I have a lammps_file.data and I need to convert it to Gromacs files (gro and top) to run my simulations.
Does anyone know how to do this?
Another choice is to convert from lammps to charmm files (psf and pdb). Once I get the charmm files I can just use Topotools to get the gromacs files I need.
Thanks
Indeed, NOW I am trying to do the same myself.
So far, you can use intermol , this should work fine to convert LAMMPS data files to Gromacs files. Once you install intermol, and you ceate a path to the intermol converter, you can use a command like:
python2.7 $conv/convert.py --lmp_in topology.data --gromacs -v
CHECK the format of your data file, I still having problemst to convert it.
If you wish to create the psf file,
you would need VMD (google it), then open the tcl terminal and write :
topo readlammpsdata topology.data full
animate write psf topology.psf
The 1st line is for loading yur LAMMPS data file, if you are in the folder where
that files is located
2nd convert the data to psf CHARMM
Also, you could try this. In this paper, they provide a tood to conver
CHARMM topologies to gromacs here. Thus, you convert to psf, then to gro top.
Related
I would like to convert this book Mastering the Lightning Network, which is freely available through GitHub to a pdf for personal use.
Unfortunately, I have only figured out how to "translate" single files using asciidoc or asciidoctor-pdf. The options for folders don't seem to work with the configuration of the repository.
There has to be an easy way to translate everything, including all files and pictures. Would be very thankful if somebody could help me out.
As far as I know it is not possible to convert a folder containing AsciiDoc files to a pdf, a simple script could do it but the problem would be in what order do you want your files to be converted?
The simplest solution for you is to create your own content.adoc file and use the include macro to select what files you want to convert and in what order, it could look something like this:
= Mastering the Lightning Network
include::01_introduction.asciidoc[]
include::02_getting_started.asciidoc[]
include::03_how_ln_works.asciidoc[]
include::04_node_client.asciidoc[]
include::05_node_operations.asciidoc[]
include::06_lightning_architecture.asciidoc[]
include::07_payment_channels.asciidoc[]
include::08_routing_htlcs.asciidoc[]
include::09_channel_operation.asciidoc[]
include::10_onion_routing.asciidoc[]
include::11_gossip_channel_graph.asciidoc[]
include::12_path_finding.asciidoc[]
include::13_wire_protocol.asciidoc[]
include::14_encrypted_transport.asciidoc[]
include::15_payment_requests.asciidoc[]
include::16_security_privacy_ln.asciidoc[]
include::17_conclusion.asciidoc[]
and you convert using asciidoctor-pdf content.adoc
You could try using imagemagick:
magick *.jpg out.pdf
I am trying to convert a scanned page to text using both pytesseract and tesseract command line on Ubuntu. The results are remarkably different (pytesseract performs way better than tesseract command line) and I am unable to understand why. I looked at the default values for the parameters and tried altering some of the parameter values in tesseract command line (like psm ) but I am unable to get the same result as pytesseract. Due to lack of proper documentation in pytesseract I am not able to figure out what default values for parameters are used.
Here is my pytesseract code
print(pytesseract.image_to_string(Image.open('test.tiff'))
Looking at the source code of pytesseract, it seems the image is always converted into a .bmp file.
Working with a .bmp file and psm of 6 at the command line with Tesseract gives same result as pytesseract.
Also, tesseract can work with uncompressed bmp files only. Hence, if ImageMagick is used to convert .pdf to .bmp, the following will work
convert -density 300 -quality 100 mypdf.pdf BMP3:mypdf.bmp
tesseract mypdf.bmp -psm 6 mypdf txt
In tessaract v5 3.0+
Pytessaract does not convert images to BMP. You can verify this by commenting out cleanup(f.name) in the save context manager, which is found within the source code /pytesseract/pytesseract.py. The filename of the temp file will also need to retrieved (Pytessaract was saving files within temp files directory of the user, ie. "[path-to-user]\AppData\Local[file-name]". I found what Pytesseract is actually doing is in the prepare function.
Basically, taking the temp file and using that same file with the tesseract command directly will yeild the same results
I want to open my 3D point cloud in MATLAB. But they are in .las files. How can I display them in MATLAB???
I heard about .ply file can open 3D point data on MATLAB. So I want to know how to convert las files to ply files.
There is a .las file reader for matlab here:
https://es.mathworks.com/matlabcentral/fileexchange/48073-lasdata
Once you have the data in matlab you can use these point cloud tools, which are part of the computer vision toolbox:
https://es.mathworks.com/help/vision/3-d-point-cloud-processing.html
If you want to embrace the open source force, I'm writing a Python (easy transition from matlab) library for point cloud processing:
https://github.com/daavoo/pyntcloud
You can use the free and open-source CloudCompare software.
On the command line:
CloudCompare -O file_to_convert.las -C_EXPORT_FMT PLY -SAVE_CLOUDS
Take care to the order of the options: it seems that -SAVE_CLOUDS must be at the end.
That will result in a binary-format PLY file in the same directory as the file to convert, named using the original filename and the date of export, like: file_to_convert_2019-07-18_13h32_06_751.ply
I found no way to specify the output file name (should you find one please comment below).
Should you want a more predictable name, add option -NO_TIMESTAMP before the option -SAVE_CLOUDS (but then you risk overwriting files so be careful).
More help (such as how to export in ASCII-format) in the documentation.
I timed this on powerful PC, it took 170s to convert a 2.7GB LAS file with 102M points (XYZ,intensity,time).
if you have LAStools installed, you can use las2txt to convert your *.las/*.laz files into *.xyz format which MeshLab can import natively as a point cloud, which may then be converted into a Mesh.
There are a multitude of caveats to that depending on the source of your data-set.
I need to convert my SFF file to PDF, then i need verify the document. i.e SFF file and converted file.
For that, I think to convert SFF file to image file and PDF file to image file.
Then comparing the both file using image processing.
To do this method:
Im searching for a program to convert SFF to BMP
Does anyone know such a program or has another idea how to do the job?
Thank you in advance...
Looks like you need reaConvertor. It　appears to be a matured tool you can rely on. There is an online version of the tool here
I think:
https://github.com/Sonderstorch/sfftools
will do what you need (convert sff -> tiff/jpeg/..) and then you can use imageMagic (for example) to go to PDF.
Clearly not a current well used image format, however if you have legacy.sff Structured Fax Format, they are similar (not exactly identical) to a Monochrome G4 format.
By far the simplest programmable method to convert is using IrfanView which can Read Modify and Resave as other formats in batches.
Out put can be any other modern image type including Mono.BMP, G4.fax or as PDF (with or without GhostScript)
I have a pretty big .kml file (it is the property of my company, and I can legally use it), what I want to import into an .osm file, downloaded from download.geofabrik.de. I can open this .osm map in softwares, for completely offline usage, such as Marble.
My question is: can I somehow merge this kml and osm file, so when I open the merged file in Marble, the routes described by the kml are also visible? So basically, I want to merge a.kml with b.osm, resulting in c.osm, what I can use offline.
Is it possible? If yes, can you direct me in the right direction?
Any help is appreciated, thanks!
Some notes:
I have tried GPSBabel, it indicates that it can convert .kml to .osm. It generates a 65MB .osm file from my 12MB .kml, but when I open it in Marble, it does not show any routes, so it looks like a dead end. :/
The weird thing is, GPSBabel produced an input what QGIS could open. I merged the two .osm file with osmosis, but the problem is, the output is invalid, nothing can open it.
JOSM does not open the original .osm file, what is 1GB of size.
ps: I have posted this on help.openstreetmap.org as well, but for now, nobody could help me, so I am trying to get some answer here, maybe... Sorry for the "repost", and thanks for the help! :)
What you want to do is honestly the wrong way to go about it, but still possible.
The first step is to use ogr2osm with the command-line flags --positive-id, --add-version, --add-timestampand with--id 3000000000` (or some other number larger than the largest node ID in the file.
You will then have a .osm file that Osmosis or Osmconvert can merge with another file, in this case your downloaded software. In the case of osmosis, osmosis --read-xml internal.osm --sort --read-xml extract.osm --sort --merge --write-xml combined.osm (untested)
A more common way would be to download the shapefiles for the region from geofabrik then use ogr2ogr and similar tools to combine them with the .kml file in the output format of your choice.
Keep in mind that if you distribute this "derivative database" you have created, it has to be licensed under the ODbL. This does not apply if you're distributing it internally only.