surface coloring MVP

choppa/render/Template.html

@@ -165,22 +165,9 @@
                          // set protein sticks and surface
                          viewer.setStyle({model: 0}, {stick: {colorscheme: "whiteCarbon", radius:0.15}});
                          // define a coloring function based on our residue ranges. We can't call .addSurface separate times because the surfaces won't be merged nicely. 
-                         var colorAsSnake = function(atom) {                         if (['155_A','196_A','186_A','227_A','284_A','33_A','93_A','6_A','180_A','191_A','142_A','153_A','222_A','279_A','156_A','1_A','69_A','233_A','244_A','263_A','198_A','285_A','121_A','277_A','94_A','228_A','45_A','18_A','220_A','37_A','116_A','261_A','67_A','78_A','212_A','280_A','272_A','21_A','234_A','264_A','81_A','160_A','283_A','24_A','84_A','106_A','46_A','259_A','8_A','19_A','232_A','243_A','224_A'].includes(atom.resi+'_'+atom.chain)){ 
- return '#ff8a6c' 
- } else if (['166_A','117_A','128_A','139_A','22_A','79_A','235_A','41_A','52_A','197_A','109_A','120_A','265_A','3_A','14_A','82_A','216_A','295_A','44_A','189_A','63_A','208_A','150_A','161_A','306_A','112_A','268_A','74_A','85_A','219_A','287_A','36_A','181_A','115_A','238_A','143_A','66_A','200_A','211_A','28_A','173_A','230_A','192_A','203_A','9_A','145_A','290_A','39_A','118_A','252_A','175_A','58_A','80_A','214_A','137_A','271_A','282_A','293_A','31_A','205_A','99_A','195_A','206_A','168_A','110_A','42_A','187_A','140_A','151_A','170_A','53_A','64_A','266_A','26_A','122_A','34_A','56_A','113_A','258_A','269_A','209_A','182_A','124_A','135_A','231_A','154_A','165_A','299_A','10_A','146_A','291_A','29_A','40_A','174_A','242_A','2_A','147_A','59_A','215_A','302_A','51_A','176_A','138_A','149_A','294_A','217_A','111_A','245_A','256_A','5_A','179_A','207_A','218_A','130_A','275_A','286_A','13_A','248_A','131_A','54_A','210_A','267_A','16_A','172_A','141_A','114_A','171_A','76_A','133_A','144_A','278_A','289_A','27_A','201_A','95_A','240_A','163_A','57_A','202_A','164_A','126_A','183_A','194_A','262_A','11_A','136_A','98_A'].includes(atom.resi+'_'+atom.chain)){ 
- return '#ffffff' 
- } else if (['105_B','116_B','261_B','10_B','67_B','78_B','89_B','212_B','223_B','146_B','29_B','40_B','280_B','174_B','185_B','291_B','108_B','242_B','2_B','253_B','136_B','147_B','59_B','70_B','204_B','215_B','98_B','272_B','21_B','155_B','166_B','177_B','302_B','234_B','167_A','117_B','128_B','139_B','264_B','196_B','101_B','158_B','283_B','294_B','32_B','43_B','25_A','100_B','111_B','245_B','256_B','5_B','62_B','73_B','207_B','218_B','130_B','275_B','13_B','24_B','35_B','169_B','286_B','92_B','226_B','237_B','248_B','131_B','305_B','54_B','188_B','199_B','210_B','93_B','267_B','16_B','150_B','161_B','172_B','229_B','112_B','123_B','180_B','191_B','65_B','142_B','153_B','278_B','289_B','27_B','84_B','95_B','240_B','46_B','57_B','68_B','202_B','297_B','125_B','8_B','19_B','30_B','164_B','259_B','270_B','87_B','221_B','232_B','243_B','281_B','126_B','300_B','38_B','49_B','183_B','194_B','77_B','251_B','11_B','262_B','145_B','156_B','269_B','213_B','224_B','96_B','107_B','118_B','175_B','60_B','137_B','273_B','22_B','205_B','79_B','90_B','235_B','292_B','303_B','41_B','52_B','186_B','197_B','109_B','120_B','254_B','265_B','3_B','14_B','148_B','71_B','82_B','216_B','227_B','110_B','284_B','33_B','44_B','167_B','178_B','189_B','72_B','246_B','129_B','140_B','151_B','63_B','208_B','91_B','102_B','25_B','159_B','170_B','55_B','132_B','257_B','268_B','6_B','295_B','74_B','85_B','219_B','276_B','36_B','47_B','287_B','181_B','298_B','104_B','115_B','238_B','249_B','260_B','299_B','143_B','66_B','200_B','211_B','222_B','134_B','17_B','28_B','162_B','173_B','279_B','230_B','241_B','124_B','135_B','192_B','203_B','86_B','97_B','9_B','154_B','165_B','290_B','39_B','127_B','252_B','1_B','184_B','58_B','69_B','80_B','214_B','271_B','282_B','293_B','20_B','31_B','88_B','99_B','233_B','244_B','301_B','50_B','61_B','195_B','206_B','62_A','263_B','12_B','23_B','157_B','168_B','274_B','51_B','225_B','236_B','119_B','42_B','176_B','187_B','198_B','81_B','255_B','4_B','138_B','149_B','160_B','285_B','217_B','179_B','304_B','53_B','64_B','121_B','266_B','277_B','15_B','26_B','83_B','94_B','228_B','239_B','122_B','34_B','45_B','56_B','190_B','296_B','113_B','7_B','18_B','247_B','141_B','152_B','258_B','75_B','209_B','220_B','103_B','114_B','288_B','221_A','37_B','171_B','182_B','76_B','250_B','133_B','144_B','201_B','106_B','231_B','163_B','48_B','193_B'].includes(atom.resi+'_'+atom.chain)){ 
- return '#642df0' 
- } else if (['60_A','90_A','101_A','158_A','292_A','303_A','254_A','148_A','71_A','178_A','55_A','123_A','257_A','298_A','104_A','260_A','134_A','162_A','77_A','107_A','20_A','88_A','301_A','50_A','61_A','12_A','23_A','157_A','225_A','236_A','72_A','255_A','4_A','129_A','91_A','102_A','159_A','304_A','15_A','239_A','296_A','190_A','247_A','7_A','152_A','288_A','250_A','97_A','48_A','105_A','127_A','89_A','185_A','253_A','204_A','177_A','119_A','32_A','43_A','100_A','73_A','35_A','169_A','92_A','226_A','237_A','305_A','188_A','199_A','229_A','103_A','65_A','297_A','68_A','125_A','281_A','270_A','30_A','87_A','300_A','38_A','49_A','251_A'].includes(atom.resi+'_'+atom.chain)){ 
- return '#ff9e83' 
- } else if (['273_A','276_A','47_A','249_A','17_A','86_A','193_A','223_A','70_A'].includes(atom.resi+'_'+atom.chain)){ 
- return '#ff7454' 
- } else if (['246_A'].includes(atom.resi+'_'+atom.chain)){ 
- return '#ff3f25' 
- } else if (['241_A','96_A','274_A','83_A','75_A','184_A','213_A'].includes(atom.resi+'_'+atom.chain)){ 
- return '#ff5c3d' 
- } else if (['132_A','108_A'].includes(atom.resi+'_'+atom.chain)){ 
- return '#ff0707' 
+                         var colorAsSnake = function(atom) {
+                          atom_residx = String(atom.resi)
+                                {{SURFACE_COLOR_INSERT}}
                                           }};                         viewer.addSurface("MS", {colorfunc: colorAsSnake, opacity: 0.9}) 
 
                          viewer.setStyle({bonds: 0}, {sphere:{radius:0.5}}); //water molecules

choppa/render/logoplots.py

@@ -30,6 +30,41 @@
         'Y': '#84380b',
         'X': '#000000', # add 'X' so that LogoMaker doesn't log to stdout
     }
+WHITE_EMPTY_SQUARE = "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"
+
+def render_singleres_logoplot(res):
+    """
+    Renders a simple, single-letter 'logoplot', normally for showing the wildtype residue. The plot
+    is square and is typically rendered top center downstream.
+    """
+    _, ax = plt.subplots(figsize=(4, 4))
+
+    # create Logo object
+    logomaker.Logo(
+        pd.DataFrame({res:1}, index=[0]),
+        font_name="Sans Serif",
+        color_scheme=LOGOPLOT_WITHOUT_CONF_COLORSCHEME,
+        flip_below=False,
+        show_spines=True,
+        ax=ax
+    )
+
+    plt.xticks([])
+    plt.yticks([])
+    # plt.savefig("debug_logoplot.png", dpi=70, bbox_inches="tight") # uncomment for testing
+    # plt object directly to base64 string instead of tmpfile
+    lp_bytes = io.BytesIO()
+    plt.savefig(
+        lp_bytes,  
+        format='png', 
+        dpi=70, # DPI 70 seems to be ~smallest we can get away with
+        bbox_inches="tight",
+        )
+    lp_bytes.seek(0)
+    lp_base64 = base64.b64encode(lp_bytes.read())
+    plt.close()
+
+    return lp_base64 
 
 class LogoPlot():
     """
@@ -70,8 +105,8 @@ def divide_fitness_types(self):
                 else:
                     fit_mutants[mutant['aa']] = [mutant['fitness']]
 
-        return {wildtype: wildtype_fitness}, unfit_mutants, fit_mutants
-    
+        return {wildtype: wildtype_fitness}, unfit_mutants, fit_mutants  
+
     def render_logoplot(self, mutants, global_min_confidence=False, global_max_confidence=False, lhs=True, wildtype=False):
         """
         Creates a logoplot as a base64 string. Also annotes with confidence values if present.
@@ -80,7 +115,7 @@ def render_logoplot(self, mutants, global_min_confidence=False, global_max_confi
         """  
         if len(mutants) == 0:
             # this can happen when there are no mutants in this category. Return an empty white-sqare base64 instead.
-            return "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"
+            return WHITE_EMPTY_SQUARE
         plt.switch_backend('Agg') # prevents plt from opening a figure on OS
         if wildtype: # we want this to be a bit smaller and square because it'll always have 1 residue.
             _, ax = plt.subplots(figsize=(4, 4))