toruniina/afmize

generate pseudo-AFM image file from structure file

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afmize's Issues

Rotation of initial PDB file structure.

Hi :)
I want to get an image of the rotated structure in AFMize.
Do you know how to rotate the coordinates? Or can you implement it? :)

makeしたときにでるエラー

buildディレクトリを作成して移動し、cmakeは実行できましたが、
makeをしたら以下のコメントが出ました。

[ 12%] Building CXX object src/CMakeFiles/afmize.dir/afmize.cpp.o
/home/shino/afmize/src/afmize.cpp: In instantiation of ‘main(int, char**)::<lambda(auto:1)> [with auto:1 = afmize::system]’:
/home/shino/afmize/src/afmize.cpp:355:60: required from here
/home/shino/afmize/src/afmize.cpp:345:17: internal compiler error: Segmentation fault
if(stage_align) // align the lower edge of bounding box to stage
^
Please submit a full bug report,
with preprocessed source if appropriate.
See file:///usr/share/doc/gcc-5/README.Bugs for instructions.
src/CMakeFiles/afmize.dir/build.make:62: recipe for target 'src/CMakeFiles/afmize.dir/afmize.cpp.o' failed
make[2]: *** [src/CMakeFiles/afmize.dir/afmize.cpp.o] Error 1
CMakeFiles/Makefile2:96: recipe for target 'src/CMakeFiles/afmize.dir/all' failed
make[1]: *** [src/CMakeFiles/afmize.dir/all] Error 2
Makefile:94: recipe for target 'all' failed
make: *** [all] Error 2

解決策の検討をよろしくお願いいたします。

Unnecessary comma

In a CSV file, it seems that comma at the end of each line is unnecessary.

installation

I am using a MAC OSX computer and I have installed the CMake and git but in principle Xcode should have the C++14 compiler. However, when run git submodule update —init command, I am receiving the following error message.

fatal: not a git repository (or any of the parent directories): .git

I dont know what is the reason.
IS there a specific directory that I should go?

Thank you for your reply.

Best regards,

Boost library not found error

I am trying to install afmize but at the 'cmake ..' stage, I get the error below. It seems that the boost library cannot be downloaded from the link in CMakeLists.txt. I would appreciate your help! I am using Windows, with Cmake, git, and C++ compiler.

-- Boost library not found. Donwloading...

CMake Error at CMakeLists.txt:22 (file):
file DOWNLOAD HASH mismatch
for file: [C:/Users/S/afmize/extlib/boost_1_72_0.tar.gz]
expected hash: [c66e88d5786f2ca4dbebb14e06b566fb642a1a6947ad8cc9091f9f445134143f]
actual hash: [e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855]
status: [22;"HTTP response code said error"]

CMake Error at CMakeLists.txt:31 (message):
failed to download Boost library."HTTP response code said error"

Height and position of scale bar

Hi !
Now, the length of scale bar can be specified, but its height and position cannot.
When generating a high resolution image, I was faced with the problem that the scale bar was missing.
I'm so happy if the scale-bar height and position can be specified as well as its length can.
In addition, I'm glad if I can hide the scale bar when needed because the scale bar cannot be hidden completely by setting its length to be zero.

Best,
Sotaro

Height range of color scale

Hello!
It would be grateful if a height range of color scale for AFM images can be specified explicitly.
This leads to easily making and comparing pseudo AFM videos.
Additionally, it would be helpful if information on the height range used is available.

Best regards,
Sotaro