Workflow for Lightning Fast Molecular Docking Part One

Mon, 1 Jun 2020 13:10:00 +0530

Compiling AutoDock Vina on iOS

Why? Because I can.

Installing makedepend

makedepend is a Unix tool used to generate dependencies of C source files. Most modern programes do not use this anymore, but then again AutoDock Vina's source code hasn't been changed since 2011. The first hurdle came when I saw that there was no makedepend command, neither was there any package on any development repository for iOS. So, I tracked down the original source code for makedepend (https://github.com/DerellLicht/makedepend). According to the repository this is actually the source code for the makedepend utility that came with some XWindows distribution back around Y2K. I am pretty sure there is a problem with my current compiler configuration because I had to manually edit the Makefile to provide the path to the iOS SDKs using the -isysroot flag.

Editting the Makefile

Original Makefile ( I used the provided mac Makefile base )

BASE=/usr/local
+BOOST_VERSION=1_41
+BOOST_INCLUDE = $(BASE)/include
+C_PLATFORM=-arch i386 -arch ppc -isysroot /Developer/SDKs/MacOSX10.5.sdk -mmacosx-version-min=10.4
+GPP=/usr/bin/g++
+C_OPTIONS= -O3 -DNDEBUG
+BOOST_LIB_VERSION=
+
+include ../../makefile_common
+

I installed Boost 1.68.0-1 from Sam Bingner's repository. ( Otherwise I would have had to compile boost too 😫 )

Editted Makefile

BASE=/usr
+BOOST_VERSION=1_68
+BOOST_INCLUDE = $(BASE)/include
+C_PLATFORM=-arch arm64 -isysroot /var/sdks/Latest.sdk
+GPP=/usr/bin/g++
+C_OPTIONS= -O3 -DNDEBUG
+BOOST_LIB_VERSION=
+
+include ../../makefile_common
+

Updating the Source Code

Of course since Boost 1.41 many things have been added and deprecated, that is why I had to edit the source code to make it work with version 1.68

Error 1 - No Matching Constructor

../../../src/main/main.cpp:50:9: error: no matching constructor for initialization of 'path' (aka 'boost::filesystem::path')
+return path(str, boost::filesystem::native);
+

This was an easy fix, I just commented this and added a return statement to return the path

return path(str)
+

Error 2 - No Member Named 'nativefilestring'

../../../src/main/main.cpp:665:57: error: no member named 'native_file_string' in 'boost::filesystem::path'
+                std::cerr << "\n\nError: could not open \"" << e.name.native_file_string() << "\" for " << (e.in ? "reading" : "writing") << ".\n";
+                                                               ~~~~~~ ^
+../../../src/main/main.cpp:677:80: error: no member named 'native_file_string' in 'boost::filesystem::path'
+                std::cerr << "\n\nParse error on line " << e.line << " in file \"" << e.file.native_file_string() << "\": " << e.reason << '\n';
+                                                                                      ~~~~~~ ^
+2 errors generated.
+

Turns out native_file_string was deprecated in Boost 1.57 and replaced with just string

Error 3 - Library Not Found

This one still boggles me because there was no reason for it to not work, as a workaround I downloaded the DEB, extracted it and used that path for compiling.

Error 4 - No Member Named 'nativefilestring' Again.

But, this time in another file and I quickle fixed it

Moment of Truth

Obviously it was working on my iPad, but would it work on another device? I transfered the compiled binary and

The package is available on my repository and only depends on boost. ( Both, Vina and Vina-Split are part of the package)

Navan Chauhan