jrf@student45-OptiPlex-7000:/usr/lib/Dockey$ ./Dockey
Segmentation fault (core dumped)
jrf@student45-OptiPlex-7000:/usr/lib/Dockey$ sudo ./Dockey
[sudo] password for jrf:
Segmentation fault

我想在dockey中，直观的比较配体对接前后，相对于目标受体的位置变化，因此想到如下操作。

导入受体1wma，导入配体obj1，对接平台autodock4，参数为默认值。
对接完成后，poses栏中，单击best poses。
在pymol命令栏，输入fetch 1wma导入初始蛋白，在sequence中选择原位置的目标配体，提取为obj01。
显示complex结果，obj01，隐藏1wma初始蛋白。

问题1：以上，可以是否可以反映出直观比较配体对接前后，相对位置的变化呢？

我输入 align complex, obj01
提示错误代码：
PyMOL>PyMOL>align obj01, obj02
Match-Error: unable to open matrix file 'C:\Program Files (x86)\Dockey\pymol\pymol_path\data/pymol/matrices/BLOSUM62'.

并且，我复制了一份complex也不能解决这个问题，但是我导出complex的pdb文件，在pymol 2.5 平台上可以实现以下代码：

PyMOL>align 1wma-r, obj01
Match: read scoring matrix.
Match: assigning 276 x 1 pairwise scores.
MatchAlign: aligning residues (276 vs 1)...
MatchAlign: score 5.000
ExecutiveAlign: 27 atoms aligned.
ExecutiveRMS: 1 atoms rejected during cycle 1 (RMSD=2.97).
Executive: RMSD = 2.734 (26 to 26 atoms)

这是在分子对接中常用来计算RMSD值的代码。

问题2：作者可否加入自动计算RMSD值的脚本，这样真的会方便很多，因为autodock引擎计算的rRMSD和cRMSD值通常不作为参考数据。

Traceback (most recent call last):
File "MolKit\hydrogenBuilder.py", line 65, in addHydrogens
File "MolKit\molecule.py", line 102, in getattr
File "MolKit\tree.py", line 496, in getattr
File "MolKit\listSet.py", line 170, in getattr
File "MolKit\molecule.py", line 366, in getattr
AttributeError: member babel_type not found

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "process.py", line 328, in run
File "process.py", line 490, in do
File "process.py", line 289, in prepare_receptor
File "prepare.py", line 204, in prepare_autodock_receptor
File "AutoDockTools\MoleculePreparation.py", line 570, in init
File "AutoDockTools\MoleculePreparation.py", line 140, in init
File "AutoDockTools\MoleculePreparation.py", line 190, in repairMol
File "AutoDockTools\MoleculePreparation.py", line 203, in addHydrogens
File "MolKit\hydrogenBuilder.py", line 69, in addHydrogens
File "PyBabel\atomTypes.py", line 141, in assignHybridization
File "PyBabel\atomTypes.py", line 294, in valence_two
File "PyBabel\util.py", line 55, in bond_angle
ZeroDivisionError: ('Input used:', [28.999, 41.694, 2.992], [28.999, 41.694, 2.992], [28.999, 41.694, 2.992])

After docking finished, I can't see the best docked poses

When I start work I not see "Molecule details". Molecule was imported from the RCSB database. Maybe it is problem.

Traceback (most recent call last):
File "MolKit\hydrogenBuilder.py", line 65, in addHydrogens
File "MolKit\molecule.py", line 102, in getattr
File "MolKit\tree.py", line 496, in getattr
File "MolKit\listSet.py", line 170, in getattr
File "MolKit\molecule.py", line 366, in getattr
AttributeError: member babel_type not found

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "process.py", line 328, in run
File "process.py", line 490, in do
File "process.py", line 289, in prepare_receptor
File "prepare.py", line 204, in prepare_autodock_receptor
File "AutoDockTools\MoleculePreparation.py", line 570, in init
File "AutoDockTools\MoleculePreparation.py", line 140, in init
File "AutoDockTools\MoleculePreparation.py", line 190, in repairMol
File "AutoDockTools\MoleculePreparation.py", line 203, in addHydrogens
File "MolKit\hydrogenBuilder.py", line 69, in addHydrogens
File "PyBabel\atomTypes.py", line 141, in assignHybridization
File "PyBabel\atomTypes.py", line 294, in valence_two
File "PyBabel\util.py", line 55, in bond_angle
ZeroDivisionError: ('Input used:', [-16.484, -36.189, -13.694], [-16.484, -36.189, -13.694], [-16.484, -36.189, -13.694])
[
test0305.zip
](url)

Hi,

I really liked the tool. Im trying to import and visualize precomputed docking poses into dockey rather than generating again using autodock?. Is there any option to import precomputed poses for analysis?.

Looking forward for your suggestions.

1. 受体蛋白：PDB_ID: 1Y5I, 处理：加氢、去水、去有机物、去除B、C链。
2. 配体Pubchem CID: 943
3. 对接结构失败
4. 显示如下：
   Traceback (most recent call last):
   File "MolKit\hydrogenBuilder.py", line 65, in addHydrogens
   File "MolKit\molecule.py", line 102, in getattr
   File "MolKit\tree.py", line 496, in getattr
   File "MolKit\listSet.py", line 170, in getattr
   File "MolKit\molecule.py", line 366, in getattr
   AttributeError: member babel_type not found

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "process.py", line 328, in run
File "process.py", line 490, in do
File "process.py", line 289, in prepare_receptor
File "prepare.py", line 204, in prepare_autodock_receptor
File "AutoDockTools\MoleculePreparation.py", line 570, in init
File "AutoDockTools\MoleculePreparation.py", line 140, in init
File "AutoDockTools\MoleculePreparation.py", line 190, in repairMol
File "AutoDockTools\MoleculePreparation.py", line 203, in addHydrogens
File "MolKit\hydrogenBuilder.py", line 69, in addHydrogens
File "PyBabel\atomTypes.py", line 141, in assignHybridization
File "PyBabel\atomTypes.py", line 294, in valence_two
File "PyBabel\util.py", line 55, in bond_angle
ZeroDivisionError: ('Input used:', [-124.512, -87.645, 8.462], [-124.512, -87.645, 8.462], [-124.512, -87.645, 8.462])
请问这是对接程序的问题还是受体蛋白的问题？如何解决呢？

杜老师您好！使用Dockey时，出现了无法显示docking pose，无法显示interactions的问题。双击poses中的项目无法显示对接结构，如图所示：

且此时选择“Save selected pose"，导出的PDB文件大小为0字节（文件属性中如此显示），使用记事本打开为空白内容。

先前其他项目的对接中，docking pose和interactions是可以显示的。尚不清楚何种设置导致了这个问题，但怀疑与pdbfixer和pdb2pqr的取消勾选有关。在此项目中，勾选pdbfixer和pdb2pqr后，无法成功运行对接。

谢谢！

Waiting is always displayed when running the program

老师我在运行时一直显示waiting，具体界面如图：https://raw.githubusercontent.com/1334581771/figurebed/main/img/202310121109908.png
https://raw.githubusercontent.com/1334581771/figurebed/main/img/202310121110560.png

cannot show the docking poses in the PyMOL Sidebar
cannot analyze the interactions

作者你好！很感谢您所制作的dockey，给了我们很大的帮助！
我想问一下现在的dockey是否可以将对接的结果输出为一个表格之类的文件，可以让我们更方便的读取到每一个配体的对接分数之类的，我在帮助文档中只看到了导出单一配体的配对情况，但是貌似没有介绍可以将所有配体的对接信息一起导出的，所以想问一下现在10.2版本的dockey支持这个功能嘛？

Molecules cannot be imported from ZINC and no bug information.

Traceback (most recent call last):
File "MolKit\hydrogenBuilder.py", line 65, in addHydrogens
File "MolKit\molecule.py", line 102, in getattr
File "MolKit\tree.py", line 496, in getattr
File "MolKit\listSet.py", line 170, in getattr
File "MolKit\molecule.py", line 366, in getattr
AttributeError: member babel_type not found

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "process.py", line 318, in run
File "process.py", line 481, in do
File "process.py", line 279, in prepare_receptor
File "prepare.py", line 204, in prepare_autodock_receptor
File "AutoDockTools\MoleculePreparation.py", line 570, in init
File "AutoDockTools\MoleculePreparation.py", line 140, in init
File "AutoDockTools\MoleculePreparation.py", line 190, in repairMol
File "AutoDockTools\MoleculePreparation.py", line 203, in addHydrogens
File "MolKit\hydrogenBuilder.py", line 69, in addHydrogens
File "PyBabel\atomTypes.py", line 141, in assignHybridization
File "PyBabel\atomTypes.py", line 294, in valence_two
File "PyBabel\util.py", line 55, in bond_angle
ZeroDivisionError: ('Input used:', [15.352, 38.929, 203.579], [15.352, 38.929, 203.579], [15.352, 38.929, 203.579])

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "process.py", line 322, in run
File "process.py", line 250, in update_error
File "process.py", line 232, in send_message
File "multiprocessing\connection.py", line 206, in send
File "multiprocessing\connection.py", line 280, in _send_bytes
BrokenPipeError: [WinError 232] 管道正在被关闭。

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "multiprocessing\process.py", line 314, in _bootstrap
File "process.py", line 329, in run
File "process.py", line 247, in update_finished
File "process.py", line 232, in send_message
File "multiprocessing\connection.py", line 206, in send
File "multiprocessing\connection.py", line 280, in _send_bytes
BrokenPipeError: [WinError 232] 管道正在被关闭。

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "main.py", line 27, in
File "Lib\site-packages\PyInstaller\hooks\rthooks\pyi_rth_multiprocessing.py", line 52, in _freeze_support
File "multiprocessing\spawn.py", line 116, in spawn_main
File "multiprocessing\spawn.py", line 129, in _main
File "multiprocessing\process.py", line 329, in _bootstrap
AttributeError: 'NoneType' object has no attribute 'write'

Traceback (most recent call last):
File "MolKit\hydrogenBuilder.py", line 65, in addHydrogens
File "MolKit\molecule.py", line 102, in getattr
File "MolKit\tree.py", line 496, in getattr
File "MolKit\listSet.py", line 170, in getattr
File "MolKit\molecule.py", line 366, in getattr
AttributeError: member babel_type not found

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "process.py", line 318, in run
File "process.py", line 481, in do
File "process.py", line 279, in prepare_receptor
File "prepare.py", line 204, in prepare_autodock_receptor
File "AutoDockTools\MoleculePreparation.py", line 570, in init
File "AutoDockTools\MoleculePreparation.py", line 140, in init
File "AutoDockTools\MoleculePreparation.py", line 190, in repairMol
File "AutoDockTools\MoleculePreparation.py", line 203, in addHydrogens
File "MolKit\hydrogenBuilder.py", line 69, in addHydrogens
File "PyBabel\atomTypes.py", line 141, in assignHybridization
File "PyBabel\atomTypes.py", line 294, in valence_two
File "PyBabel\util.py", line 55, in bond_angle
ZeroDivisionError: ('Input used:', [15.174, 30.846, -37.139], [15.174, 30.846, -37.139], [15.174, 30.846, -37.139])

I saw another post related to this error where the solution was in Edit -> Settings -> Receptor preprocessing tab. However, on MacOS, the edit tab does not have a Settings panel, nor does any of the other panels. Attached is a screenshot. Is there a workaround to this?

Here is the error:

Traceback (most recent call last):
File "MolKit/hydrogenBuilder.py", line 65, in addHydrogens
File "MolKit/molecule.py", line 102, in getattr
File "MolKit/tree.py", line 496, in getattr
File "MolKit/listSet.py", line 170, in getattr
File "MolKit/molecule.py", line 366, in getattr
AttributeError: member babel_type not found

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "process.py", line 318, in run
File "process.py", line 335, in do
File "process.py", line 279, in prepare_receptor
File "prepare.py", line 204, in prepare_autodock_receptor
File "AutoDockTools/MoleculePreparation.py", line 570, in init
File "AutoDockTools/MoleculePreparation.py", line 140, in init
File "AutoDockTools/MoleculePreparation.py", line 190, in repairMol
File "AutoDockTools/MoleculePreparation.py", line 203, in addHydrogens
File "MolKit/hydrogenBuilder.py", line 69, in addHydrogens
File "PyBabel/atomTypes.py", line 141, in assignHybridization
File "PyBabel/atomTypes.py", line 294, in valence_two
File "PyBabel/util.py", line 55, in bond_angle
ZeroDivisionError: ('Input used:', [-33.236, 47.639, 26.683], [-33.236, 47.639, 26.683], [-33.236, 47.639, [26.683])

I defined the binding pocket by drawing custom box, however, the generated docking conformations are not in it.

OSError: [WinError 193] %1 不是有效的 Win32 应用程序。

对接了好几次，都是对接失败，报错AttributeError: member babel_type not found

Nice work !
As the title, is it possible to install dockey into a conda environment ? Or current installation must use system libraries?

Hello,
I have been following the instructions to install dockey but when I try to open the app it fails to open and I do not getn ya ny sort of messages anywhere.
I am trying to install in on a MacOS Monterey 12.6
Any suggestions on what might be going on and how to solve it?
Thanks

hi

when I imported the receptor and tried to draw the grid box, the window for drawing the box does not appear and the program is stuck.

Progress为100%，但status为Running。软件一直保持不动，怎么回事！

你好，请问为什么我在windows上安装完成之后无法导入受体结构？pdb导入是灰色的。

老师您好，这个程序为什么一直停在这啊，压根不运行

#4 #2 #(https://github.com/lmdu/dockey/assets/147358728/b5664311-6152-41d9-89ed-5372b2e33f22)

I tried to install Dockey on Ubuntu22.04. I tried all the three suggested methods. However, none of them worked. I got an error, segmentation fault (core dumped), as shown in attachments. Could you help me to solve the problem? Thanks!