number=2459 @@serial_number=2455 @@serial_number=1910 @@serial_number=2064 @@serial_number=1908 @@serial_number=1909 @@serial_number=1926
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color pocket3_atoms color_pocket3
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name pocket4_atoms @@serial_number=1488 @@serial_number=1490 @@serial_number=1486 @@serial_number=1495 @@serial_number=1497 @@serial_number=1513 @@serial_number=1619 @@serial_number=1620 @@serial_number=2039 @@serial_number=1754 @@serial_number=1757 @@serial_number=1750 @@serial_number=1528 @@serial_number=1756 @@serial_number=1769 @@serial_number=1489 @@serial_number=1766 @@serial_number=1917 @@serial_number=1498 @@serial_number=1499 @@serial_number=1900 @@serial_number=2030 @@serial_number=2031 @@serial_number=2034 @@serial_number=2035 @@serial_number=2038 @@serial_number=1896 @@serial_number=1897 @@serial_number=1902 @@serial_number=1899 @@serial_number=1901 @@serial_number=2017
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color pocket4_atoms color_pocket4
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name pocket5_atoms @@serial_number=2936 @@serial_number=2937 @@serial_number=2772 @@serial_number=2924 @@serial_number=2926 @@serial_number=2927 @@serial_number=2928 @@serial_number=2925 @@serial_number=2895 @@serial_number=2896 @@serial_number=2898 @@serial_number=1637 @@serial_number=2935 @@serial_number=2938 @@serial_number=2940 @@serial_number=2674 @@serial_number=2708 @@serial_number=2686 @@serial_number=2688 @@serial_number=2705 @@serial_number=2707 @@serial_number=2770 @@serial_number=2771 @@serial_number=2939 @@serial_number=2789 @@serial_number=2881 @@serial_number=2791 @@serial_number=2792 @@serial_number=2793
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color pocket5_atoms color_pocket5
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name pocket6_atoms @@serial_number=1482 @@serial_number=1860 @@serial_number=1861 @@serial_number=2652 @@serial_number=2653 @@serial_number=1481 @@serial_number=1491 @@serial_number=1502 @@serial_number=2666 @@serial_number=2659 @@serial_number=2663 @@serial_number=2667 @@serial_number=1492 @@serial_number=1870 @@serial_number=1874 @@serial_number=2280 @@serial_number=2281 @@serial_number=2282 @@serial_number=2283 @@serial_number=2284 @@serial_number=1857 @@serial_number=1856 @@serial_number=2263 @@serial_number=2259 @@serial_number=2656
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color pocket6_atoms color_pocket6
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name pocket7_atoms @@serial_number=2411 @@serial_number=2503 @@serial_number=2558 @@serial_number=2559 @@serial_number=2309 @@serial_number=2312 @@serial_number=2413 @@serial_number=2330 @@serial_number=2848 @@serial_number=2822 @@serial_number=2823 @@serial_number=2847 @@serial_number=2298 @@serial_number=2297 @@serial_number=2299 @@serial_number=2329
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color pocket7_atoms color_pocket7
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open data/1fbl.pdb_points.pdb.gz
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color by bfactor #2 palette lime:red range 0,0.7
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set bgcolor #242455
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transparency 0
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graphics silhouettes false
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lighting soft
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@@ -0,0 +1,83 @@
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from pymol import cmd,stored
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set depth_cue, 1
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set fog_start, 0.4
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set_color b_col, [36,36,85]
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set_color t_col, [10,10,10]
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set bg_rgb_bottom, b_col
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set bg_rgb_top, t_col
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set bg_gradient
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set spec_power = 200
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set spec_refl = 0
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load "data/1fbl.pdb", protein
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create ligands, protein and organic
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select xlig, protein and organic
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delete xlig
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hide everything, all
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color white, elem c
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color bluewhite, protein
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#show_as cartoon, protein
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show surface, protein
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#set transparency, 0.15
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show sticks, ligands
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set stick_color, magenta
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# SAS points
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load "data/1fbl.pdb_points.pdb.gz", points
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hide nonbonded, points
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show nb_spheres, points
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set sphere_scale, 0.2, points
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cmd.spectrum("b", "green_red", selection="points", minimum=0, maximum=0.7)
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stored.list=[]
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cmd.iterate("(resn STP)","stored.list.append(resi)") # read info about residues STP
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lastSTP=stored.list[-1] # get the index of the last residue
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hide lines, resn STP
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cmd.select("rest", "resn STP and resi 0")
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for my_index in range(1,int(lastSTP)+1): cmd.select("pocket"+str(my_index), "resn STP and resi "+str(my_index))
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for my_index in range(1,int(lastSTP)+1): cmd.show("spheres","pocket"+str(my_index))
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for my_index in range(1,int(lastSTP)+1): cmd.set("sphere_scale","0.4","pocket"+str(my_index))
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for my_index in range(1,int(lastSTP)+1): cmd.set("sphere_transparency","0.1","pocket"+str(my_index))
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set_color pcol1 = [0.361,0.576,0.902]
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select surf_pocket1, protein and id [963,990,991,992,993,994,1027,1033,1035,1036,1025,1026,664,667,670,671,676,971,679,958,959,960,961,962,938,942,943,972,661,934,929,988,989,1016,682,700,692,693,696,32,33,1105,1106,1111,1117,651,653,644,646,1112,1113,1118,1119,658,659,1122,1124,657]
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set surface_color, pcol1, surf_pocket1
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set_color pcol2 = [0.329,0.278,0.702]
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select surf_pocket2, protein and id [758,760,173,514,515,761,730,728,746,171,172,501,472,499,498,564,582,560,570,532,561]
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set surface_color, pcol2, surf_pocket2
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set_color pcol3 = [0.698,0.361,0.902]
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select surf_pocket3, protein and id [2107,2109,2144,2152,2091,2092,1991,2150,2151,2161,2163,2444,1890,1891,2426,2439,2459,2455,1910,2064,1908,1909,1926]
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set surface_color, pcol3, surf_pocket3
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set_color pcol4 = [0.702,0.278,0.639]
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select surf_pocket4, protein and id [1488,1490,1486,1495,1497,1513,1619,1620,2039,1754,1757,1750,1528,1756,1769,1489,1766,1917,1498,1499,1900,2030,2031,2034,2035,2038,1896,1897,1902,1899,1901,2017]
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set surface_color, pcol4, surf_pocket4
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set_color pcol5 = [0.902,0.361,0.545]
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select surf_pocket5, protein and id [2936,2937,2772,2924,2926,2927,2928,2925,2895,2896,2898,1637,2935,2938,2940,2674,2708,2686,2688,2705,2707,2770,2771,2939,2789,2881,2791,2792,2793]
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set surface_color, pcol5, surf_pocket5
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set_color pcol6 = [0.702,0.353,0.278]
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select surf_pocket6, protein and id [1482,1860,1861,2652,2653,1481,1491,1502,2666,2659,2663,2667,1492,1870,1874,2280,2281,2282,2283,2284,1857,1856,2263,2259,2656]
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set surface_color, pcol6, surf_pocket6
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set_color pcol7 = [0.902,0.729,0.361]
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select surf_pocket7, protein and id [2411,2503,2558,2559,2309,2312,2413,2330,2848,2822,2823,2847,2298,2297,2299,2329]
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set surface_color, pcol7, surf_pocket7
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deselect
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orient
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@@ -1,75 +0,0 @@
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from pymol import cmd,stored
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set depth_cue, 1
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set fog_start, 0.4
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set_color b_col, [36,36,85]
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set_color t_col, [10,10,10]
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set bg_rgb_bottom, b_col
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set bg_rgb_top, t_col
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set bg_gradient
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set spec_power = 200
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set spec_refl = 0
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load "data/1fbl.pdb", protein
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create ligands, protein and organic
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select xlig, protein and organic
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delete xlig
|
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hide everything, all
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||||
|
||||
color white, elem c
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color bluewhite, protein
|
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#show_as cartoon, protein
|
||||
show surface, protein
|
||||
#set transparency, 0.15
|
||||
|
||||
show sticks, ligands
|
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set stick_color, magenta
|
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# SAS points
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load "data/1fbl.pdb_points.pdb.gz", points
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hide nonbonded, points
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show nb_spheres, points
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set sphere_scale, 0.2, points
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cmd.spectrum("b", "green_red", selection="points", minimum=0, maximum=0.7)
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stored.list=[]
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cmd.iterate("(resn STP)","stored.list.append(resi)") # read info about residues STP
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lastSTP=stored.list[-1] # get the index of the last residue
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hide lines, resn STP
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cmd.select("rest", "resn STP and resi 0")
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for my_index in range(1,int(lastSTP)+1): cmd.select("pocket"+str(my_index), "resn STP and resi "+str(my_index))
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for my_index in range(1,int(lastSTP)+1): cmd.show("spheres","pocket"+str(my_index))
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for my_index in range(1,int(lastSTP)+1): cmd.set("sphere_scale","0.4","pocket"+str(my_index))
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for my_index in range(1,int(lastSTP)+1): cmd.set("sphere_transparency","0.1","pocket"+str(my_index))
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|
||||
|
||||
|
||||
set_color pcol1 = [0.361,0.576,0.902]
|
||||
select surf_pocket1, protein and id [991,992,993,994,1033,1035,1036,1026,664,670,676,971,679,958,959,960,961,962,963,938,942,972,934,929,943,989,1016,32,692,700,33,1118,1119,658,659,1122,1124,651,1112,1106]
|
||||
set surface_color, pcol1, surf_pocket1
|
||||
set_color pcol2 = [0.490,0.278,0.702]
|
||||
select surf_pocket2, protein and id [2109,2144,2091,2092,1991,2150,2151,2161,2163,2444,1891,2426,2439,1910,2064,1909,1890,1926]
|
||||
set surface_color, pcol2, surf_pocket2
|
||||
set_color pcol3 = [0.902,0.361,0.682]
|
||||
select surf_pocket3, protein and id [760,761,730,728,746,173,514,515,171,172,501,472,499,532,560]
|
||||
set surface_color, pcol3, surf_pocket3
|
||||
set_color pcol4 = [0.702,0.408,0.278]
|
||||
select surf_pocket4, protein and id [1488,1497,1513,1619,1620,1769,1490,1756,1757,1489,1766,1917,1499,2030,2031,2034,2035]
|
||||
set surface_color, pcol4, surf_pocket4
|
||||
|
||||
|
||||
deselect
|
||||
|
||||
orient
|
||||
|
||||
@@ -1,5 +0,0 @@
|
||||
name , rank, score, probability, sas_points, surf_atoms, center_x, center_y, center_z, residue_ids, surf_atom_ids
|
||||
pocket1 , 1, 9.77, 0.525, 70, 40, 70.5274, 83.4375, -11.5099, A_103 A_180 A_181 A_182 A_183 A_184 A_186 A_214 A_215 A_218 A_219 A_222 A_226 A_227 A_228 A_238 A_239 A_240, 32 33 651 658 659 664 670 676 679 692 700 929 934 938 942 943 958 959 960 961 962 963 971 972 989 991 992 993 994 1016 1026 1033 1035 1036 1106 1112 1118 1119 1122 1124
|
||||
pocket2 , 2, 3.04, 0.101, 37, 18, 89.2267, 98.6419, 26.7534, A_337 A_339 A_341 A_348 A_357 A_360 A_362 A_366 A_367 A_368 A_400 A_402, 1890 1891 1909 1910 1926 1991 2064 2091 2092 2109 2144 2150 2151 2161 2163 2426 2439 2444
|
||||
pocket3 , 3, 2.94, 0.095, 34, 15, 61.1038, 70.7493, -13.6472, A_119 A_156 A_160 A_162 A_164 A_168 A_191 A_194 A_196, 171 172 173 472 499 501 514 515 532 560 728 730 746 760 761
|
||||
pocket4 , 4, 1.87, 0.037, 27, 17, 90.8572, 95.9207, 10.7905, A_290 A_291 A_293 A_304 A_320 A_321 A_340 A_353 A_354, 1488 1489 1490 1497 1499 1513 1619 1620 1756 1757 1766 1769 1917 2030 2031 2034 2035
|
||||
|
@@ -1,368 +0,0 @@
|
||||
chain, residue_label, residue_name, score, zscore, probability, pocket
|
||||
A, 100, PHE, 0.5863, -0.0527, 0.0491, 0
|
||||
A, 101, VAL, 0.1968, -0.2697, 0.0067, 0
|
||||
A, 102, LEU, 0.0989, -0.3243, 0.0023, 0
|
||||
A, 103, THR, 0.6058, -0.0418, 0.0523, 1
|
||||
A, 104, PRO, 0.0206, -0.3680, 0.0005, 0
|
||||
A, 105, GLY, 0.0092, -0.3743, 0.0003, 0
|
||||
A, 106, ASN, 0.0249, -0.3656, 0.0006, 0
|
||||
A, 107, PRO, 0.0174, -0.3698, 0.0005, 0
|
||||
A, 108, ARG, 0.0243, -0.3659, 0.0006, 0
|
||||
A, 109, TRP, 0.0866, -0.3312, 0.0019, 0
|
||||
A, 110, GLU, 0.0384, -0.3581, 0.0008, 0
|
||||
A, 111, ASN, 0.0742, -0.3381, 0.0016, 0
|
||||
A, 112, THR, 0.0271, -0.3643, 0.0006, 0
|
||||
A, 113, HIS, 0.0742, -0.3381, 0.0016, 0
|
||||
A, 114, LEU, 0.0632, -0.3442, 0.0013, 0
|
||||
A, 115, THR, 0.0382, -0.3582, 0.0008, 0
|
||||
A, 116, TYR, 0.0714, -0.3396, 0.0015, 0
|
||||
A, 117, ARG, 0.0224, -0.3670, 0.0005, 0
|
||||
A, 118, ILE, 0.0366, -0.3590, 0.0008, 0
|
||||
A, 119, GLU, 1.0303, 0.1948, 0.1491, 3
|
||||
A, 120, ASN, 0.0779, -0.3360, 0.0017, 0
|
||||
A, 121, TYR, 0.1145, -0.3156, 0.0028, 0
|
||||
A, 122, THR, 0.0163, -0.3704, 0.0004, 0
|
||||
A, 123, PRO, 0.0185, -0.3691, 0.0005, 0
|
||||
A, 124, ASP, 0.0206, -0.3680, 0.0005, 0
|
||||
A, 125, LEU, 0.1977, -0.2693, 0.0067, 0
|
||||
A, 126, SER, 0.0248, -0.3656, 0.0006, 0
|
||||
A, 127, ARG, 0.1113, -0.3174, 0.0027, 0
|
||||
A, 128, GLU, 0.0397, -0.3573, 0.0008, 0
|
||||
A, 129, ASP, 0.2691, -0.2295, 0.0115, 0
|
||||
A, 130, VAL, 0.0862, -0.3314, 0.0019, 0
|
||||
A, 131, ASP, 0.0672, -0.3420, 0.0014, 0
|
||||
A, 132, ARG, 0.2657, -0.2313, 0.0112, 0
|
||||
A, 133, ALA, 0.3319, -0.1945, 0.0168, 0
|
||||
A, 134, ILE, 0.0525, -0.3502, 0.0011, 0
|
||||
A, 135, GLU, 0.1450, -0.2986, 0.0041, 0
|
||||
A, 136, LYS, 0.6173, -0.0354, 0.0542, 0
|
||||
A, 137, ALA, 0.0002, -0.3794, 0.0002, 0
|
||||
A, 138, PHE, 0.0770, -0.3366, 0.0017, 0
|
||||
A, 139, GLN, 0.1328, -0.3054, 0.0036, 0
|
||||
A, 140, LEU, 0.1585, -0.2911, 0.0047, 0
|
||||
A, 141, TRP, 0.0676, -0.3418, 0.0014, 0
|
||||
A, 142, SER, 0.1231, -0.3108, 0.0032, 0
|
||||
A, 143, ASN, 0.1959, -0.2703, 0.0066, 0
|
||||
A, 144, VAL, 0.1321, -0.3058, 0.0035, 0
|
||||
A, 145, SER, 0.0061, -0.3760, 0.0003, 0
|
||||
A, 146, PRO, 0.0286, -0.3635, 0.0006, 0
|
||||
A, 147, LEU, 0.1067, -0.3200, 0.0026, 0
|
||||
A, 148, THR, 0.1447, -0.2988, 0.0041, 0
|
||||
A, 149, PHE, 0.1362, -0.3036, 0.0037, 0
|
||||
A, 150, THR, 0.1135, -0.3162, 0.0028, 0
|
||||
A, 151, LYS, 0.1105, -0.3179, 0.0027, 0
|
||||
A, 152, VAL, 0.0485, -0.3524, 0.0010, 0
|
||||
A, 153, SER, 0.0704, -0.3402, 0.0015, 0
|
||||
A, 154, GLU, 0.0210, -0.3677, 0.0005, 0
|
||||
A, 155, GLY, 0.0064, -0.3759, 0.0003, 0
|
||||
A, 156, GLN, 0.0271, -0.3644, 0.0006, 3
|
||||
A, 157, ALA, 0.0219, -0.3672, 0.0005, 0
|
||||
A, 158, ASP, 0.0828, -0.3333, 0.0018, 0
|
||||
A, 159, ILE, 0.0033, -0.3776, 0.0003, 0
|
||||
A, 160, MET, 0.9464, 0.1481, 0.1269, 3
|
||||
A, 161, ILE, 0.7581, 0.0431, 0.0818, 0
|
||||
A, 162, SER, 1.0132, 0.1853, 0.1445, 3
|
||||
A, 163, PHE, 0.0534, -0.3497, 0.0011, 0
|
||||
A, 164, VAL, 0.1232, -0.3108, 0.0032, 3
|
||||
A, 165, ARG, 0.0404, -0.3569, 0.0008, 0
|
||||
A, 166, GLY, 0.0114, -0.3731, 0.0004, 0
|
||||
A, 167, ASP, 0.0143, -0.3715, 0.0004, 0
|
||||
A, 168, HIS, 0.1673, -0.2862, 0.0051, 3
|
||||
A, 169, ARG, 0.0373, -0.3586, 0.0008, 0
|
||||
A, 170, ASP, 0.3326, -0.1941, 0.0169, 0
|
||||
A, 171, ASN, 0.0857, -0.3317, 0.0019, 0
|
||||
A, 172, SER, 0.2911, -0.2172, 0.0133, 0
|
||||
A, 173, PRO, 0.0421, -0.3560, 0.0009, 0
|
||||
A, 174, PHE, 0.0574, -0.3475, 0.0012, 0
|
||||
A, 175, ASP, 0.0343, -0.3604, 0.0007, 0
|
||||
A, 176, GLY, 0.0088, -0.3745, 0.0003, 0
|
||||
A, 177, PRO, 0.0826, -0.3334, 0.0018, 0
|
||||
A, 178, GLY, 0.2319, -0.2502, 0.0089, 0
|
||||
A, 179, GLY, 0.2707, -0.2285, 0.0116, 0
|
||||
A, 180, ASN, 1.6667, 0.5495, 0.3284, 1
|
||||
A, 181, LEU, 0.5081, -0.0963, 0.0370, 1
|
||||
A, 182, ALA, 3.4334, 1.5343, 0.6739, 1
|
||||
A, 183, HIS, 3.4902, 1.5660, 0.6815, 1
|
||||
A, 184, ALA, 2.6624, 1.1046, 0.5529, 1
|
||||
A, 185, PHE, 0.9324, 0.1403, 0.1234, 0
|
||||
A, 186, GLN, 0.3475, -0.1858, 0.0182, 1
|
||||
A, 187, PRO, 0.0494, -0.3519, 0.0010, 0
|
||||
A, 188, GLY, 0.0776, -0.3362, 0.0017, 0
|
||||
A, 189, PRO, 0.0802, -0.3348, 0.0017, 0
|
||||
A, 190, GLY, 0.0561, -0.3482, 0.0011, 0
|
||||
A, 191, ILE, 0.9980, 0.1768, 0.1404, 3
|
||||
A, 192, GLY, 0.0692, -0.3409, 0.0015, 0
|
||||
A, 193, GLY, 0.0119, -0.3728, 0.0004, 0
|
||||
A, 194, ASP, 0.9252, 0.1363, 0.1216, 3
|
||||
A, 195, ALA, 0.6133, -0.0376, 0.0535, 0
|
||||
A, 196, HIS, 0.9880, 0.1713, 0.1377, 3
|
||||
A, 197, PHE, 0.0000, -0.3795, 0.0002, 0
|
||||
A, 198, ASP, 0.0007, -0.3790, 0.0002, 0
|
||||
A, 199, GLU, 0.0204, -0.3681, 0.0005, 0
|
||||
A, 200, ASP, 0.0313, -0.3620, 0.0007, 0
|
||||
A, 201, GLU, 0.0563, -0.3481, 0.0012, 0
|
||||
A, 202, ARG, 0.1086, -0.3190, 0.0026, 0
|
||||
A, 203, TRP, 0.0215, -0.3675, 0.0005, 0
|
||||
A, 204, THR, 0.3933, -0.1603, 0.0228, 0
|
||||
A, 205, LYS, 0.6021, -0.0438, 0.0516, 0
|
||||
A, 206, ASN, 0.4865, -0.1083, 0.0341, 0
|
||||
A, 207, PHE, 0.1933, -0.2717, 0.0065, 0
|
||||
A, 208, ARG, 0.1223, -0.3113, 0.0031, 0
|
||||
A, 209, ASP, 0.2679, -0.2302, 0.0114, 0
|
||||
A, 210, TYR, 0.3250, -0.1983, 0.0161, 0
|
||||
A, 211, ASN, 0.5608, -0.0668, 0.0450, 0
|
||||
A, 212, LEU, 0.2492, -0.2405, 0.0101, 0
|
||||
A, 213, TYR, 0.6233, -0.0321, 0.0553, 0
|
||||
A, 214, ARG, 1.0926, 0.2295, 0.1661, 1
|
||||
A, 215, VAL, 1.1105, 0.2395, 0.1711, 1
|
||||
A, 216, ALA, 0.0158, -0.3706, 0.0004, 0
|
||||
A, 217, ALA, 0.0000, -0.3795, 0.0002, 0
|
||||
A, 218, HIS, 3.7453, 1.7082, 0.7135, 1
|
||||
A, 219, GLU, 3.7748, 1.7246, 0.7170, 1
|
||||
A, 220, LEU, 0.0000, -0.3795, 0.0002, 0
|
||||
A, 221, GLY, 0.0000, -0.3795, 0.0002, 0
|
||||
A, 222, HIS, 4.0934, 1.9022, 0.7509, 1
|
||||
A, 223, SER, 0.0006, -0.3791, 0.0002, 0
|
||||
A, 224, LEU, 0.0014, -0.3787, 0.0002, 0
|
||||
A, 225, GLY, 0.0845, -0.3324, 0.0019, 0
|
||||
A, 226, LEU, 1.0232, 0.1909, 0.1472, 1
|
||||
A, 227, SER, 1.0418, 0.2012, 0.1521, 1
|
||||
A, 228, HIS, 4.3482, 2.0442, 0.7745, 1
|
||||
A, 229, SER, 0.3569, -0.1805, 0.0191, 0
|
||||
A, 230, THR, 0.2870, -0.2195, 0.0129, 0
|
||||
A, 231, ASP, 0.4405, -0.1339, 0.0283, 0
|
||||
A, 232, ILE, 1.0044, 0.1804, 0.1421, 0
|
||||
A, 233, GLY, 0.7892, 0.0604, 0.0887, 0
|
||||
A, 234, ALA, 0.8689, 0.1049, 0.1075, 0
|
||||
A, 235, LEU, 0.8973, 0.1207, 0.1145, 0
|
||||
A, 236, MET, 0.1265, -0.3089, 0.0033, 0
|
||||
A, 237, TYR, 1.2459, 0.3150, 0.2093, 0
|
||||
A, 238, PRO, 2.5814, 1.0594, 0.5377, 1
|
||||
A, 239, ASN, 0.8113, 0.0728, 0.0938, 1
|
||||
A, 240, TYR, 1.0336, 0.1967, 0.1499, 1
|
||||
A, 241, ILE, 1.0623, 0.2127, 0.1578, 0
|
||||
A, 242, TYR, 0.6169, -0.0356, 0.0541, 0
|
||||
A, 243, THR, 1.0067, 0.1817, 0.1427, 0
|
||||
A, 244, GLY, 0.2077, -0.2637, 0.0073, 0
|
||||
A, 245, ASP, 0.7730, 0.0514, 0.0852, 0
|
||||
A, 246, VAL, 0.7015, 0.0116, 0.0700, 0
|
||||
A, 247, GLN, 0.8216, 0.0785, 0.0962, 0
|
||||
A, 248, LEU, 0.3612, -0.1781, 0.0195, 0
|
||||
A, 249, SER, 0.3242, -0.1988, 0.0161, 0
|
||||
A, 250, GLN, 0.0671, -0.3420, 0.0014, 0
|
||||
A, 251, ASP, 0.5056, -0.0976, 0.0367, 0
|
||||
A, 252, ASP, 0.0813, -0.3341, 0.0018, 0
|
||||
A, 253, ILE, 0.1855, -0.2761, 0.0060, 0
|
||||
A, 254, ASP, 0.1656, -0.2872, 0.0050, 0
|
||||
A, 255, GLY, 0.0880, -0.3304, 0.0020, 0
|
||||
A, 256, ILE, 0.0825, -0.3335, 0.0018, 0
|
||||
A, 257, GLN, 0.0179, -0.3695, 0.0005, 0
|
||||
A, 258, ALA, 0.0397, -0.3573, 0.0008, 0
|
||||
A, 259, ILE, 0.0200, -0.3683, 0.0005, 0
|
||||
A, 260, TYR, 0.0171, -0.3700, 0.0004, 0
|
||||
A, 261, GLY, 0.0111, -0.3733, 0.0004, 0
|
||||
A, 262, PRO, 0.0258, -0.3651, 0.0006, 0
|
||||
A, 263, SER, 0.0373, -0.3587, 0.0008, 0
|
||||
A, 264, GLU, 0.0438, -0.3550, 0.0009, 0
|
||||
A, 265, ASN, 0.0210, -0.3677, 0.0005, 0
|
||||
A, 266, PRO, 0.0279, -0.3639, 0.0006, 0
|
||||
A, 267, VAL, 0.0102, -0.3738, 0.0004, 0
|
||||
A, 268, GLN, 0.0415, -0.3563, 0.0008, 0
|
||||
A, 269, PRO, 0.1411, -0.3008, 0.0039, 0
|
||||
A, 270, SER, 0.1538, -0.2937, 0.0045, 0
|
||||
A, 271, GLY, 0.1209, -0.3121, 0.0031, 0
|
||||
A, 272, PRO, 0.0212, -0.3677, 0.0005, 0
|
||||
A, 273, GLN, 0.3875, -0.1635, 0.0222, 0
|
||||
A, 274, THR, 0.2083, -0.2634, 0.0073, 0
|
||||
A, 275, PRO, 0.2263, -0.2533, 0.0085, 0
|
||||
A, 276, GLN, 0.3368, -0.1917, 0.0173, 0
|
||||
A, 277, VAL, 0.2312, -0.2506, 0.0088, 0
|
||||
A, 278, CYS, 0.1749, -0.2820, 0.0055, 0
|
||||
A, 279, ASP, 0.1950, -0.2708, 0.0066, 0
|
||||
A, 280, SER, 0.1181, -0.3136, 0.0030, 0
|
||||
A, 281, LYS, 0.0830, -0.3332, 0.0018, 0
|
||||
A, 282, LEU, 0.1455, -0.2984, 0.0041, 0
|
||||
A, 283, THR, 0.1634, -0.2884, 0.0049, 0
|
||||
A, 284, PHE, 0.1181, -0.3137, 0.0030, 0
|
||||
A, 285, ASP, 0.1488, -0.2965, 0.0043, 0
|
||||
A, 286, ALA, 0.0377, -0.3585, 0.0008, 0
|
||||
A, 287, ILE, 0.0131, -0.3722, 0.0004, 0
|
||||
A, 288, THR, 0.0395, -0.3574, 0.0008, 0
|
||||
A, 289, THR, 0.8047, 0.0691, 0.0923, 0
|
||||
A, 290, LEU, 0.5340, -0.0818, 0.0409, 4
|
||||
A, 291, ARG, 0.8059, 0.0697, 0.0925, 4
|
||||
A, 292, GLY, 0.4034, -0.1546, 0.0239, 0
|
||||
A, 293, GLU, 0.2966, -0.2142, 0.0137, 4
|
||||
A, 294, LEU, 0.0003, -0.3793, 0.0002, 0
|
||||
A, 295, MET, 0.0436, -0.3552, 0.0009, 0
|
||||
A, 296, PHE, 0.0000, -0.3795, 0.0002, 0
|
||||
A, 297, PHE, 0.0000, -0.3795, 0.0002, 0
|
||||
A, 298, LYS, 0.1681, -0.2858, 0.0052, 0
|
||||
A, 299, ASP, 0.1661, -0.2869, 0.0051, 0
|
||||
A, 300, ARG, 0.8416, 0.0897, 0.1009, 0
|
||||
A, 301, PHE, 0.2805, -0.2231, 0.0124, 0
|
||||
A, 302, TYR, 0.0510, -0.3510, 0.0010, 0
|
||||
A, 303, MET, 0.0273, -0.3642, 0.0006, 0
|
||||
A, 304, ARG, 0.2061, -0.2646, 0.0072, 4
|
||||
A, 305, THR, 0.0500, -0.3516, 0.0010, 0
|
||||
A, 306, ASN, 0.4343, -0.1374, 0.0276, 0
|
||||
A, 307, SER, 0.2484, -0.2410, 0.0100, 0
|
||||
A, 308, PHE, 0.3544, -0.1819, 0.0189, 0
|
||||
A, 309, TYR, 0.3307, -0.1951, 0.0167, 0
|
||||
A, 310, PRO, 0.1885, -0.2744, 0.0062, 0
|
||||
A, 311, GLU, 0.1706, -0.2844, 0.0053, 0
|
||||
A, 312, VAL, 0.0868, -0.3311, 0.0019, 0
|
||||
A, 313, GLU, 0.2440, -0.2435, 0.0097, 0
|
||||
A, 314, LEU, 0.1932, -0.2718, 0.0065, 0
|
||||
A, 315, ASN, 0.1979, -0.2691, 0.0067, 0
|
||||
A, 316, PHE, 0.9436, 0.1465, 0.1262, 0
|
||||
A, 317, ILE, 0.1205, -0.3123, 0.0031, 0
|
||||
A, 318, SER, 0.1928, -0.2720, 0.0065, 0
|
||||
A, 319, VAL, 0.2769, -0.2251, 0.0121, 0
|
||||
A, 320, PHE, 0.3676, -0.1746, 0.0202, 4
|
||||
A, 321, TRP, 0.4438, -0.1321, 0.0287, 4
|
||||
A, 322, PRO, 0.0460, -0.3538, 0.0009, 0
|
||||
A, 323, GLN, 0.0558, -0.3484, 0.0011, 0
|
||||
A, 324, VAL, 0.0441, -0.3549, 0.0009, 0
|
||||
A, 325, PRO, 0.0627, -0.3445, 0.0013, 0
|
||||
A, 326, ASN, 0.1814, -0.2783, 0.0058, 0
|
||||
A, 327, GLY, 0.0472, -0.3531, 0.0010, 0
|
||||
A, 328, LEU, 0.0614, -0.3452, 0.0013, 0
|
||||
A, 329, GLN, 0.0961, -0.3259, 0.0022, 0
|
||||
A, 330, ALA, 0.0162, -0.3704, 0.0004, 0
|
||||
A, 331, ALA, 0.0131, -0.3722, 0.0004, 0
|
||||
A, 332, TYR, 0.2752, -0.2261, 0.0120, 0
|
||||
A, 333, GLU, 0.8135, 0.0740, 0.0943, 0
|
||||
A, 334, ILE, 0.7341, 0.0297, 0.0768, 0
|
||||
A, 335, ALA, 0.7233, 0.0237, 0.0745, 0
|
||||
A, 336, ASP, 0.2315, -0.2504, 0.0088, 0
|
||||
A, 337, ARG, 0.4673, -0.1190, 0.0316, 2
|
||||
A, 338, ASP, 0.0683, -0.3414, 0.0014, 0
|
||||
A, 339, GLU, 0.6939, 0.0073, 0.0684, 2
|
||||
A, 340, VAL, 0.3418, -0.1889, 0.0177, 4
|
||||
A, 341, ARG, 0.8427, 0.0903, 0.1012, 2
|
||||
A, 342, PHE, 0.0704, -0.3402, 0.0015, 0
|
||||
A, 343, PHE, 0.0053, -0.3765, 0.0003, 0
|
||||
A, 344, LYS, 0.0437, -0.3551, 0.0009, 0
|
||||
A, 345, GLY, 0.0214, -0.3675, 0.0005, 0
|
||||
A, 346, ASN, 0.0151, -0.3710, 0.0004, 0
|
||||
A, 347, LYS, 0.0419, -0.3561, 0.0009, 0
|
||||
A, 348, TYR, 0.8434, 0.0907, 0.1013, 2
|
||||
A, 349, TRP, 0.0432, -0.3554, 0.0009, 0
|
||||
A, 350, ALA, 0.5089, -0.0958, 0.0372, 0
|
||||
A, 351, VAL, 0.3450, -0.1871, 0.0180, 0
|
||||
A, 352, ARG, 0.3314, -0.1947, 0.0167, 0
|
||||
A, 353, GLY, 0.4078, -0.1521, 0.0244, 4
|
||||
A, 354, GLN, 0.4438, -0.1321, 0.0287, 4
|
||||
A, 355, ASP, 0.0594, -0.3464, 0.0012, 0
|
||||
A, 356, VAL, 0.0179, -0.3695, 0.0005, 0
|
||||
A, 357, LEU, 0.0890, -0.3298, 0.0020, 2
|
||||
A, 358, TYR, 0.1045, -0.3212, 0.0025, 0
|
||||
A, 359, GLY, 0.0628, -0.3445, 0.0013, 0
|
||||
A, 360, TYR, 0.8901, 0.1167, 0.1127, 2
|
||||
A, 361, PRO, 0.0343, -0.3604, 0.0007, 0
|
||||
A, 362, LYS, 0.6710, -0.0054, 0.0640, 2
|
||||
A, 363, ASP, 0.0129, -0.3723, 0.0004, 0
|
||||
A, 364, ILE, 0.0007, -0.3790, 0.0002, 0
|
||||
A, 365, HIS, 0.0164, -0.3703, 0.0004, 0
|
||||
A, 366, ARG, 0.1371, -0.3031, 0.0038, 2
|
||||
A, 367, SER, 0.6973, 0.0092, 0.0691, 2
|
||||
A, 368, PHE, 0.8040, 0.0687, 0.0921, 2
|
||||
A, 369, GLY, 0.0778, -0.3361, 0.0017, 0
|
||||
A, 370, PHE, 0.0657, -0.3428, 0.0014, 0
|
||||
A, 371, PRO, 0.1676, -0.2860, 0.0051, 0
|
||||
A, 372, SER, 0.0247, -0.3657, 0.0006, 0
|
||||
A, 373, THR, 0.1715, -0.2839, 0.0053, 0
|
||||
A, 374, VAL, 0.1353, -0.3040, 0.0037, 0
|
||||
A, 375, LYS, 0.1006, -0.3234, 0.0024, 0
|
||||
A, 376, ASN, 0.0426, -0.3557, 0.0009, 0
|
||||
A, 377, ILE, 0.0465, -0.3536, 0.0009, 0
|
||||
A, 378, ASP, 0.1268, -0.3088, 0.0033, 0
|
||||
A, 379, ALA, 0.0195, -0.3686, 0.0005, 0
|
||||
A, 380, ALA, 0.0184, -0.3692, 0.0005, 0
|
||||
A, 381, VAL, 0.0349, -0.3600, 0.0007, 0
|
||||
A, 382, PHE, 0.4664, -0.1195, 0.0314, 0
|
||||
A, 383, GLU, 0.1765, -0.2811, 0.0056, 0
|
||||
A, 384, GLU, 0.8039, 0.0687, 0.0921, 0
|
||||
A, 385, ASP, 0.0373, -0.3587, 0.0008, 0
|
||||
A, 386, THR, 0.2375, -0.2471, 0.0092, 0
|
||||
A, 387, GLY, 0.0918, -0.3283, 0.0021, 0
|
||||
A, 388, LYS, 0.2845, -0.2209, 0.0127, 0
|
||||
A, 389, THR, 0.0000, -0.3795, 0.0002, 0
|
||||
A, 390, TYR, 0.4105, -0.1506, 0.0247, 0
|
||||
A, 391, PHE, 0.0000, -0.3795, 0.0002, 0
|
||||
A, 392, PHE, 0.0023, -0.3782, 0.0003, 0
|
||||
A, 393, VAL, 0.1649, -0.2875, 0.0050, 0
|
||||
A, 394, ALA, 0.0816, -0.3340, 0.0018, 0
|
||||
A, 395, HIS, 0.0868, -0.3311, 0.0019, 0
|
||||
A, 396, GLU, 0.1756, -0.2816, 0.0055, 0
|
||||
A, 397, CYS, 0.0509, -0.3511, 0.0010, 0
|
||||
A, 398, TRP, 0.1962, -0.2701, 0.0066, 0
|
||||
A, 399, ARG, 0.4601, -0.1230, 0.0306, 0
|
||||
A, 400, TYR, 0.5013, -0.1000, 0.0361, 2
|
||||
A, 401, ASP, 0.0555, -0.3485, 0.0011, 0
|
||||
A, 402, GLU, 0.8097, 0.0719, 0.0934, 2
|
||||
A, 403, TYR, 0.0641, -0.3437, 0.0013, 0
|
||||
A, 404, LYS, 0.0135, -0.3719, 0.0004, 0
|
||||
A, 405, GLN, 0.0524, -0.3503, 0.0011, 0
|
||||
A, 406, SER, 0.0809, -0.3344, 0.0018, 0
|
||||
A, 407, MET, 0.1097, -0.3183, 0.0027, 0
|
||||
A, 408, ASP, 0.1959, -0.2702, 0.0066, 0
|
||||
A, 409, THR, 0.0678, -0.3417, 0.0014, 0
|
||||
A, 410, GLY, 0.0565, -0.3480, 0.0012, 0
|
||||
A, 411, TYR, 0.4213, -0.1446, 0.0260, 0
|
||||
A, 412, PRO, 0.1375, -0.3028, 0.0038, 0
|
||||
A, 413, LYS, 0.2158, -0.2592, 0.0078, 0
|
||||
A, 414, MET, 0.0409, -0.3566, 0.0008, 0
|
||||
A, 415, ILE, 0.0148, -0.3712, 0.0004, 0
|
||||
A, 416, ALA, 0.0330, -0.3611, 0.0007, 0
|
||||
A, 417, GLU, 0.0264, -0.3648, 0.0006, 0
|
||||
A, 418, GLU, 0.3283, -0.1965, 0.0164, 0
|
||||
A, 419, PHE, 0.0555, -0.3485, 0.0011, 0
|
||||
A, 420, PRO, 0.0226, -0.3669, 0.0005, 0
|
||||
A, 421, GLY, 0.0633, -0.3442, 0.0013, 0
|
||||
A, 422, ILE, 0.0625, -0.3447, 0.0013, 0
|
||||
A, 423, GLY, 0.0630, -0.3443, 0.0013, 0
|
||||
A, 424, ASN, 0.0676, -0.3418, 0.0014, 0
|
||||
A, 425, LYS, 0.1803, -0.2790, 0.0058, 0
|
||||
A, 426, VAL, 0.0831, -0.3332, 0.0018, 0
|
||||
A, 427, ASP, 0.1773, -0.2807, 0.0056, 0
|
||||
A, 428, ALA, 0.0393, -0.3576, 0.0008, 0
|
||||
A, 429, VAL, 0.0184, -0.3692, 0.0005, 0
|
||||
A, 430, PHE, 0.0287, -0.3634, 0.0006, 0
|
||||
A, 431, GLN, 0.7617, 0.0451, 0.0826, 0
|
||||
A, 432, LYS, 0.5886, -0.0514, 0.0495, 0
|
||||
A, 433, ASP, 0.6096, -0.0397, 0.0529, 0
|
||||
A, 434, GLY, 0.0381, -0.3582, 0.0008, 0
|
||||
A, 435, PHE, 0.3123, -0.2054, 0.0150, 0
|
||||
A, 436, LEU, 0.0028, -0.3779, 0.0003, 0
|
||||
A, 437, TYR, 1.2080, 0.2939, 0.1986, 0
|
||||
A, 438, PHE, 0.0129, -0.3723, 0.0004, 0
|
||||
A, 439, PHE, 0.0129, -0.3723, 0.0004, 0
|
||||
A, 440, HIS, 0.1039, -0.3216, 0.0025, 0
|
||||
A, 441, GLY, 0.0762, -0.3370, 0.0016, 0
|
||||
A, 442, THR, 0.0582, -0.3470, 0.0012, 0
|
||||
A, 443, ARG, 0.0748, -0.3378, 0.0016, 0
|
||||
A, 444, GLN, 0.9015, 0.1231, 0.1155, 0
|
||||
A, 445, TYR, 0.2509, -0.2396, 0.0102, 0
|
||||
A, 446, GLN, 0.8646, 0.1025, 0.1064, 0
|
||||
A, 447, PHE, 0.0050, -0.3767, 0.0003, 0
|
||||
A, 448, ASP, 0.0426, -0.3557, 0.0009, 0
|
||||
A, 449, PHE, 0.4075, -0.1523, 0.0244, 0
|
||||
A, 450, LYS, 0.0456, -0.3541, 0.0009, 0
|
||||
A, 451, THR, 0.0140, -0.3716, 0.0004, 0
|
||||
A, 452, LYS, 0.2891, -0.2183, 0.0131, 0
|
||||
A, 453, ARG, 0.0130, -0.3722, 0.0004, 0
|
||||
A, 454, ILE, 0.0434, -0.3553, 0.0009, 0
|
||||
A, 455, LEU, 0.0502, -0.3515, 0.0010, 0
|
||||
A, 456, THR, 0.6377, -0.0240, 0.0578, 0
|
||||
A, 457, LEU, 0.1150, -0.3154, 0.0029, 0
|
||||
A, 458, GLN, 0.9360, 0.1423, 0.1243, 0
|
||||
A, 459, LYS, 0.3229, -0.1995, 0.0159, 0
|
||||
A, 460, ALA, 0.0221, -0.3672, 0.0005, 0
|
||||
A, 461, ASN, 0.1549, -0.2931, 0.0045, 0
|
||||
A, 462, SER, 1.0288, 0.1940, 0.1487, 0
|
||||
A, 463, TRP, 1.5103, 0.4624, 0.2856, 0
|
||||
A, 464, PHE, 0.0896, -0.3295, 0.0020, 0
|
||||
A, 465, ASN, 0.0767, -0.3367, 0.0016, 0
|
||||
A, 466, CYS, 0.1336, -0.3050, 0.0036, 0
|
||||
|
@@ -1,195 +0,0 @@
|
||||
version: 2.5-dev.12
|
||||
git head: aae633f5
|
||||
|
||||
Params[
|
||||
apoholo_use_for_eval = false
|
||||
apoholo_use_for_train = false
|
||||
atom_table_feat_keep_sgn = false
|
||||
atom_table_feat_pow = 2.0
|
||||
atom_table_features = [apRawValids, apRawInvalids, atomicHydrophobicity]
|
||||
average_feat_vectors = false
|
||||
avg_pow = 1.0
|
||||
avg_weighted = false
|
||||
balance_class_weights = false
|
||||
balance_density = false
|
||||
balance_density_radius = 2.0
|
||||
cache_datasets = false
|
||||
chains = keep
|
||||
check_vectors = false
|
||||
classifier = FastRandomForest
|
||||
classifier_train_stats = false
|
||||
clear_prim_caches = false
|
||||
clear_sec_caches = false
|
||||
collect_eval_vectors = false
|
||||
collect_only_once = true
|
||||
conserv_cloud_radius = 10.0
|
||||
conservation_dirs = []
|
||||
conservation_exponent = 1
|
||||
crossval_threads = 1
|
||||
dataset_base_dir = C:\PHD\WORKSPACE\P2RANK\p2rank-private\distro\test_data
|
||||
deep_surrounding = false
|
||||
delete_models = true
|
||||
delete_vectors = true
|
||||
electrostatics_dirs = []
|
||||
eval_tolerances = [0, 1, 2, 4, 10, 99]
|
||||
extended_pocket_cutoff = 3.5
|
||||
extra_features = []
|
||||
fail_fast = false
|
||||
fail_on_conserv_seq_mismatch = false
|
||||
false_positive_cost = 2.0
|
||||
feat_aa_properties = []
|
||||
feat_asa_neigh_radius = 6.0
|
||||
feat_asa_probe_radius = 1.4
|
||||
feat_asa_probe_radius2 = 3.0
|
||||
feat_crang_contact_dist = 3.0
|
||||
feat_csv_columns = []
|
||||
feat_csv_directories = []
|
||||
feat_csv_ignore_missing = false
|
||||
feat_pmass_natoms = 70
|
||||
feat_pmass_nsasp = 40
|
||||
feat_pmass_radius = 11.0
|
||||
feat_propensity_tables = SprintT1070
|
||||
feat_stmotif_motifs = [C2H2, C4, C3H1, E1H2, C2H1, H3, D1H2, C3, D1H1, E1H1, C1H3, C2, H2]
|
||||
feat_stmotif_radius = 4.0
|
||||
feat_stmotif_useradius = true
|
||||
feature_filters = []
|
||||
feature_importances = false
|
||||
features = [chem, volsite, protrusion, bfactor]
|
||||
folds = 5
|
||||
fpocket_command = fpocket
|
||||
grid_cell_edge = 2.0
|
||||
grid_cutoff_radius = 3.4
|
||||
hopt_cache_labeled_points = false
|
||||
hopt_max_iterations = 1000
|
||||
hopt_objective = DCA_4_0
|
||||
hopt_optimizer = spearmint
|
||||
hopt_python_command = python
|
||||
hopt_spearmint_dir =
|
||||
hopt_train_only_once = false
|
||||
identify_peptides_by_labeling = false
|
||||
ignore_het_groups = [HOH, DOD, WAT, NAG, MAN, UNK, GLC, ABA, MPD, GOL, SO4, PO4]
|
||||
inner_classifier = FastRandomForest
|
||||
installDir = C:\PHD\WORKSPACE\P2RANK\p2rank-private\distro
|
||||
label_residues = true
|
||||
ligand_clustering_distance = 1.7
|
||||
ligand_derived_point_labeling = true
|
||||
ligand_induced_volume_cutoff = 2.5
|
||||
ligand_protein_contact_distance = 4.0
|
||||
ligc_prot_dist = 5.5
|
||||
load_conservation = false
|
||||
loaded_pockets_limit = 0
|
||||
log_cases = true
|
||||
log_level = INFO
|
||||
log_scores_to_file =
|
||||
log_to_console = true
|
||||
log_to_file = true
|
||||
loop = 1
|
||||
max_train_instances = 0
|
||||
meta_classifier_iterations = 5
|
||||
min_ligand_atoms = 5
|
||||
model = default
|
||||
neighbourhood_radius = 6.0
|
||||
neutral_points_margin = 5.5
|
||||
out_file = <null>
|
||||
out_format = keep
|
||||
out_prefix_date = false
|
||||
out_subdir = <null>
|
||||
output_base_dir = C:\PHD\WORKSPACE\P2RANK\p2rank-private\distro\test_output
|
||||
output_only_stats = false
|
||||
pair_hist_bins = 5
|
||||
pair_hist_deep = true
|
||||
pair_hist_normalize = false
|
||||
pair_hist_radius = 6.0
|
||||
pair_hist_smooth = false
|
||||
pair_hist_subsample_limit = 0
|
||||
parallel = true
|
||||
plb_rescorer_atomic = false
|
||||
ploop_delete_runs = false
|
||||
ploop_zip_runs = false
|
||||
point_max_distfrom_pocket = 4.5
|
||||
point_min_distfrom_protein = 2.5
|
||||
point_sampler = SurfacePointSampler
|
||||
point_sampling_strategy = surface
|
||||
point_score_pow = 2.0
|
||||
positive_def_ligtypes = [relevant]
|
||||
positive_point_ligand_distance = 2.6
|
||||
pred_clustering_dist = 3.0
|
||||
pred_min_cluster_size = 3
|
||||
pred_point_threshold = 0.35
|
||||
pred_protein_surface_cutoff = 3.5
|
||||
predict_residues = false
|
||||
predictions = true
|
||||
probatp_res_transformer = residue/default_ProbabilityScoreTransformer.json
|
||||
probatp_transformer = default_ProbabilityScoreTransformer.json
|
||||
protr_hist_bins = 5
|
||||
protr_hist_cumulative = false
|
||||
protr_hist_relative = false
|
||||
protrusion_radius = 10.0
|
||||
r_generate_plots = true
|
||||
r_plot_stddevs = false
|
||||
r_threads = 2
|
||||
randomize_seed = false
|
||||
rescorer = ModelBasedRescorer
|
||||
residue_point_score_pow = -1.0
|
||||
residue_score_extra_dist = 2.0
|
||||
residue_score_only_exposed = false
|
||||
residue_score_sum_to_avg = 0.0
|
||||
residue_score_threshold = 1.0
|
||||
residue_score_transform = NONE
|
||||
residue_table_features = []
|
||||
rf_bagsize = 100
|
||||
rf_batch_prediction = true
|
||||
rf_depth = 0
|
||||
rf_ensure_leaves_normalized = false
|
||||
rf_features = 0
|
||||
rf_flatten = false
|
||||
rf_flatten_as_legacy = true
|
||||
rf_threads = 0
|
||||
rf_trees = 100
|
||||
sample_negatives_from_decoys = false
|
||||
sampling_multiplier = 3
|
||||
score_pockets_by = p2rank
|
||||
score_point_limit = 0
|
||||
seed = 42
|
||||
selected_stats = [DCA_4_0, DCA_4_2, DCA_4_4, DCC_10_0, DCC_10_2, DSOR_02_0, DSOR_02_2, DSWO_05_0, DSWO_05_2, point_MCC, point_TPX, point_LOG_LOSS, AVG_DSO_SUCC, AVG_LIGCOV_SUCC, AVG_POCKETS, AVG_POCKET_SAS_POINTS, AVG_POCKET_SAS_POINTS_TRUE_POCKETS, TIME_MINUTES]
|
||||
smooth_representation = false
|
||||
smoothing_radius = 4.5
|
||||
solvent_radius = 1.6
|
||||
ss_cloud_radius = 10.0
|
||||
stats_collect_predictions = true
|
||||
stats_curves = false
|
||||
stdout_timestamp =
|
||||
strict_inner_points = false
|
||||
subsampl_high_protrusion_negatives = false
|
||||
subsample = false
|
||||
supersample = false
|
||||
surface_additional_cutoff = 2.5
|
||||
target_class_ratio = 0.1
|
||||
target_class_weight_ratio = 0.1
|
||||
tessellation = 2
|
||||
threads = 17
|
||||
train_lig_cutoff = 0.0
|
||||
train_pockets = 9
|
||||
train_protein_limit = 0
|
||||
train_random_rotated_copies = 0
|
||||
train_score_transformers = []
|
||||
train_score_transformers_for_residues = false
|
||||
train_tessellation = 2
|
||||
train_tessellation_negatives = 2
|
||||
use_kdtree_cutout_sphere_thrashold = 150
|
||||
use_only_positive_score = true
|
||||
use_optimized_surface = true
|
||||
vis_all_surface = false
|
||||
vis_copy_proteins = true
|
||||
vis_generate_proteins = true
|
||||
vis_highlight_ligands = false
|
||||
visualizations = true
|
||||
weight_dist_param = 4.5
|
||||
weight_function = INV
|
||||
weight_power = 2.0
|
||||
weight_sigma = 2.2
|
||||
zip_log_file = false
|
||||
zip_visualizations = false
|
||||
zscoretp_res_transformer = residue/default_ZscoreTpTransformer.json
|
||||
zscoretp_transformer = default_ZscoreTpTransformer.json
|
||||
]
|
||||
@@ -1,75 +0,0 @@
|
||||
|
||||
from pymol import cmd,stored
|
||||
|
||||
set depth_cue, 1
|
||||
set fog_start, 0.4
|
||||
|
||||
set_color b_col, [36,36,85]
|
||||
set_color t_col, [10,10,10]
|
||||
set bg_rgb_bottom, b_col
|
||||
set bg_rgb_top, t_col
|
||||
set bg_gradient
|
||||
|
||||
set spec_power = 200
|
||||
set spec_refl = 0
|
||||
|
||||
load "data/1fbl.pdb", protein
|
||||
create ligands, protein and organic
|
||||
select xlig, protein and organic
|
||||
delete xlig
|
||||
|
||||
hide everything, all
|
||||
|
||||
color white, elem c
|
||||
color bluewhite, protein
|
||||
#show_as cartoon, protein
|
||||
show surface, protein
|
||||
#set transparency, 0.15
|
||||
|
||||
show sticks, ligands
|
||||
set stick_color, magenta
|
||||
|
||||
|
||||
|
||||
|
||||
# SAS points
|
||||
|
||||
load "data/1fbl.pdb_points.pdb.gz", points
|
||||
hide nonbonded, points
|
||||
show nb_spheres, points
|
||||
set sphere_scale, 0.2, points
|
||||
cmd.spectrum("b", "green_red", selection="points", minimum=0, maximum=0.7)
|
||||
|
||||
|
||||
stored.list=[]
|
||||
cmd.iterate("(resn STP)","stored.list.append(resi)") # read info about residues STP
|
||||
lastSTP=stored.list[-1] # get the index of the last residue
|
||||
hide lines, resn STP
|
||||
|
||||
cmd.select("rest", "resn STP and resi 0")
|
||||
|
||||
for my_index in range(1,int(lastSTP)+1): cmd.select("pocket"+str(my_index), "resn STP and resi "+str(my_index))
|
||||
for my_index in range(1,int(lastSTP)+1): cmd.show("spheres","pocket"+str(my_index))
|
||||
for my_index in range(1,int(lastSTP)+1): cmd.set("sphere_scale","0.4","pocket"+str(my_index))
|
||||
for my_index in range(1,int(lastSTP)+1): cmd.set("sphere_transparency","0.1","pocket"+str(my_index))
|
||||
|
||||
|
||||
|
||||
set_color pcol1 = [0.361,0.576,0.902]
|
||||
select surf_pocket1, protein and id [991,992,993,994,1033,1035,1036,1026,664,670,676,971,679,958,959,960,961,962,963,938,942,972,934,929,943,989,1016,32,692,700,33,1118,1119,658,659,1122,1124,651,1112,1106]
|
||||
set surface_color, pcol1, surf_pocket1
|
||||
set_color pcol2 = [0.490,0.278,0.702]
|
||||
select surf_pocket2, protein and id [2109,2144,2091,2092,1991,2150,2151,2161,2163,2444,1891,2426,2439,1910,2064,1909,1890,1926]
|
||||
set surface_color, pcol2, surf_pocket2
|
||||
set_color pcol3 = [0.902,0.361,0.682]
|
||||
select surf_pocket3, protein and id [760,761,730,728,746,173,514,515,171,172,501,472,499,532,560]
|
||||
set surface_color, pcol3, surf_pocket3
|
||||
set_color pcol4 = [0.702,0.408,0.278]
|
||||
select surf_pocket4, protein and id [1488,1497,1513,1619,1620,1769,1490,1756,1757,1489,1766,1917,1499,2030,2031,2034,2035]
|
||||
set surface_color, pcol4, surf_pocket4
|
||||
|
||||
|
||||
deselect
|
||||
|
||||
orient
|
||||
|
||||
Binary file not shown.
@@ -1,84 +0,0 @@
|
||||
|
||||
from pymol import cmd,stored
|
||||
|
||||
set depth_cue, 1
|
||||
set fog_start, 0.4
|
||||
|
||||
set_color b_col, [36,36,85]
|
||||
set_color t_col, [10,10,10]
|
||||
set bg_rgb_bottom, b_col
|
||||
set bg_rgb_top, t_col
|
||||
set bg_gradient
|
||||
|
||||
set spec_power = 200
|
||||
set spec_refl = 0
|
||||
|
||||
load "data/1fbl.pdb", protein
|
||||
create ligands, protein and organic
|
||||
select xlig, protein and organic
|
||||
delete xlig
|
||||
|
||||
hide everything, all
|
||||
|
||||
color white, elem c
|
||||
color bluewhite, protein
|
||||
#show_as cartoon, protein
|
||||
show surface, protein
|
||||
#set transparency, 0.15
|
||||
|
||||
show sticks, ligands
|
||||
set stick_color, magenta
|
||||
|
||||
|
||||
|
||||
|
||||
# SAS points
|
||||
|
||||
load "data/1fbl.pdb_points.pdb.gz", points
|
||||
hide nonbonded, points
|
||||
show nb_spheres, points
|
||||
set sphere_scale, 0.2, points
|
||||
cmd.spectrum("b", "green_red", selection="points", minimum=0, maximum=0.7)
|
||||
|
||||
|
||||
stored.list=[]
|
||||
cmd.iterate("(resn STP)","stored.list.append(resi)") # read info about residues STP
|
||||
lastSTP=stored.list[-1] # get the index of the last residue
|
||||
hide lines, resn STP
|
||||
|
||||
cmd.select("rest", "resn STP and resi 0")
|
||||
|
||||
for my_index in range(1,int(lastSTP)+1): cmd.select("pocket"+str(my_index), "resn STP and resi "+str(my_index))
|
||||
for my_index in range(1,int(lastSTP)+1): cmd.show("spheres","pocket"+str(my_index))
|
||||
for my_index in range(1,int(lastSTP)+1): cmd.set("sphere_scale","0.4","pocket"+str(my_index))
|
||||
for my_index in range(1,int(lastSTP)+1): cmd.set("sphere_transparency","0.1","pocket"+str(my_index))
|
||||
|
||||
|
||||
|
||||
set_color pcol1 = [0.361,0.576,0.902]
|
||||
select surf_pocket1, protein and id [963,990,991,992,993,994,1027,1033,1035,1036,1025,1026,664,667,670,671,676,971,679,958,959,960,961,962,938,942,943,972,661,934,929,988,989,1016,682,700,692,693,696,32,33,1105,1106,1111,1117,651,653,644,646,1112,1113,1118,1119,658,659,1122,1124,657]
|
||||
set surface_color, pcol1, surf_pocket1
|
||||
set_color pcol2 = [0.329,0.278,0.702]
|
||||
select surf_pocket2, protein and id [758,760,173,514,515,761,730,728,746,171,172,501,472,499,498,564,582,560,570,532,561]
|
||||
set surface_color, pcol2, surf_pocket2
|
||||
set_color pcol3 = [0.698,0.361,0.902]
|
||||
select surf_pocket3, protein and id [2107,2109,2144,2152,2091,2092,1991,2150,2151,2161,2163,2444,1890,1891,2426,2439,2459,2455,1910,2064,1908,1909,1926]
|
||||
set surface_color, pcol3, surf_pocket3
|
||||
set_color pcol4 = [0.702,0.278,0.639]
|
||||
select surf_pocket4, protein and id [1488,1490,1486,1495,1497,1513,1619,1620,2039,1754,1757,1750,1528,1756,1769,1489,1766,1917,1498,1499,1900,2030,2031,2034,2035,2038,1896,1897,1902,1899,1901,2017]
|
||||
set surface_color, pcol4, surf_pocket4
|
||||
set_color pcol5 = [0.902,0.361,0.545]
|
||||
select surf_pocket5, protein and id [2936,2937,2772,2924,2926,2927,2928,2925,2895,2896,2898,1637,2935,2938,2940,2674,2708,2686,2688,2705,2707,2770,2771,2939,2789,2881,2791,2792,2793]
|
||||
set surface_color, pcol5, surf_pocket5
|
||||
set_color pcol6 = [0.702,0.353,0.278]
|
||||
select surf_pocket6, protein and id [1482,1860,1861,2652,2653,1481,1491,1502,2666,2659,2663,2667,1492,1870,1874,2280,2281,2282,2283,2284,1857,1856,2263,2259,2656]
|
||||
set surface_color, pcol6, surf_pocket6
|
||||
set_color pcol7 = [0.902,0.729,0.361]
|
||||
select surf_pocket7, protein and id [2411,2503,2558,2559,2309,2312,2413,2330,2848,2822,2823,2847,2298,2297,2299,2329]
|
||||
set surface_color, pcol7, surf_pocket7
|
||||
|
||||
|
||||
deselect
|
||||
|
||||
orient
|
||||
|
||||
File diff suppressed because it is too large
Load Diff
@@ -684,11 +684,17 @@ class Params {
|
||||
boolean feature_importances = false
|
||||
|
||||
/**
|
||||
* produce pymol visualisations
|
||||
* produce visualisations
|
||||
*/
|
||||
@RuntimeParam
|
||||
boolean visualizations = true
|
||||
|
||||
/**
|
||||
* Renderers used to produce visualizations. Available renderers: [pymol, chimerax]
|
||||
*/
|
||||
@RuntimeParam
|
||||
List<String> vis_renderers = ["pymol", "chimerax"]
|
||||
|
||||
/**
|
||||
* visualize all surface points (not just inner pocket points)
|
||||
*/
|
||||
|
||||
@@ -1,266 +0,0 @@
|
||||
package cz.siret.prank.program.rendering
|
||||
|
||||
import cz.siret.prank.domain.*
|
||||
import cz.siret.prank.domain.labeling.LabeledPoint
|
||||
import cz.siret.prank.geom.Atoms
|
||||
import cz.siret.prank.prediction.pockets.rescorers.ModelBasedRescorer
|
||||
import cz.siret.prank.program.params.Parametrized
|
||||
import cz.siret.prank.utils.ColorUtils
|
||||
import cz.siret.prank.utils.Futils
|
||||
import groovy.transform.CompileStatic
|
||||
import groovy.util.logging.Slf4j
|
||||
import org.biojava.nbio.structure.Atom
|
||||
import org.zeroturnaround.zip.NameMapper
|
||||
import org.zeroturnaround.zip.ZipUtil
|
||||
|
||||
import java.awt.*
|
||||
import java.util.List
|
||||
|
||||
import static cz.siret.prank.utils.Futils.writeFile
|
||||
|
||||
/**
|
||||
* Generates PyMol visualizations.
|
||||
*
|
||||
* Used for visualization of binding site predictions.
|
||||
*/
|
||||
@Slf4j
|
||||
@CompileStatic
|
||||
class OldPymolRenderer implements Parametrized {
|
||||
|
||||
String outdir
|
||||
|
||||
OldPymolRenderer(String outputDir) {
|
||||
this.outdir = outputDir
|
||||
}
|
||||
|
||||
static String pyColor(Color c) {
|
||||
sprintf "[%5.3f,%5.3f,%5.3f]", c.red/255, c.green/255, c.blue/255
|
||||
}
|
||||
|
||||
void render(Dataset.Item item, ModelBasedRescorer rescorer, PredictionPair pair) {
|
||||
|
||||
String label = item.label
|
||||
|
||||
String pmlf = "$outdir/${label}.pml"
|
||||
String pointsDir = "$outdir/data"
|
||||
|
||||
Futils.mkdirs(pointsDir)
|
||||
|
||||
String pointsf = "$pointsDir/${label}_points.pdb.gz"
|
||||
String pointsfRelName = "data/${label}_points.pdb.gz"
|
||||
|
||||
String proteinf = Futils.absPath(item.proteinFile)
|
||||
String proteinfabs = proteinf
|
||||
if (params.vis_copy_proteins) {
|
||||
String name = Futils.shortName(proteinf)
|
||||
String newf = "$pointsDir/$name"
|
||||
String newfrel = "data/$name"
|
||||
|
||||
log.info "copying [$proteinf] to [$newf]"
|
||||
Futils.copy(proteinf, newf)
|
||||
|
||||
proteinf = newfrel
|
||||
proteinfabs = newf
|
||||
}
|
||||
|
||||
writeFile(pmlf, renderMainPmlScript(proteinf, pointsfRelName, pair))
|
||||
|
||||
Writer pdb = Futils.getGzipWriter(pointsf)
|
||||
int i = 0
|
||||
for (LabeledPoint lp : rescorer.labeledPoints) {
|
||||
double beta = lp.score
|
||||
Atom p = lp.point
|
||||
def lab = "STP"
|
||||
|
||||
pdb.printf "HETATM%5d H %3s 1 %2d %8.3f%8.3f%8.3f 0.50%6.3f\n", i, lab, lp.pocket, p.x, p.y, p.z, beta
|
||||
i++
|
||||
}
|
||||
pdb.close()
|
||||
|
||||
|
||||
if (params.zip_visualizations) {
|
||||
List<File> fileList = [new File(pmlf), new File(pointsf)]
|
||||
if (params.vis_copy_proteins) {
|
||||
fileList.add(new File(proteinfabs))
|
||||
}
|
||||
File zipFile = new File("$outdir/${label}_visualization.zip")
|
||||
NameMapper mapper = { String fileName ->
|
||||
return fileName.endsWith(".pml") ? fileName : "data/".concat(fileName)
|
||||
}
|
||||
ZipUtil.packEntries(fileList.toArray(new File[0]) as File[], zipFile, mapper)
|
||||
fileList.forEach({ File f -> f.delete() })
|
||||
}
|
||||
}
|
||||
|
||||
private String renderMainPmlScript(String proteinFile, String pointsFileRelative, PredictionPair pair) {
|
||||
// language=python
|
||||
"""
|
||||
from pymol import cmd,stored
|
||||
|
||||
set depth_cue, 1
|
||||
set fog_start, 0.4
|
||||
|
||||
set_color b_col, [36,36,85]
|
||||
set_color t_col, [10,10,10]
|
||||
set bg_rgb_bottom, b_col
|
||||
set bg_rgb_top, t_col
|
||||
set bg_gradient
|
||||
|
||||
set spec_power = 200
|
||||
set spec_refl = 0
|
||||
|
||||
load "$proteinFile", protein
|
||||
create ligands, protein and organic
|
||||
select xlig, protein and organic
|
||||
delete xlig
|
||||
|
||||
hide everything, all
|
||||
|
||||
color white, elem c
|
||||
color bluewhite, protein
|
||||
#show_as cartoon, protein
|
||||
show surface, protein
|
||||
#set transparency, 0.15
|
||||
|
||||
show sticks, ligands
|
||||
set stick_color, magenta
|
||||
|
||||
|
||||
${renderLigands(pair.holoProtein)}
|
||||
|
||||
# SAS points
|
||||
|
||||
load "$pointsFileRelative", points
|
||||
hide nonbonded, points
|
||||
show nb_spheres, points
|
||||
set sphere_scale, 0.2, points
|
||||
cmd.spectrum("b", "green_red", selection="points", minimum=0, maximum=0.7)
|
||||
|
||||
|
||||
stored.list=[]
|
||||
cmd.iterate("(resn STP)","stored.list.append(resi)") # read info about residues STP
|
||||
lastSTP=stored.list[-1] # get the index of the last residue
|
||||
hide lines, resn STP
|
||||
|
||||
cmd.select("rest", "resn STP and resi 0")
|
||||
|
||||
for my_index in range(1,int(lastSTP)+1): cmd.select("pocket"+str(my_index), "resn STP and resi "+str(my_index))
|
||||
for my_index in range(1,int(lastSTP)+1): cmd.show("spheres","pocket"+str(my_index))
|
||||
for my_index in range(1,int(lastSTP)+1): cmd.set("sphere_scale","0.4","pocket"+str(my_index))
|
||||
for my_index in range(1,int(lastSTP)+1): cmd.set("sphere_transparency","0.1","pocket"+str(my_index))
|
||||
|
||||
${colorExposedAtoms(pair)}
|
||||
|
||||
${colorPocketSurfaces(pair)}
|
||||
|
||||
deselect
|
||||
|
||||
orient
|
||||
""".stripIndent()
|
||||
}
|
||||
|
||||
private String colorPocketSurfaces(PredictionPair pair) {
|
||||
StringBuilder res = new StringBuilder()
|
||||
|
||||
int N = pair.prediction.reorderedPockets.size()
|
||||
|
||||
List<Color> colors = ColorUtils.createSpectrum(N, 0.6d, 0.6d, 1.20d)
|
||||
|
||||
int i = 1
|
||||
pair.prediction.reorderedPockets.each { Pocket pocket ->
|
||||
String ids = pocket.surfaceAtoms.indexes.join(",")
|
||||
String name = "surf_pocket$i"
|
||||
String ncol = "pcol$i"
|
||||
|
||||
res << "set_color $ncol = " + pyColor(colors[i-1]) + "\n"
|
||||
res << "select $name, protein and id [$ids] \n"
|
||||
res << "set surface_color, $ncol, $name \n"
|
||||
i++
|
||||
}
|
||||
|
||||
return res.toString()
|
||||
}
|
||||
|
||||
private String colorExposedAtoms(PredictionPair pair) {
|
||||
// return pair.prediction.protein.exposedAtoms.list.collect { "set surface_color, grey30, id $it.PDBserial \n set sphere_color, grey30, id $it.PDBserial" }.join("\n")
|
||||
|
||||
return ""
|
||||
}
|
||||
|
||||
private String renderLigands(Protein protein) {
|
||||
|
||||
if (!params.vis_highlight_ligands) {
|
||||
return "" // keep ligands rendered as purple sticks
|
||||
}
|
||||
|
||||
// or highlight them: render as red balls
|
||||
|
||||
"""
|
||||
# relevant ligands
|
||||
${renderLigands("ligands_relevant", "violet", protein.relevantLigands)}
|
||||
|
||||
# ignored ligands
|
||||
${renderLigands("ligands_ignored", "lightorange", protein.allIgnoredLigands)}
|
||||
"""
|
||||
}
|
||||
|
||||
private String renderLigands(String label, String color, List<Ligand> ligands) {
|
||||
|
||||
Atoms ligandAtoms = Atoms.join(ligands*.atoms)
|
||||
|
||||
if (ligandAtoms.empty) return ""
|
||||
|
||||
List<String> ligandAtomIds = ligandAtoms.collect {it.PDBserial.toString() }
|
||||
String idsOrList = ligandAtomIds.collect {"id $it" }.join(" or ")
|
||||
|
||||
"""
|
||||
select $label, $idsOrList
|
||||
show spheres, $label
|
||||
color $color, $label
|
||||
"""
|
||||
}
|
||||
|
||||
/* random notes:
|
||||
|
||||
#set ray_shadow, 0
|
||||
#set depth_cue, 0
|
||||
#set ray_trace_fog, 0
|
||||
//#set antialias, 2
|
||||
set bg_rgb_top, [10,10,10]
|
||||
set bg_rgb_bottom, [36,36,85]
|
||||
|
||||
|
||||
#create protein, fprotein and polymer
|
||||
#delete fprotein
|
||||
|
||||
#color bluewhite, fprotein
|
||||
#remove solvent
|
||||
#set stick_color, magenta
|
||||
#hide lines
|
||||
#show sticks
|
||||
|
||||
#set sphere_scale, 0.33
|
||||
#show_as sticks, ligands
|
||||
|
||||
#show spheres, ligand
|
||||
|
||||
#select pockets, resn STP
|
||||
#print stored.list
|
||||
|
||||
#show spheres, resn STP
|
||||
|
||||
#for my_index in range(2,int(lastSTP)+2): cmd.color(my_index,"pocket"+str(my_index))
|
||||
|
||||
#load $pointsf0RelName, points0
|
||||
#hide nonbonded, points0
|
||||
#show nb_spheres, points0
|
||||
#cmd.spectrum("b", "yellow_blue", selection="points0", minimum=0.3, maximum=1)
|
||||
|
||||
#set ray_trace_mode, 1
|
||||
|
||||
// predefined gradients: http://kpwu.wordpress.com/2007/11/27/pymol-example-coloring-surface-by-b-factor/
|
||||
// http://cupnet.net/pdb_format/
|
||||
// http://www.pymolwiki.org/index.php/Colorama
|
||||
*/
|
||||
|
||||
}
|
||||
@@ -11,9 +11,9 @@ import cz.siret.prank.geom.Atoms
|
||||
import cz.siret.prank.geom.Struct
|
||||
import cz.siret.prank.program.Main
|
||||
import cz.siret.prank.program.PrankException
|
||||
import cz.siret.prank.program.rendering.PymolRenderer
|
||||
import cz.siret.prank.program.rendering.RenderingModel
|
||||
import cz.siret.prank.program.routines.Routine
|
||||
import cz.siret.prank.program.visualization.RenderingModel
|
||||
import cz.siret.prank.program.visualization.renderers.NewPymolRenderer
|
||||
import cz.siret.prank.utils.*
|
||||
import groovy.transform.CompileStatic
|
||||
import groovy.util.logging.Slf4j
|
||||
@@ -282,7 +282,7 @@ class AnalyzeRoutine extends Routine {
|
||||
csv << "${item.label}, $nchains, $chainIds, $nres, $nlabres, ${s.positives}, ${s.negatives}, ${s.unlabeled}\n"
|
||||
|
||||
if (params.visualizations) {
|
||||
new PymolRenderer("$outdir/visualizations", new RenderingModel(
|
||||
new NewPymolRenderer("$outdir/visualizations", new RenderingModel(
|
||||
proteinFile: item.proteinFile,
|
||||
label: item.label,
|
||||
protein: item.protein,
|
||||
@@ -313,7 +313,7 @@ class AnalyzeRoutine extends Routine {
|
||||
}
|
||||
|
||||
if (params.visualizations) {
|
||||
new PymolRenderer("$outdir/visualizations", new RenderingModel(
|
||||
new NewPymolRenderer("$outdir/visualizations", new RenderingModel(
|
||||
proteinFile: item.proteinFile,
|
||||
label: item.label,
|
||||
protein: item.protein,
|
||||
|
||||
@@ -11,9 +11,9 @@ import cz.siret.prank.prediction.pockets.rescorers.PocketRescorer
|
||||
import cz.siret.prank.prediction.pockets.results.PredictionSummary
|
||||
import cz.siret.prank.prediction.transformation.ScoreTransformer
|
||||
import cz.siret.prank.program.ml.Model
|
||||
import cz.siret.prank.program.rendering.OldPymolRenderer
|
||||
import cz.siret.prank.program.routines.Routine
|
||||
import cz.siret.prank.program.routines.results.PredictResults
|
||||
import cz.siret.prank.program.visualization.PredictionVisualizer
|
||||
import cz.siret.prank.utils.Futils
|
||||
import groovy.transform.CompileStatic
|
||||
import groovy.util.logging.Slf4j
|
||||
@@ -95,7 +95,7 @@ class PredictPocketsRoutine extends Routine {
|
||||
rescorer.reorderPockets(pair.prediction, item.context) // in this context reorderPockets() makes predictions
|
||||
|
||||
if (produceVisualizations) {
|
||||
new OldPymolRenderer(visDir).render(item, rescorer, pair)
|
||||
new PredictionVisualizer(outdir).generateVisualizations(item, rescorer, pair)
|
||||
}
|
||||
|
||||
if (outputPredictionFiles) {
|
||||
|
||||
@@ -6,8 +6,8 @@ import cz.siret.prank.domain.PredictionPair
|
||||
import cz.siret.prank.features.FeatureExtractor
|
||||
import cz.siret.prank.prediction.pockets.rescorers.*
|
||||
import cz.siret.prank.program.ml.Model
|
||||
import cz.siret.prank.program.rendering.OldPymolRenderer
|
||||
import cz.siret.prank.program.routines.results.EvalResults
|
||||
import cz.siret.prank.program.visualization.PredictionVisualizer
|
||||
import cz.siret.prank.utils.Futils
|
||||
import groovy.transform.CompileStatic
|
||||
import groovy.util.logging.Slf4j
|
||||
@@ -90,7 +90,7 @@ class EvalPocketsRoutine extends EvalRoutine {
|
||||
rescorer.reorderPockets(pair.prediction, item.context)
|
||||
|
||||
if (params.visualizations) {
|
||||
new OldPymolRenderer(visDir).render(item, (ModelBasedRescorer)rescorer, pair)
|
||||
new PredictionVisualizer(outdir).generateVisualizations(item, (ModelBasedRescorer)rescorer, pair)
|
||||
}
|
||||
|
||||
if (params.predictions) {
|
||||
|
||||
@@ -7,9 +7,9 @@ import cz.siret.prank.geom.Atoms
|
||||
import cz.siret.prank.geom.samplers.SampledPoints
|
||||
import cz.siret.prank.prediction.metrics.ClassifierStats
|
||||
import cz.siret.prank.program.ml.Model
|
||||
import cz.siret.prank.program.rendering.PymolRenderer
|
||||
import cz.siret.prank.program.rendering.RenderingModel
|
||||
import cz.siret.prank.program.routines.results.EvalResults
|
||||
import cz.siret.prank.program.visualization.RenderingModel
|
||||
import cz.siret.prank.program.visualization.renderers.NewPymolRenderer
|
||||
import cz.siret.prank.utils.Futils
|
||||
import groovy.transform.CompileStatic
|
||||
|
||||
@@ -90,7 +90,7 @@ class EvalResiduesRoutine extends EvalRoutine {
|
||||
}
|
||||
|
||||
if (params.visualizations) {
|
||||
new PymolRenderer("$outdir/visualizations", new RenderingModel(
|
||||
new NewPymolRenderer("$outdir/visualizations", new RenderingModel(
|
||||
proteinFile: item.proteinFile,
|
||||
label: item.label,
|
||||
protein: item.protein,
|
||||
|
||||
@@ -0,0 +1,126 @@
|
||||
package cz.siret.prank.program.visualization
|
||||
|
||||
import cz.siret.prank.domain.Dataset
|
||||
import cz.siret.prank.domain.PredictionPair
|
||||
import cz.siret.prank.domain.labeling.LabeledPoint
|
||||
import cz.siret.prank.prediction.pockets.rescorers.ModelBasedRescorer
|
||||
import cz.siret.prank.program.params.Parametrized
|
||||
import cz.siret.prank.program.visualization.renderers.ChimeraXRenderer
|
||||
import cz.siret.prank.program.visualization.renderers.PymolRenderer
|
||||
import cz.siret.prank.utils.ColorUtils
|
||||
import cz.siret.prank.utils.Futils
|
||||
import groovy.transform.CompileStatic
|
||||
import groovy.util.logging.Slf4j
|
||||
import org.biojava.nbio.structure.Atom
|
||||
|
||||
import java.awt.*
|
||||
import java.util.List
|
||||
|
||||
/**
|
||||
* Visualizes pocket predictions.
|
||||
*/
|
||||
@Slf4j
|
||||
@CompileStatic
|
||||
class PredictionVisualizer implements Parametrized {
|
||||
|
||||
String outdir
|
||||
|
||||
PredictionVisualizer(String outdir) {
|
||||
this.outdir = visualizationsDir(outdir)
|
||||
}
|
||||
|
||||
//===========================================================================================================//
|
||||
|
||||
static String visualizationsDir(String outdir) {
|
||||
return "$outdir/visualizations"
|
||||
}
|
||||
|
||||
static List<Color> generatePocketColors(int n) {
|
||||
return ColorUtils.createSpectrum(n, 0.6d, 0.6d, 1.20d)
|
||||
}
|
||||
|
||||
//===========================================================================================================//
|
||||
|
||||
static void writeLabeledPointsPdb(String pointsf, List<LabeledPoint> labeledPoints) {
|
||||
Writer pdb = Futils.getGzipWriter(pointsf)
|
||||
int i = 0
|
||||
for (LabeledPoint lp : labeledPoints) {
|
||||
double beta = lp.score
|
||||
Atom p = lp.point
|
||||
def lab = "STP"
|
||||
|
||||
pdb.printf "HETATM%5d H %3s 1 %2d %8.3f%8.3f%8.3f 0.50%6.3f\n", i, lab, lp.pocket, p.x, p.y, p.z, beta
|
||||
i++
|
||||
}
|
||||
pdb.close()
|
||||
}
|
||||
|
||||
// void conditionallyZipVisualizations(List<File> fileList, String label) {
|
||||
// if (params.zip_visualizations) {
|
||||
// List<File> fileList = [new File(pmlf), new File(pointsf)]
|
||||
// if (params.vis_copy_proteins) {
|
||||
// fileList.add(new File(proteinfAbs))
|
||||
// }
|
||||
// File zipFile = new File("$outdir/${label}_visualization.zip")
|
||||
// NameMapper mapper = { String fileName ->
|
||||
// return fileName.endsWith(".pml") ? fileName : "data/".concat(fileName)
|
||||
// }
|
||||
// ZipUtil.packEntries(fileList.toArray(new File[0]) as File[], zipFile, mapper)
|
||||
// fileList.forEach({ File f -> f.delete() })
|
||||
// }
|
||||
// }
|
||||
|
||||
//===========================================================================================================//
|
||||
|
||||
void generateVisualizations(Dataset.Item item, ModelBasedRescorer rescorer, PredictionPair pair) {
|
||||
|
||||
String label = item.label
|
||||
|
||||
//String pmlf = "$outdir/${label}.pml"
|
||||
|
||||
String dataDir = Futils.mkdirs("$outdir/data")
|
||||
|
||||
|
||||
// SAS points
|
||||
|
||||
String pointsFileRelative = "data/${label}_points.pdb.gz"
|
||||
String pointsFile = "$outdir/$pointsFileRelative"
|
||||
|
||||
writeLabeledPointsPdb(pointsFile, rescorer.labeledPoints)
|
||||
|
||||
// protein files
|
||||
|
||||
String proteinFile = Futils.absPath(item.proteinFile)
|
||||
String proteinFileAbs = proteinFile
|
||||
if (params.vis_copy_proteins) {
|
||||
String name = Futils.shortName(proteinFile)
|
||||
String newf = "$dataDir/$name"
|
||||
String newfrel = "data/$name"
|
||||
|
||||
log.info "copying [$proteinFile] to [$newf]"
|
||||
Futils.copy(proteinFile, newf)
|
||||
|
||||
proteinFile = newfrel
|
||||
proteinFileAbs = newf
|
||||
}
|
||||
|
||||
// renderers
|
||||
|
||||
if ('pymol' in params.vis_renderers) {
|
||||
try {
|
||||
new PymolRenderer(outdir).renderPredictions(item, pair, proteinFile, pointsFileRelative)
|
||||
} catch (Exception e) {
|
||||
log.error("Error rendering PyMol visualization for $label", e)
|
||||
}
|
||||
}
|
||||
if ('chimerax' in params.vis_renderers) {
|
||||
try {
|
||||
new ChimeraXRenderer(outdir).renderPredictions(item, pair, proteinFile, pointsFileRelative)
|
||||
} catch (Exception e) {
|
||||
log.error("Error rendering ChimeraX visualization for $label", e)
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
}
|
||||
@@ -1,4 +1,4 @@
|
||||
package cz.siret.prank.program.rendering
|
||||
package cz.siret.prank.program.visualization
|
||||
|
||||
import cz.siret.prank.domain.Protein
|
||||
import cz.siret.prank.domain.labeling.BinaryLabeling
|
||||
@@ -43,9 +43,7 @@ class RenderingModel implements Parametrized {
|
||||
|
||||
//Color fnColor = new Color(109, 186, 192) // cyan
|
||||
|
||||
|
||||
|
||||
//Color tpColor = Color.BLUE
|
||||
//Color tpColor = Color.BLUE
|
||||
//Color fpColor = Color.MAGENTA
|
||||
//Color fnColor = Color.CYAN
|
||||
|
||||
@@ -0,0 +1,91 @@
|
||||
package cz.siret.prank.program.visualization.renderers
|
||||
|
||||
import cz.siret.prank.domain.Dataset
|
||||
import cz.siret.prank.domain.Pocket
|
||||
import cz.siret.prank.domain.PredictionPair
|
||||
import cz.siret.prank.utils.ColorUtils
|
||||
import groovy.transform.CompileStatic
|
||||
import groovy.util.logging.Slf4j
|
||||
|
||||
import static cz.siret.prank.program.visualization.PredictionVisualizer.generatePocketColors
|
||||
import static cz.siret.prank.utils.Futils.writeFile
|
||||
|
||||
/**
|
||||
* Generates ChimeraX visualization of pocket predictions.
|
||||
*/
|
||||
@Slf4j
|
||||
@CompileStatic
|
||||
class ChimeraXRenderer {
|
||||
|
||||
String bgColor = "#242455"
|
||||
String proteinColor = "#d9d9ff"
|
||||
String ligandColor = "magenta"
|
||||
String transparency = "0" // 0-100(full transparency)
|
||||
|
||||
//===========================================================================================================//
|
||||
|
||||
String outdir
|
||||
|
||||
ChimeraXRenderer(String outdir) {
|
||||
this.outdir = outdir
|
||||
}
|
||||
|
||||
void renderPredictions(Dataset.Item item, PredictionPair pair, String proteinFile, String pointsFileRelative) {
|
||||
|
||||
String label = item.label
|
||||
String file = "$outdir/${label}_chimerax.cxc"
|
||||
|
||||
writeFile(file, renderMainScript(proteinFile, pointsFileRelative, pair))
|
||||
|
||||
}
|
||||
|
||||
//===========================================================================================================//
|
||||
|
||||
private String renderMainScript(String proteinFile, String pointsFileRelative, PredictionPair pair) {
|
||||
"""
|
||||
open $proteinFile
|
||||
surf
|
||||
hide solvent
|
||||
color protein $proteinColor
|
||||
color ligand $ligandColor
|
||||
|
||||
|
||||
${colorPockets(pair)}
|
||||
|
||||
|
||||
open $pointsFileRelative
|
||||
color by bfactor #2 palette lime:red range 0,0.7
|
||||
|
||||
|
||||
set bgcolor $bgColor
|
||||
transparency $transparency
|
||||
graphics silhouettes false
|
||||
lighting soft
|
||||
"""
|
||||
}
|
||||
|
||||
private StringBuilder colorPockets(PredictionPair pair) {
|
||||
StringBuilder res = new StringBuilder()
|
||||
|
||||
List<Pocket> pockets = pair.prediction.reorderedPockets
|
||||
int n = pockets.size()
|
||||
List<String> colors = generatePocketColors(n).collect { ColorUtils.colorToHex(it) }
|
||||
|
||||
|
||||
for (int i = 0; i != n; i++) {
|
||||
res << "color name color_pocket${i + 1} ${colors[i]}\n"
|
||||
}
|
||||
res << "\n"
|
||||
|
||||
|
||||
for (int i = 0; i != n; i++) {
|
||||
Pocket pocket = pockets[i]
|
||||
res << "name pocket${i + 1}_atoms " << pocket.surfaceAtoms.collect { "@@serial_number=${it.PDBserial}" }.join(" ") << "\n"
|
||||
res << "color pocket${i + 1}_atoms color_pocket${i + 1}\n"
|
||||
res << "\n"
|
||||
}
|
||||
|
||||
return res
|
||||
}
|
||||
|
||||
}
|
||||
@@ -1,18 +1,19 @@
|
||||
package cz.siret.prank.program.rendering
|
||||
package cz.siret.prank.program.visualization.renderers
|
||||
|
||||
import cz.siret.prank.domain.labeling.BinaryLabeling
|
||||
import cz.siret.prank.domain.labeling.LabeledPoint
|
||||
import cz.siret.prank.domain.labeling.LabeledResidue
|
||||
import cz.siret.prank.domain.labeling.ResidueLabeling
|
||||
import cz.siret.prank.program.params.Parametrized
|
||||
import cz.siret.prank.program.visualization.RenderingModel
|
||||
import cz.siret.prank.utils.Futils
|
||||
import groovy.transform.CompileStatic
|
||||
import groovy.util.logging.Slf4j
|
||||
import org.biojava.nbio.structure.Atom
|
||||
|
||||
import java.awt.*
|
||||
import java.util.List
|
||||
|
||||
import static cz.siret.prank.program.visualization.PredictionVisualizer.writeLabeledPointsPdb
|
||||
|
||||
/**
|
||||
* Generates PyMol visualization of RenderingModel.
|
||||
*
|
||||
@@ -20,7 +21,7 @@ import java.util.List
|
||||
*/
|
||||
@Slf4j
|
||||
@CompileStatic
|
||||
class PymolRenderer implements Parametrized {
|
||||
class NewPymolRenderer implements Parametrized {
|
||||
|
||||
String outdir
|
||||
RenderingModel model
|
||||
@@ -29,7 +30,7 @@ class PymolRenderer implements Parametrized {
|
||||
String pmlFile
|
||||
String dataDir
|
||||
|
||||
PymolRenderer(String outdir, RenderingModel model) {
|
||||
NewPymolRenderer(String outdir, RenderingModel model) {
|
||||
this.outdir = outdir
|
||||
this.model = model
|
||||
}
|
||||
@@ -218,7 +219,7 @@ cmd.spectrum("b", "rainbow", selection="protein", minimum=0, maximum=1)
|
||||
String pointsfAbs = "$dataDir/${label}_points.pdb.gz"
|
||||
String pointsfRel = "data/" + Futils.shortName(pointsfAbs)
|
||||
|
||||
writeLabeledPoints(pointsfAbs, model.labeledPoints)
|
||||
writeLabeledPointsPdb(pointsfAbs, model.labeledPoints)
|
||||
|
||||
"""
|
||||
load "$pointsfRel", points
|
||||
@@ -246,19 +247,6 @@ cmd.set("sphere_scale","0.3","rest")
|
||||
|
||||
}
|
||||
|
||||
void writeLabeledPoints(String fname, List<LabeledPoint> labeledPoints) {
|
||||
Writer pdb = Futils.getGzipWriter(fname)
|
||||
int i = 0
|
||||
for (LabeledPoint lp : labeledPoints) {
|
||||
double beta = lp.score
|
||||
Atom p = lp.point
|
||||
def lab = "STP"
|
||||
pdb.printf "HETATM%5d H %3s 1 %2d %8.3f%8.3f%8.3f 0.50%6.3f\n", i, lab, lp.pocket, p.x, p.y, p.z, beta
|
||||
i++
|
||||
}
|
||||
pdb.close()
|
||||
}
|
||||
|
||||
//===========================================================================================================//
|
||||
|
||||
static String pyColor(Color c) {
|
||||
@@ -0,0 +1,211 @@
|
||||
package cz.siret.prank.program.visualization.renderers
|
||||
|
||||
import cz.siret.prank.domain.*
|
||||
import cz.siret.prank.geom.Atoms
|
||||
import cz.siret.prank.program.params.Parametrized
|
||||
import cz.siret.prank.program.visualization.PredictionVisualizer
|
||||
import groovy.transform.CompileStatic
|
||||
import groovy.util.logging.Slf4j
|
||||
|
||||
import java.awt.*
|
||||
import java.util.List
|
||||
|
||||
import static cz.siret.prank.utils.Futils.writeFile
|
||||
|
||||
/**
|
||||
* Generates PyMol visualization of Pocket predictions.
|
||||
*/
|
||||
@Slf4j
|
||||
@CompileStatic
|
||||
class PymolRenderer implements Parametrized {
|
||||
|
||||
String outdir
|
||||
|
||||
PymolRenderer(String outputDir) {
|
||||
this.outdir = outputDir
|
||||
}
|
||||
|
||||
static String pyColor(Color c) {
|
||||
sprintf "[%5.3f,%5.3f,%5.3f]", c.red/255, c.green/255, c.blue/255
|
||||
}
|
||||
|
||||
void renderPredictions(Dataset.Item item, PredictionPair pair, String proteinFile, String pointsFileRelative) {
|
||||
|
||||
String label = item.label
|
||||
String pmlf = "$outdir/${label}_pymol.pml"
|
||||
|
||||
writeFile(pmlf, renderMainScript(proteinFile, pointsFileRelative, pair))
|
||||
|
||||
}
|
||||
|
||||
private String renderMainScript(String proteinFile, String pointsFileRelative, PredictionPair pair) {
|
||||
// language=python
|
||||
"""
|
||||
from pymol import cmd,stored
|
||||
|
||||
set depth_cue, 1
|
||||
set fog_start, 0.4
|
||||
|
||||
set_color b_col, [36,36,85]
|
||||
set_color t_col, [10,10,10]
|
||||
set bg_rgb_bottom, b_col
|
||||
set bg_rgb_top, t_col
|
||||
set bg_gradient
|
||||
|
||||
set spec_power = 200
|
||||
set spec_refl = 0
|
||||
|
||||
load "$proteinFile", protein
|
||||
create ligands, protein and organic
|
||||
select xlig, protein and organic
|
||||
delete xlig
|
||||
|
||||
hide everything, all
|
||||
|
||||
color white, elem c
|
||||
color bluewhite, protein
|
||||
#show_as cartoon, protein
|
||||
show surface, protein
|
||||
#set transparency, 0.15
|
||||
|
||||
show sticks, ligands
|
||||
set stick_color, magenta
|
||||
|
||||
|
||||
${renderLigands(pair.holoProtein)}
|
||||
|
||||
# SAS points
|
||||
|
||||
load "$pointsFileRelative", points
|
||||
hide nonbonded, points
|
||||
show nb_spheres, points
|
||||
set sphere_scale, 0.2, points
|
||||
cmd.spectrum("b", "green_red", selection="points", minimum=0, maximum=0.7)
|
||||
|
||||
|
||||
stored.list=[]
|
||||
cmd.iterate("(resn STP)","stored.list.append(resi)") # read info about residues STP
|
||||
lastSTP=stored.list[-1] # get the index of the last residue
|
||||
hide lines, resn STP
|
||||
|
||||
cmd.select("rest", "resn STP and resi 0")
|
||||
|
||||
for my_index in range(1,int(lastSTP)+1): cmd.select("pocket"+str(my_index), "resn STP and resi "+str(my_index))
|
||||
for my_index in range(1,int(lastSTP)+1): cmd.show("spheres","pocket"+str(my_index))
|
||||
for my_index in range(1,int(lastSTP)+1): cmd.set("sphere_scale","0.4","pocket"+str(my_index))
|
||||
for my_index in range(1,int(lastSTP)+1): cmd.set("sphere_transparency","0.1","pocket"+str(my_index))
|
||||
|
||||
${colorExposedAtoms(pair)}
|
||||
|
||||
${colorPocketSurfaces(pair)}
|
||||
|
||||
deselect
|
||||
|
||||
orient
|
||||
"""
|
||||
}
|
||||
|
||||
private String colorPocketSurfaces(PredictionPair pair) {
|
||||
StringBuilder res = new StringBuilder()
|
||||
|
||||
int nPockets = pair.prediction.reorderedPockets.size()
|
||||
List<Color> colors = PredictionVisualizer.generatePocketColors(nPockets)
|
||||
|
||||
int i = 1
|
||||
pair.prediction.reorderedPockets.each { Pocket pocket ->
|
||||
String ids = pocket.surfaceAtoms.indexes.join(",")
|
||||
String name = "surf_pocket$i"
|
||||
String ncol = "pcol$i"
|
||||
|
||||
res << "set_color $ncol = " + pyColor(colors[i-1]) + "\n"
|
||||
res << "select $name, protein and id [$ids] \n"
|
||||
res << "set surface_color, $ncol, $name \n"
|
||||
i++
|
||||
}
|
||||
|
||||
return res.toString()
|
||||
}
|
||||
|
||||
private String colorExposedAtoms(PredictionPair pair) {
|
||||
// return pair.prediction.protein.exposedAtoms.list.collect { "set surface_color, grey30, id $it.PDBserial \n set sphere_color, grey30, id $it.PDBserial" }.join("\n")
|
||||
|
||||
return ""
|
||||
}
|
||||
|
||||
private String renderLigands(Protein protein) {
|
||||
|
||||
if (!params.vis_highlight_ligands) {
|
||||
return "" // keep ligands rendered as purple sticks
|
||||
}
|
||||
|
||||
// or highlight them: render as red balls
|
||||
|
||||
"""
|
||||
# relevant ligands
|
||||
${renderLigands("ligands_relevant", "violet", protein.relevantLigands)}
|
||||
|
||||
# ignored ligands
|
||||
${renderLigands("ligands_ignored", "lightorange", protein.allIgnoredLigands)}
|
||||
"""
|
||||
}
|
||||
|
||||
private String renderLigands(String label, String color, List<Ligand> ligands) {
|
||||
|
||||
Atoms ligandAtoms = Atoms.join(ligands*.atoms)
|
||||
|
||||
if (ligandAtoms.empty) return ""
|
||||
|
||||
List<String> ligandAtomIds = ligandAtoms.collect {it.PDBserial.toString() }
|
||||
String idsOrList = ligandAtomIds.collect {"id $it" }.join(" or ")
|
||||
|
||||
"""
|
||||
select $label, $idsOrList
|
||||
show spheres, $label
|
||||
color $color, $label
|
||||
"""
|
||||
}
|
||||
|
||||
/* random notes:
|
||||
|
||||
#set ray_shadow, 0
|
||||
#set depth_cue, 0
|
||||
#set ray_trace_fog, 0
|
||||
//#set antialias, 2
|
||||
set bg_rgb_top, [10,10,10]
|
||||
set bg_rgb_bottom, [36,36,85]
|
||||
|
||||
|
||||
#create protein, fprotein and polymer
|
||||
#delete fprotein
|
||||
|
||||
#color bluewhite, fprotein
|
||||
#remove solvent
|
||||
#set stick_color, magenta
|
||||
#hide lines
|
||||
#show sticks
|
||||
|
||||
#set sphere_scale, 0.33
|
||||
#show_as sticks, ligands
|
||||
|
||||
#show spheres, ligand
|
||||
|
||||
#select pockets, resn STP
|
||||
#print stored.list
|
||||
|
||||
#show spheres, resn STP
|
||||
|
||||
#for my_index in range(2,int(lastSTP)+2): cmd.color(my_index,"pocket"+str(my_index))
|
||||
|
||||
#load $pointsf0RelName, points0
|
||||
#hide nonbonded, points0
|
||||
#show nb_spheres, points0
|
||||
#cmd.spectrum("b", "yellow_blue", selection="points0", minimum=0.3, maximum=1)
|
||||
|
||||
#set ray_trace_mode, 1
|
||||
|
||||
// predefined gradients: http://kpwu.wordpress.com/2007/11/27/pymol-example-coloring-surface-by-b-factor/
|
||||
// http://cupnet.net/pdb_format/
|
||||
// http://www.pymolwiki.org/index.php/Colorama
|
||||
*/
|
||||
|
||||
}
|
||||
@@ -8,6 +8,12 @@ import java.util.List
|
||||
@CompileStatic
|
||||
class ColorUtils {
|
||||
|
||||
static String colorToHex(Color color) {
|
||||
return "#" + Integer.toHexString(color.getRGB()).substring(2);
|
||||
}
|
||||
|
||||
//===========================================================================================================//
|
||||
|
||||
/**
|
||||
Generates a series of colors such that the
|
||||
distribution of the colors is (fairly) evenly spaced
|
||||
|
||||
Reference in New Issue
Block a user