From 20b1941b672cb133ff4ca4c5cb45ae70cdd8c5f7 Mon Sep 17 00:00:00 2001 From: Navan Chauhan Date: Mon, 1 Jun 2020 12:27:12 +0530 Subject: Publish deploy 2020-06-01 12:27 --- feed.rss | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) (limited to 'feed.rss') diff --git a/feed.rss b/feed.rss index a8f147d..3f63420 100644 --- a/feed.rss +++ b/feed.rss @@ -1,4 +1,11 @@ -Navan ChauhanWelcome to my personal fragment of the internet. Majority of the posts should be complete.https://navanchauhan.github.io/enMon, 1 Jun 2020 00:48:18 +0530Mon, 1 Jun 2020 00:48:18 +0530250https://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 11:30:00 +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
+Navan ChauhanWelcome to my personal fragment of the internet. Majority of the posts should be complete.https://navanchauhan.github.io/enMon, 1 Jun 2020 12:27:03 +0530Mon, 1 Jun 2020 12:27:03 +0530250https://navanchauhan.github.io/posts/2020-06-01-Speeding-Up-Molecular-Docking-Workflow-AutoDock-Vina-and-PyMOLWorkflow for Lightning Fast Molecular Docking Part OneThis is my workflow for lightning fast molecular docking.https://navanchauhan.github.io/posts/2020-06-01-Speeding-Up-Molecular-Docking-Workflow-AutoDock-Vina-and-PyMOLMon, 1 Jun 2020 13:10:00 +0530Workflow for Lightning Fast Molecular Docking Part One
My Setup
  • macOS Catalina ( RIP 32bit app)
  • PyMOL
  • AutoDock Vina
  • Open Babel
One Command Docking
obabel -:"$(pbpaste)" --gen3d -opdbqt -Otest.pdbqt && vina --receptor lu.pdbqt --center_x -9.7 --center_y 11.4 --center_z 68.9 --size_x 19.3 --size_y 29.9 --size_z 21.3  --ligand test.pdbqt
+
To run this command you simple copy the SMILES structure of the ligand you want an it automatically takes it from your clipboard, generates the 3D structure in the AutoDock PDBQT format using Open Babel and then docks it with your receptor using AutoDock Vina, all with just one command.
Let me break down the commands
obabel -:"$(pbpaste)" --gen3d -opdbqt -Otest.pdbqt
+
pbpaste and pbcopy are macOS commands for pasting and copying from and to the clipboard. Linux users may install the xclip and xsel packages from their respective package managers and then insert these aliases into their bash_profile, zshrc e.t.c
alias pbcopy='xclip -selection clipboard'
+alias pbpaste='xclip -selection clipboard -o'
+
$(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 11:30:00 +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
 [  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:
-- 
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