conformer | PyTorch implementation of `` Conformer | Machine Learning library
kandi X-RAY | conformer Summary
kandi X-RAY | conformer Summary
Transformer models are good at capturing content-based global interactions, while CNNs exploit local features effectively. Conformer combine convolution neural networks and transformers to model both local and global dependencies of an audio sequence in a parameter-efficient way. Conformer significantly outperforms the previous Transformer and CNN based models achieving state-of-the-art accuracies. This repository contains only model code, but you can train with conformer at openspeech.
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Top functions reviewed by kandi - BETA
- Compute embedding
- Compute the relative position of pos_score
conformer Key Features
conformer Examples and Code Snippets
Community Discussions
Trending Discussions on conformer
QUESTION
I generated a bunch of conformers for a molecule. For each conformed, I want to save the coordinates in a SDF file. I tried the following, but the coordinates in the sdf file is different from that of the conformer.
...ANSWER
Answered 2021-Oct-19 at 16:26When you use SDWriter.write you need to supply the ID of the conformer you wish to write to the file:
QUESTION
A new deep-learning algorithm for drug-discovery based on images, requires splitting a file containing ~3000 chemical compounds in png files containing individual 2D 200 x 200 pixel images (.: SN00001400.png, SN00002805.png, SN00002441.png........). Not need any conformers, nor any other 3D information.
I could send an initial f1.sdf example containing 9 compound images, names and smiles, one for each compound row.
Using rdkit 2017.09.1 in Anaconda3 with Python 3.6, 3.7 or 3.8, Jupyter notebooks and/or Python prompt, in 2 e7 64 computers within Windows 8 professional, I am looking for a simple Python code to split the images, convert them to a 200 x 200 pixel png file (carios), named them by their corresponding compound ID and save them into a different directory (.: images), ready to be tested.
I try many different web codes and combinations but despite intensive testing, they did not work :-(.
Following some of my best (?) code trials.
rdkit imports tested
...ANSWER
Answered 2021-Jan-21 at 20:42You were right!.
I performed a "conda install -c conda-forge rdkit" in a newly created Anaconda3 environment, and most of the commands suddenly WORKED!!!. THANK YOU VERY MUCH!!!!
I developed the code below..... but I got stopped because I cannot find a way to transfer each of the corresponding comp_id to the names of the png files that code for the beautiful png images. Any ideas? THANKS!!!
from rdkit import Chem
from rdkit.Chem import AllChem
from rdkit.Chem import Draw
from rdkit.Chem.Draw import rdMolDraw2D
from rdkit.Chem.Draw.rdMolDraw2D import MolDraw2DSVG
from rdkit.Chem.Draw.rdMolDraw2D import MolDraw2DCairo
from rdkit.Chem.Draw import MolToFile
from rdkit.Chem import rdDepictor
from rdkit.Chem import MolFromSmiles
suppl = Chem.SDMolSupplier('f1.sdf')
for mol in suppl:
QUESTION
I am running some molecular simulations, and I have a file with coordinates (a .xyz file, which is basically a file with tabbed columns) and I need to send it another file, which will be my input file for my simulation.
To give you a picture, this is how my input files look like with my coordinates (there is more stuff at the bottom that remains untouched):
inputfile.py
ANSWER
Answered 2021-Jan-09 at 08:19import re
def insert_data(conformer_filepath,input_filepath,output_filepath):
#grab conformer data
with open(conformer_filepath,'r') as f:
conformer_text = f.read()
conformer_data = re.search('conformer[^\n]+\n(.+)',conformer_text,re.M|re.S).group(1)
#this looks for the line that has conformer in it and takes all lines after it
#grab input file before and after text
with open(input_filepath,'r') as f:
input_text = f.read()
input_pre,input_post = re.search('(^.+\n0 1\n).+?(\n}.*)$',input_text,re.M|re.S).groups()
#this looks for the "0 1" line and takes everything before that. Then it skips down to the next curly bracket which is at the start of a line and takes that and everything past it.
#write them to the output file
with open(output_filepath,'w') as f:
f.write(input_pre + conformer_data + input_post)
#this writes the three pieces collected to the output file
QUESTION
I'm trying to generate conformers for a number of small-molecule ligands to eventually do docking with. I generated the conformers using RDkit's EmbedMultipleConfs function. However, when subsequently visually inspecting the conformers in PyMol I noticed that RDKit did not preserve correct angles for aromatic moieties. For instance, in one my ligands with a benzene group it did not preserve the planarity of this group, instead assigning random angles to this benzene group as if it were a cyclohexane.
There seem to be no problems with aromaticity when just loading the molecule.
Is there a way to fix this?
Part of the code for generating conformers:
...ANSWER
Answered 2020-Jul-05 at 22:10I believe that your problem is probably that you are reading the input from a PDB file. PDB files do not contain the bond orders of small molecules. Your best bet is to assign the correct bond orders from a template molecule as below:
QUESTION
I have a function like this:
...ANSWER
Answered 2020-Jan-14 at 22:36The reason for the error is FetchableRecord.Type is not the same as ModelA.Type or ModelB.Type. Even if both of the structs conform to FetchableRecord protocol, constraining the models (by conforming to a certain protocol) does not affect the "Types", more technically speaking:
ModelA.self == FetchableRecord.self OR ModelB.self == FetchableRecord.self is false.
In order to resolve this issue, you could implement the method's signiture as:
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Install conformer
Currently we only support installation from source code using setuptools. Checkout the source code and run the following commands:.
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