@import url('https://fonts.googleapis.com/css2?family=Geist:wght@300;400;500&family=Geist+Mono:wght@300;400;500&family=Cormorant+Garamond:wght@300;400;500&display=swap');

/* light mode (default) */
:root {
  --bg:            #f4f6f9;
  --surface:       #ebeef3;
  --surface-hover: #e1e5ec;
  --border:        #ced3dc;
  --border-hover:  #748cab;
  --text:          #0d1321;
  --muted:         #3e5c76;
  --dim:           #dde1e9;
  --font-sans:     'Geist', -apple-system, sans-serif;
  --font-mono:     'Geist Mono', 'SF Mono', 'Menlo', monospace;
  --font-display:  'Cormorant Garamond', Georgia, serif;
  --color-text-primary:   #0d1321;
  --color-text-secondary: #3e5c76;
  --color-border:         #ced3dc;
  --color-background:     #f4f6f9;
  --color-surface:        #ebeef3;
  --color-surface-light:  #e1e5ec;
  --color-primary:        #3e5c76;
  --border-radius:        2px;
  --glass-bg:             rgba(255,255,255,0.55);
  --glass-border:         rgba(0,0,0,0.12);
  --glass-shadow:         0 2px 10px rgba(0,0,0,0.08), 0 4px 20px rgba(0,0,0,0.05), inset 0 1px 0 rgba(255,255,255,0.9);
  --glass-bg-hover:       rgba(255,255,255,0.75);
}

/* dark mode — via OS preference or explicit class */
@media (prefers-color-scheme: dark) {
  :root:not(.light-mode) {
    --bg:            #0d1321;
    --surface:       #1d2d44;
    --surface-hover: #253752;
    --border:        #2a3f5c;
    --border-hover:  #3e5c76;
    --text:          #f4f6f9;
    --muted:         #748cab;
    --dim:           #141c2e;
    --color-text-primary:   #f4f6f9;
    --color-text-secondary: #748cab;
    --color-border:         #2a3f5c;
    --color-background:     #0d1321;
    --color-surface:        #1d2d44;
    --color-surface-light:  #253752;
    --glass-bg:             rgba(255,255,255,0.06);
    --glass-border:         rgba(255,255,255,0.12);
    --glass-shadow:         0 2px 10px rgba(0,0,0,0.4), 0 4px 20px rgba(0,0,0,0.3), inset 0 1px 0 rgba(255,255,255,0.08);
    --glass-bg-hover:       rgba(255,255,255,0.12);
  }
}

html.dark-mode {
  --bg:            #0d1321;
  --surface:       #1d2d44;
  --surface-hover: #253752;
  --border:        #2a3f5c;
  --border-hover:  #3e5c76;
  --text:          #f4f6f9;
  --muted:         #748cab;
  --dim:           #141c2e;
  --color-text-primary:   #f4f6f9;
  --color-text-secondary: #748cab;
  --color-border:         #2a3f5c;
  --color-background:     #0d1321;
  --color-surface:        #1d2d44;
  --color-surface-light:  #253752;
  --glass-bg:             rgba(255,255,255,0.06);
  --glass-border:         rgba(255,255,255,0.12);
  --glass-shadow:         0 2px 10px rgba(0,0,0,0.4), 0 4px 20px rgba(0,0,0,0.3), inset 0 1px 0 rgba(255,255,255,0.08);
  --glass-bg-hover:       rgba(255,255,255,0.12);
}

*, *::before, *::after { box-sizing: border-box; }

html { background: var(--bg); }

body {
  font-family: var(--font-sans);
  font-size: 0.9rem;
  line-height: 1.7;
  background: var(--bg);
  color: var(--text);
  margin: 0;
  padding: 2rem;
  -webkit-font-smoothing: antialiased;
  text-transform: lowercase;
  display: flex;
  flex-direction: column;
  min-height: 100vh;
  box-sizing: border-box;
  padding-bottom: 5rem;
}

a { color: inherit; text-decoration: none; }

::selection { background: var(--text); color: var(--bg); }

.container {
  max-width: 1200px;
  margin: 0 auto;
  background: transparent;
  padding: 0;
  border: none;
  box-shadow: none;
  border-radius: 0;
  flex: 1;
}

header {
  display: flex;
  flex-wrap: wrap;
  align-items: flex-start;
  justify-content: space-between;
  padding: 1.25rem 1.5rem;
  margin-bottom: 2rem;
  border-bottom: 1px solid transparent;
}

header h1 {
  font-family: var(--font-mono);
  font-size: 0.875rem;
  font-weight: 400;
  color: var(--text);
  letter-spacing: 0.04em;
  margin: 0;
  flex: 0 1 auto;
  order: 1;
}

header nav {
  flex: 0 0 auto;
  order: 2;
}

header p {
  font-family: var(--font-mono);
  font-size: 0.625rem;
  color: var(--muted);
  letter-spacing: 0.08em;
  margin: 0.5rem 0 0;
  flex: 0 0 100%;
  order: 3;
}


nav { margin: 0; }

.nav-link {
  font-family: var(--font-mono);
  font-size: 0.625rem;
  letter-spacing: 0.1em;
  color: var(--muted);
  background: var(--glass-bg);
  border: 1px solid var(--glass-border);
  border-radius: 999px;
  padding: 4px 14px;
  backdrop-filter: blur(72px) saturate(200%);
  -webkit-backdrop-filter: blur(72px) saturate(200%);
  box-shadow: var(--glass-shadow);
  transition: color 0.2s, background 0.2s, box-shadow 0.2s, transform 0.2s;
  display: inline-flex;
  align-items: center;
  gap: 0.3rem;
}
.nav-link:hover {
  color: var(--text);
  background: var(--glass-bg-hover);
  transform: translate(-2px);
}

.header-logo { display: none; }

main { padding: 0; }

h2 {
  font-family: var(--font-mono);
  font-size: 0.7rem;
  font-weight: 400;
  letter-spacing: 0.12em;
  color: var(--muted);
  margin: 0 0 1rem 0;
}

h3 {
  font-family: var(--font-mono);
  font-size: 0.7rem;
  font-weight: 400;
  letter-spacing: 0.1em;
  color: var(--muted);
  margin: 0 0 0.75rem 0;
}

label {
  font-family: var(--font-mono);
  font-size: 0.65rem;
  letter-spacing: 0.08em;
  color: var(--muted);
}

textarea, input[type="number"], input[type="text"], select {
  width: 100%;
  padding: 0.6rem 0.75rem;
  background: var(--dim);
  border: 1px solid var(--border);
  border-radius: var(--border-radius);
  font-family: var(--font-mono);
  font-size: 0.75rem;
  color: var(--text);
  resize: vertical;
  transition: border-color 0.2s;
  -webkit-appearance: none;
  appearance: none;
}

textarea::placeholder, input::placeholder { color: var(--muted); opacity: 0.6; }

textarea:focus, input:focus, select:focus {
  outline: none;
  border-color: var(--border-hover);
}

textarea[readonly] {
  opacity: 0.7;
  cursor: default;
}

select {
  background-image: url("data:image/svg+xml,%3Csvg xmlns='http://www.w3.org/2000/svg' width='10' height='6'%3E%3Cpath d='M0 0l5 6 5-6z' fill='%23748cab'/%3E%3C/svg%3E");
  background-repeat: no-repeat;
  background-position: right 0.75rem center;
  padding-right: 2rem;
  cursor: pointer;
}

/* glass button base */
button, .upload-btn {
  appearance: none !important;
  -webkit-appearance: none !important;
  display: inline-flex !important;
  align-items: center !important;
  justify-content: center !important;
  gap: 0.4rem !important;
  font-family: var(--font-mono) !important;
  font-size: 0.7rem !important;
  letter-spacing: 0.08em !important;
  color: var(--muted) !important;
  background: var(--glass-bg) !important;
  border: 1px solid var(--glass-border) !important;
  border-radius: 999px !important;
  padding: 0.45rem 1.1rem !important;
  cursor: pointer !important;
  backdrop-filter: blur(72px) saturate(200%) !important;
  -webkit-backdrop-filter: blur(72px) saturate(200%) !important;
  box-shadow: var(--glass-shadow) !important;
  transition: color 0.2s, background 0.2s, box-shadow 0.2s, transform 0.2s !important;
  white-space: nowrap !important;
  width: auto !important;
  text-transform: lowercase !important;
}

button:hover, .upload-btn:hover {
  color: var(--text) !important;
  background: var(--glass-bg-hover) !important;
  transform: translate(-2px) !important;
}

/* green glass — convert / calculate */
#convert-btn, #calculate-btn {
  color: #16a34a !important;
  background: rgba(34,197,94,0.08) !important;
  border-color: rgba(34,197,94,0.3) !important;
  box-shadow: 0 2px 10px rgba(34,197,94,0.08), inset 0 1px 0 rgba(34,197,94,0.15) !important;
}
#convert-btn:hover, #calculate-btn:hover {
  color: #15803d !important;
  background: rgba(34,197,94,0.14) !important;
  border-color: rgba(34,197,94,0.5) !important;
}

/* red glass — clear */
#clear-btn {
  color: #dc2626 !important;
  background: rgba(220,38,38,0.08) !important;
  border-color: rgba(220,38,38,0.3) !important;
  box-shadow: 0 2px 10px rgba(220,38,38,0.08), inset 0 1px 0 rgba(220,38,38,0.1) !important;
}
#clear-btn:hover {
  color: #b91c1c !important;
  background: rgba(220,38,38,0.14) !important;
  border-color: rgba(220,38,38,0.5) !important;
}

/* blue glass — copy / download */
#copy-btn, #download-btn, #download-pqr, #download-dx, #copy-result-btn {
  color: #2563eb !important;
  background: rgba(37,99,235,0.08) !important;
  border-color: rgba(37,99,235,0.3) !important;
  box-shadow: 0 2px 10px rgba(37,99,235,0.08), inset 0 1px 0 rgba(37,99,235,0.1) !important;
}
#copy-btn:hover, #download-btn:hover, #download-pqr:hover, #download-dx:hover {
  color: #1d4ed8 !important;
  background: rgba(37,99,235,0.14) !important;
  border-color: rgba(37,99,235,0.5) !important;
}

/* upload button — dashed outline */
.upload-btn {
  display: block !important;
  text-align: center !important;
  margin-bottom: 0.75rem !important;
  width: 100% !important;
  border-style: dashed !important;
}

/* viewer / sasa control buttons */
#center-btn, #spin-btn, .control-button,
#toggle-spin, #center-view, #toggle-surface, #test-viewer {
  color: var(--muted) !important;
}

/* yellow glass — simplified mode */
#simple-mode-btn {
  color: #d97706 !important;
  background: rgba(245,158,11,0.08) !important;
  border-color: rgba(245,158,11,0.3) !important;
  box-shadow: 0 2px 10px rgba(245,158,11,0.08), inset 0 1px 0 rgba(245,158,11,0.1) !important;
}
#simple-mode-btn:hover {
  background: rgba(245,158,11,0.14) !important;
  border-color: rgba(245,158,11,0.5) !important;
}

.output-controls {
  display: flex;
  gap: 0.5rem;
  margin-bottom: 0.75rem;
}

.converter-grid {
  display: grid;
  grid-template-columns: 1fr 1fr;
  gap: 1px;
  background: transparent;
}

.converter-grid > .io-box:first-child {
  border-right: 1px solid transparent;
}


.converter-grid > button,
.calculator-layout > button {
  width: auto;
  justify-self: center;
  align-self: start;
  min-width: 160px;
  margin-top: 1.25rem;
}

.io-box {
  background: var(--bg);
  padding: 1.5rem;
  display: flex;
  flex-direction: column;
  gap: 0.75rem;
  border-bottom: 1px solid transparent;
}

.calculator-layout {
  display: grid;
  grid-template-columns: 1fr 1fr;
  gap: 1px;
  background: transparent;
}

.calculator-layout > .io-box:first-child {
  border-right: 1px solid transparent;
}

.calculator-layout .io-box { background: var(--bg); }

.calculator-layout #calculate-btn,
.calculator-layout #clear-btn {
  width: 100%;
  margin-top: 0;
  border-radius: 999px;
}

.viewer-layout {
  display: flex;
  gap: 1px;
  background: transparent;
  align-items: flex-start;
}

#viewer-controls {
  flex: 0 0 260px;
  background: var(--bg);
  padding: 1.5rem;
  border: none;
  border-radius: 0;
}

#viewer-controls h3 {
  border-bottom: 1px solid transparent;
  padding-bottom: 0.5rem;
  margin-bottom: 1rem;
}

.control-group { margin-bottom: 1.25rem; }

.control-group label {
  display: block;
  margin-bottom: 0.4rem;
}

#viewer-controls .action-buttons {
  display: flex;
  gap: 0.5rem;
}
#viewer-controls .action-buttons button { flex: 1; }

#file-name-display-3d {
  margin-top: 0.75rem;
  font-family: var(--font-mono);
  font-size: 0.625rem;
  color: var(--muted);
  word-break: break-all;
}

#viewport {
  flex: 0 0 520px;
  width: 520px;
  height: 520px;
  border: none;
  outline: 1px solid var(--border);
  background: var(--bg);
}

.results-table-container {
  max-height: 400px;
  overflow-y: auto;
  border: 1px solid var(--border);
}

.results-table {
  width: 100%;
  border-collapse: collapse;
}

.results-table th, .results-table td {
  padding: 0.5rem 0.75rem;
  text-align: left;
  border-bottom: 1px solid var(--border);
  font-family: var(--font-mono);
  font-size: 0.7rem;
}

.results-table th {
  background: var(--surface);
  font-weight: 500;
  color: var(--muted);
  position: sticky;
  top: 0;
}

.results-table tr:last-child td { border-bottom: none; }
.results-table tr:hover td { background: var(--surface); }

.results-table .sub-header {
  font-weight: 500;
  background: var(--dim);
  text-align: center;
  color: var(--muted);
}

.placeholder-text {
  font-family: var(--font-mono);
  font-size: 0.7rem;
  color: var(--muted);
  padding: 1rem;
}

.upload-section {
  text-align: center;
  border: 1px dashed var(--border);
  padding: 2rem;
  background: var(--bg);
}

.upload-section .description {
  font-size: 0.75rem;
  color: var(--muted);
  margin: 0 0 1rem 0;
}

.hidden { display: none !important; }

.pdb-info-container {
  display: flex;
  gap: 1px;
  background: var(--border);
  margin: 1.5rem 0;
  flex-wrap: wrap;
}

.info-card {
  background: var(--bg);
  padding: 1rem 1.5rem;
  text-align: center;
  flex: 1;
}

.info-card h3 {
  margin: 0 0 0.25rem 0;
  font-size: 0.6rem;
  color: var(--muted);
}

.info-card p {
  margin: 0;
  font-size: 1.1rem;
  font-weight: 400;
  color: var(--text);
}

.info-card p.small-text {
  font-size: 0.7rem;
  word-break: break-word;
}

.plot-container {
  border: none;
  padding: 0;
  aspect-ratio: 1 / 1;
  width: 100%;
  max-width: 700px;
  margin: 0 auto;
  background: var(--bg);
}

#progress-container { margin-top: 1.5rem; width: 100%; }

#progress-text {
  text-align: center;
  font-family: var(--font-mono);
  font-size: 0.65rem;
  color: var(--muted);
  margin-bottom: 0.5rem;
}

.progress-bar-background {
  width: 100%;
  height: 4px;
  background: var(--surface);
  border: 1px solid var(--border);
  overflow: hidden;
}

#progress-bar {
  width: 0%;
  height: 100%;
  background: var(--border-hover);
  transition: width 0.4s ease;
}

.column-selector {
  display: flex;
  gap: 1rem;
}
.selector-group {
  flex: 1;
  display: flex;
  flex-direction: column;
  gap: 0.4rem;
}

.stats-box {
  font-family: var(--font-mono);
  font-size: 0.65rem;
  color: var(--muted);
  margin-top: 0.5rem;
}

.parameters-box, .params-box {
  border: 1px solid var(--border);
  padding: 1rem;
  margin-top: 0.75rem;
}

.parameters-box h3, .params-box h3 {
  margin: 0 0 0.75rem 0;
  border-bottom: 1px solid var(--border);
  padding-bottom: 0.5rem;
}

.param-group {
  display: flex;
  align-items: center;
  gap: 0.75rem;
  margin-bottom: 0.75rem;
  flex-wrap: wrap;
}

.param-group label { min-width: 140px; font-size: 0.65rem; }

.param-group input[type="number"] {
  width: 80px;
  flex: none;
}

.param-info {
  font-family: var(--font-mono);
  font-size: 0.6rem;
  color: var(--muted);
  opacity: 0.7;
}

.plot-container-hydro {
  width: 100%;
}

#hydrophobicity-plot {
  width: 100%;
}

.status-box {
  border: 1px solid var(--border);
  padding: 1rem;
  font-family: var(--font-mono);
  font-size: 0.7rem;
  color: var(--muted);
  margin-bottom: 0.75rem;
}

.info-note {
  border: 1px solid rgba(245,158,11,0.3) !important;
  background: rgba(245,158,11,0.06) !important;
  padding: 1rem;
  margin-bottom: 1.5rem;
}

.info-note h3 {
  color: #d97706 !important;
  font-size: 0.7rem !important;
  margin: 0 0 0.5rem 0 !important;
}

.info-note p {
  font-size: 0.7rem !important;
  line-height: 1.6 !important;
  color: var(--muted) !important;
  margin: 0 0 0.4rem 0 !important;
}

.sasa-summary {
  font-family: var(--font-mono);
  font-size: 0.75rem;
  color: var(--text);
}

footer {
  position: fixed;
  bottom: 0;
  left: 0;
  right: 0;
  height: 20%;
  z-index: 10;
  background: linear-gradient(to top, var(--bg) 30%, transparent 100%);
  pointer-events: none;
  display: flex;
  flex-direction: column;
  align-items: center;
  justify-content: flex-end;
  padding: 0 3rem 1.25rem;
  gap: 0.5rem;
  font-family: var(--font-mono);
  font-size: 0.625rem;
  color: var(--muted);
  letter-spacing: 0.04em;
}

.footer-links {
  display: flex;
  gap: 1.5rem;
  pointer-events: auto;
}

footer a { color: var(--muted); transition: color 0.2s; }
footer a:hover { color: var(--text); }

@media (max-width: 768px) {
  body { padding: 1rem; }

  .converter-grid,
  .calculator-layout {
    grid-template-columns: 1fr;
    background: transparent;
    gap: 1rem;
  }

  .viewer-layout {
    flex-direction: column;
    background: transparent;
    gap: 1rem;
  }
  #viewer-controls { flex: none; width: 100%; }

  .column-selector { flex-direction: column; }
}