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?
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
dnf downgrade chemfiles-0.9.3 and potentially the same for chemfiles-devel.
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 :
chemfiles::Trajectory trj("testfile.dcd");
auto testframe=trj.read();
cout << "Distance between oxygen " << 1 << " and " << 5 << "is" << testframe.distance(1,5) << "\n";
auto position = testframe.positions();
auto diff = position[5] - position[1];
cout << "Distance from positions" << diff.norm() << "\n";
The coordinates returned by Frame.positions() are in Angstroms, is that correct?
yes, that's the idea. We need to improve the doc on this front.
I am getting vastly different values from both methods. If I use the distance() method then I get 0.18 Angstroms, but from vector subtraction, I get 9.56 Angstroms (which matches the one I get from VMD).
Frame::distance uses periodic boundary condition, and you can check the distances being used by looking at frame.cell().lengths() and frame.cell().angles(). If you want to remove all periodic boundary conditions, you need to use an infinite cell, which you can set with frame.set_cell(UnitCell())
I'm working on a software that use Chemfiles to read and write molecule files.
I have an issue with the .mmcif parser, and more especially with the pdbx_struct_oper_list attribute that doesn't seems to be read.
For example with 6NCL (PDB id) in mmtf format, Chemfiles is able to read the assembly data and duplicate the structure with the right transformations.
But in .mmcif, the assembly parameters are not read (or not applied).
Do I forgot a special action to apply these parameters ?
Thank you for your reply.