After digging a bit more in the VMD dtrplugin code, it seems that it support more than what is exported through the VMD API, and it would make sense to extract https://github.com/chemfiles/molfiles/blob/chemfiles/src/dtrplugin.hxx and https://github.com/chemfiles/molfiles/blob/chemfiles/src/dtrplugin.cxx and use them directly. In particular, they support reading only part of the trajectory, which helps reducing the amount of memory required.
The main thing we would need is at least one trajectory to use as test case, even better if we can get multiple files, to check all the different variation of the format: https://mdtraj.org/1.9.3/api/generated/mdtraj.load_dtr.html#mdtraj.load_dtr
Are you talking about the binaries from OpenSuse build, i.e. http://chemfiles.org/chemfiles/latest/installation.html#pre-compiled-binaries?
These are following the usual linux naming scheme:
chemfiles package only contains the shared library, chemfiles-static contains the static library & chemfiles-dev (Debian & friends) / chemfiles-devel (CentOS & friends) contains the headers.
I realize this is not very clear on the documentation, I'll update it (unless you want to send a PR for this! :smiley:)
Hi again, I'm trying to figure out how to use SubSelection as implemented in chemfiles/chemfiles#327 and can't quite figure it out. I basically have the use case that was requested (say, find all atoms within 5A of residue ALA). Can't I do two sub-selections "distance(resname == ALA, resname != ALA) < 5"? Thanks much
For your topology question, you can use this overload of
Trajectory::set_topology
Hi, sorry more questions. I'm reading MD coordinates from one file and topology from another using trj.set_topology and it works great. Now I want to add some new atomic properties and use them across multiple frames. It seems I can only access a topology and its atoms one frame at a time. One simple way to do that might be to define a topology from a file, add my properties and then use traj.set_topology(modifeid_topology) but there doesn't seem to be a way to just define a new topology from a file (topo = Topology(filename)), only if assigning it to a trajectory. Am I missing something? Thanks
I'm not quite sure what you mean =) So have one file (
file1) with coordinates and another one (file2) with a topology that you want to modify and then use for reading file1? The easiest way to do this would be something like // get topology from the first frame of the file
auto topology = Trajectory("file2").read().topology();
// modify topology
topology[12].set("foo", false);
// use the modified topology to read the other file
auto traj = Trajectory("file1");
traj.set_topology(topology);
// read, etc.
auto frame = traj.read();
Hey there, I'm a new user of chemfiles/cfiles and I have some questions:
in the hbonds analysis using cfiles:
in the hbonds analysis using cfiles:
- if the trajectory is in xyz format but the system is periodic, so if I used the cell argument, will it make any difference?
- if yes, does it wrap the atoms within the cell?
However, using the option do not modify the structure and change the positions of the atoms (i.e. wrap them). It just changes the way distances are computed
Hi I'm analyzing a trajectory that includes ~ 35000 water atoms. I'd like to select and remove them from a frame before doing further analysis, using code essentially like in the examples (C++ Tutorials). This works perfectly for any other residue I select, but for waters, most of them get removed, but not all. About 32750 get removed, so my hunch is there's some limit somewhere? Feels close to max(short int). Does this kind of behavior ring any bells? Any additional selections on the remaining atoms results in "/usr/include/chemfiles/external/optional.hpp:685: std::experimental::optional<T&>::operator->() const [with T = const chemfiles::Residue]::<lambda()>: Assertion `false && "ref"' failed." Thanks much for any helpful hints
If the failed assertion comes from chemfiles, that's a bug on our side! What is the selection you are using? It sounds like you are checking a residue property/residue name.
so my hunch is there's some limit somewhere?
The limit should be max size_t, i.e. 4294967295 for 32-bit systems & 18446744073709551615 on 64-bits
For example: how can we guarantee that threading is supported with all compilers (including MSVC), and if we can not how to ensure the code can still run single-threaded; which parallelisation strategy (tasks, split the input data in chunks, work stealing, ...) is the best one in this case; how can we ensure the abscence of data races (maybe add thread sanitizer in CI?); and a few others
For sure, it is a big change and this should be discussed carefully in order to choose the best option and the best design for the library as it will impact everything else. Maybe a good start would be the use of the mulithreading API in VMD (under BSD-3 license) as it is cross-platform and seems to offer the possibility to run single-threaded codes as well.
I would be a bit worried of importing code from VMD, since it is not the cleanest and easiest code to use. I don't know what the threading API they have looks like, but I've had bad experiences with the plugins. Also, VMD codebase is not under the BSD license, the plugins are under the UIUC license which looks a lot like the BSD one. The core of the code is under a non standard open source license: https://www.ks.uiuc.edu/Research/vmd/current/LICENSE.html
To get back at the problem at hand here, I think using a cell list for neighbors search in bond search would yield more gains for less pains that trying to use multithreading here. The current algorithm is O(N^2), a cell list would be O(N) (cf https://hoomd-blue.readthedocs.io/en/stable/nlist.html)
The header is mentionning BSD-3 license but I understand your concerns about using VMD code.
Actually, as they are doing both using a cell list algorithm and running it on multithreads I thought about having multithreading as well on chemfiles. But I understand that this is a complex implementation which will impact several aspects of the library's code. It should be discussed extensively before choosing an option. I will keep you updated about my version of the code with a cell list algorithm.
Hi, I had chemfiles 0.9.3 installed with dnf on centos 8 working fine. Then I had to remove and re-install for various reasons and now I just realized that the newly installed chemfiles is version 0.10 and that appears to be the only version available via packages. Also, the website http://chemfiles.org/chemfiles/latest now appears to refer to version "0.11-dev". I'm not sure what this means. Code that was working before with 0.9 now fails with a segfault using 0.10 version. I can install 0.9.3 from source but just wanted to check what's happening. Thanks
Sorry about that, we are in the process of releasing 0.10, and we did not intend for it to reach users yet. I guess you are getting chemfiles as a pre-compiled binary here: http://chemfiles.org/chemfiles/latest/installation.html#pre-compiled-binaries ? I though that using a pre-release tag (0.10.0-rc1) meant that users would not get the update yet.
You should be able to use dnf to get back to 0.9.3 with
dnf downgrade chemfiles-0.9.3 and potentially the same for chemfiles-devel.
Out of interest, and to prevent this from happening again, which language are you using chemfiles from? If it is C or C++, could you share the compiled binary with me, potentially in private? I would like for users to get a proper error when trying to use a different version of chemfiles instead of a segfault.
dnf info chemfiles
Last metadata expiration check: 1 day, 1:07:05 ago on Mon 23 Nov 2020 11:31:44 AM EST.
Available Packages
Name : chemfiles
Version : 0.10.0
Release : 3.1
Architecture : aarch64
Size : 1.1 M
Source : chemfiles-0.10.0-3.1.src.rpm
Repository : home_Luthaf
Summary : Modern library for chemistry file reading and writing
URL : http://chemfiles.com/
License : BSD
Description :
Name : chemfiles
Version : 0.10.0
Release : 3.1
Architecture : src
Size : 4.5 M
Source : None
Repository : home_Luthaf
Summary : Modern library for chemistry file reading and writing
URL : http://chemfiles.com/
License : BSD
Description :
Name : chemfiles
Version : 0.10.0
Release : 3.1
Architecture : x86_64
Size : 1.3 M
Source : chemfiles-0.10.0-3.1.src.rpm
Repository : home_Luthaf
Summary : Modern library for chemistry file reading and writing
URL : http://chemfiles.com/
License : BSD
Description :
Name : chemfiles
Version : 0.9.3
Release : 7.11
Architecture : ppc64le
Size : 1.2 M
Source : chemfiles-0.9.3-7.11.src.rpm
Repository : home_Luthaf
Summary : Modern library for chemistry file reading and writing
URL : http://chemfiles.com/
License : BSD
Description :
Can you update repository metadata in any way? Here it tells me that the most recent version should be 0.9.3: https://build.opensuse.org/package/binaries/home:Luthaf/chemfiles/CentOS_8
Or maybe uninstall 0.10 first?
That's one point I'd like to improve on chemfiles core before the 1.0 release. The structure proposed at the end of this post (https://khinsen.wordpress.com/2013/04/10/lessons-from-sixteen-years-of-molecular-simulation-in-python/) with AtomGroups looks interesting.
Hi everyone @/all :wave: ! The version 0.10 of chemfiles have just been finalized, and is now available in all package managers. See https://github.com/chemfiles/chemfiles/releases/tag/0.10.0 or the changelog for more details on what changed!
@jmintser_gitlab just a heads up, I could not find a way to provide both 0.9.3 and 0.10 on build.opensuse.org, so the repo will only contain the 0.10 version. If you want to stay on 0.9.3 for a while, you'll have to build it from sources. Sorry about the inconvenience!