From c34171884fed4b64ee58f9e9c06b26761cd3f367 Mon Sep 17 00:00:00 2001 From: Navan Chauhan Date: Thu, 25 Jun 2020 18:17:44 +0530 Subject: Publish deploy 2020-06-25 18:17 --- feed.rss | 5 +++-- posts/2020-05-31-compiling-open-babel-on-ios/index.html | 3 ++- sitemap.xml | 2 +- tags/tutorial/index.html | 2 +- 4 files changed, 7 insertions(+), 5 deletions(-) diff --git a/feed.rss b/feed.rss index 215ddb1..56e2319 100644 --- a/feed.rss +++ b/feed.rss @@ -1,4 +1,4 @@ -Navan ChauhanWelcome to my personal fragment of the internet. Majority of the posts should be complete.https://navanchauhan.github.io/enTue, 2 Jun 2020 23:25:41 +0530Tue, 2 Jun 2020 23:25:41 +0530250https://navanchauhan.github.io/posts/2020-06-02-Compiling-AutoDock-Vina-on-iOSCompiling AutoDock Vina on iOSCompiling AutoDock Vina on iOShttps://navanchauhan.github.io/posts/2020-06-02-Compiling-AutoDock-Vina-on-iOSTue, 2 Jun 2020 23:23:00 +0530Compiling 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 +Navan ChauhanWelcome to my personal fragment of the internet. Majority of the posts should be complete.https://navanchauhan.github.io/enThu, 25 Jun 2020 18:17:35 +0530Thu, 25 Jun 2020 18:17:35 +0530250https://navanchauhan.github.io/posts/2020-06-02-Compiling-AutoDock-Vina-on-iOSCompiling AutoDock Vina on iOSCompiling AutoDock Vina on iOShttps://navanchauhan.github.io/posts/2020-06-02-Compiling-AutoDock-Vina-on-iOSTue, 2 Jun 2020 23:23:00 +0530Compiling 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 @@ -33,7 +33,8 @@ include ../../makefile_common
$(pbpaste)

This is used in bash to evaluate the results of a command. In this scenario we are using it to get the contents of the clipboard.

The rest of the command is a normal Open Babel command to generate a 3D structure in PDBQT format and then save it as test.pdbqt

&&

This tells the termianl to only run the next part if the previous command runs succesfuly without any errors.

vina --receptor lu.pdbqt --center_x -9.7 --center_y 11.4 --center_z 68.9 --size_x 19.3 --size_y 29.9 --size_z 21.3 --ligand test.pdbqt -

This is just the docking command for AutoDock Vina. In the next part I will tell how to use PyMOL and a plugin to directly generate the coordinates in Vina format --center_x -9.7 --center_y 11.4 --center_z 68.9 --size_x 19.3 --size_y 29.9 --size_z 21.3 without needing to type them manually.

]]>
https://navanchauhan.github.io/posts/2020-05-31-compiling-open-babel-on-iosCompiling Open Babel on iOSCompiling Open Babel on iOShttps://navanchauhan.github.io/posts/2020-05-31-compiling-open-babel-on-iosSun, 31 May 2020 23:30:00 +0530Compiling Open Babel on iOS

Due to the fact that my summer vacations started today, I had the brilliant idea of trying to run open babel on my iPad. To give a little background, I had tried to compile AutoDock Vina using a cross-compiler but I had miserably failed.

I am running the Checkr1n jailbreak on my iPad and the Unc0ver jailbreak on my phone.

But Why?

Well, just because I can. This is literally the only reason I tried compiling it and also partially because in the long run I want to compile AutoDock Vina so I can do Molecular Docking on the go.

Let's Go!

How hard can it be to compile open babel right? It is just a simple software with clear and concise build instructions. I just need to use cmake to build and the make to install.

It is 11 AM in the morning. I install clang, cmake and make from the Sam Bingner's repository, fired up ssh, downloaded the source code and ran the build command.`clang

Fail No. 1

I couldn't even get cmake to run, I did a little digging arond StackOverflow and founf that I needed the iOS SDK, sure no problem. I waited for Xcode to update and transfered the /Applications/Xcode.app/Contents/Developer/Platforms/iPhoneOS.platform/Developer/SDKs/iPhoneOS.sdk to /var/sdks/ on my iPad

Them I told cmake that this is the location for my SDK 😠. Succesful! Now I just needed to use make.

Fail No. 2

It was giving the error that thread-local-storage was not supported on this device.

[ 0%] Building CXX object src/CMakeFiles/openbabel.dir/alias.cpp.o +

This is just the docking command for AutoDock Vina. In the next part I will tell how to use PyMOL and a plugin to directly generate the coordinates in Vina format --center_x -9.7 --center_y 11.4 --center_z 68.9 --size_x 19.3 --size_y 29.9 --size_z 21.3 without needing to type them manually.

]]>
https://navanchauhan.github.io/posts/2020-05-31-compiling-open-babel-on-iosCompiling Open Babel on iOSCompiling Open Babel on iOShttps://navanchauhan.github.io/posts/2020-05-31-compiling-open-babel-on-iosSun, 31 May 2020 23:30:00 +0530Compiling Open Babel on iOS

Due to the fact that my summer vacations started today, I had the brilliant idea of trying to run open babel on my iPad. To give a little background, I had tried to compile AutoDock Vina using a cross-compiler but I had miserably failed.

I am running the Checkr1n jailbreak on my iPad and the Unc0ver jailbreak on my phone.

But Why?

Well, just because I can. This is literally the only reason I tried compiling it and also partially because in the long run I want to compile AutoDock Vina so I can do Molecular Docking on the go.

Let's Go!

How hard can it be to compile open babel right? It is just a simple software with clear and concise build instructions. I just need to use cmake to build and the make to install.

It is 11 AM in the morning. I install clang, cmake and make from the Sam Bingner's repository, fired up ssh, downloaded the source code and ran the build command.`clang

Fail No. 1

I couldn't even get cmake to run, I did a little digging arond StackOverflow and founf that I needed the iOS SDK, sure no problem. I waited for Xcode to update and transfered the SDKs to my iPad

scp -r /Applications/Xcode.app/Contents/Developer/Platforms/iPhoneOS.platform/Developer/SDKs/iPhoneOS.sdk root@192.168.1.8:/var/sdks/ +

Them I told cmake that this is the location for my SDK 😠. Succesful! Now I just needed to use make.

Fail No. 2

It was giving the error that thread-local-storage was not supported on this device.

[ 0%] Building CXX object src/CMakeFiles/openbabel.dir/alias.cpp.o [ 1%] Building CXX object src/CMakeFiles/openbabel.dir/atom.cpp.o In file included from /var/root/obabel/ob-src/src/atom.cpp:28: In file included from /var/root/obabel/ob-src/include/openbabel/ring.h:29: diff --git a/posts/2020-05-31-compiling-open-babel-on-ios/index.html b/posts/2020-05-31-compiling-open-babel-on-ios/index.html index 2b1a9fb..37af7e3 100644 --- a/posts/2020-05-31-compiling-open-babel-on-ios/index.html +++ b/posts/2020-05-31-compiling-open-babel-on-ios/index.html @@ -1,4 +1,5 @@ -Compiling Open Babel on iOS | Navan Chauhan
5 minute readCreated on May 31, 2020Last modified on June 2, 2020

Compiling Open Babel on iOS

Due to the fact that my summer vacations started today, I had the brilliant idea of trying to run open babel on my iPad. To give a little background, I had tried to compile AutoDock Vina using a cross-compiler but I had miserably failed.

I am running the Checkr1n jailbreak on my iPad and the Unc0ver jailbreak on my phone.

But Why?

Well, just because I can. This is literally the only reason I tried compiling it and also partially because in the long run I want to compile AutoDock Vina so I can do Molecular Docking on the go.

Let's Go!

How hard can it be to compile open babel right? It is just a simple software with clear and concise build instructions. I just need to use cmake to build and the make to install.

It is 11 AM in the morning. I install clang, cmake and make from the Sam Bingner's repository, fired up ssh, downloaded the source code and ran the build command.`clang

Fail No. 1

I couldn't even get cmake to run, I did a little digging arond StackOverflow and founf that I needed the iOS SDK, sure no problem. I waited for Xcode to update and transfered the /Applications/Xcode.app/Contents/Developer/Platforms/iPhoneOS.platform/Developer/SDKs/iPhoneOS.sdk to /var/sdks/ on my iPad

Them I told cmake that this is the location for my SDK 😠. Succesful! Now I just needed to use make.

Fail No. 2

It was giving the error that thread-local-storage was not supported on this device.

[ 0%] Building CXX object src/CMakeFiles/openbabel.dir/alias.cpp.o +Compiling Open Babel on iOS | Navan Chauhan
5 minute readCreated on May 31, 2020Last modified on June 25, 2020

Compiling Open Babel on iOS

Due to the fact that my summer vacations started today, I had the brilliant idea of trying to run open babel on my iPad. To give a little background, I had tried to compile AutoDock Vina using a cross-compiler but I had miserably failed.

I am running the Checkr1n jailbreak on my iPad and the Unc0ver jailbreak on my phone.

But Why?

Well, just because I can. This is literally the only reason I tried compiling it and also partially because in the long run I want to compile AutoDock Vina so I can do Molecular Docking on the go.

Let's Go!

How hard can it be to compile open babel right? It is just a simple software with clear and concise build instructions. I just need to use cmake to build and the make to install.

It is 11 AM in the morning. I install clang, cmake and make from the Sam Bingner's repository, fired up ssh, downloaded the source code and ran the build command.`clang

Fail No. 1

I couldn't even get cmake to run, I did a little digging arond StackOverflow and founf that I needed the iOS SDK, sure no problem. I waited for Xcode to update and transfered the SDKs to my iPad

scp -r /Applications/Xcode.app/Contents/Developer/Platforms/iPhoneOS.platform/Developer/SDKs/iPhoneOS.sdk root@192.168.1.8:/var/sdks/ +

Them I told cmake that this is the location for my SDK 😠. Succesful! Now I just needed to use make.

Fail No. 2

It was giving the error that thread-local-storage was not supported on this device.

[ 0%] Building CXX object src/CMakeFiles/openbabel.dir/alias.cpp.o [ 1%] Building CXX object src/CMakeFiles/openbabel.dir/atom.cpp.o In file included from /var/root/obabel/ob-src/src/atom.cpp:28: In file included from /var/root/obabel/ob-src/include/openbabel/ring.h:29: diff --git a/sitemap.xml b/sitemap.xml index c966ce3..53c3d59 100644 --- a/sitemap.xml +++ b/sitemap.xml @@ -1 +1 @@ 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\ No newline at end of file diff --git a/tags/tutorial/index.html b/tags/tutorial/index.html index 9bec523..d561bfd 100644 --- a/tags/tutorial/index.html +++ b/tags/tutorial/index.html @@ -1 +1 @@ -Navan Chauhan

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