For programming questions that involve chemistry - such as questions about programmatically working with chemical formulae, simulating chemical processes, or using chemistry-related libraries and APIs. Non-programming questions about chemistry are off-topic here, but may be on-topic on chemistry.stackexchange.com.
Questions tagged [chemistry]
275 questions
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RDKit Function Issues: Python argument types in Mol.GetSubstructMatches(Mol, str) did not match C++ signature
Been programming a program to determine various functional groups from an inputted molecule. Was working great until 2 days ago. Started getting the error below. Below is a simplified exerpt of the code that generates the same error. Any suggestions…
Bigfoot Mountain
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- 2
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1 answer
issue encountered using Backend Estimator using providers from qiskit_braket_providers
I am carrying out a ground state estimation of a molecule via qiskit-nature workflows. As explained in qiskit documentation I define a VQE solver by means of a backend estimator that runs on a specific backend. Normally I use different backends…
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How to produce contour plots for clustered (x,y,z) data in matplotlib?
I have a set of three-dimensional spectral data in (x, y, z) coordinate form. The x-axis corresponds to spectral frequencies, the y-axis corresponds to a calculated coefficient based on my data for each frequency, and the z-axis corresponds to the…
Nathan Black
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Cannot debug getVecs, getCoupls, and findCCvec functions in Python script with certain Mus_df values
I have the following code that gets some input files and calculates some values. The issue is, the code is working for Mus_df values 1,2,3,4,6,12 but not 5,7,8,9,10,11. The error indicates that CCvecs is None-type. Can you help me?
import numpy as…
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How to import a SDF or sd file in python?
This would be my first time asking a problem here and I am a bit new to programming so please bear with me. Now, I was trying to import a list of compounds from ChemBL so as to get these compounds to be displayed in a grid and categorize them.…
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2 answers
Get 3D Chemical Structures - Python Automation
I am working in python and i want to get a series of 3D images for the molecules I'm using.
I have .mol files stored in my folder and for each of them I would like to obtain a 3D render of its 'stick' representation.
With py3Dmol i can get a 3D…
Mirk
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Coodinates generate and molecule functionnalization
I need help please. Can someone guide me on how to generate the xyz coordinates of all functionalized Azulene molecules knowing the positions of the functional groups (1,3,9) and the functional groups (C(CN)2, COCH3, Br)?
I search the answer on the…
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issues encountered in using scikit-quant optimizers in Qiskit VQE workflows (Aer backend)
as I am testing all optimizers advised in qiskit.algorithms.optimizers reference page to evaluate their performance in a VQE qiskit nature workflow on the Aer backend with and without noise model, I decided to call scikit-quant optimizers BOBYQA,…
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Sympy Troubleshooting: unsupported operand type(s) for +: 'ImmutableDenseNDimArray' and 'NegativeOne'
I'm trying to determine the entropy of adsorbed hydrogen gas, leaving the temperature "T" as a symbolic variable in Python using the sympy library, and am running into issues as a result
Originally, the process was completed numerically, which…
Luke Pretzie
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Generation of Duval Triangle for OLTC
In my angular 6 project, I am using plotly.js-dist to generate duval triangle. I need to implement Duval Triangle for OLTC. I have the values for CH4, C2H2 and C2H4. in library I need to understand how to add the values to axis based on the given…
Pradip Solace
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How to make a comprehensive composition table efficiently
I am trying to make a comprehensive compositon table for composite development (in chemistry field) based on the specific rules.
The rules are
The numbers in a table mean the weight percentage of each raw material in the ccomposite
There are three…
hiro
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- 4
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2 answers
Indexing of strings (molecule SMILES)
Also, please can someone adjust or give me advice on how to look at the second order of parenthesis. Same process as this, but with only parenthesis in second order (this code is first order). Can you make it so I can easily adjust? By second order…
YZman
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Discrepancy Between MATLAB and Python
I have a MATLAB script for calculating the entropy of a molecule according to its vibrational frequencies, and which I know to be correct by comparing it with experimental results. The MATLAB script is as…
Luke Pretzie
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Why does my program always say that the request was not found in the dictionary?
Every time I input a request I get an error saying the request was not found. Does anyone know what the problem is?
def get_elem(req):
for element in elements_dict:
if req.upper() == element:
return elements_dict[element]
…
Roee Weglein
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- 1
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Converting an Isometric SMILE into its atoms and non-hydrogen neighbours
Hope whoever is reading this is well.
I have an issue with my code. I am trying to convert an isometric SMILE, a descriptor of a molecule, into its atomic groups and neightbours.
My code is below.
import rdkit
from rdkit import Chem
def…
YZman
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