Hdplus and fullhd perf

Cargo.toml

@@ -18,6 +18,7 @@ ratatui = "0.29"
 crossterm = "0.28"
 ratatui-image = { version = "9.0.0", default-features = false, features = ["crossterm"] }
 image = "0.25"
+libc = "0.2"
 pdbtbx = { version = "0.12", features = ["rstar"] }
 clap = { version = "4", features = ["derive"] }
 anyhow = "1"
@@ -26,6 +27,7 @@ flate2 = "1"
 rayon = "1"
 reqwest = { version = "0.12", features = ["blocking"], optional = true }
 serde = { version = "1", features = ["derive"] }
+toml = "0.8"
 serde_json = "1"
 tempfile = { version = "3.27.0", optional = true }
 tokio = { version = "1", features = ["rt", "macros"], optional = true }

README.md

@@ -34,6 +34,7 @@ Terminal molecular structure viewer — load, rotate, and explore proteins, nucl
 - **RNA/DNA support** — backbone, wireframe, and cartoon modes with base-type coloring
 - **Small molecule rendering** — ligands as ball-and-stick, ions as spheres
 - **Interface analysis** — inter-chain contacts, binding pockets, and interaction visualization (H-bonds, salt bridges, hydrophobic contacts)
+- **Sequence panel** — scroll every chain's sequence, select residues, and show them as ball-and-stick in the 3D view
 - **7 color schemes** — structure, chain, element (CPK), B-factor, rainbow, pLDDT (AlphaFold)
 - **Interactive controls** — vim-style rotation, zoom, pan with auto-rotation
 - **PDB & mmCIF** — both formats supported, with RCSB PDB fetch (`--fetch`)
@@ -248,10 +249,50 @@ leave the prior frame, state, and revision unchanged.
 | `I` | Interface interactions |
 | `g` | Toggle ligands |
 | `[`/`]` | Prev/next chain |
+| `S` | Sequence panel |
+| `b` | Ball-and-stick for the selection |
+| `z` | Centre the view on the selection |
 | `Space` | Auto-rotate |
 | `?` | Help |
 | `q` | Quit |
 
+While the sequence panel is open it takes the arrow keys; `h`/`j`/`k`/`l` still
+rotate the view, so you can turn the structure while picking residues.
+
+| Key | Action in the sequence panel |
+|-----|------------------------------|
+| `←`/`→` | Move the cursor one residue (across chain ends) |
+| `↑`/`↓` | Move one row |
+| `Shift`+arrow | Extend the selection from the cursor |
+| `PgUp`/`PgDn` | Move a screenful |
+| `Home`/`End` | Start / end of the chain |
+| `Enter` | Select or deselect the residue |
+| `A` | Select or deselect the whole chain |
+| `x` | Clear the selection |
+| `[`/`]` | Jump to the previous / next chain |
+| `<`/`>` | Shrink / grow the panel |
+| `S` / `Esc` | Close the panel |
+
+## Sequence Panel & Residue Selection
+
+Press `S` to open a scrollable panel listing the sequence of every chain in
+one-letter codes — amino acids and nucleotides alike, numbered in the gutter and
+grouped in tens. Each chain gets a header with its type, length, and residue
+range, so a 52-chain ribosome reads as one continuous list.
+
+The cursor moves with the arrow keys; `Enter` picks a residue, `Shift`+arrow
+extends a range, and `A` takes a whole chain. Picked residues are drawn in the
+3D view as ball-and-stick over whatever mode is active, with the selection color
+on carbons and CPK colors elsewhere, z-buffered so a side chain that really is
+behind the structure stays behind it. `b` turns the ball-and-stick off, leaving a
+marker sphere per residue; `z` centres the view on the selection, which is how
+you find a handful of residues inside something the size of a ribosome. The
+selection survives closing the panel, and the status bar keeps its count.
+
+Letters are colored by the active color scheme, so the panel and the structure
+read as one picture; the selection and cursor colors come from `[selection]` in
+the palette file.
+
 ## Color Schemes
 
 | Scheme | Description |
@@ -263,6 +304,33 @@ leave the prior frame, state, and revision unchanged.
 | **Rainbow** | N-terminus (blue) to C-terminus (red). |
 | **pLDDT** | AlphaFold confidence (blue=high, orange=low). |
 
+### Customizing the palette
+
+Every fixed color above can be changed from a TOML file. ProteinView reads
+`~/.config/proteinview/palette.toml` (or `$XDG_CONFIG_HOME/proteinview/palette.toml`)
+when it exists, and `--palette <FILE>` overrides that:
+
+```bash
+proteinview examples/1UBQ.pdb --palette my-palette.toml
+```
+
+Every key is optional — anything you leave out keeps its built-in default, so a
+file this short is valid:
+
+```toml
+[structure]
+helix = "#00FFFF"
+```
+
+Colors are six hex digits, with or without a leading `#`, in either case.
+Element symbols merge onto the built-in CPK table, so overriding carbon leaves
+the rest alone, while `[chain] colors` replaces the chain cycle outright. Unknown
+keys are rejected rather than ignored, so a typo tells you rather than silently
+doing nothing.
+
+See [`docs/palette.example.toml`](docs/palette.example.toml) for a fully
+commented file listing every setting at its default value.
+
 ## Terminal Support
 
 | Terminal | Braille | HD | FullHD |

docs/palette.example.toml

@@ -0,0 +1,106 @@
+# ProteinView color palette
+#
+# Copy to ~/.config/proteinview/palette.toml to have it picked up automatically,
+# or point at it explicitly:
+#
+#     proteinview structure.pdb --palette docs/palette.example.toml
+#
+# Every key is optional. Anything you leave out keeps its built-in default, so a
+# file containing nothing but a single color is perfectly valid. Colors are six
+# hexadecimal digits, with or without a leading '#', in either case.
+#
+# Unknown keys are an error rather than being ignored, so a typo tells you
+# instead of silently doing nothing.
+
+# --- Structure scheme (the default, keyed by secondary structure) ------------
+[structure]
+helix = "FF0080"
+sheet = "FFC800"
+turn  = "6080FF"
+coil  = "00CC00"
+
+# --- Nucleic acid bases ------------------------------------------------------
+# Used for DNA/RNA residues under the Structure scheme.
+[nucleotide]
+adenine  = "DC3C3C"
+uracil   = "3C3CDC"
+thymine  = "3C3CDC"
+guanine  = "3CB43C"
+cytosine = "DCC828"
+inosine  = "9664B4"
+
+# --- Chain scheme ------------------------------------------------------------
+# Cycled by chain id. Order matters, and the list replaces the default outright
+# rather than merging, so give it as many colors as you want in the rotation.
+[chain]
+colors = [
+  "00B4FF",
+  "FF6400",
+  "00DC64",
+  "FF3296",
+  "B464FF",
+  "FFDC00",
+  "00C8C8",
+  "FF9696",
+]
+
+# --- Element scheme (CPK) ----------------------------------------------------
+[element]
+# Color for any element not listed below.
+fallback = "C8C8C8"
+
+# These *merge* onto the built-in table, so overriding carbon leaves every other
+# element alone. Keys are element symbols and are matched case-insensitively.
+[element.symbols]
+C  = "909090"
+N  = "3050F8"
+O  = "FF0D0D"
+S  = "FFFF30"
+H  = "FFFFFF"
+P  = "FF8000"
+FE = "E06633"
+MG = "00B400"
+ZN = "7D80B0"
+CA = "3DFF00"
+MN = "9C7AC7"
+CO = "F090A0"
+CU = "C88033"
+NI = "50D050"
+CL = "1FF01F"
+BR = "A62929"
+
+# --- pLDDT scheme (AlphaFold confidence bands) -------------------------------
+[plddt]
+very_high = "0053D6"  # >= 90
+high      = "65CBF3"  # >= 70
+low       = "FFDB13"  # >= 50
+very_low  = "FF7D45"  # <  50
+
+# --- B-factor scheme ---------------------------------------------------------
+# Endpoints of a linear gradient across roughly the 5..80 B-factor range.
+[bfactor]
+low  = "0000FF"
+high = "FF0000"
+
+# --- Interface highlighting ('f') --------------------------------------------
+[interface]
+focus_contact   = "00FF64"  # focus chain, touching a partner
+focus_other     = "28643C"  # focus chain, away from the interface
+partner_contact = "FFA500"  # partner chain, touching the focus chain
+partner_other   = "64503C"  # partner chain, away from the interface
+ligand          = "FFFFFF"  # ligands, kept bright so they stay visible
+
+# --- Small molecules ---------------------------------------------------------
+[ligand]
+ligand  = "FF00FF"
+ion     = "00FFFF"
+rainbow = "FF00FF"  # ligands under the Rainbow scheme
+
+# --- Sequence panel selection ('S') ------------------------------------------
+# Residues picked in the sequence panel.  Carbons of the ball-and-stick overlay
+# take `carbon`; every other element keeps its CPK color, so a picked residue
+# still reads as itself.
+[selection]
+carbon = "00E68C"  # ball-and-stick carbons of picked residues
+marker = "00E68C"  # marker sphere shown when ball-and-stick is off ('b')
+cursor = "FFC800"  # the sequence panel's cursor cell