COCONUT | read molecules from various file types
kandi X-RAY | COCONUT Summary
kandi X-RAY | COCONUT Summary
This compiles is designed to read molecules from various file types (SMILES, SDF, MOL, csv, tsv), check them for errors and connectivity, compute a large number of molecular parameters and properties, and store everything in a Mongo database. Unless you want to modify the code, we recomment using the compiled JAR that can be downloaded here:
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Top functions reviewed by kandi - BETA
- Runs the analysis
- Sets the UniqueProductDescriptors
- Called when the process is finished
- This is the main implementation of this implementation
- Runs the NPL fragments
- Splits a list of ether bracket atoms into a list of aromatic bonds
- Removes circular sugar containers from a molecule
- Extract the additional features for synthetic molecules
- Creates an AtomContainer for a synthetic molecule
- The main method
- Reads the SMILES file
- Generate a list of unique smiles
- Returns true if the given molecule has at least one sugar
- Partitions the provided molecule to unconnected fragments
- Generate unique smiles
- Gets the source
- Returns a string representation of this taxonomy
- Get all tax ranks
- Selects the largest fragment of a molecule
- Edit the given atom
- Start the downloader
- Checks to see if the provided molecule contains a sugar molecule
- Generates the pseudo SMILES code of a molecule
- Read InChi file
- Reads a SMILES file
- Read SMILES files from a file
COCONUT Key Features
COCONUT Examples and Code Snippets
Community Discussions
Trending Discussions on COCONUT
QUESTION
This is not a Duplicate question, I spent 3 days searching here and there is no other question similar to mine!
This javascript generates random words only when called from one single div, or the first one when trying different DOM Methods to get Elements.
I've tried several options and combinations with getElementsBy ID, Tag, Name, Class, and CSS Selector.
However after several days searching and testing, I can't make it work in more than one div.
I need to use the same array as the only source for all my 36 divs, to generate random words from an onClick event on each of them.
I'm open to edit it, or completely change it.
This is what I have currently working for the first div using getElementsByClassName which I suppose should be the correct way as I need to call this script from several elements, not just one:
...ANSWER
Answered 2021-Jun-13 at 21:11You can create a loop to add the click handler to all fruits
QUESTION
Given a list of lists (e.g. the input_ls
below): Do you know of a function which gives me the minimal list of lists (as a dictionary), with which I can construct the initial input_ls
by "adding up" those lists (e.g. the output_dict
below)?
ANSWER
Answered 2021-May-28 at 15:15I think the function len() can help you.
The len() function returns the number of items in an object.
Exemple :
QUESTION
I am working on a project in which I need to post a new Course to my API. I tested this with POSTMAN and API works just fine, however when I try to post data using react fetch data is corrupted. While sending single strings like dishName: "pizza" works just fine and is shown in database I cannot manage to send an array of objects. I tried to do it in many ways like:
...ANSWER
Answered 2021-May-27 at 21:44You are setting the ingredients
state as a string, so you are basically 'stringify' a string which will result in JSON SyntaxError
. If you want to send an array that way you must specify the array bracket [
and ]
in order to make it a valid array.
To solve it just change:
QUESTION
I am having a problem with having it printing out a response of each item in my list, but if I get rid of the loop responsible, I can't check a users input, for example, if they put 'almond', it will say it doesn't know, because in my list, it says 'almonds'.
That is why I do a loop through each element, so it will search for the word in the element, but the loop prints that it can't find the answer a few times (unnecessarily!) and then the answer.
I hope this is understandable, and here is my code:
...ANSWER
Answered 2021-May-23 at 14:32you need to loop through the two lists seperately:
QUESTION
Everything that I push into arr1
should have been removed from the mapping of arr2
, but instead the new pushed value is returned. Why is that?
ANSWER
Answered 2021-May-23 at 17:25- Do not keep the JSX elements in state (arr1). state variable to just have the data only.
- setArr1(...arr1, t.currentTarget.value) --> Not setting as array here. Update to setArr1([...arr1, t.currentTarget.value])
Try the snippet.
QUESTION
I am trying to extract set of keywords such as ['lemon', 'apple', 'coconut'] etc. from the paths such as "\var\prj\lemon_123\xyz", "\var\prj\123_apple\coconut", "\var\prj\lemonade\coconutapple", "\var\prj\apple\lemon"
The expected output is little complex:
Paths MatchedKeywords "/var/prj/lemon_123/xyz" lemon "/var/prj/123_apple/coconut" apple, coconut "/var/prj/lemonade/coconutapple" "/var/prj/apple/lemon" apple, lemonkeep in mind that the third row does not have the exact word which start with /, \s, \d or _ thats why there is no match. The regular expression is kind of like this: \s\d_/[\s\d_/]. I tried using:
df['Paths'].str.findall(r'[^\s\d_/]lemon|apple|coconut[\s\d_/$]', flags=re.IGNORECASE)
But it is still showing 'lemon' and 'coconut' in the third row.
Thank you in advance.
...ANSWER
Answered 2021-May-21 at 18:41Your regex is not correct for what you're looking to match, which is easy to see with visualization tools like https://regexper.com/ (no affiliation; just grabbed the top Google result).
You have: [^\s\d_/]lemon|apple|coconut[\s\d_/$]
but likely want something like: [\s\d_/](lemon|apple|coconut)[\s\d_/]
QUESTION
So I had a task to do a shop class, products class a basket class bla bla bla, I did all of this, tested, everything is working fine and that has nothing to do with the problem. Now what I had to do is create discounts and a chain of responsibility, like let's say I create 3 discounts and it goes through pointers and checks which one is suitable. So I did it, it does work, when I was debugging I checked, that it stops on the discount it needs to, returns me the price with the discount applied BUT THEN it somehow is going back by pointers and returning again what I don't need. I will make this more clear after I show the code and I will provide an example. So this is my Discount.h
which holds a pointer to the next Discount and the main virtual countDiscount();
function that plays the role in all of this.
ANSWER
Answered 2021-May-19 at 18:39int FixatedDiscount::countDiscount(Basket b) {
int totalPrice = b.countPrice(); //this method just counts the value of the basket which for our example is 120
if (totalPrice >= limit) {
totalPrice -= discount;
std::cout << "Handled when limit is " << limit << " and discount is: " << discount << " returning total price: " << totalPrice << std::endl;
}
else if (next != NULL) {
next->countDiscount(b);
}
else {
std::cout << "I am the last handler" << std::endl;
}
return totalPrice;
}
QUESTION
I want to separate this list into two different list. The pattern that I saw the fruit is the number 1.
always followed by fruit, while animal placed between whitespace except the last one.
ANSWER
Answered 2021-May-04 at 07:59text = ['1.banana dog 2.apple cat 3.grape tiger 4.orange snake']
textlist = text[0].split()
fruitlist = []
animallist = []
for word in textlist:
if "." in word:
fruitlist.append(word.split(".")[1])
else:
animallist.append(word)
fruit = " ".join(fruitlist)
animal= " ".join(animallist)
QUESTION
So basically I have an array of items : [ apple, banana , peach , pear , coconut , orange ... and so on ]
I want to display them in an embed but since embed has a character limit , I want to display only 10 elements per page and whenever the user reacts with arrow emojis - it will take them to the other page- so basically paginating an embed. But no matter how many ways I try , I cannot seem to do that- Help is very appreciated!
P.S - I deleted my codes out of frustration so I can't provide a code- well my code wouldn't be any help anyways-
...ANSWER
Answered 2021-May-01 at 02:57I would suggest the discord.js-pagination module for this. It allows you to provide an array of embeds and then it handles all the difficult stuff.
QUESTION
Having a difficult time describing this which is probably why I'm not certain what function/what I'm looking for. Would appreciate someone describing what this function is called.
Basically, I have about a dozen .csv files, each with lists of a few hundred genes each. None of the lists includes all gene names.
What I'm looking to do, is to merge all those lists together and get a comprehensive list of all genes with an indication of which files said genes show up in. I don't need the values, just 1s and 0s to indicate if those names show up in said file is plenty.
I can already tell this may not make sense, so this analogy may help:
Let's say I have three files, Fruit A, Fruit B, and Fruit C. Fruit A has 2 apples, 3 bananas, and 1 orange. Fruit B has 1 apple and 1 coconut. Fruit C has 2 oranges and a lime. I want to merge it and produce a file that looks like this:
FRUIT NAME Fruit A Fruit B Fruit C Apple 1 1 0 Banana 1 0 0 Orange 1 0 1 Coconut 0 1 0 Lime 0 0 1Any advice would be greatly appreciated.
...ANSWER
Answered 2021-Apr-27 at 05:03- first convert all three files (.csv) into individual vectors, as you have stated that these are lists only.
- then take unique elements out of these lists.
- use
%in%
operator to generate your individual file columns
Community Discussions, Code Snippets contain sources that include Stack Exchange Network
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No vulnerabilities reported
Install COCONUT
You can use COCONUT like any standard Java library. Please include the the jar files in your classpath. You can also use any IDE and you can run and debug the COCONUT component as you would do with any other Java program. Best practice is to use a build tool that supports dependency management such as Maven or Gradle. For Maven installation, please refer maven.apache.org. For Gradle installation, please refer gradle.org .
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