How to compress repeating branches in directed graph?

I work a lot with directed graphs resulting from heap dumps of Java programs. One thing that characterizes them is that they contain lots of repeating patterns. I would like to find a way of...

Automatically cropping an image with python/PIL

Can anyone help me figure out what's happening in my image auto-cropping script? I have a png image with a large transparent area/space. I would like to be able to automatically crop that space...

Retrieve all molecules from smiles file

I am working on .smiles files. File structure of .smiles file is : http://en.wikipedia.org/wiki/Chemical_file_format#SMILES I want to get all the atoms from the smiles file. It means that If there...

Many to many relationship with a composite key on SQLAlchemy

Let's say I have the following model: class Molecule(Base): db = Column(Integer, primary_key=True) id = Column(Integer, primary_key=True) data = Column(Integer) class Atom(Base): id =...

to get molecular name from smiles format using python

I have number of molecules in smiles format and I want to get molecular name from smiles format of molecule and I want to use python for that conversion. for example : CN1CCC[[email protected]]1c2cccnc2 -...

Force no default selection in selectInput()

The Shiny documentation mentions that for selectInput(): selected The value (or, if none was supplied, the title) of the navigation item that should be selected by default. If NULL, the first...

How to avoid re-compiling generated source code

Generating boilerplate source code with sbt works fine: sourceGenerators in Compile <+= sourceManaged in Compile map { srcDir => DslBoilerplate.generate(srcDir, Seq( ...

How to disable logged warnings in Pybel?

I am using Pybel - a Python wrapper around the OpenBabel API, and I am trying to disable warnings such as these: ============================== *** Open Babel Warning in ParseComplex Illegal...

pytest: How do I read a list of fixtures from a file?

I would like to pytest (via TestInfra) to assert the presence of packages on a host. I have a list of packages that should be there in a text file, which I can read and put in an array. I would...

Converting molecule name to SMILES?

I was just wondering, is there any way to convert IUPAC or common molecular names to SMILES? I want to do this without having to manually convert every single one utilizing online systems. Any...

python : tkinter treeview colors are not updating

This is my first post, please excuse me if I made mistake in the format, I will gladly change it if required. I'm creating an interface for scientific datas analysis using Tkinter. For a list of...

How to convert Smiles to Fingerprint with rdkit?

I have to convert a list of Smiles in a list of Fingerprints with rdkit. But I don't know how. I searched for solutions in the internet, but there is actually no Example working... Does anyone...

How to generate a graph from a SMILES molecule representation?

I have a dataset of molecules represented with SMILES strings. I was trying to represent this as graphs. Is there a way to do so? For instance, let's say I have string...

Unable to install ansible-galaxy roles from within a Jenksinfile to build and deploy infrastructure with (git)scm referenced roles

I have the following jenkinsfile pipeline { agent { dockerfile { args "-u root -v /var/run/docker.sock:/var/run/docker.sock" } } environment { ...

Test dependant Ansible roles with molecule and gilt, zero documentation

Currently building multiple Ansible roles for my company some of which will be marked as dependant on one another(think like a deploy [application] containers role thats dependant on the role...

Atomic Design, is a modal an organism?

There is a tile (molecule) with an image, some text and a play button. When the button is triggered a video should be shown via a modal. I think a modal should be an organism, but i want the modal...

How to display text with subscripts or superscripts in the Title Bar?

I would like to be able to show subscripted text in the Title Bar of a Windows Form or WPF Window. The reason for this is simple. Our project team has written a molecule editor: Instead of just...

TZ variable passed to jest not taking effect with Jenkins docker slaves

I am using docker slaves for build via Docker plugin for jenkins. I have no issues with my builds but however in one repository we're passing TZ variable to jest as shown below for a particular...

Pandas dataframe select rows where a list-column contains a specific set of elements

This is a follow-up to the following post: https://stackoverflow.com/questions/53342715/pandas-dataframe-select-rows-where-a-list-column-contains-any-of-a-list-of-strin I want to be able to select...

from dgl.data.chem import mol_to_bigraph, smiles_to_bigraph does not work

I am working on graph classification problem based on molecules. My data is SMILES, and I want to convert it into graph and build model using DGL package. I have installed the dgl package by using...

Calculate descriptors with RDkit

I am trying to calculate all the descriptors (both 2D/3D) for a list of molecules with RDkit in python. When I run: MolecularDescriptorCalculator.CalcDescriptors(mol, simplelist) it...

How to find keywords in a text file using python's sklearn

I want to create a way to optimize my resume using a python script. To do this, I am trying to find keywords used in the job listing that I can add to my resume to make it stand out when it is run...

Cant install package via ansible snap module

I just want to do a simple task via ansible using molecule. The following code below: - name: Continue to install applications snap: name: "{{ item }}" classic: true loop: -...

How do I get molecular structural information from SMILES

My question is: is there any algorithm that can convert a SMILES structure into a topological fingerprint? For example if glycerol is the input the answer would be 3 x -OH , 2x -CH2 and 1x...

Parsing a genbank file format with biopython's SeqIO

I'm trying to parse a protein genbank file format, Here's an example file (example.protein.gpff) LOCUS NP_001346895 208 aa linear PRI 20-JAN-2018 DEFINITION ...

AttributeError: 'Dataset' object has no attribute 'value'

I got this error when using a package to read hdf5 files: dataset.value Error: Traceback (most recent call last): File "train.py", line 163, in <module> train(0, False, args.gpu_list,...

How can I define local dependencies between roles in a collection in ansible?

I have a question about dependencies between roles in a collection. In general, I am concerned if it is possible to define dependencies between roles in a collection - local dependencies like a...

Atomic Design with Redux: Where to place components using the store?

I have a molecule that uses the state to control the visibility of another UI element using the store. Is it suitable to use the store from any where when applying Atomic Design or should there be...

Run function immidiately after REST-API is hit

There are these two applications: WordPress-site with REST-API. Let's call this Brandon. Another system, using the REST-API. Let's call this Jeremy. I know about the WordPress Stack Exchange,...

Rdkit Mol object getProp("_Name") is empty. How to get ID?

So I have been looking through the documentation but couldn't find anything relevant. In the SDF file, Chembl name is empty but I do have entry on the chembl ID which I want. Here' 15 12 2 0 ...