Let's say I have a text file that looks like this:
<number> <name> <type> <inputs...>
1 XOR1 XOR A B
2 SUM XOR 1 C
What would be the best approach to generate the truth table for this circuit?
That depends on what you have available, and how big your file is.
Perl is optimized for reading files and generating simple text output. It doesn't have a library of boolean operators, but they're easy enough to write. I'd use that if I just wanted text-in, text-out.
If I wanted to display the data online AND generate a results file, I'd use PHP to read the data and write the table to a CSV file that could either be opened in Excel, or posted online in an HTML table.
If your data is in a REALLY BIG data file, I'd use SQL.
If your data is in a really huge file that you want to be accessible to authorized users online, and you want THEM to be able to create truth tables, I'd use Oracle's APEX to create an easy interface for them to build their own truth tables and play around with the data without altering it.
If you're in an electrical engineering environment, use the tools designed for your problem -- Verilog or similar.
Whatcha got? Whatcha wanna do with it?
-- Ada
I prefer using C#. I already have the code to 'parse' the input
text file. I just don't know where to start in terms of
actually 'simulating' it. The output can simply be a text file
with inputs and output values – Don 12 mins ago
How many inputs and how many outputs in the circuit you want to simulate?
The size of the simulation determines how it can most easily be run. If the circuit is small(ish), you can enter the inputs and circuit values into vector arrays, then cross them to get the output matrix.
Matlab is ideal for this, as it was written for processing arrays.
Again: Whatcha got, and whatcha wanna do with it?
-- Ada
Related
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 -CH.
I'm trying to build a python script that can predict the density of a mixture using an artificial neural network. As an input I want to have the structure/fingerprint of my molecules starting from the SMILES structure.
I'm already familiar with -rdkit and the morganfingerprint but that is not what i'm looking for. I'm also aware that I can use the 'matching substructure' search in rdkit, but then I would have to define all the different subgroups. Is there any more convenient/shorter way?
For most of the structures, there's no existing option to find the fragments. However, there's a module in rdkit that can provide you the number of fragments especially when it's a function group. Check it out here. As an example, let's say you want to find the number of aliphatic -OH groups in your molecule. You can simply call the following function to do that
from rdkit.Chem.Fragments import fr_Al_OH
fr_Al_OH(mol)
or the following would return the number of aromatic -OH groups:
from rdkit.Chem.Fragments import fr_Ar_OH
fr_Ar_OH(mol)
Similarly, there are 83 more functions available. Some of them would be useful for your task. For the ones, you don't get the pre-written function, you can always go to the source code of these rdkit modules, figure out how they did it, and then implement them for your features. But as you already mentioned, the way would be to define a SMARTS string and then fragment matching. The fragment matching module can be found here.
If you want to predict densities of pure components before predicting the mixtures I recommend the following paper:
https://pubs.acs.org/doi/abs/10.1021/acs.iecr.6b03809
You can use the fragments specified by rdkit as mnis proposes. Or you could specify the groups as SMARTS patterns and look for them yourself using GetSubstructMatches as you proposed yourself.
Dissecting a molecule into specific groups is not as straightforward as it might appear in the first place. You could also use an algorithm I published a while ago:
https://jcheminf.biomedcentral.com/articles/10.1186/s13321-019-0382-3
It includes a list of SMARTS for the UNIFAC model, but you could also use them for other things, like density prediction.
I have a table that contains text fields. In those fields I store text. There are around 20 to 50 sentences in each field depending on the row. I am making an auto-complete HTML object with HTML and PHP, and I would like to start typing the beginning of a word and that the database return sentences containing those words (Like Microsoft office 2007/2010 navigation pane).
I need mysql to return those words or sentences as a separate result, so i can manipulate them further.
Example:
--------------------------------------------------------------------
| id | title |content |
--------------------------------------------------------------------
1 | test 1 | PHP is a very nice language and has nice features.
2 | test 2 | Spain is a nice country to visit and has nice language.
3 | test 3 | Perl isn\'t as nice a language as PHP.
I need mysql query to return following as different result:
1,"nice language"
1,"nice features"
2,"nice country"
2,"nice langugage"
3,"nicea a language"
Here is my sql query:
SELECT id, SUBSTR(content,POSITION('nice' IN content),50)
FROM entries
MATCH (title,entry) AGAINST ('nice' WITH QUERY EXPANSION)
New Answer
OP is actually asking nothing to do with php and javascript - his question concerns doing string manipulation directly within MySQL.
String manipulation isn't really the main focus of a DBMS. When dealing with "words" in a fluid text sense, there's a lot of logic required to determine where the next word boundary is, and you don't want your database doing this really. Plus, any queries written to do this will probably be incredibly difficult to read.
It depends exactly what you are doing, but it's quite likely that a DB only approach will be slower because there will be more function calls: SQL functions are pretty limited.
And for re-usability and best practice, what if you wanted to change your database in the future to say MongoDB? You'd need to re-write the whole damned awkward query.
No, my suggestion would be to pull the whole value using standard MySQL into PHP, throw it into PCRE, very simple regex, job done. It's better to show what you're actually doing in your PHP code as it's more "intention revealing".
At least 33% of a developer's work is picking the right tool for the job. PHP is the right tool in this example.
Original Answer
You have included the tags php and javascript, so I'm guessing (although your question needs more clarification on this) that you obviously want this 'autocomplete' running client-side. So as a result, you have to get your data from server-side to client-side first.
Twitter Bootstrap has something really cool called Typeahead. This uses JavaScript to perform (what I think) you require: the example on that page shows how you can type a country and it'll auto-complete it for you. It looks like this:
How do you get this working? Include the required JavaScript file first, and then write your HTML.
Here's some from the source code of the bootstrap page so you can see how it works:
<input type="text" data-provide="typeahead" data-items="4" data-source='["Alabama","Alaska","Arizona","Arkansas","California"]'>
Can you see how the data-source attribute is the one that gives the typeahead the information you want? You want to connect to MySQL, grab your data, and shove these into the data-source array for the JavaScript to work with, as above.
So, on your page load, you connect to MySQL and you pull all the relevant strings you would like to be "auto-complete-able" from the Database. You then put these as new Data attributes for the typeahead, and that's pretty much it!
--
Edit: There's a fork of twitter bootstrap's typeahead that allows AJAX calls, so you could use this to perform the data retrieval asynchronously (if you can figure it out, I'd recommend this approach).
I am storing a series of events to a CSV file, each event type comes with a different set of data.
To illustrate, say I have two events (there will be many more):
Running, which has a data set containing speed and incline.
Sleeping, which has a data set containing snores.
There are two options to store this data in CSV records:
Option A
Storing each possible item of data in it's own field...
speed, incline, snores
therefore...
15mph, 20%, ,
, , 12
16mph, 20%, ,
14mph, 20%, ,
Option B
Storing each event in its own record...
event, value1...
therefore...
running, 15mph, 20%
sleeping, 12
running, 16mph, 20%
running, 14mph, 20%
Without a specific CSV specification, the consensus seems to be:
Each record "should" contain the same number of comma-separated fields.
Context
There are a number of events which each have a large & different set of data values.
CSV data is to be of use to other developers (I will/could/should/won't use either structure).
The 'other developers' to be toward the novice end of the spectrum and/or using resource limited systems. CSV is accessible.
The CSV format is being provided non-exclusively as feature not requirement. Although, if said application is providing a CSV file it should be provided in the correct manner from now on.
Question
Would it be valid – in this case - to go with Option B?
Thoughts
Option B maintains a level of human readability, which is an advantage say CSV is read by human not processor. Neither method is more complex to parse using a custom parser, but will Option B void the usefulness of a CSV format with other libraries, frameworks, applications et al. With Option A future changes/versions to the data set of an individual event may break the CSV structure (zombie , , to maintain forwards compatibility); whereas Option B will fail gracefully.
edit
This may be aimed at students and frameworks like OpenFrameworks, Plask, Proccessing et al. where CSV is easier to implement.
Any "other frameworks, libraries and applications" I've ever used all handle CSV parsing differently, so trying to conform to one or many of these standards might over-complicate your end result. My recommendation would be to keep it simple and use what works for your specific task. If human readbility is a requirement, then CSV in the form of Option B would work fine. Otherwise, you may want to consider JSON or XML.
As you say there is no "CSV Standard" with regard to contents. The real answer depend on what you are doing and why. You mention "other frameworks, libraries and applications". The one thing I've learnt is "Dont over engineer". i.e. Don't write reams of code today on the assumption that you will plug it into some other framework tomorrow.
I'd say option B is fine, unless you have specific requirements to use other apps etc.
< edit >
Having re-read your context, I'd probably pick one output format and use it, and forget about having multiple formats:
Having multiple output formats is a source of inconsistency (e.g. bug in one format but not another).
Having multiple formats means more code that needs to be
tested
documented
supported
< /edit >
Is there any reason you can't use XML? Yes, it's slightly more difficult to parse, at least for novices, but if so they probably need the practice. File size would be much greater, of course, but it's compressible.
In your experience, in Fortran 90, what is the best way to store large arrays in output files? Previously, I had been trying to write large arrays to ASCII text files. For example, I would do something like this (thanks to the recommendation at the bottom of the page In Fortran 90, what is a good way to write an array to a text file, row-wise?):
PROGRAM testing1
IMPLICIT NONE
INTEGER :: i, j, k
INTEGER, DIMENSION(4,10) :: a
k=1
DO i=1,4
DO j=1,10
a(i,j)=k
k=k+1
END DO
END DO
OPEN(UNIT=12, FILE="output.txt", ACTION="WRITE", STATUS="REPLACE")
DO i=1,4
DO j=1,10
WRITE(12, "(i2,x)", ADVANCE="NO") a(i,j)
END DO
WRITE(12, *)
END DO
CLOSE(UNIT=12)
END PROGRAM testing1
This works, but as pointed out by the topmost reply at In Fortran 90, what is a good way to write an array to a text file, row-wise?, writing large arrays to text files is very slow and creates files that are somewhat larger in size than is necessary. The poster there recommended instead writing to an unformatted Fortran binary, using something like:
PROGRAM testing2
IMPLICIT NONE
INTEGER :: i, j, k
INTEGER, DIMENSION(4,10) :: a
k=1
DO i=1,4
DO j=1,10
a(i,j)=k
k=k+1
END DO
END DO
OPEN(UNIT=13, FILE="output.dat", ACTION="WRITE", STATUS="REPLACE", &
FORM="UNFORMATTED")
WRITE(13) a
CLOSE(UNIT=13)
END PROGRAM testing2
This seems to work, and is indeed much faster and results in smaller file sizes, as promised by the reply here. However, what do I do if I would like to be able to later work with the data stored in Fortran binary (e.g., output.dat above) and analyze its contents? For example, what if I want to open the array stored in the binary in a program such as Microsoft Excel?
When I mentioned matlab in my previous post, the reply suggested that I open the binary as a hexadecimal file and figure out and extract the records from there. But, I am nervous that I am getting into deep water since I have no prior experience in hexadecimal sleuthing. When I asked on the matlab board (here: http://www.mathworks.com/matlabcentral/answers/12639-advice-on-reading-an-unformatted-fortran-binary-file-into-matlab) about reading Fortran files into matlab, the person there suggested that using Fortran stream might be easy. But is Fortran stream (i.e., using the directive ACCESS="STREAM" in the OPEN command) likely to be similar in time and file size to the ASCII text file that I created in my first example above?
Or, do you know if there is any other software that can automatically read Fortran binaries into some sort of human readable form? (Or, do you know of any good tutorials on either hexadecimal sleuthing or Fortran stream?)
Thank you very much for your time.
Stream is a choice independent of the choice of formatted / unformatted -- one is "access", the other "format" The default for Fortran I/O is record oriented access. The typical approach of a Fortran compiler for records (at least unformatted) to write a 4-byte record length before and after each record. (The "after" is to make reading backwards easier.) Using a hex edit you could verify these extra data items that I described and skip them in MatLab. But they are not part of the language standard and are not portable and are certainly not obvious in other languages. If you select stream and unformatted you will just get the raw sequence of bytes corresponding to your data items -- no extra data items to worry about in the other language! In my experience this output tends to be fairly easy to read in other languages (not tried in MatLab). If this is a small & simple project with portability of the files to other computers not an issue, I would probably use this approach (stream & unformatted) rather than a file format specification such as HDF5 or FITS. I'd write the array as write (13) a, as in your final example. Depending on the other language, you might have to transpose the dimensions. If this is a major and long-lived project with portability a concern, then a portable and standard file interface is worth considering.
I don't know whether any of these formats can be read from Excel. More research.... You might have to write a program to read the binary file of whatever format and output a file in a format that Excel understands.
(converting comment into an answer for posterity)
Are you specifically trying to get information into Matlab? If you are, I highly recommend HDF5. This is the portable binary format you have been looking for.
For converting a Fortran binary to HDF5, you're going to have to read in the original Fortran binary and then write out the same data to an HDF5 file. If you have the Fortran source, this should be pretty easy. Allocate your arrays, make sure you read the arrays in the same order as you wrote them and then write out your new shiny HDF5 file.
The HDF5 group has tutorials with examples in C and Fortran. There is likely an example very close to what you're trying to do. When you build HDF5, make sure to manually enable Fortran support. It is disabled by default.
%In MATLAB
fid=fopen('YOUR_FILE.direct','r'); %Fortran Direct ACCESS
frewind(fid);
tbb=ones(367,45203);
for i =1:367
temp=fread(fid,[45203],'single');
tbb(i,:)=temp;
end
fclose(fid)
For my C class I've written a simple statistics program -- it calculates max, min, mean, etc. Anyway, I've gotten the program successfully compiled, so all I need to do now is actually test it; the only problem is that I don't have anything to test with.
In my case, I need a list of doubles -- my program needs to accept between 2 and 1,000,000; Is there some resource online that can produce lists of otherwise meaningless data? I know Lorem Ipsum gets used for typesetting, and I'm wondering if there's something similar for various types of numerical data.
Or am I out of luck, and I'll have to just create my own junk data?
The problem with testing software is not the source of the data, but the test set. I mean, can you test an int sum(int a, int b) method by just inputting random numbers to it? No, you need to know what to expect. This is a test set: inputs and expected outputs.
What do you say when you discover that 548888876+99814465=643503341? How can you tell this is the real result?
More than finding random numbers to give your program, you must somehow know the results of your computation in advance in order to compare it.
There are a few ways to do it: what I suggest you is to pick a random number generator (amphetamachine +1) and use the data both on your code and on a program that you already know is good, ie. Matlab for your purposes. After computing your statistics with both, compare your results and see if you coded good or need to do some debug.
By the way, I volountarily altered the result of the above sum...
What about just generating a random double?
Random r = new Random();
for (int i = 0; i < 100000; i++)
{
double number = r.NextDouble();
//do something with the value
}
Since the data you need will depend on the program, there is no source of generic data that I know of.
If you are able to write that program, you should be able to write a script to generate dummy data for yourself.
Just use a loop to print out random numbers within the range your program can accept.
Generate a file with random bytes:
$ dd \
of=random-bytes \
if=/dev/urandom \
bs=1024 \
count=1024
http://www.generatedata.com/#generator
I've used that data generator before with some success. To be fair, it will usually involve copy/pasting the data it generates into some other format that you'll be able to read in.
You can generate your own data for this specific case quite easily though. Loop a random number of times with a terminating condition of 1,000,000. Generating random doubles within the range you expect. Feed that in and away you go.
Generating your own test data in this case is probably the best option.
You could take the first million digits of pi and chop them up into however many doubles you want.
The first few could be 3.14159, 2.65358, 9.79323, 8.46264, 3.38327, 9.50288, 4.19716, and 9.39937, for example.