cfiles | Analysing trajectories with chemfiles

by chemfiles C++ Version: Current License: Non-SPDX

X-Ray Key Features Code Snippets Community Discussions(10)Vulnerabilities Install Support

kandi X-RAY | cfiles Summary

cfiles is a C++ library. cfiles has no bugs, it has no vulnerabilities and it has low support. However cfiles has a Non-SPDX License. You can download it from GitHub.

cfiles is a collection of post-processing algorithms for molecular or quantum chemical simulations. It offer both data managing capacities and analysis of simulation output. cfiles is implemented using the chemfiles library for reading and writing trajectory data. You can ask questions about cfiles in the chat, or in github issues.

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Security

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Support

cfiles has a low active ecosystem.

It has 8 star(s) with 3 fork(s). There are 3 watchers for this library.

It had no major release in the last 6 months.

There are 10 open issues and 16 have been closed. On average issues are closed in 97 days. There are no pull requests.

It has a neutral sentiment in the developer community.

The latest version of cfiles is current.

Quality

cfiles has no bugs reported.

Security

cfiles has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.

License

cfiles has a Non-SPDX License.

Non-SPDX licenses can be open source with a non SPDX compliant license, or non open source licenses, and you need to review them closely before use.

Reuse

cfiles releases are not available. You will need to build from source code and install.

Installation instructions, examples and code snippets are available.

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cfiles Key Features

No Key Features are available at this moment for cfiles.

cfiles Examples and Code Snippets

No Code Snippets are available at this moment for cfiles.

Community Discussions

Trending Discussions on cfiles

Optimizing GROUP BY of jsonb array values in Postgres

make - Get path to file without filename

Replacing iterative INSERT from SELECT with recursion or functions to traverse paths in Postgres

Improving performance of ORDER BY on jsonb cross join with inner join group by

Aggregating distinct values from JSONB arrays combined with SQL group by

Improving performance of Postgres jsonb queries combined with relational queries

Java FileSystemWatcher not catch file created event until all files be written while write file with high frequency

esp-idf : I can't include mdebtls directory in a component

Read in files from list of lists

How to get Makefile to put obj files in separate directory?

QUESTION

Optimizing GROUP BY of jsonb array values in Postgres

Asked 2021-Mar-19 at 00:20

Updated for better hardware

I have the following simplified schema in Postgres12 whereby a dataset has many cfiles and each cfile has property_values stored as jsonb:

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ANSWER

Answered 2021-Mar-18 at 21:46

I think you will have a tough time doing much better with the current schema. Could you normalize the data do you have a table with one row per (tid,"Sample Names",id) combo, or perhaps just one row per unique ("Sample Names") or per (tid,"Sample Names")?

Although I don't think there is a generic answer to "As well as filtering by columns from the other joined tables". An answer would depend on how selective the filter is and whether it is indexable.

Source https://stackoverflow.com/questions/66694811

QUESTION

make - Get path to file without filename

Asked 2021-Feb-09 at 20:53

I have in my Makefile a rule to get all src files:

...

ANSWER

Answered 2021-Feb-09 at 20:50

dirname is your friend. (dont't forget man dirname)

Source https://stackoverflow.com/questions/66126871

QUESTION

Replacing iterative INSERT from SELECT with recursion or functions to traverse paths in Postgres

Asked 2021-Feb-04 at 02:10

In my schema a dataset has many cfiles and a cfile has one dataset. Each cfile also has a number of dynamic property values stored in jsonb.

Fiddle here

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ANSWER

Answered 2021-Feb-04 at 02:10

I'll load up the output of "find /lib /bin /etc" which is about 27k lines into a table...

Source https://stackoverflow.com/questions/66034969

QUESTION

Improving performance of ORDER BY on jsonb cross join with inner join group by

Asked 2021-Jan-24 at 13:25

I have two tables in PostgreSQL 12: a dataset has many cfiles and a cfile has one dataset

...

ANSWER

Answered 2021-Jan-24 at 03:38

DISTINCT in aggregate functions is not PostgreSQL's strong side.

Perhaps this will perform better:

Source https://stackoverflow.com/questions/65865741

QUESTION

Aggregating distinct values from JSONB arrays combined with SQL group by

Asked 2021-Jan-22 at 19:15

I am trying to aggregate distinct values from JSONB arrays in a SQL GROUP BY statement:

One dataset has many cfiles and a cfile only ever has one dataset

...

ANSWER

Answered 2021-Jan-22 at 18:55

jsonb_array_elements is a set returning function and should be used in the FROM clause. Using it in the SELECT list makes things unnecessarily complicated:

Source https://stackoverflow.com/questions/65850946

QUESTION

Improving performance of Postgres jsonb queries combined with relational queries

Asked 2021-Jan-21 at 17:39

I have a single SELECT that queries both regular postgres tables and a jsonb column. When I SELECT the entire jsonb column, the query is fast (574 ms). However when I instead select a top-level path of the same jsonb column, the query slows down by 6x (3241ms). My final query needs to access the string array values from 4 of these top-level jsonb paths, which slows the query right down to 5 seconds.

I have about 50K records in the cfiles table and the jsonb column cfiles.property_values is structured like this:

...

ANSWER

Answered 2021-Jan-21 at 15:50

Your slow query is deTOASTing the large jsonb data for all 44255 rows, and then carrying the parsed-out values through the sort to pick out the top 20 rows. (I don't know why it does the deTOASTing eagerly like that). So 44235 JSONB were deTOASTed just to be thrown away.

Your fast query is (presumably) returning TOAST pointers from the hash join, sorting the rows with those small pointers, and then deTOASTing only the 20 survivors. In the case of EXPLAIN ANALYZE, it doesn't even deTOAST the survivors, it just throws the pointers away.

That is the "why", as for what to do about it, if you truly can't alter any of the query below the very top part, I doubt there is anything you can do about it on the server side.

If you can modify the query more substantially, then you can improve the run time with a CTE. Have the CTE select the entire jsonb, and then the select on the CTE pulls the value out of it.

Source https://stackoverflow.com/questions/65820380

QUESTION

Java FileSystemWatcher not catch file created event until all files be written while write file with high frequency

Asked 2020-Dec-16 at 08:58

I'm trying to watching file created event on Directory using FileSystemWatcher of Spring boot devtools filewatch package It's work fine when catch created event when file be written. But I facing a problem when write file with high frequency. FileSystemWatcher will waiting until all files be written then fire created event for each file.

So, I want FileSystemWatcher will fire created event when each file written, not wait to all file be written then fire events. How can I do that. Here is my code:

Watching Configuration

...

ANSWER

Answered 2020-Dec-16 at 08:58

I've found the root cause by the folder which store file be locked by writer process. With high frequency, it will be locked until writer complete. So that, I've change my code to another way. I use common.io package to watching folder and just lock file which being write not lock folder. So that, my writer app and listener app can work parallel

Source https://stackoverflow.com/questions/65228392

QUESTION

esp-idf : I can't include mdebtls directory in a component

Asked 2020-Sep-27 at 07:39

On esp32, using esp-idf, I built a module called webSocket.c/.h . it includes

...

ANSWER

Answered 2020-Sep-27 at 07:39

Added

Source https://stackoverflow.com/questions/64079177

QUESTION

Read in files from list of lists

Asked 2020-Feb-06 at 05:37

I have a bunch of files for which I created lists for such as below:

...

ANSWER

Answered 2020-Feb-06 at 05:37

fread (or any other way to read data) reads only one file at a time. You can try.

Source https://stackoverflow.com/questions/60088259

QUESTION

How to get Makefile to put obj files in separate directory?

Asked 2019-Dec-04 at 16:09

If my Makefile looks like this:

...

ANSWER

Answered 2019-Dec-04 at 16:09

When $(OBJ_DIR)/%.o: $(SRC_DIR)/%.c is resolved, it expand to

Source https://stackoverflow.com/questions/59180047

Community Discussions, Code Snippets contain sources that include Stack Exchange Network

Vulnerabilities

No vulnerabilities reported

Install cfiles

To build it you can run. You can then copy the cfiles executable to some place in your path. Note: When using the C++ standard library from GCC 4.8, cfiles rely on the boost_regex library, which can be installed using your favorite package manager.

Support

You are welcome to contribute to cfiles, whatever your skill level. You can help with new analysis algorithms, improving existing ones, adding or improving documentation, etc. If you plan adding new code, please open an issue about it for discussion. Don't forget to run the tests when changing the code; and to add new tests when adding new algorithms. The tests are Python scripts in the tests directory, checking the output of the algorithms. Here is a short check list to contribute to cfiles. If there is anything you don't understand, or if you have any question, please ask! You can reach me on github issues, by email, or in the chat.

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