pdbqtf

pdbqtf is a command line tool for fixing problematic chemical elements in PDBQT files.

Features

• fix problematic question mark (?) elements in PDBQT files
• batch fixing
• in-place fixing or save as new file

pdbqtf accepts the following ways of input:

• standard input: pdbqtf
• file input: pdbqtf file.pdbqt
• input redirect: pdbqtf <(cat file.pdbqt)
• pipe input: cat file.pdbqt | pdbqtf

Supported operating systems and compilers

All systems with compilers in conformance with the C++17 standard, e.g.

• Linux x86_64 and g++ 8.3.1 or higher
• Mac OS X x86_64 and clang 7 or higher
• Windows x86_64 and msvc 19.14 or higher

Compilation from source code

Get Boost

pdbqtf depends on the Program Options component in Boost C++ Libraries. Boost 1.75.0 was tested. There are several ways to get Boost.

With vcpkg on Windows, macOS or Linux:

# Note: this will download and build from source
vcpkg install boost-program-options

With nuget on Windows:

nuget install boost_program_options-vc142

With apt on Ubuntu/Debian:

sudo apt install libboost-program-options-dev

With Homebrew on macOS:

brew install boost

With PowerShell on Windows:

$Url = "https://sourceforge.net/projects/boost/files/boost-binaries/1.75.0/boost_1_75_0-msvc-14.2-64.exe"
(New-Object System.Net.WebClient).DownloadFile($Url, "$env:TEMP\boost.exe")
Start-Process -Wait -FilePath "$env:TEMP\boost.exe" "/SILENT","/SP-","/SUPPRESSMSGBOXES"

Build from Source on Linux or Windows:

Download Boost 1.75 and unpack the archive to boost_1_75_0/include.

Build on Linux run:

cd boost_1_75_0/include
./bootstrap.sh
./b2 --build-dir=../build/linux_x64 --stagedir=../ -j 8 link=static address-model=64

Or, on Windows run:

cd boost_1_75_0\include
bootstrap.bat
b2 --build-dir=../build/win_x64 --stagedir=../ -j 8 link=static address-model=64

Then add the path of the boost_1_75_0 directory the to the BOOST_ROOT environment variable.

Build with CMake

This project uses cross-platform build system CMake to build from source. It detects your environment and decides the most appropriate compiler toolset. The minimum version of CMake required is 3.20. To build, simply run

cmake -B build
cmake --build build --config Release

The generated objects and executable will be placed in the build folder.

Optionally, on Linux or macOS one may install the output binary to the system (usually /usr/local/bin) by running

sudo cmake --install build

On Windows, the script should be run without sudo but under Administrator. The executable will be copied to an individual directory under Program Files.

Build with Visual Studio

Visual Studio 2019 solution and project files are provided. To compile, simply run

msbuild /t:Build /p:Configuration=Release

Or one may open pdbqtf.sln in Visual Studio 2019 and do a full rebuild.

The generated objects will be placed in the obj folder, and the generated executable will be placed in the bin folder.

Usage

First add pdbqtf to the PATH environment variable.

To display a full list of available options, simply run the program with the --help argument

pdbqtf --help

See the Features section above for usages in different input ways.

Author

Maozi Chen