Boost.Python.Argument.Error

[darose93]

I am currently attempting to run this program on a Mac and have been able to open up the GUI, however, once I input the files and start the calculations python will immediately crash. The error code below was displayed so I updated my boost package to boost-1.67.0-py37_4 however this did not appear to have any effect.

Boost.Python.ArgumentError: Python argument types in rdkit.Chem.rdinchi.MolToInchi(NoneType, str) did not match C++ signature: MolToInchi(RDKit::ROMol mol, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > options='')

I have minimal experience working with python so any insight into this issue would be really appreciated.

[HowarthA]

Hi, Despite being developed and tested most extensively on Linux, DP4-AI will run on a macOS. What version of rdkit do you have installed? The inchi generation code is running smoothly on my Mac (OS Mojave) using Python 3.7 and rdkit version 2019.09.3.0.

[darose93]

Hi, I am also running Mac (OS Mojave) using Python 3.7 with the rdkit version rdkit-2020.03.1.0. I later realized that issue was related to the .sdf file format. For some reason, my exported file had the incorrect heading/formatting which once I fixed that issue did go away. I then ran into another problem moments later dealing with the sdf2tinker executable. I have copied the error message below.

Setting up Tinker files...

/bin/sh: /Applications/DP4-AI-master/sdf2tinkerxyz: cannot execute binary file

Traceback (most recent call last):

File "PyDP4_GUI.py", line 2001, in runPyDP4

self.NMRData, self.Isomers, self.settings, self.DP4Data =

PyDP4.main(ui.table_widget.Tab1.settings)

File "/Applications/DP4-AI-master/PyDP4.py", line 210, in main

TinkerInputs = Tinker.SetupTinker(settings)

File "/Applications/DP4-AI-master/Tinker.py", line 54, in SetupTinker

outp = subprocess.check_output(convinp + inpf + '.sdf', shell=True)

File "/Users/newuser/opt/anaconda3/lib/python3.7/subprocess.py", line 411, in check_output

**kwargs).stdout

File "/Users/newuser/opt/anaconda3/lib/python3.7/subprocess.py", line 512, in run

output=stdout, stderr=stderr)

subprocess.CalledProcessError: Command '/Applications/DP4-AI-master/sdf2tinkerxyz -k /Applications/DP4-AI-master/default.key <BYH1_new1.sdf' returned non-zero exit status 126.

Abort trap: 6

I attempted to redownload the executable but that ultimately led to the same error message.

I really appreciate your help with this!

Doug Rose

On Wed, Apr 22, 2020 at 4:03 AM HowarthA notifications@github.com wrote:

Hi, Despite being developed and tested most extensively on Linux, DP4-AI will run on a macOS. What version of rdkit do you have installed? The inchi generation code is running smoothly on my Mac (OS Mojave) using Python 3.7 and rdkit version 2019.09.3.0.

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[KristapsE]

sdf2tinkerxyz is a Linux binary that converts the sdf file to tinker xyz format, so the problem in hindsight is not unexpected. TINKER on Mac OS is definitely a combination we haven't tried yet.

You should try downloading the Mac OS binary for sdf2tinkerxyz copy it over the file you downloaded from the GitHub.

http://sdf2xyz2sdf.sourceforge.net/?Downloads

[KristapsE]

I assume that this fixed the issue, so I will close this issue now.