/*
 * R2DT 2D+3D viewer styles (r2dt-2d-3d-viewer.css).
 * Loaded after pdb-rna-viewer-0.3.0.css in generated index.html.
 */

/* --- Toolbar accents (match toggle on-state) --------------------------- */

:root {
  --r2dt-accent: #7a96b0;
  --r2dt-accent-soft-bg: #e8eef3;
  --r2dt-accent-soft-border: #a8bac9;
  --r2dt-accent-badge-bg: #dde5ec;
  --r2dt-accent-badge-text: #5c7388;
  --r2dt-bp-glyph: #909090;
  --r2dt-font-ui: -apple-system, BlinkMacSystemFont, "Segoe UI", Roboto,
    sans-serif;
  --r2dt-font-diagram: Helvetica, Arial, sans-serif;
}

/* --- 2D panel fonts ---------------------------------------------------- */

#pdb-rna-viewer,
.r2dt-panel--2d,
#mainMenu.r2dt-toolbar {
  font-family: var(--r2dt-font-ui);
}

#pdb-rna-viewer svg.rnaTopoSvg text,
.r2dt-panel--2d svg.rnaTopoSvg text {
  font-family: var(--r2dt-font-diagram);
  font-weight: 700;
}

/* --- Toolbar ----------------------------------------------------------- */

#mainMenu.r2dt-toolbar {
  height: auto;
  min-height: 40px;
  line-height: normal;
  background: #f8f9fa;
  color: #374151;
  border: none;
  position: relative;
  z-index: 30;
  overflow: visible;
  flex: none;
  width: 100%;
  display: block;
}

#mainMenu.r2dt-toolbar form {
  margin: 0;
  padding: 8px 12px;
  gap: 10px 12px;
  flex-wrap: nowrap;
  align-items: center;
  justify-content: flex-start;
  min-width: 0;
  overflow: visible;
}

#mainMenu.r2dt-toolbar .menu-dropdown {
  position: relative;
}

.r2dt-toolbar-title {
  font-size: 13px;
  font-weight: 500;
  color: #6b7280;
  letter-spacing: 0.01em;
  white-space: nowrap;
  overflow: hidden;
  text-overflow: ellipsis;
  flex: 1 1 0;
  min-width: 0;
  max-width: 100%;
  margin-right: 2px;
}

.r2dt-toolbar-group {
  display: inline-flex;
  align-items: center;
  gap: 8px;
  flex: 0 0 auto;
  flex-wrap: nowrap;
}

.r2dt-toolbar-group + .r2dt-toolbar-group {
  padding-left: 12px;
  border-left: 1px solid #e5e7eb;
}

/* Section labels add noise at the 600px panel width — hide them. */
.r2dt-toolbar-group-label {
  display: none;
}

/* --- Toggle switches --------------------------------------------------- */

.r2dt-toggle {
  display: inline-flex;
  align-items: center;
  gap: 8px;
  cursor: pointer;
  user-select: none;
  font-size: 13px;
  color: #374151;
  min-height: 32px;
}

.r2dt-toggle input {
  position: absolute;
  opacity: 0;
  width: 0;
  height: 0;
  pointer-events: none;
}

.r2dt-toggle-track {
  position: relative;
  flex: none;
  width: 34px;
  height: 20px;
  background: #e5e7eb;
  border-radius: 999px;
  transition: background 0.15s ease;
}

.r2dt-toggle-track::after {
  content: "";
  position: absolute;
  top: 2px;
  left: 2px;
  width: 16px;
  height: 16px;
  background: #fff;
  border-radius: 50%;
  box-shadow: 0 1px 2px rgba(0, 0, 0, 0.12);
  transition: transform 0.15s ease;
}

.r2dt-toggle input:checked + .r2dt-toggle-track {
  background: var(--r2dt-accent);
}

.r2dt-toggle input:checked + .r2dt-toggle-track::after {
  transform: translateX(14px);
}

.r2dt-toggle input:focus-visible + .r2dt-toggle-track {
  outline: 2px solid #b8c9d9;
  outline-offset: 2px;
}

.r2dt-toggle-label {
  line-height: 1.2;
}

/* Nested-BP row injected by the plugin — restyle in place */
.r2dt-toolbar-group--pairs .r2dt-nested-wrap {
  display: inline-flex;
  align-items: center;
  flex: none;
  position: relative;
}

.r2dt-toolbar-group--pairs .r2dt-nested-wrap input {
  position: absolute;
  opacity: 0;
  width: 0;
  height: 0;
  pointer-events: none;
}

.r2dt-toolbar-group--pairs .r2dt-nested-toggle {
  display: inline-flex;
  align-items: center;
  gap: 8px;
  cursor: pointer;
  user-select: none;
  font-size: 13px;
  color: #374151;
  min-height: 32px;
  margin: 0;
  white-space: nowrap;
}

.r2dt-toolbar-group--pairs .r2dt-nested-toggle span {
  position: relative;
  padding-left: 42px;
  line-height: 20px;
}

.r2dt-toolbar-group--pairs .r2dt-nested-toggle span::before {
  content: "";
  position: absolute;
  left: 0;
  top: 0;
  width: 34px;
  height: 20px;
  background: #e5e7eb;
  border-radius: 999px;
  transition: background 0.15s ease;
}

.r2dt-toolbar-group--pairs .r2dt-nested-toggle span::after {
  content: "";
  position: absolute;
  left: 2px;
  top: 2px;
  width: 16px;
  height: 16px;
  background: #fff;
  border-radius: 50%;
  box-shadow: 0 1px 2px rgba(0, 0, 0, 0.12);
  transition: transform 0.15s ease;
}

.r2dt-toolbar-group--pairs .r2dt-nested-wrap input:checked + .r2dt-nested-toggle span::before {
  background: var(--r2dt-accent);
}

.r2dt-toolbar-group--pairs .r2dt-nested-wrap input:checked + .r2dt-nested-toggle span::after {
  transform: translateX(14px);
}

.r2dt-toolbar-group--pairs .r2dt-nested-wrap input:focus-visible + .r2dt-nested-toggle span::before {
  outline: 2px solid #b8c9d9;
  outline-offset: 2px;
}

/* --- Filter dropdown button -------------------------------------------- */

#mainMenu.r2dt-toolbar .menu-dropdown button,
.r2dt-btn {
  background: #fff;
  color: #374151;
  border: 1px solid #d1d5db;
  border-radius: 6px;
  padding: 6px 10px;
  min-height: 32px;
  font-size: 13px;
  font-family: inherit;
  cursor: pointer;
  display: inline-flex;
  align-items: center;
  gap: 6px;
  box-shadow: 0 1px 2px rgba(0, 0, 0, 0.04);
  transition: background 0.15s ease, border-color 0.15s ease;
}

#mainMenu.r2dt-toolbar .menu-dropdown button:hover,
.r2dt-btn:hover {
  background: #f3f4f6;
  border-color: #9ca3af;
}

#mainMenu.r2dt-toolbar .menu-dropdown.show button {
  background: var(--r2dt-accent-soft-bg);
  border-color: var(--r2dt-accent-soft-border);
}

.r2dt-filter-badge {
  display: inline-flex;
  align-items: center;
  justify-content: center;
  min-width: 2.2em;
  padding: 1px 6px;
  border-radius: 999px;
  background: #e5e7eb;
  color: #374151;
  font-size: 11px;
  font-weight: 600;
  line-height: 1.4;
}

.menu-dropdown.show .r2dt-filter-badge {
  background: var(--r2dt-accent-badge-bg);
  color: var(--r2dt-accent-badge-text);
}

#bpFilterBtnIcon {
  margin-left: 0;
  font-size: 11px;
  color: #6b7280;
  transition: transform 0.15s ease;
}

.menu-dropdown.show #bpFilterBtnIcon {
  transform: rotate(180deg) translate(0, -1px);
}

#bpFilterBtnHelp,
#bpFilterBtn .help-icon {
  display: none !important;
}

/* --- Filter dropdown panel --------------------------------------------- */

#mainMenu.r2dt-toolbar .menu-dropdown-content {
  display: none;
}

/* Docked in the 2D panel (like the base-pair list) so it is not clipped by
   the toolbar or covered by the SVG diagram. */
#pdb-rna-viewer #checkboxes.r2dt-bp-filter-panel {
  display: none;
  position: absolute;
  left: auto;
  right: 8px;
  bottom: 48px;
  top: auto;
  width: auto;
  min-width: 280px;
  max-width: 340px;
  max-height: min(480px, 60vh);
  overflow-y: auto;
  background: #fff;
  border: 1px solid rgba(229, 231, 235, 0.95);
  border-radius: 8px;
  box-shadow: 0 -4px 24px rgba(0, 0, 0, 0.12);
  padding: 10px;
  z-index: 100;
  float: none;
  box-sizing: border-box;
}

.r2dt-filter-panel-title {
  font-size: 12px;
  font-weight: 600;
  color: #374151;
  margin: 0 0 8px;
  padding-bottom: 8px;
  border-bottom: 1px solid #eef0f2;
  line-height: 1.3;
}

#checkboxes.r2dt-bp-filter-panel table {
  display: grid;
  grid-template-columns: 1fr 1fr;
  gap: 4px 8px;
  width: 100%;
  border-collapse: separate;
  border-spacing: 0;
}

#checkboxes.r2dt-bp-filter-panel tbody,
#checkboxes.r2dt-bp-filter-panel tr {
  display: contents;
}

#checkboxes.r2dt-bp-filter-panel td {
  display: block;
  padding: 0;
}

#checkboxes.r2dt-bp-filter-panel td:has(#Checkbox_All) {
  grid-column: 1 / -1;
}

#checkboxes.r2dt-bp-filter-panel label {
  display: flex;
  align-items: center;
  gap: 6px;
  padding: 6px 8px;
  border-radius: 6px;
  font-size: 13px;
  color: #374151;
  text-align: left;
  transition: background 0.12s ease;
}

.r2dt-bp-family-label {
  flex: none;
}

.r2dt-bp-glyph-wrap {
  flex: none;
  display: inline-flex;
  align-items: center;
  line-height: 0;
  margin-left: auto;
}

.r2dt-bp-glyph {
  display: block;
  color: var(--r2dt-bp-glyph);
}

/* Residue readout (bottom-right: hover + selected) ---------------------- */

#pdb-rna-viewer .pdb-rna-view-tooltip,
#pdb-rna-viewer .pdb-rna-view-tooltip-highlight {
  font-size: calc(11px + 4pt);
  font-weight: 400;
  line-height: 1.35;
  color: #6b7280;
}

#pdb-rna-viewer .pdb-rna-view-tooltip strong,
#pdb-rna-viewer .pdb-rna-view-tooltip-highlight strong {
  font-weight: 500;
  color: #6b7280;
}

/* Clear-selection (×) button inside the selection tooltip. */
.r2dt-deselect-btn {
  appearance: none;
  margin-left: 6px;
  padding: 0;
  width: 18px;
  height: 18px;
  border: 1px solid #d1d5db;
  border-radius: 50%;
  background: #fff;
  color: #6b7280;
  font-size: 11px;
  line-height: 1;
  cursor: pointer;
  vertical-align: middle;
  display: inline-flex;
  align-items: center;
  justify-content: center;
  transition: background 0.12s ease, border-color 0.12s ease, color 0.12s ease;
}

.r2dt-deselect-btn:hover {
  background: #f3f4f6;
  border-color: #9ca3af;
  color: #374151;
}

.r2dt-deselect-btn:focus-visible {
  outline: 2px solid #b8c9d9;
  outline-offset: 1px;
}

#checkboxes.r2dt-bp-filter-panel label:hover {
  background: #f3f4f6;
}

#checkboxes.r2dt-bp-filter-panel input[type="checkbox"] {
  accent-color: var(--r2dt-accent);
  width: 15px;
  height: 15px;
  margin: 0;
  flex: none;
}

/* --- Legend inside base-pairs panel ------------------------------------ */

.r2dt-bp-legend-more {
  margin-top: 10px;
  padding-top: 10px;
  border-top: 1px solid #eef0f2;
}

.r2dt-bp-legend-more summary {
  cursor: pointer;
  font-size: 12px;
  font-weight: 500;
  color: #5c7388;
  list-style: none;
  user-select: none;
}

.r2dt-bp-legend-more summary::-webkit-details-marker {
  display: none;
}

.r2dt-bp-legend-more summary::before {
  content: "▸ ";
  font-size: 11px;
  color: #9ca3af;
}

.r2dt-bp-legend-more[open] summary::before {
  content: "▾ ";
}

.r2dt-bp-legend-more .r2dt-bp-legend-panel {
  margin-top: 8px;
}

.r2dt-bp-legend-intro {
  margin: 0 0 10px;
  font-size: 11px;
  line-height: 1.45;
  color: #6b7280;
}

.r2dt-bp-legend-table {
  width: 100%;
  border-collapse: collapse;
  font-size: 11px;
  color: #374151;
}

.r2dt-bp-legend-table th,
.r2dt-bp-legend-table td {
  border: 1px solid #e5e7eb;
  padding: 3px 6px;
  text-align: center;
  vertical-align: middle;
}

.r2dt-bp-legend-table thead th {
  font-weight: 600;
  background: #f9fafb;
}

.r2dt-bp-legend-table tbody th {
  white-space: nowrap;
  font-weight: 600;
  text-align: left;
}

.r2dt-bp-legend-table svg {
  display: inline-block;
  vertical-align: middle;
  height: 14px;
  width: auto;
}

.r2dt-bp-legend-cite {
  margin: 10px 0 0;
  font-size: 11px;
  color: #6b7280;
}

.r2dt-bp-legend-cite a {
  color: #5c7388;
}

/* --- Base pair list (docked inside 2D panel) --------------------------- */

.r2dt-bp-list-dropdown {
  position: relative;
  display: inline-flex;
}

#mainMenu.r2dt-toolbar .bp-list-btn {
  white-space: nowrap;
}

#pdb-rna-viewer .bp-list-dialog.r2dt-bp-list-panel {
  position: absolute;
  left: auto;
  right: 8px;
  bottom: 48px;
  top: auto;
  flex-direction: column;
  width: min(248px, calc(100% - 16px));
  height: min(220px, 38%);
  max-height: min(220px, 38%);
  overflow: hidden;
  background: rgba(255, 255, 255, 0.94);
  border: 1px solid rgba(229, 231, 235, 0.95);
  border-radius: 8px;
  box-shadow: 0 -2px 16px rgba(0, 0, 0, 0.08);
  padding: 6px 8px;
  z-index: 25;
  font-size: 12px;
  color: #374151;
  box-sizing: border-box;
}

.r2dt-bp-list-panel-title {
  flex: none;
  font-size: 11px;
  font-weight: 600;
  color: #6b7280;
  margin: 0 0 4px;
  padding-bottom: 4px;
  border-bottom: 1px solid #eef0f2;
  line-height: 1.2;
}

#pdb-rna-viewer .bp-list-dialog ul {
  flex: 1 1 auto;
  min-height: 0;
  list-style: none !important;
  margin: 0;
  padding: 0 !important;
  overflow-y: auto !important;
  overscroll-behavior: contain;
  -webkit-overflow-scrolling: touch;
}

#pdb-rna-viewer .bp-list-dialog li {
  display: flex;
  align-items: center;
  justify-content: space-between;
  gap: 10px;
  padding: 1px 4px;
  border-radius: 4px;
  cursor: pointer;
  font-size: 12px;
  line-height: 1.2;
  color: #374151;
  transition: background 0.12s ease;
}

.r2dt-bp-list-pair {
  flex: 1 1 auto;
  min-width: 0;
  white-space: nowrap;
  overflow: hidden;
  text-overflow: ellipsis;
}

.r2dt-bp-list-family {
  flex: none;
  font-size: 11px;
  font-weight: 500;
  color: #6b7280;
  letter-spacing: 0.02em;
}

.r2dt-bp-list-item--nonwc .r2dt-bp-list-pair {
  color: #6b7280;
}

.r2dt-bp-list-item--nonwc .r2dt-bp-list-family {
  color: #9ca3af;
}

.r2dt-bp-list-tag {
  flex: none;
  font-size: 10px;
  font-weight: 500;
  color: #9ca3af;
  letter-spacing: 0.03em;
  text-transform: lowercase;
  padding: 1px 5px;
  border-radius: 3px;
  background: #f3f4f6;
  line-height: 1.3;
}

#pdb-rna-viewer .bp-list-dialog li:hover,
.r2dt-panel--2d .bp-list-dialog li:hover {
  background: #f3f4f6;
}

.r2dt-bp-list-item--nonwc:hover .r2dt-bp-list-tag {
  background: #e8eaed;
}

/* --- Floating panel controls (top-right zoom) -------------------------- */

#pdb-rna-viewer .pdb-rna-view-btn-group {
  display: flex;
  gap: 4px;
}

#pdb-rna-viewer .pdb-rna-view-btn {
  display: inline-flex;
  align-items: center;
  justify-content: center;
  padding: 6px;
  line-height: 0;
  vertical-align: middle;
}

#pdb-rna-viewer .pdb-rna-view-btn svg {
  display: block;
  width: 20px;
  height: 20px;
}

.pdb-rna-view-btn {
  background: #fff;
  color: #374151;
  border: 1px solid #d1d5db;
  border-radius: 6px;
  padding: 5px 7px;
  box-shadow: 0 1px 2px rgba(0, 0, 0, 0.06);
}

.pdb-rna-view-btn:hover {
  background: #f3f4f6;
  border-color: #9ca3af;
}

#pdb-rna-viewer,
.r2dt-panel--2d {
  display: flex;
  flex-direction: column;
  position: relative;
  overflow: hidden;
  border: 1px solid #e5e7eb;
  border-radius: 8px;
  background: #fff;
  box-sizing: border-box;
}

#pdb-molstar,
.r2dt-panel--3d {
  border: 1px solid #e5e7eb;
  border-radius: 8px;
  background: #fff;
  box-sizing: border-box;
  /* Allow Mol* "outside" control panels (bottom:-295px) to show below the canvas. */
  overflow: visible;
}

#pdb-molstar .msp-layout-main {
  overflow: hidden;
  border-radius: 7px;
}

#pdb-molstar .msp-plugin-content {
  border: none;
}

.pdb-rna-view-container {
  flex: 1 1 auto;
  min-height: 0;
  border: none;
  border-radius: 0;
  overflow: hidden;
  height: auto !important;
  width: 100%;
  display: block;
}

#pdb-rna-viewer #mainMenu.r2dt-toolbar {
  height: auto !important;
  line-height: normal !important;
  min-height: 44px;
}

.help-tooltip {
  border-radius: 8px;
  box-shadow: 0 8px 24px rgba(0, 0, 0, 0.12);
  font-size: 12px;
}

/* --- Embed root layout (R2DTViewer.create) -------------------------------- */

.r2dt-viewer-root {
  --r2dt-panel-size: 600px;
  --r2dt-viewer-height: 600px;
  max-width: calc(var(--r2dt-panel-size) * 2 + 16px);
}

.r2dt-viewer-root[data-layout="stacked"] .r2dt-viewer-vis {
  flex-direction: column;
}

.r2dt-viewer-root[data-layout="2d-only"] .r2dt-panel--3d,
.r2dt-viewer-root[data-layout="3d-only"] .r2dt-panel--2d {
  display: none;
}

.r2dt-viewer-vis {
  display: flex;
  gap: 16px;
  align-items: flex-start;
}

.r2dt-viewer-root #pdb-rna-viewer,
.r2dt-viewer-root #pdb-molstar {
  width: var(--r2dt-panel-size);
  height: var(--r2dt-viewer-height);
  flex: none;
}

.r2dt-viewer-root #pdb-molstar {
  position: relative;
}

.r2dt-viewer-lbn {
  margin-top: 20px;
  max-width: calc(var(--r2dt-panel-size) * 2 + 16px);
}

.r2dt-viewer-lbn-title {
  font-size: 14px;
  font-weight: 600;
  margin: 0 0 6px;
}

/* --- Compare layout (R2DTViewer.createCompare) --------------------------- */

.r2dt-compare-root {
  --r2dt-compare-panel-height: 480px;
}

.r2dt-compare-grid {
  display: flex;
  gap: 12px;
  align-items: flex-start;
}

.r2dt-compare-slot {
  flex: 1 1 0;
  min-width: 0;
}

.r2dt-compare-slot-title {
  font-size: 13px;
  margin: 0 0 8px;
  font-weight: 600;
}

.r2dt-compare-tag {
  color: #888;
  font-weight: 400;
}

.r2dt-compare-root .r2dt-viewer-root {
  max-width: none;
}

.r2dt-compare-root .r2dt-panel--2d,
.r2dt-compare-root .r2dt-panel--3d {
  width: 100%;
  height: var(--r2dt-compare-panel-height);
  flex: none;
}

.r2dt-compare-molstar-root .r2dt-panel--3d {
  position: relative;
}

.r2dt-viewer-lbn .lbn-body {
  overflow-x: auto;
  background: #fafafa;
  border: 1px solid #e0e0e0;
  border-radius: 4px;
  padding: 8px 12px;
}

.lbn-row {
  font-family: "Courier New", Courier, monospace;
  font-size: 12px;
  white-space: pre;
  line-height: 1.6;
}

.lbn-label {
  display: inline-block;
  width: 7ch;
  color: #888;
}

.lbn-nt,
.lbn-bp,
.lbn-dot {
  display: inline-block;
  width: 1ch;
  text-align: center;
  vertical-align: bottom;
}

.lbn-nt {
  cursor: pointer;
  border-radius: 2px;
}

.lbn-nt:hover {
  background: #d0eaf8;
}

.lbn-bp {
  cursor: pointer;
  font-weight: bold;
  border-radius: 2px;
}

.lbn-bp:hover {
  background: #d0eaf8;
}

.lbn-selected {
  background: #ffe066 !important;
  outline: 1px solid #e6b800;
}

.lbn-partner {
  background: #ffc0cb !important;
  outline: 1px solid #d0607a;
}

/* Pairs hidden in the current 2D view are dimmed (kept in place so the
   columns stay aligned). Selection highlight still overrides this. */
.lbn-bp.lbn-bp-hidden {
  color: #c9ced6;
  font-weight: normal;
}

.lbn-row--hidden .lbn-label {
  color: #c9ced6;
}

.r2dt-viewer-lbn-caption {
  margin: 0 0 8px;
  font-size: 12px;
  color: #6b7280;
  line-height: 1.4;
}