Configuration parsers¶

All parsers inherit from BaseParser and override the _parse_stream and, possibly, the _parse_file methods. After a parser has been initialised it can be used to build a single system through its make_system() method or a whole trajectory by using it to initialise a Trajectory object.

`BaseParser`
`OxDNAParser`	Use oxDNA/topology files to build systems.
`GroParser`
`LAMMPSDataFileParser`	Overloaded function.
`LAMMPSDumpParser`
`LJKAParser`
`PatchyParticlesParser`	Build systems out of PatchyParticles configurations.

class baggianalysis.core.BaseParser(self: baggianalysis.core.BaseParser) → None ¶

Bases: pybind11_builtins.pybind11_object

_parse_file(self: baggianalysis.core.BaseParser, arg0: str) → baggianalysis.core.System ¶

make_system(self: baggianalysis.core.BaseParser, arg0: str) → baggianalysis.core.System ¶

set_topology(self: baggianalysis.core.BaseParser, arg0: baggianalysis.core.Topology) → None ¶

class baggianalysis.core.OxDNAParser(*args, **kwargs)¶

Bases: baggianalysis.core.BaseParser

Use oxDNA/topology files to build systems.

Overloaded function.

__init__(self: baggianalysis.core.OxDNAParser, topology_file: str) -> None

Initialise the parser by using the Default topology parser to parse the given topology file.

Parameters: topology_file (str) – The topology file to be used for initialisation.

__init__(self: baggianalysis.core.OxDNAParser, topology_parser: baggianalysis.core.oxDNA_topology.Default) -> None

Initialise the parser by using the given topology parser.

Parameters: topology – An oxDNA topology parser, which should be an instance of an object inheriting from the Default topology parser.

class baggianalysis.core.oxDNA_topology.Default(self: baggianalysis.core.oxDNA_topology.Default, arg0: str) → None ¶

Bases: pybind11_builtins.pybind11_object

N(self: baggianalysis.core.oxDNA_topology.Default) → int ¶

Return the number of particles as specified in the topology file.

Returns: The number of particles as specified in the topology file.
Return type: int

N_A(self: baggianalysis.core.oxDNA_topology.Default) → int ¶

A default oxDNA topology contains either a single number (the total number of particles, N) or two numbers (N and the number of particles of the first species, NA). This method returns N in the former case and NA in the latter.

Returns: The number of particles of species A as specified in the topology file.
Return type: int

type(self: baggianalysis.core.oxDNA_topology.Default, p_idx: int) → str ¶

The type of the particle with the given index.

Parameters: p_idx (int) – The index of the particle whose type one wants to know.
Returns: The type of the given particle.
Return type: str

class baggianalysis.core.oxDNA_topology.TSP(self: baggianalysis.core.oxDNA_topology.TSP, arg0: str) → None ¶

Bases: baggianalysis.core.oxDNA_topology.Default

N_arms(self: baggianalysis.core.oxDNA_topology.TSP, arg0: int) → int ¶

N_monomers_per_arm(self: baggianalysis.core.oxDNA_topology.TSP, arg0: int) → int ¶

N_stars(self: baggianalysis.core.oxDNA_topology.TSP) → int ¶

class baggianalysis.core.GroParser(self: baggianalysis.core.GroParser, arg0: float) → None ¶: Bases: baggianalysis.core.BaseParser

class baggianalysis.core.LAMMPSDataFileParser(*args, **kwargs)¶

Bases: baggianalysis.core.BaseParser

Overloaded function.

__init__(self: baggianalysis.core.LAMMPSDataFileParser, arg0: str) -> None
__init__(self: baggianalysis.core.LAMMPSDataFileParser, arg0: int, arg1: int) -> None

class baggianalysis.core.LAMMPSDumpParser(self: baggianalysis.core.LAMMPSDumpParser, rescaled_coords: bool = False) → None ¶: Bases: baggianalysis.core.BaseParser

class baggianalysis.core.LJKAParser(self: baggianalysis.core.LJKAParser) → None ¶: Bases: baggianalysis.core.BaseParser

class baggianalysis.core.PatchyParticlesParser(*args, **kwargs)¶

Bases: baggianalysis.core.BaseParser

Build systems out of PatchyParticles configurations. These files store the particles’ positios and orientation matrices.

Overloaded function.

__init__(self: baggianalysis.core.PatchyParticlesParser) -> None

Default constructor: the parser will assume that the particles have four patches arranged on a tetrahedron.

__init__(self: baggianalysis.core.PatchyParticlesParser, base_patches: List[glm::tvec3<scalar, P>]) -> None

The object can also be built by providing a list of vectors storing the base patches, that is, those vectors that, when multiplied by the orientation matrix, yield the particles’ patches.

__init__(self: baggianalysis.core.PatchyParticlesParser, patch_filename: str) -> None

Obtain the list of vectors storing the base patches from the given file.