Format classes¶chemfiles::Format¶The Format class defines the interface to implement in order to add a new format to chemfiles. It is possible to implement only one of Format::read; Format::read_step or Format::write. In that case, only the corresponding operations will be available from the corresponding chemfiles::Trajectory.
Subclassed by chemfiles::AmberNetCDFFormat, chemfiles::LAMMPSDataFormat, chemfiles::Molfile< F >, chemfiles::PDBFormat, chemfiles::TinkerFormat, chemfiles::TNGFormat, chemfiles::XYZFormat
Public Functions
read_step(size_t step, Frame &frame)¶Read a specific step from the trajectory file.
FormatError: if the file does not follow the format FileError: if their is an OS error while reading the filestep: The step to read frame: The frame to fill read(Frame &frame)¶Read a specific step from the trajectory file.
FormatError: if the file does not follow the format FileError: if their is an OS error while reading the fileframe: The frame to fill write(const Frame &frame)¶Write a frame to the trajectory file.
FormatError: if the file does not follow the format FileError: if their is an OS error while reading the fileframe: The frame to be writen nsteps() = 0¶Get the number of frames in the associated file.
These classes implement the format interface defined previously.
chemfiles::XYZFormat¶XYZ file format reader and writer.
Inherits from chemfiles::Format
chemfiles::PDBFormat¶PDB file format reader and writer.
For multi-frame trajectories, we follow the convention of VMD to use multiple END records, separating the steps.
Inherits from chemfiles::Format
chemfiles::AmberNetCDFFormat¶Amber NetCDF file format reader.
Inherits from chemfiles::Format
chemfiles::TNGFormat¶TNG file format reader.
Inherits from chemfiles::Format
chemfiles::LAMMPSDataFormat¶LAMMPS Data file format reader and writer.
LAMMPS data files are not fully stand-alone, as one needs to know the atom style to read the data. This reader will try to guess the atom style by checking the first line of the header for atom_style <style>, and by reading any comment after the Atoms section name. If no atom style is specified, the code default to full and send a warning.
The code alse tries to read atomic names at the end of data lines. For example, the atom at index 44 will have C2 as atomic name.
44 44 2 0.000000 1.094000 2.061000 69.552002 # C2 RES
Inherits from chemfiles::Format
chemfiles::TinkerFormat¶Tinker XYZ file format.
The format is described here: http://chembytes.wikidot.com/tnk-tut00#toc2. Additionally to the original Tinker XYZ format, chemfiles also supports the files with unit cell data, as introduced in Tinker 6.3.
This format is associated with the .arc extension, but not the .xyz extension, which is used for the standard XYZ format.
Inherits from chemfiles::Format
chemfiles::Molfile¶Use of VMD Molfile plugins as format reader. This class is templated by a value in the MolfileFormat enum.
Inherits from chemfiles::Format
chemfiles::MolfileFormat¶List all the VMD molfile plugins enabled. For more documentation about VMD molfile plugins, please see: http://www.ks.uiuc.edu/Research/vmd/plugins/molfile/
Values:
DCD¶DCD binary file format.
GRO¶Gromacs .gro file format.
TRR¶Gromacs .trr file format.
XTC¶Gromacs .xtc file format.
TRJ¶Gromacs .trj file format.
LAMMPS¶Lammps trajectory files.
MOL2¶MOL2 file format.
MOLDEN¶Molden file format.