Good evening,
I am trying to convert a standard InChI string to a non-standard InChI string with fixed-hydrogen-layer:
Example:
Standard inChI for Uracil:
InChI=1S/C4H4N2O2/c7-3-1-2-5-4(8)6-3/h1-2H,(H2,5,6,7,8)
Desired outcome:
InChI=1/C4H4N2O2/c7-3-1-2-5-4(8)6-3/h1-2H,(H2,5,6,7,8)/f/h5-6H
InChIkey for Uracil: ISAKRJDGNUQOIC-UHFFFAOYSA-N
My question is if this is at all theoretically possible without further information and if not, are there other ways to achieve this goal, e.g. using an existing database?
The ultimate goal is to convert the InChI string with hydrogen layer into a mol file to be able to map chromatogram peaks against it, so I installed OpenBabel which can do the trick, but it can not solve the aforementioned conversion between the InChIs.
I already found the cactus website which allows to convert from InChIkey (which I can generate from the standard InChI that I have) to the desired non-standard InChI (with hydrogen layer) via inserting the InChIkey into the url like so:
http://cactus.nci.nih.gov/chemical/structure/ISAKRJDGNUQOIC-UHFFFAOYSA-N/inchi.
The problem here is that it returns multiple correct non-standard InChI strings (with fixed hydrogen layer). One of them is the standard for uracil that I am after but I don't see a way to figure out how to pick the correct one automatically. As you can imagine I want to run this in an automated fashion for hundreds of conversions.
I appreciate your help.
Loddi
Related
When using the Windows-Machine-Learning library, the input and output to the onnx models is often either TensorFloat or ImageFeatureValue format.
My question: What is the difference between these? It seems like I am able to change the form of the input in the automatically created model.cs file after onnx import (for body pose detection) from TensorFloat to ImageFeatureValue and the code still runs. This makes it e.g. easier to work with videoframes, since I can then create my input via ImageFeatureValue.CreateFromVideoFrame(frame).
Is there a reason why this might lead to problems and what are the differences between these when using videoframes as input, I don't see it from the documentation? Or why does the model.cs script create a TensorFloat instead of an ImageFeatureValue in the first place anyway if the input is a videoframe?
Found the answer here.
If Windows ML does not support your model's color format or pixel range, then you can implement conversions and tensorization. You'll create an NCHW four-dimensional tensor for 32-bit floats for your input value. See the Custom Tensorization Sample for an example of how to do this.
I already did a lot of research and realized that clear information about "How to generate PDF/A-1a" or "...convert to PDF/A-1a" is really rare. I found some information to convert to PDF/A-1a via GhostScript, but I didn't make it to get it working. So, maybe there are some necessary conditions for the data missing in the first place. Conditions like propper metadata of the PDF, structured data for readability by a screen reader, alternative text for pictures, and a declaration of the given language of the text. I need a proper working GhostScript command with the corresponding gs version and the mandatory file conditions to generate or even convert to PDF/A-1a. PDF/A-1b means nothing to me because I'm already able to convert to that.
Thanks for any help.
I am new to this site and I would like to get some inputs regarding parsing STDF files. Generally speaking, I am trying to parse a STDF file to gather only the results (numbers) and not the rest of the line. If I am able to achieve this, I would then like to compare all the numbers together through a bubble sort or insertion sort and see if any numbers are equal to each other. I am capable of doing this in C/C++ and Java but I have no experience parsing documents using Scripts.
Could anyone push me in the right direction? What should I be reading to learn my way around this?
Are you already using an STDF library?
You did not mention one, so I assume not.
You should find a library you are comfortable with (the list changes over time, but you can find some by Googling or looking at the STDF page on Wikipedia) rather than attempting to parse STDF yourself, unless you have a good reason to recreate the STDF parser wheel.
An STDF file contains many tests. It generally does not make sense to compare the results for different tests, so I assume you are looking for matching values within the set of results for each test.
I would use your chosen STDF parser to read the value of each test for each part. Keep a set of the results for each test. As you read each new result, check the set to see if already exists. If it does, you have found the case you were looking for, otherwise add the result to the set.
I have a legacy VB application that still has some life in it, and I am wanting to translate it to another language.
I plan to write a Ruby script, possibly utilising a parser, to extract all strings from the three million lines of source, replace them with constants, and move them to a string resource file that can be used to provide translations.
Is anyone aware of a script/library that could be used to intelligently extract the strings?
I'm not aware of any existing off-the-shelf tool that you could use. We created a tool like this at my work and it worked well. The FRM file format is quite simple (although only briefly documented). We wrote a tool that (1) extracted all strings from control definitions and (2) generated the code to reload them at runtime during Form_Load.
Is it possible to update an rdf file dynamically from user generated input through a webform? The exact scenario would beskos concept definitions being created and updated through user input to html forms.
I was considering xpath but is there a better / generally accepted / best practice way of doing this kind of thing?
For this type of thing there are IMO two approaches:
1 - Using Named Graphs in a Triple Store
Rather than editing an actual fixed file you use a Graph which is stored as a named graph in a Triple Store that supports triple level updates (i.e. you can change individual Triples in a Graph). For example you could use a store like Virtuoso or a Jena based store (Jena SDB/TDB) to do this, basically any store that supports the SPARUL language or has it's own equivalent.
2 - Using a fixed RDF file and altering it
From your mention of XPath I assume that you are intending to store your file as RDF/XML. While XPath would potentially work for this it's going to be dependent on the exact serialization of your file and may get very complex. If your app is going to allow users to submit and edit their own files then they'll be no guarantees over how the RDF has been serialized into RDF/XML so your XPath expressions might not work. If you control all the serialization and processing of the RDF/XML then you can keep it in a format that your XPath will work on.
From my point of view the simplest way to do this approach is to load the file into memory using an appropriate RDF library, manipulate it in memory and then persist the whole thing back to disk when the user is done (or at regular intervals or whatever is appropriate to your application)