Configuration exporters¶
Interface for configuration-exporting classes. |
|
Export configurations to the cogli1 file format, used for visualisation purposes. |
|
Export configurations to the oxDNA file format. |
|
Export configurations to the LAMMPS data file format. |
-
class
baggianalysis.core.
BaseExporter
(self: baggianalysis.core.BaseExporter) → None¶ Bases:
pybind11_builtins.pybind11_object
Interface for configuration-exporting classes.
The default constructor does not take any parameters.
-
write
(self: baggianalysis.core.BaseExporter, system: baggianalysis.core.System, filename: str) → None¶ Print out a single system.
-
write_topology
(self: baggianalysis.core.BaseExporter, arg0: baggianalysis.core.System, arg1: str) → None¶ Some formats have a topology file on top of configuration (and/or trajectory) files. By default this method is called by both
write()
andwrite_topology()
and hence should be extended by child classes that export to formats that use topology files.- Parameters
system –
-
-
class
baggianalysis.core.
Cogli1Exporter
(*args, **kwargs)¶ Bases:
baggianalysis.core.BaseExporter
Export configurations to the cogli1 file format, used for visualisation purposes.
Overloaded function.
__init__(self: baggianalysis.core.Cogli1Exporter) -> None
This constructor makes the exporter print each particle as a red sphere of radius 0.5.
__init__(self: baggianalysis.core.Cogli1Exporter, arg0: Callable[[baggianalysis.core.Particle], baggianalysis.core.Cogli1Particle]) -> None
This constructor takes as a parameter a callable that maps each particle into a
Cogli1Particle
that will be interpreted by the exporter and printed in cogli1 format.An example of such a callable is the following:
def cogli1_mapper(p): c_p = ba.Cogli1Particle() if p.position[0] > 0: c_p.size = 1.0 c_p.color = "0,1,0" if p.position[1] > 0: c_p.show = False return c_p
The function defined above will give all those particles that have an x coordinate larger than 0 a size of 1.0 and a green color. Particles with a y coordinate larger than 0 will be hidden. The other particles will be red and have a size of 0.5.
- Parameters
mapper (callable) – A callable that takes a particle and returns a
Cogli1Particle
.
-
class
baggianalysis.core.
Cogli1Particle
(self: baggianalysis.core.Cogli1Particle) → None¶ Bases:
pybind11_builtins.pybind11_object
A utility class used by
Cogli1Exporter
to customise its output.By default, the particle is visible, has a size of 0.5 and a red color.
-
property
color
¶ The color of the particle. It can be a name (“red”) or an RGB string (“1,0,0”). Defaults to “red”.
- Type
-
property
-
class
baggianalysis.core.
GenericOxDNAExporter
(self: baggianalysis.core.GenericOxDNAExporter, arg0: bool) → None¶ Bases:
baggianalysis.core.BaseExporter
Export configurations to the oxDNA file format. The exporter will generate a topology and a configuration file. Note that the filename passed to the
write()
method is used as-is for the configuration file and as a suffix, prefixed bytopology_
, for the topology file.The constructor takes one parameter which tells the exporter whether the topology line should also contain the number of particles of type A.
- Parameters
also_print_N_A (bool) – If True, the exporter will print the number of particles of type A in addition to the number of particles in the topology file.
-
class
baggianalysis.core.
LAMMPSDataFileExporter
(self: baggianalysis.core.LAMMPSDataFileExporter, arg0: str) → None¶ Bases:
baggianalysis.core.BaseExporter
Export configurations to the LAMMPS data file format.
The constructor takes one mandatory argument.