RDKit is a popular open-source library for chemoinformatics and machine learning applied to chemoinformatics.
RDKit is a popular open-source library for chemoinformatics and machine learning applied to chemoinformatics.
Questions tagged [rdkit]
251 questions
0
votes
1 answer
Function cannot open file after py2exe compile
I'm using rdkit.
After a build using py2exe, when I call the Draw.MolToImage method there is an error:
Warning: unable to load font metrics from dir
C:\pythonApp\dist\library.zip\rd
kit\sping\PIL\pilfonts
Traceback (most recent call last):
File…
mahoney
- 11
0
votes
1 answer
Function to Button in Python using PyQt4
I am trying to create a button in a window that will ultimately run a function that I have written from code. My GUI code so far is as follows:
import sys
from PyQt4 import QtGui, QtCore
class PAINSFILTER(QtGui.QMainWindow):
def __init__(self):
…
olanre
- 31
- 1
- 1
- 4
0
votes
0 answers
Bit match analogue for array of words (fingerprints)
I'm trying to perform a substructure search on chemical database, using Avalon fingerprint precomputed for every compound.
There is a method to compare these fingerprints in RDKit:
DataStructs.AllProbeBitsMatch ( fp1, fp2 )
Docs describe this method…
Artico
- 101
- 6
0
votes
1 answer
rdkit svg flavors and rendering inline svg on django dev server
Hi I am trying to serve svg inline in a document rendered by a Django template where the svg ( 2D line drawings) and the document context are dynamically generated. The svg_string is put into my django context and rendered by the template.
{{…
harijay
- 11,303
- 12
- 38
- 52
-1
votes
1 answer
how can I address the error which calls “SMILES Pass Error”
When I run the python script, it shows the problem "SMILES Pass Error"imageimage2image3.
Codes show as below.
def convert_vocab_to_smiles_fn(smi_vocab_coding_padded,
token_EOS=SmilesVocab.smi_vocab.index('')):
…
yan
- 1
- 2
-1
votes
1 answer
rdkit.Chem.rdmolfiles.MolToMolFile(NoneType, str)
I am trying to convert smi to sdf format using rdkit python library. I am running following line of python code.
def convertir_smi_sdf(file_smi):
leer = [i for i in open(file_smi)]
print(f"Total de smi: {len(leer)}")
cont = 0
…
Rogelio Gomez
- 1
- 2
-1
votes
1 answer
Obtain information about bonded neighbors to all atoms in a molecule in python
I am coding in python a script and I need to obtain from a PDB file information about what atoms are bonded with each other in an automatized way.
For example, if we had ethane obtain a dictionary as…
Ignasi
- 11
- 1
-1
votes
1 answer
Install Rdkit in jupyter notebook, using Anaconda enviornment
How to install rdkit library in my jupyter notebook. I am using Anaconda environment.
Urvesh
- 331
- 4
- 15
-1
votes
1 answer
How can I set error message if it is not belongs to training datasets?
I have been implemented successfully recommendation engine but having a problem with that if I put any unrelated value still giving output it must be shown that " you have entered wrong value"
Here is output
correct smiles output
If I put wrong…
mastane lael
- 33
- 6
-1
votes
2 answers
Cannot allocate memory for array, rdkit converting to numpy array error
I have a list of 2215 molecules encoded as 2048 bit vectors. What I'm trying to do is to create 2D array from it. I am using rdkit library to convert to numpy arrays. The code worked without a problem few weeks ago and now there is a memory error…
Jozef
- 7
- 2
-1
votes
1 answer
convert SMILES column to ROMol column with in the same pandas data frame
How can I convert SMILES column to new SDF(ROMol) column in the same pandas data frame using RDkit or other?
for example:
ID SMILES
1 Oc1ccc2c(noc2c1)c3cccc4ccc(O)cc34
2 Oc1cc(C=C)c2cc(ccc2c1)c3ccc(O)c(F)c3
3 …
Naravut Suvannang
- 187
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- 11