From 1bcb7e57e17b136e9005030f1e56cf2aee6c3705 Mon Sep 17 00:00:00 2001
From: Samuel Ellis <sjellis@vt.edu>
Date: Fri, 22 May 2020 10:53:29 -0400
Subject: [PATCH 1/3] Adding a partial to hold an icon for each page of the
 website.

---
 themes/minimal/layouts/partials/models_icon.html       | 1 +
 themes/minimal/layouts/partials/protein_icon.html      | 1 +
 themes/minimal/layouts/partials/simulation_icon.html   | 1 +
 themes/minimal/layouts/partials/structure_icon.html    | 1 +
 themes/minimal/layouts/partials/target_icon.html       | 1 +
 themes/minimal/layouts/partials/therapeutics_icon.html | 1 +
 themes/minimal/layouts/partials/trajectory_icon.html   | 1 +
 7 files changed, 7 insertions(+)
 create mode 100755 themes/minimal/layouts/partials/models_icon.html
 create mode 100755 themes/minimal/layouts/partials/protein_icon.html
 create mode 100755 themes/minimal/layouts/partials/simulation_icon.html
 create mode 100755 themes/minimal/layouts/partials/structure_icon.html
 create mode 100755 themes/minimal/layouts/partials/target_icon.html
 create mode 100755 themes/minimal/layouts/partials/therapeutics_icon.html
 create mode 100755 themes/minimal/layouts/partials/trajectory_icon.html

diff --git a/themes/minimal/layouts/partials/models_icon.html b/themes/minimal/layouts/partials/models_icon.html
new file mode 100755
index 00000000..decc2967
--- /dev/null
+++ b/themes/minimal/layouts/partials/models_icon.html
@@ -0,0 +1 @@
+⊧
\ No newline at end of file
diff --git a/themes/minimal/layouts/partials/protein_icon.html b/themes/minimal/layouts/partials/protein_icon.html
new file mode 100755
index 00000000..c2adb301
--- /dev/null
+++ b/themes/minimal/layouts/partials/protein_icon.html
@@ -0,0 +1 @@
+🝪
\ No newline at end of file
diff --git a/themes/minimal/layouts/partials/simulation_icon.html b/themes/minimal/layouts/partials/simulation_icon.html
new file mode 100755
index 00000000..1782c8ab
--- /dev/null
+++ b/themes/minimal/layouts/partials/simulation_icon.html
@@ -0,0 +1 @@
+⮔
\ No newline at end of file
diff --git a/themes/minimal/layouts/partials/structure_icon.html b/themes/minimal/layouts/partials/structure_icon.html
new file mode 100755
index 00000000..a2121ba2
--- /dev/null
+++ b/themes/minimal/layouts/partials/structure_icon.html
@@ -0,0 +1 @@
+◳
\ No newline at end of file
diff --git a/themes/minimal/layouts/partials/target_icon.html b/themes/minimal/layouts/partials/target_icon.html
new file mode 100755
index 00000000..4fc864cf
--- /dev/null
+++ b/themes/minimal/layouts/partials/target_icon.html
@@ -0,0 +1 @@
+🞜
\ No newline at end of file
diff --git a/themes/minimal/layouts/partials/therapeutics_icon.html b/themes/minimal/layouts/partials/therapeutics_icon.html
new file mode 100755
index 00000000..3cd913b8
--- /dev/null
+++ b/themes/minimal/layouts/partials/therapeutics_icon.html
@@ -0,0 +1 @@
+💊
\ No newline at end of file
diff --git a/themes/minimal/layouts/partials/trajectory_icon.html b/themes/minimal/layouts/partials/trajectory_icon.html
new file mode 100755
index 00000000..9b9f9bc3
--- /dev/null
+++ b/themes/minimal/layouts/partials/trajectory_icon.html
@@ -0,0 +1 @@
+↝
\ No newline at end of file

From 15921e18896efb8fb9775bfc6aa2d8bafa2ec5b5 Mon Sep 17 00:00:00 2001
From: Samuel Ellis <sjellis@vt.edu>
Date: Fri, 22 May 2020 10:53:53 -0400
Subject: [PATCH 2/3] Adding icon for each page to menu bar.

---
 config.toml | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)
 mode change 100644 => 100755 config.toml

diff --git a/config.toml b/config.toml
old mode 100644
new mode 100755
index 03040947..cfddca3a
--- a/config.toml
+++ b/config.toml
@@ -29,13 +29,13 @@ ignoreFiles = ["README.md$"]
     [[menu.main]]
         parent = "Biology"
         url = "/proteins/"
-        name = "Proteins and Virion"
+        name = "🝪 Proteins and Virion"
         weight = 1
 
     [[menu.main]]
         parent = "Biology"
         url = "/targets/"
-        name = "Target Modalities"
+        name = "🞜 Target Modalities"
         weight = 2
 
 
@@ -47,19 +47,19 @@ ignoreFiles = ["README.md$"]
     [[menu.main]]
         parent = "Viral/Host Structural Data"
         url = "/structures"
-        name = "Structures"
+        name = "◳ Structures"
         weight = 1
 
     [[menu.main]]
         parent = "Viral/Host Structural Data"
         url = "/models"
-        name = "Models"
+        name = "⊧ Models"
         weight = 2
 
     [[menu.main]]
         parent = "Viral/Host Structural Data"
         url = "/simulations"
-        name = "Simulations"
+        name = "⮔ Simulations"
         weight = 2
 
 [[menu.main]]
@@ -71,7 +71,7 @@ ignoreFiles = ["README.md$"]
     [[menu.main]]
         parent = "Therapeutics"
         url = "/therapeutics"
-        name = "All Therapeutics"
+        name = "💊 All Therapeutics"
         weight = 1
 
     [[menu.main]]

From d11cbe02e0f75951480e6f767566d9876bd08c1a Mon Sep 17 00:00:00 2001
From: Samuel Ellis <sjellis@vt.edu>
Date: Fri, 22 May 2020 10:54:20 -0400
Subject: [PATCH 3/3] Adding icon partials to references of each page type.

---
 themes/minimal/layouts/models/single.html              | 2 +-
 themes/minimal/layouts/partials/model-entry.html       | 4 ++--
 themes/minimal/layouts/partials/protein-entry.html     | 4 ++--
 themes/minimal/layouts/partials/simulation-entry.html  | 8 ++++----
 themes/minimal/layouts/partials/structure-entry.html   | 8 ++++----
 themes/minimal/layouts/partials/target-entry.html      | 4 ++--
 themes/minimal/layouts/partials/therapeutics-data.html | 4 ++--
 themes/minimal/layouts/simulations/single.html         | 2 +-
 themes/minimal/layouts/structures/single.html          | 2 +-
 9 files changed, 19 insertions(+), 19 deletions(-)
 mode change 100644 => 100755 themes/minimal/layouts/models/single.html
 mode change 100644 => 100755 themes/minimal/layouts/simulations/single.html
 mode change 100644 => 100755 themes/minimal/layouts/structures/single.html

diff --git a/themes/minimal/layouts/models/single.html b/themes/minimal/layouts/models/single.html
old mode 100644
new mode 100755
index 03161125..47b4a112
--- a/themes/minimal/layouts/models/single.html
+++ b/themes/minimal/layouts/models/single.html
@@ -98,7 +98,7 @@ <h3 align="left" class="anchor" id="{{ .name | anchorize }}"><b><a href='{{index
                     {{ end }}
                 {{ end }}
                 {{ if $localScratch.Get "has_content" }}
-                    <h3 align="left"><u><a style="color:black;" href='{{ $t_map.link }}'>{{$t_map.name}}</a></u></h3>
+                    <h3 align="left"><u><a style="color:black;" href='{{ $t_map.link }}'>{{ partial "target_icon" }} {{$t_map.name}}</a></u></h3>
                     <!-- Finally Models -->
                     {{ range sort $.Site.Data.models "rating" "desc" }}
                         {{ $protein := $localScratch.Get "protein" }}
diff --git a/themes/minimal/layouts/partials/model-entry.html b/themes/minimal/layouts/partials/model-entry.html
index 6107ea97..45f2c1b8 100755
--- a/themes/minimal/layouts/partials/model-entry.html
+++ b/themes/minimal/layouts/partials/model-entry.html
@@ -24,7 +24,7 @@ <h5 align="center">{{ .model.creator }}</h5>
       <h5 align="left"><b>Represented Proteins: </b>
       {{ range $pname := .model.proteins }}
          {{ $plink := print ($localScratch.Get "context").Site.BaseURL "/proteins/#" ( $pname | anchorize) }}
-         <a href="{{ $plink }}"><kbd class="bg-primary" style="">{{ $pname }}</kbd></a>
+         <a href="{{ $plink }}"><kbd class="bg-primary" style="">{{ partial "protein_icon" }} {{ $pname }}</kbd></a>
       {{ end }}
       </h5>
 
@@ -71,7 +71,7 @@ <h5 align="left"><b>Simulations:</b></h5>
                 {{ $anchor := print ( $sim.title | anchorize) "-" ( $.protein | anchorize) "-" ( $.target | anchorize) }}
                 <h5 align="left">
                 <p>
-                <a href='{{ $localScratch.Get "BaseURL" }}/simulations/#{{ $anchor }}'><kbd class="alert-secondary">{{ $sim.title }}</kbd></a>
+                <a href='{{ $localScratch.Get "BaseURL" }}/simulations/#{{ $anchor }}'><kbd class="alert-secondary">{{ partial "simulation_icon" }} {{ $sim.title }}</kbd></a>
                 {{ partial "general-marker" $sim }}
                 </p>
                 </h5>
diff --git a/themes/minimal/layouts/partials/protein-entry.html b/themes/minimal/layouts/partials/protein-entry.html
index eb56b9b8..4d52b9a3 100755
--- a/themes/minimal/layouts/partials/protein-entry.html
+++ b/themes/minimal/layouts/partials/protein-entry.html
@@ -79,7 +79,7 @@ <h5 align="left">
         {{ $anchor := print ( $model.name | anchorize) "-" ( $.protein.protein | anchorize) "-" ( $target | anchorize) }}
         {{ $model_url := print $.context.Site.BaseURL "/models/#" $anchor }}
         <a href='{{ $model_url }}'>
-          <kbd class="alert-info">{{  $model.name | title }}{{partial "stars" $model.rating}}</kbd>
+          <kbd class="alert-info">{{ partial "models_icon" }} {{  $model.name | title }}{{partial "stars" $model.rating}}</kbd>
         </a>
         {{ partial "general-marker" $model }}
       </p>
@@ -99,7 +99,7 @@ <h5 align="left">
         {{ if and (in .proteins $.protein.protein) (lt ($localScratch.Get "postedSim") 2) }}
         <!-- TODO: Map the anchor to *a* target instead of just the protein heade-->
             <p>
-                <a href='{{ $localScratch.Get "BaseURL" }}/simulations/#{{ $.protein.name | anchorize }}'><kbd class="alert-secondary">{{ $sim.title}}</kbd></a>
+                <a href='{{ $localScratch.Get "BaseURL" }}/simulations/#{{ $.protein.name | anchorize }}'><kbd class="alert-secondary">{{ partial "simulation_icon" }} {{ $sim.title}}</kbd></a>
                 {{ partial "general-marker" $sim }}
                 <!-- Add to the counter -->
                 {{ $localScratch.Set "postedSim" (add ($localScratch.Get "postedSim") 1 )}}
diff --git a/themes/minimal/layouts/partials/simulation-entry.html b/themes/minimal/layouts/partials/simulation-entry.html
index f54695f7..ea91329a 100755
--- a/themes/minimal/layouts/partials/simulation-entry.html
+++ b/themes/minimal/layouts/partials/simulation-entry.html
@@ -77,7 +77,7 @@ <h5 align="left">
         <h5 align="left">
             <b>Trajectory:</b>
             {{ if .simulation.trajectory }}
-                <a href="{{ .simulation.trajectory }}"><kbd class="alert-secondary">Get Trajectory ({{.simulation.size}})</kbd></a>
+                <a href="{{ .simulation.trajectory }}"><kbd class="alert-secondary">{{ partial "trajectory_icon" }} Get Trajectory ({{.simulation.size}})</kbd></a>
             {{ else }}
                 ---
             {{ end }}
@@ -87,7 +87,7 @@ <h5 align="left">
         <h5 align="left">
             <b>Represented Proteins:</b>
             {{ range .simulation.proteins }}
-                <a href='{{ index ($localScratch.Get "protein_map") . }}'><kbd class="bg-primary">{{ . }}</kbd></a> 
+                <a href='{{ index ($localScratch.Get "protein_map") . }}'><kbd class="bg-primary">{{ partial "protein_icon" }} {{ . }}</kbd></a> 
             {{ else }}
                 ---
             {{ end }}
@@ -98,7 +98,7 @@ <h5 align="left">
             <b>Represented Structures:</b>
             {{ range .simulation.structures }}
                 {{ $anchor := print ( . | upper | anchorize) "-" ( $.protein | anchorize) }}
-                <a href='{{ $.context.Site.BaseURL }}/structures/#{{ $anchor }}'><kbd class="alert-danger">{{.}}</kbd></a>
+                <a href='{{ $.context.Site.BaseURL }}/structures/#{{ $anchor }}'><kbd class="alert-danger">{{ partial "structure_icon" }} {{.}}</kbd></a>
             {{ else }}
                 ---
             {{ end }}
@@ -112,7 +112,7 @@ <h5 align="left">
                 {{ range $mname, $mdata := $.context.Site.Data.models }}
                     {{ if eq $model $mname }}
                         {{ $anchor := print ( $mdata.name | anchorize) "-" ( $.protein | anchorize) "-" ( $.target | anchorize) }}
-                        <a href='{{ $.context.Site.BaseURL }}/models/#{{ $anchor }}'><kbd class="alert-info">{{ $mdata.name}}</kbd></a>
+                        <a href='{{ $.context.Site.BaseURL }}/models/#{{ $anchor }}'><kbd class="alert-info">{{ partial "models_icon" }} {{ $mdata.name}}</kbd></a>
                     {{ end }}
                 {{ end }}
             {{ else }}
diff --git a/themes/minimal/layouts/partials/structure-entry.html b/themes/minimal/layouts/partials/structure-entry.html
index 1f1aa678..b1154143 100755
--- a/themes/minimal/layouts/partials/structure-entry.html
+++ b/themes/minimal/layouts/partials/structure-entry.html
@@ -112,7 +112,7 @@ <h5 align="left">
         {{ $anchor := print ( $model.name | anchorize) "-" ( $.protein | anchorize) "-" ( $.target | anchorize) }}
         {{ $model_url := print $.context.Site.BaseURL "/models/#" $anchor }}
         <a href='{{ $model_url }}'>
-          <kbd>{{  $model.name | title }}{{partial "stars" $model.rating}}</kbd>
+          <kbd>{{ partial "models_icon" }} {{  $model.name | title }}{{partial "stars" $model.rating}}</kbd>
         </a>
         {{ partial "general-marker" $model }}
       </p>
@@ -129,7 +129,7 @@ <h5 align="left">
   <p>-->
   {{ $targets := partial "ensure-slice" .structure.targets }}
   {{ range $targets }}
-    <a href='{{ (index ($localScratch.Get "target_map") .).link }}'><kbd class="item-tag">{{ (index ($localScratch.Get "target_map") .).name | title }}</kbd></a>
+    <a href='{{ (index ($localScratch.Get "target_map") .).link }}'><kbd class="item-tag">{{ partial "target_icon" }} {{ (index ($localScratch.Get "target_map") .).name | title }}</kbd></a>
   {{ end }}
   <!--</p>-->
   </h5>
@@ -137,7 +137,7 @@ <h5 align="left">
   <h5 align="left"><b>Related Proteins:</b>
   {{ $proteins := partial "ensure-slice" .structure.proteins }}
   {{ range $proteins }}
-    <a href='{{ index ($localScratch.Get "protein_map") . }}'><kbd class="bg-primary">{{ . }}</kbd></a>
+    <a href='{{ index ($localScratch.Get "protein_map") . }}'><kbd class="bg-primary">{{ partial "protein_icon" }} {{ . }}</kbd></a>
   {{ end }}
   </h5>
 
@@ -149,7 +149,7 @@ <h5 align="left"><b>Top Simulations:</b><a href='{{ $.context.Site.BaseURL }}/si
         {{ if and ($sin) (lt ($localScratch.Get "postedSim") 2) }}
             {{ $anchor := print ( $sim.title | anchorize) "-" ( $.protein | anchorize) "-" ( $.target | anchorize) }}
             <h5 align="left"><p>
-            <a href='{{ $localScratch.Get "BaseURL" }}/simulations/#{{ $anchor }}'><kbd class="alert-secondary">{{ $sim.title }}</kbd></a>
+            <a href='{{ $localScratch.Get "BaseURL" }}/simulations/#{{ $anchor }}'><kbd class="alert-secondary">{{ partial "simulation_icon" }} {{ $sim.title }}</kbd></a>
             {{ partial "general-marker" $sim }}
             </p></h5>
             <!-- Add to the counter -->
diff --git a/themes/minimal/layouts/partials/target-entry.html b/themes/minimal/layouts/partials/target-entry.html
index ffcb3d0f..f61c3719 100755
--- a/themes/minimal/layouts/partials/target-entry.html
+++ b/themes/minimal/layouts/partials/target-entry.html
@@ -19,7 +19,7 @@ <h4 class="anchor" id="{{.context.name | anchorize }}"><b>{{ .context.name }}</b
   <!-- tag links to proteins involves in this target -->
   <h5 align="left"><b>Proteins affected:</b>
   {{ range .context.proteins }}
-    <a href='{{ index ($localScratch.Get "protein_map") . }}'><kbd class="bg-primary">{{ . }}</kbd></a>
+    <a href='{{ index ($localScratch.Get "protein_map") . }}'><kbd class="bg-primary">{{ partial "protein_icon" }} {{ . }}</kbd></a>
   {{ end }}
   </h5>
 
@@ -30,7 +30,7 @@ <h5 align="left"><b>Potential therapeutic modalities:</b><!--</h5>
     <h5 align="left">-->
       {{ range .context.therapeutic_modalities }}
        <!-- NOTE: hyperlinks do not correctly link up to the right anchor point yet -->
-       <a href='{{ index ($localScratch.Get "thera_map") . }}'><kbd class="alert-success">{{ . | title }}</kbd></a>
+       <a href='{{ index ($localScratch.Get "thera_map") . }}'><kbd class="alert-success">{{ partial "therapeutics_icon" }} {{ . | title }}</kbd></a>
       {{ end }}
     <!--</h5>-->
     </div>
diff --git a/themes/minimal/layouts/partials/therapeutics-data.html b/themes/minimal/layouts/partials/therapeutics-data.html
index 72c74685..2051ecda 100755
--- a/themes/minimal/layouts/partials/therapeutics-data.html
+++ b/themes/minimal/layouts/partials/therapeutics-data.html
@@ -45,7 +45,7 @@ <h5 align="left"><b>Read more about it:</b>
   <h5 align="left"><b>Targeting Modalities:</b>
   
   {{ range $localScratch.Get "iter" }}
-    <a href='{{ (index ($localScratch.Get "target_map") .).link }}'><kbd class="item-tag">{{ . | title}}</kbd></a>
+    <a href='{{ (index ($localScratch.Get "target_map") .).link }}'><kbd class="item-tag">{{ partial "target_icon" }} {{ . | title}}</kbd></a>
   {{ end }}
   </h5>
 {{ end }}
@@ -60,7 +60,7 @@ <h5 align="left"><b>Targeting Modalities:</b>
   <h5 align="left"><b>Known Protein Interactions:</b>
   
   {{ range $localScratch.Get "iter" }}
-    <a href='{{ index ($localScratch.Get "protein_map") . }}'><kbd class="bg-primary">{{ . }}</kbd></a>
+    <a href='{{ index ($localScratch.Get "protein_map") . }}'><kbd class="bg-primary">{{ partial "protein_icon" }} {{ . }}</kbd></a>
   {{ end }}
   </h5>
 {{ end }}
diff --git a/themes/minimal/layouts/simulations/single.html b/themes/minimal/layouts/simulations/single.html
old mode 100644
new mode 100755
index 1eddbb08..94063e8f
--- a/themes/minimal/layouts/simulations/single.html
+++ b/themes/minimal/layouts/simulations/single.html
@@ -95,7 +95,7 @@ <h3 align="left" class="anchor" id="{{ .name | anchorize }}"><b><a href='{{index
                 {{ end }}
 
                 {{ if $localScratch.Get "has_content" }}
-                    <h3 align="left"><u><a style="color:black;" href='{{ $t_map.link }}'>{{$t_map.name}}</a></u></h3>
+                    <h3 align="left"><u><a style="color:black;" href='{{ $t_map.link }}'>{{ partial "target_icon" }} {{$t_map.name}}</a></u></h3>
                     <!-- Finally Simulations -->
                     {{ range sort $.Site.Data.simulations "rating" "desc" }}
                         {{ $protein := $localScratch.Get "protein" }}
diff --git a/themes/minimal/layouts/structures/single.html b/themes/minimal/layouts/structures/single.html
old mode 100644
new mode 100755
index eec43e10..ff157100
--- a/themes/minimal/layouts/structures/single.html
+++ b/themes/minimal/layouts/structures/single.html
@@ -94,7 +94,7 @@ <h3 align="left" class="anchor" id="{{ .name | anchorize }}"><b><a href='{{index
                     {{ end }}
                 {{ end }}
                 {{ if $localScratch.Get "has_content" }}
-                    <h3 align="left"><u><a style="color:black;" href='{{ $t_map.link }}'>{{$t_map.name}}</a></u></h3>
+                    <h3 align="left"><u><a style="color:black;" href='{{ $t_map.link }}'>{{ partial "target_icon" }} {{$t_map.name}}</a></u></h3>
                     <!-- Finally Structures -->
                     {{ range sort $.Site.Data.structures "rating" "desc" }}
                         {{ $protein := $localScratch.Get "protein" }}