### Define installation rules

Source: https://github.com/steineggerlab/foldseek/blob/master/lib/mmseqs/lib/zstd/build/cmake/lib/CMakeLists.txt

Specifies the installation paths for header files and library binaries.

```cmake
INSTALL(FILES
    ${LIBRARY_DIR}/zstd.h
    ${LIBRARY_DIR}/deprecated/zbuff.h
    ${LIBRARY_DIR}/dictBuilder/zdict.h
    ${LIBRARY_DIR}/dictBuilder/cover.h
    ${LIBRARY_DIR}/common/zstd_errors.h
    DESTINATION "include")

IF (ZSTD_BUILD_SHARED)
    INSTALL(TARGETS libzstd_shared RUNTIME DESTINATION "bin"
                                   LIBRARY DESTINATION "${CMAKE_INSTALL_LIBDIR}"
                                   ARCHIVE DESTINATION "${CMAKE_INSTALL_LIBDIR}")
ENDIF()
IF (ZSTD_BUILD_STATIC)
    INSTALL(TARGETS libzstd_static ARCHIVE DESTINATION "${CMAKE_INSTALL_LIBDIR}")
ENDIF (ZSTD_BUILD_STATIC)
```

--------------------------------

### Build and Install Zstandard with Meson

Source: https://github.com/steineggerlab/foldseek/blob/master/lib/mmseqs/lib/zstd/build/meson/README.md

Commands to initialize the build directory, compile the project, and install the resulting library.

```sh
meson --buildtype=release -D with-contrib=true -D with-tests=true -D with-contrib=true builddir
cd builddir
ninja             # to build
ninja install     # to install
```

--------------------------------

### Example execution output

Source: https://github.com/steineggerlab/foldseek/blob/master/lib/mmseqs/lib/zstd/zlibWrapper/README.md

Console output from running the example test file.

```text
zlib version 1.2.8 = 0x1280, compile flags = 0x65
uncompress(): hello, hello!
gzread(): hello, hello!
gzgets() after gzseek:  hello!
inflate(): hello, hello!
large_inflate(): OK
after inflateSync(): hello, hello!
inflate with dictionary: hello, hello!
```

```text
zlib version 1.2.8 = 0x1280, compile flags = 0x65
uncompress(): hello, hello!
gzread(): hello, hello!
gzgets() after gzseek:  hello!
inflate(): hello, hello!
large_inflate(): OK
inflate with dictionary: hello, hello!
```

--------------------------------

### Install Python Script

Source: https://github.com/steineggerlab/foldseek/blob/master/lib/prostt5/CMakeLists.txt

Installs the 'convert_hf_to_gguf.py' script to the binary installation directory with specific file permissions.

```cmake
install(
    FILES convert_hf_to_gguf.py
    PERMISSIONS
        OWNER_READ
        OWNER_WRITE
        OWNER_EXECUTE
        GROUP_READ
        GROUP_EXECUTE
        WORLD_READ
        WORLD_EXECUTE
    DESTINATION ${CMAKE_INSTALL_BINDIR})
```

--------------------------------

### Install Corrosion from Source

Source: https://github.com/steineggerlab/foldseek/blob/master/lib/mmseqs/lib/corrosion/doc/src/setup_corrosion.md

Build and install Corrosion manually using CMake commands.

```bash
git clone https://github.com/corrosion-rs/corrosion.git
# Optionally, specify -DCMAKE_INSTALL_PREFIX=<target-install-path> to specify a 
# custom installation directory
cmake -Scorrosion -Bbuild -DCMAKE_BUILD_TYPE=Release
cmake --build build --config Release
# This next step may require sudo or admin privileges if you're installing to a system location,
# which is the default.
cmake --install build --config Release
```

--------------------------------

### Install and Use zstd-adaptive

Source: https://github.com/steineggerlab/foldseek/blob/master/lib/mmseqs/lib/zstd/contrib/adaptive-compression/README.md

Build the adapt tool using make. Install it to use 'zstd-adaptive' as a command-line utility. It supports file inputs or standard I/O.

```bash
make adapt
```

```bash
make install
```

```bash
zstd-adaptive [options] [file(s)]
```

--------------------------------

### Install Corrosion via Homebrew

Source: https://github.com/steineggerlab/foldseek/blob/master/lib/mmseqs/lib/corrosion/doc/src/setup_corrosion.md

Install the community-maintained Corrosion package using Homebrew.

```bash
brew install corrosion
```

--------------------------------

### Install to Staging Directory

Source: https://github.com/steineggerlab/foldseek/blob/master/lib/mmseqs/lib/zstd/build/meson/README.md

Use the DESTDIR environment variable to install the build artifacts into a specific staging directory.

```sh
DESTDIR=./staging ninja install
```

--------------------------------

### Setup main executable

Source: https://github.com/steineggerlab/foldseek/blob/master/lib/mmseqs/src/CMakeLists.txt

Defines the main mmseqs executable and includes testing subdirectories if enabled.

```cmake
if (NOT FRAMEWORK_ONLY)
    include(MMseqsSetupDerivedTarget)
    add_subdirectory(version)
    set(mmseqs_source_files mmseqs.cpp)

    add_executable(mmseqs${EXE_SUFFIX} ${mmseqs_source_files})
    mmseqs_setup_derived_target(mmseqs${EXE_SUFFIX})
    target_link_libraries(mmseqs${EXE_SUFFIX} version)
    install(TARGETS mmseqs${EXE_SUFFIX} DESTINATION bin)

    if (HAVE_TESTS)
        add_subdirectory(test)
    endif ()
endif ()
```

--------------------------------

### Install MMseqs2 with Homebrew

Source: https://github.com/steineggerlab/foldseek/blob/master/lib/mmseqs/README.md

Use Homebrew to install MMseqs2 on macOS systems.

```bash
brew install mmseqs2
```

--------------------------------

### Install Google Cloud C++ Client Library via vcpkg

Source: https://github.com/steineggerlab/foldseek/wiki/Home

Clones the vcpkg repository, bootstraps it, and installs the google-cloud-cpp package, which is required for enabling Google Cloud Storage support in Foldseek.

```bash
git clone https://github.com/microsoft/vcpkg.git
./vcpkg/bootstrap-vcpkg.sh
./vcpkg/vcpkg install google-cloud-cpp
```

--------------------------------

### Global Alignment with SSE Intrinsics Example

Source: https://github.com/steineggerlab/foldseek/blob/master/lib/mmseqs/lib/ksw2/README.md

Demonstrates how to perform a global alignment using the ksw_extz function with SSE intrinsics. It includes sequence encoding, scoring matrix setup, and CIGAR string generation. Ensure sequences are encoded to integers before calling.

```c
#include <string.h>
#include <stdio.h>
#include "ksw2.h"

void align(const char *tseq, const char *qseq, int sc_mch, int sc_mis, int gapo, int gape)
{
	int i, a = sc_mch, b = sc_mis < 0? sc_mis : -sc_mis; // a>0 and b<0
	int8_t mat[25] = { a,b,b,b,0, b,a,b,b,0, b,b,a,b,0, b,b,b,a,0, 0,0,0,0,0 };
	int tl = strlen(tseq), ql = strlen(qseq);
	uint8_t *ts, *qs, c[256];
	ksw_extz_t ez;

	memset(&ez, 0, sizeof(ksw_extz_t));
	memset(c, 4, 256);
	c['A'] = c['a'] = 0; c['C'] = c['c'] = 1;
	c['G'] = c['g'] = 2; c['T'] = c['t'] = 3; // build the encoding table
	ts = (uint8_t*)malloc(tl);
	qs = (uint8_t*)malloc(ql);
	for (i = 0; i < tl; ++i) ts[i] = c[(uint8_t)tseq[i]]; // encode to 0/1/2/3
	for (i = 0; i < ql; ++i) qs[i] = c[(uint8_t)qseq[i]];
	ksw_extz(0, ql, qs, tl, ts, 5, mat, gapo, gape, -1, -1, 0, &ez);
	for (i = 0; i < ez.n_cigar; ++i) // print CIGAR
		printf("%d%c", ez.cigar[i]>>4, "MID"[ez.cigar[i]&0xf]);
	putchar('\n');
	free(ez.cigar); free(ts); free(qs);
}

int main(int argc, char *argv[])
{
	align("ATAGCTAGCTAGCAT", "AGCTAcCGCAT", 1, -2, 2, 1);
	return 0;
}

```

--------------------------------

### Print Hello World to stdout

Source: https://github.com/steineggerlab/foldseek/blob/master/lib/mmseqs/lib/fmt/README.md

Basic example of printing a string to standard output using fmt::print.

```c++
#include <fmt/core.h>

int main() {
  fmt::print("Hello, world!\n");
}
```

--------------------------------

### Install Rust Target Standard Library

Source: https://github.com/steineggerlab/foldseek/blob/master/lib/mmseqs/lib/corrosion/doc/src/usage.md

When cross-compiling, install the standard library for the target Rust triple using rustup.

```bash
rustup target add <target-rust-triple>
```

--------------------------------

### PZstandard Piping Example

Source: https://github.com/steineggerlab/foldseek/blob/master/lib/mmseqs/lib/zstd/contrib/pzstd/README.md

Shows how to use PZstandard with standard input/output streams, useful for piping data through compression/decompression.

```bash
cat input-file | pzstd -p num-threads -# -c > /dev/null
```

--------------------------------

### Installing Foldcomp

Source: https://github.com/steineggerlab/foldseek/blob/master/lib/foldcomp/README.md

Commands to install the Python package or download static binaries for various operating systems.

```bash
# Install Foldcomp Python package
pip install foldcomp

# Download static binaries for Linux
wget https://mmseqs.com/foldcomp/foldcomp-linux-x86_64.tar.gz

# Download static binaries for Linux (ARM64)
wget https://mmseqs.com/foldcomp/foldcomp-linux-arm64.tar.gz

# Download binary for macOS
wget https://mmseqs.com/foldcomp/foldcomp-macos-universal.tar.gz

# Download binary for Windows (x64)
wget https://mmseqs.com/foldcomp/foldcomp-windows-x64.zip
```

--------------------------------

### Install cross-compiler for PowerPC on Linux

Source: https://github.com/steineggerlab/foldseek/blob/master/lib/mmseqs/lib/corrosion/doc/src/usage.md

On Ubuntu, install the g++-powerpc64le-linux-gnu package using apt-get to enable cross-compilation for 64-bit Little-Endian PowerPC.

```bash
sudo apt install g++-powerpc64le-linux-gnu
```

--------------------------------

### Install Foldseek via Command Line

Source: https://github.com/steineggerlab/foldseek/blob/master/README.md

Commands to download and install precompiled binaries for different operating systems or use the Conda package manager.

```bash
wget https://mmseqs.com/foldseek/foldseek-linux-avx2.tar.gz; tar xvzf foldseek-linux-avx2.tar.gz; export PATH=$(pwd)/foldseek/bin/:$PATH
```

```bash
wget https://mmseqs.com/foldseek/foldseek-linux-arm64.tar.gz; tar xvzf foldseek-linux-arm64.tar.gz; export PATH=$(pwd)/foldseek/bin/:$PATH
```

```bash
wget https://mmseqs.com/foldseek/foldseek-linux-gpu.tar.gz; tar xvfz foldseek-linux-gpu.tar.gz; export PATH=$(pwd)/foldseek/bin/:$PATH
```

```bash
wget https://mmseqs.com/foldseek/foldseek-osx-universal.tar.gz; tar xvzf foldseek-osx-universal.tar.gz; export PATH=$(pwd)/foldseek/bin/:$PATH
```

```bash
conda install -c conda-forge -c bioconda foldseek
```

--------------------------------

### FoldSeek Multimercluster Command Example

Source: https://github.com/steineggerlab/foldseek/blob/master/README.md

Example command for running the easy-multimercluster module with specified thresholds.

```APIDOC
## Running Multimercluster

### Description
This command demonstrates how to use the `easy-multimercluster` module for multimer-level structural clustering. It specifies input files, output directories, and various alignment thresholds.

### Command
```bash
foldseek easy-multimercluster example/ clu tmp --multimer-tm-threshold 0.65 --chain-tm-threshold 0.5 --interface-lddt-threshold 0.65
```

### Parameters
- **`example/`**: Path to the input directory containing PDB/mmCIF files.
- **`clu`**: Output directory for cluster files.
- **`tmp`**: Temporary directory for intermediate files.
- **`--multimer-tm-threshold`** (float) - Alignment - Accept alignments with multimer alignment TMscore > thr (default: 0.65).
- **`--chain-tm-threshold`** (float) - Alignment - Accept alignments if every single chain TMscore > thr (default: 0.5).
- **`--interface-lddt-threshold`** (float) - Alignment - Accept alignments with an interface LDDT score > thr (default: 0.65).
```

--------------------------------

### Foldcomp Database Setup Commands

Source: https://github.com/steineggerlab/foldseek/blob/master/lib/foldcomp/README.md

Individual commands to set up various prebuilt protein structure databases.

```python
foldcomp.setup('esmatlas')
```

```python
foldcomp.setup('esmatlas_v2023_02')
```

```python
foldcomp.setup('highquality_clust30')
```

```python
foldcomp.setup('afdb_uniprot_v4')
```

```python
foldcomp.setup('afdb_swissprot_v4')
```

```python
foldcomp.setup('h_sapiens')
```

```python
foldcomp.setup('afdb_rep_v4')
```

```python
foldcomp.setup('afdb_rep_dark_v4')
```

--------------------------------

### Install Foldseek via pre-compiled binaries

Source: https://github.com/steineggerlab/foldseek/wiki/Home

Download and extract the appropriate static binary for your operating system and architecture.

```bash
wget https://mmseqs.com/foldseek/foldseek-linux-avx2.tar.gz
tar xvzf foldseek-linux-avx2.tar.gz
export PATH=$(pwd)/foldseek/bin/:$PATH
```

```bash
wget https://mmseqs.com/foldseek/foldseek-linux-sse41.tar.gz
tar xvzf foldseek-linux-sse41.tar.gz
export PATH=$(pwd)/foldseek/bin/:$PATH
```

```bash
wget https://mmseqs.com/foldseek/foldseek-linux-gpu.tar.gz
tar xvzf foldseek-linux-gpu.tar.gz
export PATH=$(pwd)/foldseek/bin/:$PATH
```

```bash
wget https://mmseqs.com/foldseek/foldseek-osx-universal.tar.gz
tar xvzf foldseek-osx-universal.tar.gz
export PATH=$(pwd)/foldseek/bin/:$PATH
```

--------------------------------

### te_interp usage examples

Source: https://github.com/steineggerlab/foldseek/blob/master/lib/mmseqs/lib/tinyexpr/README.md

Demonstrates immediate evaluation with and without error tracking.

```C
    int error;

    double a = te_interp("(5+5)", 0); /* Returns 10. */
    double b = te_interp("(5+5)", &error); /* Returns 10, error is set to 0. */
    double c = te_interp("(5+5", &error); /* Returns NaN, error is set to 4. */
```

--------------------------------

### Evaluate expression at runtime

Source: https://github.com/steineggerlab/foldseek/blob/master/lib/mmseqs/lib/tinyexpr/README.md

A minimal example demonstrating how to evaluate a simple math expression using te_interp.

```C
    #include "tinyexpr.h"
    printf("%f\n", te_interp("5*5", 0)); /* Prints 25. */
```

--------------------------------

### Generate pkg-config file

Source: https://github.com/steineggerlab/foldseek/blob/master/lib/mmseqs/lib/zstd/build/cmake/lib/CMakeLists.txt

Creates and installs a pkg-config file for Unix-based systems to facilitate library discovery.

```cmake
IF (UNIX)
    # pkg-config
    SET(PREFIX "${CMAKE_INSTALL_PREFIX}")
    SET(LIBDIR "${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_LIBDIR}")
    SET(INCLUDEDIR "${CMAKE_INSTALL_PREFIX}/include")
    SET(VERSION "${LIBVER_MAJOR}.${LIBVER_MINOR}.${LIBVER_RELEASE}")
    ADD_CUSTOM_TARGET(libzstd.pc ALL
            ${CMAKE_COMMAND} -DIN="${LIBRARY_DIR}/libzstd.pc.in" -DOUT="libzstd.pc"
            -DPREFIX="${PREFIX}" -DLIBDIR="${LIBDIR}" -DINCLUDEDIR="${INCLUDEDIR}" -DVERSION="${VERSION}"
            -P "${CMAKE_CURRENT_SOURCE_DIR}/pkgconfig.cmake"
            COMMENT "Creating pkg-config file")

    INSTALL(FILES "${CMAKE_CURRENT_BINARY_DIR}/libzstd.pc" DESTINATION "${LIBDIR}/pkgconfig")
ENDIF (UNIX)
```

--------------------------------

### All Member Fasta Output

Source: https://github.com/steineggerlab/foldseek/blob/master/README.md

Example of the all-member FASTA file format including cluster markers.

```fasta
>Q0KJ32	
>Q0KJ32
MAGA....R
>C0W539
MVGA....R
>D6KVP9
MVGA....R
>E3HQM9	
>E3HQM9
MCAT...Q
>Q223C0
MCAR...Q
```

--------------------------------

### Execute Block Image Generation

Source: https://github.com/steineggerlab/foldseek/blob/master/lib/mmseqs/lib/block-aligner/vis/block_aligner_accuracy_vis.ipynb

Runs the Rust block_img example to generate visualization images from input files.

```python
!cd .. && cargo run --example block_img --release --features simd_avx2 --quiet -- vis/block_img1.png vis/block_img2.png
```

```text
Output:
path: vis/block_img1.png, img size: 660 x 549
path: vis/block_img2.png, img size: 384 x 428
```

--------------------------------

### Configure Pkgconfig File

Source: https://github.com/steineggerlab/foldseek/blob/master/lib/prostt5/CMakeLists.txt

Configures the 'llama.pc' file for pkgconfig, ensuring it is generated with the correct template and installed to the pkgconfig directory.

```cmake
configure_file(cmake/llama.pc.in
        "${CMAKE_CURRENT_BINARY_DIR}/llama.pc"
        @ONLY)

install(FILES "${CMAKE_CURRENT_BINARY_DIR}/llama.pc"
        DESTINATION lib/pkgconfig)
```

--------------------------------

### Define Corrosion Installation Tests

Source: https://github.com/steineggerlab/foldseek/blob/master/lib/mmseqs/lib/corrosion/test/CMakeLists.txt

Configures CMake tests to verify the installation of Corrosion, including setup and cleanup fixtures.

```cmake
option(CORROSION_TESTS_INSTALL_CORROSION
        "Install Corrosion to a test directory and let tests use the installed Corrosion"
        OFF)
if(CORROSION_TESTS_INSTALL_CORROSION)
    add_test(NAME "install_corrosion_configure"
        COMMAND
            ${CMAKE_COMMAND}
            -S "${CMAKE_CURRENT_SOURCE_DIR}/.."
            -B "${CMAKE_CURRENT_BINARY_DIR}/build-corrosion"
            -DCORROSION_VERBOSE_OUTPUT=ON
            -DCORROSION_TESTS=OFF
            -DCMAKE_BUILD_TYPE=Release
            -G${CMAKE_GENERATOR}
            "-DCMAKE_INSTALL_PREFIX=${test_install_path}"
    )
    add_test(NAME "install_corrosion_build"
            COMMAND
            ${CMAKE_COMMAND} --build "${CMAKE_CURRENT_BINARY_DIR}/build-corrosion" --config Release
            )
    add_test(NAME "install_corrosion_install"
            COMMAND
            ${CMAKE_COMMAND} --install "${CMAKE_CURRENT_BINARY_DIR}/build-corrosion" --config Release
        )
    set_tests_properties("install_corrosion_configure" PROPERTIES FIXTURES_SETUP "fixture_corrosion_configure")
    set_tests_properties("install_corrosion_build"     PROPERTIES FIXTURES_SETUP "fixture_corrosion_build")
    set_tests_properties("install_corrosion_build"     PROPERTIES FIXTURES_REQUIRED "fixture_corrosion_configure")
    set_tests_properties("install_corrosion_install"   PROPERTIES FIXTURES_REQUIRED "fixture_corrosion_build")
    set_tests_properties("install_corrosion_install"   PROPERTIES FIXTURES_SETUP "fixture_corrosion_install")

    add_test(NAME "install_corrosion_build_cleanup" COMMAND "${CMAKE_COMMAND}" -E remove_directory "${CMAKE_CURRENT_BINARY_DIR}/build-corrosion")
    set_tests_properties("install_corrosion_build_cleanup" PROPERTIES
        FIXTURES_CLEANUP
        "fixture_corrosion_configure;fixture_corrosion_build"
    )

    add_test(NAME "install_corrosion_cleanup" COMMAND "${CMAKE_COMMAND}" -E remove_directory "${test_install_path}")
    set_tests_properties("install_corrosion_cleanup" PROPERTIES
        FIXTURES_CLEANUP
        "fixture_corrosion_configure;fixture_corrosion_build;fixture_corrosion_install"
    )
endif()
```

--------------------------------

### Initialize UI Elements

Source: https://github.com/steineggerlab/foldseek/blob/master/lib/mmseqs/data/resources/krona_prelude.html

Sets up the main options container, details panel, and dataset selection controls.

```javascript
function addOptionElements(hueName, hueDefault) { options = document.createElement('div'); options.style.position = 'absolute'; options.style.top = '0px'; options.addEventListener('mousedown', function(e) {mouseClick(e)}, false); // options.onmouseup = function(e) {mouseUp(e)} document.body.appendChild(options); document.body.style.font = '11px sans-serif'; var position = 5; details = document.createElement('div'); details.style.position = 'absolute'; details.style.top = '1%'; details.style.right = '2%'; details.style.textAlign = 'right'; document.body.insertBefore(details, canvas); // <div id="details" style="position:absolute;top:1%;right:2%;text-align:right;"> details.innerHTML = '\ <span id="detailsName" style="font-weight:bold"></span>&nbsp;\ <input type="button" id="detailsExpand" onclick="expand(focusNode);"\ value="&harr;" title="Expand this wedge to become the new focus of the chart"/><br/>\ <div id="detailsInfo" style="float:right"></div>'; keyControl = document.createElement('input'); keyControl.type = 'button'; keyControl.value = showKeys ? 'x' : '…'; keyControl.style.position = ''; keyControl.style.position = 'fixed'; keyControl.style.visibility = 'hidden'; document.body.insertBefore(keyControl, canvas); var logoElement = document.getElementById('logo'); if ( logoElement ) { logoImage = logoElement.src; } else { logoImage = 'http://marbl.github.io/Krona/img/logo-med.png'; } // document.getElementById('options').style.fontSize = '9pt'; position = addOptionElement ( position, '<a style="margin:2px" target="_blank" href="https://github.com/marbl/Krona/wiki"><img style="vertical-align:middle;width:108px;height:30px;" src="' + logoImage + '" alt="Logo of Krona"/></a><input type="button" id="back" value="&larr;" title="Go back (Shortcut: &larr;)"/>\ <input type="button" id="forward" value="&rarr;" title="Go forward (Shortcut: &rarr;)"/> \ &nbsp;Search: <input type="text" id="search"/>\ <input id="searchClear" type="button" value="x" onclick="clearSearch()"/> \ <span id="searchResults"></span>' ); if ( datasets > 1 ) { var size = datasets < datasetSelectSize ? datasets : datasetSelectSize; var select = '<table style="border-collapse:collapse;padding:0px"><tr><td style="padding:0px">' + '<select id="datasets" style="min-width:100px" size="' + size + '" onchange="onDatasetChange()">'; for ( var i = 0; i < datasetNames.length; i++ ) { select += '<option>' + datasetNames[i] + '</option>'; } select += '</select></td><td style="vertical-align:top;padding:1px;">' + '<input style="display:block" title="Previous dataset (Shortcut: &uarr;)" id="prevDataset" type="button" value="&uarr;" onclick="prevDataset()" disabled="true"/>' + '<input title="Next dataset (Shortcut: &darr;)" id="nextDataset" type="button" value="&darr;" onclick="nextDataset()"/><br/></td>' + '<td style="padding-top:1px;vertical-align:top"><input title="Switch to the last dataset that was viewed (Shortcut: TAB)" id="lastDataset" type="button" style="font:11px Times new roman" value="last" onclick="selectLastDataset()"/></td></tr></table>'; position = addOptionElement(position + 5, select); datasetDropDown = document.getElementById('datasets'); datasetButtonLast = document.getElementById('lastDataset'); datasetButtonPrev = document.getElementById('prevDataset'); datasetButtonNext = document.getElementById('nextDataset'); position += datasetDropDown.clientHeight; } position = addOptionElement ( position + 5, '<input type="button" id="maxAbsoluteDepthDecrease" value="-"/>\ <span id="maxAbsoluteDepth"></span>\ &nbsp;<input type="button" id="maxAbsoluteDepthIncrease" value="+"/> Max depth', 'Maximum depth to display, counted from the top level \ and including collapsed wedges.' ); position = addOptionElement ( position, '<input type="button" id="fontSizeDecrease" value="-"/>\ <span id="fontSize"></span>\ &nbsp;<input type="button" id="fontSizeIncrease" value="+"/> Font size' ); position = addOptionElement ( position, '<input type="button" id="radiusDecrease" value="-"/>\ <input type="button" id="radiusIncrease" value="+"/> Chart size' ); if ( hueName ) { hueDisplayName = attributes[attri
```

--------------------------------

### Install Foldseek via Conda

Source: https://github.com/steineggerlab/foldseek/blob/master/README.md

Install Foldseek using the bioconda channel. This command installs the Foldseek package.

```bash
conda install -c bioconda foldseek
```

--------------------------------

### CMake Project Setup

Source: https://github.com/steineggerlab/foldseek/blob/master/lib/mmseqs/lib/corrosion/test/multitarget/multitarget/CMakeLists.txt

Initializes the CMake build system for the project, specifying the minimum version and project details. Includes a common test header.

```cmake
cmake_minimum_required(VERSION 3.15)
project(test_project VERSION 0.1.0)
include(../../test_header.cmake)
```

--------------------------------

### Install MMseqs2 with Conda

Source: https://github.com/steineggerlab/foldseek/blob/master/lib/mmseqs/README.md

Install MMseqs2 using Conda from the conda-forge and bioconda channels.

```bash
conda install -c conda-forge -c bioconda mmseqs2
```

--------------------------------

### Install Foldseek via Bioconda

Source: https://github.com/steineggerlab/foldseek/wiki/Home

Install the package using the conda package manager.

```bash
conda install -c conda-forge -c bioconda foldseek
```

--------------------------------

### Build All Configurations with VS2015

Source: https://github.com/steineggerlab/foldseek/blob/master/lib/mmseqs/lib/zstd/build/VS_scripts/README.md

Run this command to build both Release Win32 and Release x64 versions using Visual Studio 2015.

```batch
build.VS2015.cmd
```

--------------------------------

### Build All Configurations with VS2013

Source: https://github.com/steineggerlab/foldseek/blob/master/lib/mmseqs/lib/zstd/build/VS_scripts/README.md

Run this command to build both Release Win32 and Release x64 versions using Visual Studio 2013.

```batch
build.VS2013.cmd
```

--------------------------------

### Find Installed Corrosion Package

Source: https://github.com/steineggerlab/foldseek/blob/master/lib/mmseqs/lib/corrosion/doc/src/setup_corrosion.md

Locate the installed Corrosion package within a CMake project.

```cmake
find_package(Corrosion REQUIRED)
```

--------------------------------

### Run Test Suite

Source: https://github.com/steineggerlab/foldseek/blob/master/lib/mmseqs/lib/zstd/contrib/experimental_dict_builders/randomDictBuilder/README.md

Execute the project test suite using the make utility.

```bash
make test
```

--------------------------------

### Initialize Environment and Data Transformers

Source: https://github.com/steineggerlab/foldseek/blob/master/lib/mmseqs/lib/block-aligner/vis/block_aligner_bench_vis.ipynb

Imports necessary libraries and enables the Altair data server for efficient data handling.

```python
import altair as alt
from altair_saver import save
from altair import datum
import pandas as pd
from io import StringIO

alt.data_transformers.enable("data_server")
```

```text
Result:
DataTransformerRegistry.enable('data_server')
```

--------------------------------

### Clone and Build Benchmarks

Source: https://github.com/steineggerlab/foldseek/blob/master/lib/mmseqs/lib/fmt/README.md

Commands to clone the benchmark repository and prepare the build environment using CMake.

```bash
$ git clone --recursive https://github.com/fmtlib/format-benchmark.git
$ cd format-benchmark
$ cmake .
```

--------------------------------

### Example Multimer Search Output

Source: https://github.com/steineggerlab/foldseek/blob/master/README.md

This is an example of the default tab-separated output from easy-multimersearch, showing alignment details for different chains of the complexes.

```text
1tim.pdb.gz_A   8tim.pdb.gz_A   0.967   247 8   0   1   247 1   247 5.412E-43   1527    0
1tim.pdb.gz_B   8tim.pdb.gz_B   0.967   247 8   0   1   247 1   247 1.050E-43   1551    0
```

--------------------------------

### Install GCC Dependencies for Foldseek on macOS

Source: https://github.com/steineggerlab/foldseek/wiki/Home

Installs GCC version 11 and other required libraries using Homebrew for compiling Foldseek with GCC on macOS.

```bash
brew install cmake gcc@11 zlib bzip2
```

--------------------------------

### PZstandard Basic Usage Examples

Source: https://github.com/steineggerlab/foldseek/blob/master/lib/mmseqs/lib/zstd/contrib/pzstd/README.md

Demonstrates the fundamental compression and decompression commands for PZstandard. Use the -p option to specify the number of threads.

```bash
pzstd input-file -o output-file -p num-threads -#          # Compression
```

```bash
pzstd -d input-file -o output-file -p num-threads          # Decompression
```

--------------------------------

### Initialize Visualization Settings

Source: https://github.com/steineggerlab/foldseek/blob/master/lib/mmseqs/data/resources/krona_prelude.html

Sets up initial visualization parameters based on parsed URL options and default values. Configures callbacks, sorts the head, selects the initial dataset and node, and sets up interval updates and resize handling.

```javascript
addOptionElements(hueName, hueDefault); setCallBacks(); head.sort(); maxAbsoluteDepth = 0; selectDataset(datasetDefault); if ( maxDepthDefault && maxDepthDefault < head.maxDepth ) { maxAbsoluteDepth = maxDepthDefault; } else { maxAbsoluteDepth = head.maxDepth; } selectNode(nodes[nodeDefault]); setInterval(update, 20); window.onresize = handleResize; updateMaxAbsoluteDepth(); updateViewNeeded = true;
```

--------------------------------

### Create Database with Chain Naming

Source: https://context7.com/steineggerlab/foldseek/llms.txt

Initializes a structural database with specific chain naming conventions.

```bash
foldseek createdb structures/ targetDB --chain-name-mode 1
```

--------------------------------

### Install Dependencies for Foldseek on macOS

Source: https://github.com/steineggerlab/foldseek/wiki/Home

Installs necessary build tools and libraries like CMake, libomp, zlib, and bzip2 using Homebrew for compiling Foldseek on macOS.

```bash
brew install cmake libomp zlib bzip2
```

--------------------------------

### Run Nanopore Accuracy Example

Source: https://github.com/steineggerlab/foldseek/blob/master/lib/mmseqs/lib/block-aligner/vis/block_aligner_accuracy_vis.ipynb

Executes the nanopore_accuracy example using Cargo, enabling AVX2 features for performance. This command is used to generate alignment accuracy data.

```python
output = !cd .. && cargo run --example nanopore_accuracy --release --features simd_avx2 --quiet
output
```

--------------------------------

### Construct Database with makedb

Source: https://github.com/steineggerlab/foldseek/blob/master/lib/mmseqs/lib/libmarv/Readme.md

Create a database from a FASTA file using the makedb tool. Supports gzipped input files and large numbers of sequences.

```bash
mkdir -p dbfolder
./makedb input.fa(.gz) dbfolder/dbname [options]
```

--------------------------------

### Set ROCm Path in CMake

Source: https://github.com/steineggerlab/foldseek/blob/master/lib/prostt5/ggml/src/ggml-hip/CMakeLists.txt

Configures the ROCm installation path by checking the ROCM_PATH environment variable or common installation directories. Appends the path to CMAKE_PREFIX_PATH for CMake to find ROCm components.

```cmake
if (NOT EXISTS $ENV{ROCM_PATH})
    if (NOT EXISTS /opt/rocm)
        set(ROCM_PATH /usr)
    else()
        set(ROCM_PATH /opt/rocm)
    endif()
else()
    set(ROCM_PATH $ENV{ROCM_PATH})
endif()

list(APPEND CMAKE_PREFIX_PATH  ${ROCM_PATH})
list(APPEND CMAKE_PREFIX_PATH "${ROCM_PATH}/lib64/cmake")
```

--------------------------------

### Pad Database for GPU Search

Source: https://github.com/steineggerlab/foldseek/blob/master/README.md

Prepares a database with padding for efficient GPU-based searching.

```bash
# Prepare the database for GPU search
foldseek makepaddedseqdb db db_pad
# Perform GPU search
foldseek search db db_pad result_dir --gpu 1
```

--------------------------------

### Create and Index Custom Databases

Source: https://github.com/steineggerlab/foldseek/blob/master/README.md

Pre-processes structural files into a database format and optionally creates an on-disk index for faster searching.

```bash
foldseek createdb example/ targetDB
foldseek createindex targetDB tmp  #OPTIONAL generates and stores the index on disk
foldseek easy-search example/d1asha_ targetDB aln.m8 tmpFolder
```

--------------------------------

### Run Uniclust Accuracy Example

Source: https://github.com/steineggerlab/foldseek/blob/master/lib/mmseqs/lib/block-aligner/vis/block_aligner_accuracy_vis.ipynb

Executes the `uc_accuracy` example from the Foldseek Cargo project with AVX2 SIMD features enabled and quiet output. This command is used to generate the raw accuracy data.

```bash
output = !cd .. && cargo run --example uc_accuracy --release --features simd_avx2 --quiet
output
```

--------------------------------

### Compile Foldseek on Linux with GPU Support

Source: https://github.com/steineggerlab/foldseek/wiki/Home

Installs CUDA dependencies via Conda, compiles Foldseek with GPU support, and sets up the environment variables. Use -DCMAKE_CUDA_ARCHITECTURES="native" to compile for installed GPUs only.

```bash
conda create -n nvcc -c conda-forge cuda-nvcc cuda-cudart-dev libcublas-dev libcublas-static cuda-version=12.6 cmake
conda activate nvcc
mkdir build && cd build
cmake -DCMAKE_BUILD_TYPE=RELEASE -DCMAKE_INSTALL_PREFIX=. -DENABLE_CUDA=1 -DCMAKE_CUDA_ARCHITECTURES="75;80;86;89;90" ..
make -j8
make install
export PATH=$(pwd)/bin/:$PATH
```

--------------------------------

### Create Database with Pre-built Index

Source: https://context7.com/steineggerlab/foldseek/llms.txt

Create a Foldseek database from structure files and then build a pre-built index for faster repeated searches. Specify the input folder, database name, and temporary directory for the index.

```bash
foldseek createdb structures/ targetDB
foldseek createindex targetDB tmp/
```

--------------------------------

### Configure MacOS Shared Library Install Name

Source: https://github.com/steineggerlab/foldseek/blob/master/lib/mmseqs/lib/corrosion/doc/src/common_issues.md

Use these CMake commands to set the install name, current version, and compatibility version for a shared library on MacOS. Ensure the library name follows the `lib<your_crate>.dylib` convention.

```cmake
corrosion_add_target_local_rustflags(your_crate -Clink-arg=-Wl,-install_name,@rpath/libyour_crate.dylib,-current_version,${PROJECT_VERSION_MAJOR}.${PROJECT_VERSION_MINOR},-compatibility_version,${PROJECT_VERSION_MAJOR}.0)
set_target_properties(your_crate-shared PROPERTIES IMPORTED_NO_SONAME 0)
set_target_properties(your_crate-shared PROPERTIES IMPORTED_SONAME libyour_crate.dylib)
```

--------------------------------

### Reusing Compression Contexts with zlibWrapper

Source: https://github.com/steineggerlab/foldseek/blob/master/lib/mmseqs/lib/zstd/zlibWrapper/README.md

Demonstrates the steps for reusing a single compression context to improve performance. Initialize with deflateInit, use deflate for the first file, deflateReset then deflate for the second file, and finally free with deflateEnd.

```text
- initialize the context with `deflateInit`
- for the 1st file call `deflate`, `...`, `deflate`
- for the 2nd file call `deflateReset`, `deflate`, `...`, `deflate`
- free the context with `deflateEnd`
```

--------------------------------

### ZSTD_initCStream

Source: https://github.com/steineggerlab/foldseek/blob/master/lib/mmseqs/lib/zstd/doc/zstd_manual.html

Initializes a ZSTD_CStream context to start a new compression operation.

```APIDOC
## ZSTD_initCStream

### Description
Initializes a ZSTD_CStream context to start a new compression operation. Variants include ZSTD_initCStream_usingDict and ZSTD_initCStream_usingCDict for dictionary-based compression.

### Method
Function Call
```

--------------------------------

### Train Zstandard Dictionary with Fastcover Algorithm

Source: https://github.com/steineggerlab/foldseek/blob/master/lib/mmseqs/lib/zstd/programs/zstd.1.md

Use the fastcover dictionary builder algorithm with specified parameters. Requires 0 < f < 32 and 0 < accel <= 10. d must be 6 or 8. Split defaults to 75, f to 20, and accel to 1 if not specified.

```bash
zstd --train-fastcover FILEs
```

```bash
zstd --train-fastcover=d=8,f=15,accel=2 FILEs
```

--------------------------------

### Representative Fasta Output

Source: https://github.com/steineggerlab/foldseek/blob/master/README.md

Example of the representative sequence FASTA file format.

```fasta
>Q0KJ32
MAGA....R
>E3HQM9
MCAT...Q
```

--------------------------------

### Create Database from FASTA using ProstT5

Source: https://context7.com/steineggerlab/foldseek/llms.txt

Create a Foldseek database from FASTA sequences using the ProstT5 model. Ensure ProstT5 model weights are downloaded first. Specify the input FASTA file, database name, and the path to the model weights.

```bash
foldseek databases ProstT5 weights tmp/
foldseek createdb sequences.fasta seqDB --prostt5-model weights
```

--------------------------------

### Create ProstT5 Database

Source: https://github.com/steineggerlab/foldseek/blob/master/README.md

Initializes a structural database from FASTA files using the ProstT5 model.

```bash
foldseek databases ProstT5 weights tmp
foldseek createdb db.fasta db --prostt5-model weights
```

--------------------------------

### Create and Index Database

Source: https://context7.com/steineggerlab/foldseek/llms.txt

Creates a database and generates an index, optionally excluding Cα coordinates to reduce memory usage.

```bash
foldseek createdb structures/ targetDB
foldseek createindex targetDB tmp/ --index-exclude 2
```

--------------------------------

### GET ZSTD_getDictID_fromFrame

Source: https://github.com/steineggerlab/foldseek/blob/master/lib/mmseqs/lib/zstd/doc/zstd_manual.html

Retrieves the dictionary ID required to decompress a Zstandard frame.

```APIDOC
## GET ZSTD_getDictID_fromFrame

### Description
Provides the dictID required to decompress the frame stored within `src`.

### Method
C Function

### Parameters
#### Path Parameters
- **src** (const void*) - Required - Pointer to the source frame data.
- **srcSize** (size_t) - Required - Size of the source data.

### Response
#### Success Response
- **return** (unsigned) - The dictID of the frame. Returns 0 if the dictID could not be decoded.
```

--------------------------------

### Test the Docker container

Source: https://github.com/steineggerlab/foldseek/blob/master/lib/mmseqs/lib/zstd/contrib/docker/README.md

Verifies the installation by piping input through the zstd container and decompressing it.

```bash
echo foo | docker run -i --rm zstd | docker run -i --rm zstd zstdcat
foo
```

--------------------------------

### Example Output for Complex Report

Source: https://github.com/steineggerlab/foldseek/blob/master/README.md

Sample output line from the easy-multimersearch report file.

```text
1tim.pdb.gz 8tim.pdb.gz A,B A,B 0.98941 0.98941 0.999983,0.000332,0.005813,-0.000373,0.999976,0.006884,-0.005811,-0.006886,0.999959 0.298992,0.060047,0.565875  0
```

--------------------------------

### Evaluate Command-Line Expressions with Error Checking

Source: https://github.com/steineggerlab/foldseek/blob/master/lib/mmseqs/lib/tinyexpr/README.md

This example demonstrates compiling and evaluating an expression from the command line, including variable binding and error handling. Ensure the expression is passed as a command-line argument.

```C
#include "tinyexpr.h"
    #include <stdio.h>

    int main(int argc, char *argv[])
    {
        if (argc < 2) {
            printf("Usage: example2 \"expression\"\n");
            return 0;
        }

        const char *expression = argv[1];
        printf("Evaluating:\n\t%s\n", expression);

        /* This shows an example where the variables
         * x and y are bound at eval-time. */
        double x, y;
        te_variable vars[] = {{"x", &x}, {"y", &y}};

        /* This will compile the expression and check for errors. */
        int err;
        te_expr *n = te_compile(expression, vars, 2, &err);

        if (n) {
            /* The variables can be changed here, and eval can be called as many
             * times as you like. This is fairly efficient because the parsing has
             * already been done. */
            x = 3; y = 4;
            const double r = te_eval(n); printf("Result:\n\t%f\n", r);
            te_free(n);
        } else {
            /* Show the user where the error is at. */
            printf("\t%*s^\nError near here", err-1, "");
        }

        return 0;
    }
```

--------------------------------

### Tab-Separated Cluster Output

Source: https://github.com/steineggerlab/foldseek/blob/master/README.md

Example of the tab-separated output format mapping representatives to members.

```text
Q0KJ32	Q0KJ32
Q0KJ32	C0W539
Q0KJ32	D6KVP9
E3HQM9	E3HQM9
E3HQM9	F0YHT8
```

--------------------------------

### Initialize Krona Visualization

Source: https://github.com/steineggerlab/foldseek/blob/master/lib/mmseqs/data/resources/krona_prelude.html

Initializes the Krona visualization, setting up the canvas, handling browser compatibility, and parsing configuration from the 'krona' element.

```javascript
function load() { document.body.style.overflow = "hidden"; document.body.style.margin = 0; createCanvas(); if ( context == undefined ) { document.body.innerHTML = '\ <br/>This browser does not support HTML5 (see \ <a href="https://github.com/marbl/Krona/wiki/Browser%20support">Browser support</a>).\ '; return; } if ( typeof context.fillText != 'function' ) { document.body.innerHTML = '\ <br/>This browser does not support HTML5 canvas text (see \ <a href="https://github.com/marbl/Krona/wiki/Browser%20support">Browser support</a>).\ '; return; } resize(); var kronaElement = document.getElementsByTagName('krona')[0]; var magnitudeName; var hueName; var hueDefault; var hueStart; var hueEnd; var valueStart; var valueEnd; if ( kronaElement.getAttribute('collapse') != undefined ) { collapse = kronaElement.getAttribute('collapse') == 'true'; } if ( kronaElement.getAttribute('key') != undefined ) { showKeys = kronaElement.getAttribute('key') == 'true'; } for ( var element = getFirstChild(kronaElement); element; element = getNextSibling(element) ) { switch ( element.tagName.toLowerCase() ) { case 'attributes': magnitudeName = element.getAttribute('magnitude'); // for ( var attributeElement = getFirstChild(element); attributeElement; attributeElement = getNextSibling(attributeElement) ) { var tag = attributeElement.tagName.toLowerCase(); if ( tag == 'attribute' ) { var attribute = new Attribute(); attribute.name = attributeElement.firstChild.nodeValue.toLowerCase(); attribute.displayName = attributeElement.getAttribute('display'); if ( attributeElement.getAttribute('hrefBase') ) { attribute.hrefBase = attributeElement.getAttribute('hrefBase'); } if ( attributeElement.getAttribute('target') ) { attribute.target = attributeElement.getAttribute('target'); } if ( attribute.name == magnitudeName ) { magnitudeIndex = attributes.length; } if ( attributeElement.getAttribute('listAll') ) { attribute.listAll = attributeElement.getAttribute('listAll').toLowerCase(); } else if ( attributeElement.getAttribute('listNode') ) { attribute.listNode = attributeElement.getAttribute('listNode').toLowerCase(); } else if ( attributeElement.getAttribute('dataAll') ) { attribute.dataAll = attributeElement.getAttribute('dataAll').toLowerCase(); } else if ( attributeElement.getAttribute('dataNode') ) { attribute.dataNode = attribut
```

--------------------------------

### Tween Animation Class

Source: https://github.com/steineggerlab/foldseek/blob/master/lib/mmseqs/data/resources/krona_prelude.html

Manages interpolation between start and end values for animation frames.

```javascript
function Tween(start, end) { this.start = start; this.end = end; this.current = this.start; this.current = function() { if ( progress == 1 || this.start == this.end ) { return this.end; } else { return this.start + tweenFactor * (this.end - this.start); } }; this.setTarget = function(target) { this.start = this.current(); this.end = target; } }
```

--------------------------------

### Representative Multimer Fasta Output

Source: https://github.com/steineggerlab/foldseek/blob/master/README.md

Example content of the _rep_seq.fasta file containing representative sequences.

```fasta
#5o002
>5o002_A
SHGK...R
>5o002_B
SHGK...R
#194l2
>194l2_A0
KVFG...L
>194l2_A6
KVFG...L
#10mh121
...
```

--------------------------------

### Initialize Zstandard Streaming Compression

Source: https://github.com/steineggerlab/foldseek/blob/master/lib/mmseqs/lib/zstd/doc/zstd_manual.html

Functions to begin a streaming compression session with various configuration options.

```C
size_t ZSTD_compressBegin(ZSTD_CCtx* cctx, int compressionLevel);
size_t ZSTD_compressBegin_usingDict(ZSTD_CCtx* cctx, const void* dict, size_t dictSize, int compressionLevel);
size_t ZSTD_compressBegin_advanced(ZSTD_CCtx* cctx, const void* dict, size_t dictSize, ZSTD_parameters params, unsigned long long pledgedSrcSize); /**< pledgedSrcSize : If srcSize is not known at init time, use ZSTD_CONTENTSIZE_UNKNOWN */
size_t ZSTD_compressBegin_usingCDict(ZSTD_CCtx* cctx, const ZSTD_CDict* cdict); /**< note: fails if cdict==NULL */
size_t ZSTD_compressBegin_usingCDict_advanced(ZSTD_CCtx* const cctx, const ZSTD_CDict* const cdict, ZSTD_frameParameters const fParams, unsigned long long const pledgedSrcSize);   /* compression parameters are already set within cdict. pledgedSrcSize must be correct. If srcSize is not known, use macro ZSTD_CONTENTSIZE_UNKNOWN */
size_t ZSTD_copyCCtx(ZSTD_CCtx* cctx, const ZSTD_CCtx* preparedCCtx, unsigned long long pledgedSrcSize); /**<  note: if pledgedSrcSize is not known, use ZSTD_CONTENTSIZE_UNKNOWN */
```