Universe

class pylimer_tools_cpp.Universe(self: pylimer_tools_cpp.Universe, Lx: float, Ly: float, Lz: float)

Bases: pybind11_object

Represents a full Polymer Network structure, a collection of molecules.

This is the main class for representing molecular systems, containing atoms, bonds, angles, and the simulation box.

Instantiate this Universe (Collection of Molecules) providing the box lengths.

Parameters:

  • Lx – Box length in x direction

  • Ly – Box length in y direction

  • Lz – Box length in z direction

Methods Summary

add_angles(self, angles_from, angles_via, ...)

Add angles to the Universe.

add_atoms(self, ids, types, x, y, z, nx, ny, nz)

Add atoms to the Universe, vertices to the underlying graph.

add_bonds(*args, **kwargs)

Overloaded function.

add_bonds_with_types(self, bonds_from, ...)

Add bonds to the underlying atoms, edges to the underlying graph.

add_dihedral_angles(self, angles_from, ...)

Add dihedral angles to the Universe.

compute_angles(self)

Compute the angle of each angle in the molecule, respecting periodic boundaries.

compute_bond_lengths(self)

Compute the length of each bond in the molecule, respecting periodic boundaries.

compute_bond_vectors(self)

Compute the vectors of each bond in the molecule, respecting periodic boundaries.

compute_dxs(self, atom_ids_to, atom_ids_from)

Compute the dx distance for certain bonds (length in x direction).

compute_dys(self, atom_ids_to, atom_ids_from)

Compute the dy distance for certain bonds (length in y direction).

compute_dzs(self, atom_ids_to, atom_ids_from)

Compute the dz distance for certain bonds (length in z direction).

compute_end_to_end_distances(self, ...[, ...])

Compute the end-to-end distance of each strand in the network.

compute_mean_end_to_end_distance(self, ...)

Compute the mean of the end-to-end distances of each strand in the network.

compute_mean_squared_end_to_end_distance(...)

Compute the mean square of the end-to-end distances of each strand (incl.

compute_mean_strand_length(self, ...)

Compute the mean number of beads per strand.

compute_number_average_molecular_weight(...)

Compute the number average molecular weight.

compute_polydispersity_index(self, ...)

Compute the polydispersity index: the weight average molecular weight over the number average molecular weight.

compute_temperature(self[, dimensions, k_b])

Use the velocities per atom to compute the temperature from the kinetic energy of the system.

compute_total_mass(self)

Compute the total mass of this network/universe in whatever mass unit was used when set_masses() was called.

compute_weight_average_molecular_weight(...)

Compute the weight average molecular weight.

compute_weight_fractions(self)

Compute the weight fractions of each atom type in the network.

contract_vertices_along_bond_type(self, ...)

Merge vertices along a specific bond type.

count_atom_types(self)

Count how often each atom type is present.

count_atoms_in_skin_distance(self, distances)

This is a function that may help you to compute the radial distribution function.

count_loop_lengths(self[, max_length])

Find all loops (below a specific length) and count the number of atoms involved in them.

detect_angles(self)

Detect angles in the network based on the current bonds.

detect_dihedral_angles(self)

Detect dihedral angles in the network based on the current bonds.

determine_effective_functionality_per_type(self)

Find the average functionality of each atom type in the network.

determine_functionality_per_type(self)

Find the maximum functionality of each atom type in the network.

find_loops(self, crosslinker_type[, ...])

Decompose the Universe into loops.

find_minimal_order_loop_from(self, ...[, ...])

Find the loops in the network starting with one connection.

get_angles(self)

Get all angles added to this network.

get_atom(self, atom_id)

Find an atom by its ID.

get_atom_by_vertex_id(self, vertex_id)

Find an atom by the ID of the vertex of the underlying graph.

get_atom_id_by_vertex_idx(self, vertex_id)

Get the ID of the atom by the vertex ID of the underlying graph.

get_atom_types(self)

Get all types (each one for each atom) ordered by atom vertex ID.

get_atoms(self)

Get all atoms in the universe.

get_atoms_by_degree(self, functionality)

Get the atoms that have the specified number of bonds.

get_atoms_by_type(self, atom_type)

Query all atoms by their type.

get_atoms_connected_to(self, atom)

Get the atoms connected to a specified atom.

get_atoms_connected_to_vertex(self, vertex_idx)

Get the atoms connected to a specified vertex ID.

get_bonds(self)

Get all bonds.

get_box(self)

Get the underlying bounding box object.

get_chains_with_crosslinker(self, ...)

Decompose the Universe into strands (molecules, which could be either chains, or even lonely atoms), without omitting the crosslinkers (as in get_molecules()).

get_clusters(self)

Get the components of the universe that are not connected to each other.

get_edge_ids_from(self, vertex_id)

Get the edge IDs incident to a specific vertex.

get_edge_ids_from_to(self, vertex_id_from, ...)

Get the edge IDs of all edges between two specific vertices.

get_edges(self)

Get all edges.

get_masses(self)

Get the mass of one atom per type.

get_molecules(self, atom_type_to_omit)

Decompose the Universe into molecules, which could be either chains, networks, or even lonely atoms.

get_network_of_crosslinker(self, ...)

Reduce the network to contain only crosslinkers, replacing all the strands with a single bond.

get_nr_of_angles(self)

Query the number of angles that have been added to this universe.

get_nr_of_atoms(self)

Query the number of atoms in this universe.

get_nr_of_bonds(self)

Query the number of bonds associated with this universe.

get_nr_of_bonds_of_atom(self, arg0)

Count the number of immediate neighbors of an atom, specified by its ID.

get_nr_of_bonds_of_vertex(self, arg0)

Count the number of immediate neighbors of an atom, specified by its vertex ID.

get_nr_of_dihedral_angles(self)

Query the number of dihedral angles that have been added to this universe.

get_nr_of_edges_from_to(self, ...[, max_length])

Get the number of edges in the shortest path between two specific vertices.

get_timestep(self)

Query the timestep when this universe was captured.

get_vertex_degrees(self)

Get the degree (functionality) of each vertex.

get_vertex_idx_by_atom_id(self, atom_id)

Get the vertex ID of the underlying graph for an atom with a specified ID.

get_volume(self)

Query the volume of the underlying bounding box.

has_infinite_strand(self, arg0, arg1)

Check whether there is a strand (with crosslinker) in the universe that loops through periodic images without coming back.

hash_angle_type(self, angle_from, angle_via, ...)

Convert the three integers to one long number/hash.

hash_dihedral_angle_type(self, angle_from, ...)

Convert the four integers to one long number/hash.

interpolate_edges(self, crosslinker_type, ...)

Get more or less edges than currently present, interpolating between junctions.

remove_all_angles(self)

Remove all angles from the Universe.

remove_all_dihedral_angles(self)

Remove all dihedral angles from the Universe.

remove_atoms(self, atom_ids)

Remove atoms and all associated bonds by their atom IDs.

remove_bonds(self, bonds_from, bonds_to)

Remove bonds by their connected atom IDs.

remove_bonds_by_type(self, bond_type)

Remove bonds with a specific type.

replace_atom(self, atom_id, replacement_atom)

Replace the properties of an atom with the properties of another given atom.

replace_atom_type(self, atom_id, new_type)

Replace the type of an atom with another type.

resample_velocities(self, mean, variance[, ...])

Resample velocities for atoms in the universe.

set_box(self, box[, rescale_atoms])

Override the currently assigned box with the one specified.

set_box_lengths(self, lx, ly, lz[, ...])

Override the currently assigned box with one with the side lengths specified.

set_mass(self, atom_type, mass)

Set the mass for a specific atom type.

set_masses(self, mass_per_type)

Set the mass per type of atom.

set_timestep(self, timestep)

Set the timestep when this Universe was captured.

set_vertex_property(self, vertex_id, ...)

Set a specific property for a specific vertex.

simplify(self)

Remove self links and double bonds.

Methods Documentation

add_angles(self: pylimer_tools_cpp.Universe, angles_from: list[int], angles_via: list[int], angles_to: list[int], angle_types: list[int]) → None

Add angles to the Universe. No relation to the underlying graph, just a method to preserve read & write capabilities.

Parameters:

  • angles_from – Vector of atom IDs for angle start points

  • angles_via – Vector of atom IDs for angle middle points

  • angles_to – Vector of atom IDs for angle end points

  • angle_types – Vector of angle types

add_atoms(self: pylimer_tools_cpp.Universe, ids: list[int], types: list[int], x: list[float], y: list[float], z: list[float], nx: list[int], ny: list[int], nz: list[int]) → None

Add atoms to the Universe, vertices to the underlying graph.

Parameters:

  • ids – Vector of atom IDs

  • types – Vector of atom types

  • x – Vector of x coordinates

  • y – Vector of y coordinates

  • z – Vector of z coordinates

  • nx – Vector of periodic image flags in x direction

  • ny – Vector of periodic image flags in y direction

  • nz – Vector of periodic image flags in z direction

add_bonds(*args, **kwargs)

Overloaded function.

  1. add_bonds(self: pylimer_tools_cpp.Universe, bonds_from: list[int], bonds_to: list[int]) -> None

    Add bonds to the underlying atoms, edges to the underlying graph. If the connected atoms are not found, the bonds are silently skipped.

    param bonds_from:

    Vector of atom IDs for bond start points

    param bonds_to:

    Vector of atom IDs for bond end points

  2. add_bonds(self: pylimer_tools_cpp.Universe, nr_of_bonds: int, bonds_from: list[int], bonds_to: list[int], bond_types: list[int], ignore_non_existent_atoms: bool = False, simplify_universe: bool = True) -> None

    Add bonds to the underlying atoms, edges to the underlying graph.

    param nr_of_bonds:

    Number of bonds to add

    param bonds_from:

    Vector of atom IDs for bond start points

    param bonds_to:

    Vector of atom IDs for bond end points

    param bond_types:

    Vector of bond types

    param ignore_non_existent_atoms:

    Whether to skip bonds to non-existent atoms

    param simplify_universe:

    Whether to simplify the universe after adding bonds

add_bonds_with_types(self: pylimer_tools_cpp.Universe, bonds_from: list[int], bonds_to: list[int], bond_types: list[int]) → None

Add bonds to the underlying atoms, edges to the underlying graph. If the connected atoms are not found, the bonds are silently skipped.

Parameters:

  • bonds_from – Vector of atom IDs for bond start points

  • bonds_to – Vector of atom IDs for bond end points

  • bond_types – Vector of bond types

add_dihedral_angles(self: pylimer_tools_cpp.Universe, angles_from: list[int], angles_via1: list[int], angles_via2: list[int], angles_to: list[int], angle_types: list[int]) → None

Add dihedral angles to the Universe. No relation to the underlying graph, just a method to preserve read & write capabilities.

Parameters:

  • angles_from – Vector of atom IDs for dihedral start points

  • angles_via1 – Vector of atom IDs for first middle points

  • angles_via2 – Vector of atom IDs for second middle points

  • angles_to – Vector of atom IDs for dihedral end points

  • angle_types – Vector of dihedral angle types

compute_angles(self: pylimer_tools_cpp.Universe) → list[float]

Compute the angle of each angle in the molecule, respecting periodic boundaries.

Returns:

A list of angle values in radians

compute_bond_lengths(self: pylimer_tools_cpp.Universe) → list[float]

Compute the length of each bond in the molecule, respecting periodic boundaries.

Returns:

A list of bond lengths

compute_bond_vectors(self: pylimer_tools_cpp.Universe) → list[numpy.ndarray[numpy.float64[3, 1]]]

Compute the vectors of each bond in the molecule, respecting periodic boundaries.

Returns:

A list of bond vectors

compute_dxs(self: pylimer_tools_cpp.Universe, atom_ids_to: list[int], atom_ids_from: list[int]) → list[float]

Compute the dx distance for certain bonds (length in x direction).

Parameters:

  • atom_ids_to – Vector of destination atom IDs

  • atom_ids_from – Vector of source atom IDs

Returns:

Vector of x-direction distances

compute_dys(self: pylimer_tools_cpp.Universe, atom_ids_to: list[int], atom_ids_from: list[int]) → list[float]

Compute the dy distance for certain bonds (length in y direction).

Parameters:

  • atom_ids_to – Vector of destination atom IDs

  • atom_ids_from – Vector of source atom IDs

Returns:

Vector of y-direction distances

compute_dzs(self: pylimer_tools_cpp.Universe, atom_ids_to: list[int], atom_ids_from: list[int]) → list[float]

Compute the dz distance for certain bonds (length in z direction).

Parameters:

  • atom_ids_to – Vector of destination atom IDs

  • atom_ids_from – Vector of source atom IDs

Returns:

Vector of z-direction distances

compute_end_to_end_distances(self: pylimer_tools_cpp.Universe, crosslinker_type: int, derive_image_flags: bool = False) → list[float]

Compute the end-to-end distance of each strand in the network.

Note

Internally, this uses either compute_end_to_end_distance() or compute_end_to_end_distance_with_derived_image_flags(), depending on derive_image_flags. Invalid strands (where said function returns 0.0 or -1.0) are ignored.

Parameters:

  • crosslinker_type – The type of crosslinker atoms

  • derive_image_flags – Whether to derive image flags from connectivity

Returns:

List of end-to-end distances

compute_mean_end_to_end_distance(self: pylimer_tools_cpp.Universe, crosslinker_type: int, derive_image_flags: bool = False) → float

Compute the mean of the end-to-end distances of each strand in the network.

Note

Internally, this uses either compute_end_to_end_distance() or compute_end_to_end_distance_with_derived_image_flags(), depending on derive_image_flags. Invalid strands (where said function returns 0.0 or -1.0) are ignored.

Parameters:

  • crosslinker_type – The type of crosslinker atoms

  • derive_image_flags – Whether to derive image flags from connectivity

Returns:

Mean end-to-end distance

compute_mean_squared_end_to_end_distance(self: pylimer_tools_cpp.Universe, crosslinker_type: int, only_those_with_two_crosslinkers: bool = False, derive_image_flags: bool = False) → float

Compute the mean square of the end-to-end distances of each strand (incl. crosslinks) in the network.

Note

Internally, this uses either compute_end_to_end_distance() or compute_end_to_end_distance_with_derived_image_flags(), depending on derive_image_flags. Invalid strands (where said function returns 0.0 or -1.0) are ignored.

Parameters:

  • crosslinker_type – The type of crosslinker atoms

  • only_those_with_two_crosslinkers – Whether to only consider strands with two crosslinkers

  • derive_image_flags – Whether to derive image flags from connectivity

Returns:

Mean squared end-to-end distance

compute_mean_strand_length(self: pylimer_tools_cpp.Universe, crosslinker_type: int) → float

Compute the mean number of beads per strand.

Parameters:

crosslinker_type – The type of crosslinker atoms

Returns:

Mean strand length

compute_number_average_molecular_weight(self: pylimer_tools_cpp.Universe, crosslinker_type: int) → float

Compute the number average molecular weight.

Note

Crosslinkers are ignored completely.

Parameters:

crosslinker_type – The type of crosslinker atoms

Returns:

Number average molecular weight

compute_polydispersity_index(self: pylimer_tools_cpp.Universe, crosslinker_type: int) → float

Compute the polydispersity index: the weight average molecular weight over the number average molecular weight.

compute_temperature(self: pylimer_tools_cpp.Universe, dimensions: int = 3, k_b: float = 1.0) → float

Use the velocities per atom to compute the temperature from the kinetic energy of the system.

Parameters:

  • dimensions – Number of dimensions (typically 3)

  • k_b – Boltzmann constant value

Returns:

Computed temperature

compute_total_mass(self: pylimer_tools_cpp.Universe) → float

Compute the total mass of this network/universe in whatever mass unit was used when set_masses() was called.

Returns:

Total mass of the universe

compute_weight_average_molecular_weight(self: pylimer_tools_cpp.Universe, crosslinker_type: int) → float

Compute the weight average molecular weight.

Note

Crosslinkers are ignored completely.

Parameters:

crosslinker_type – The type of crosslinker atoms

Returns:

Weight average molecular weight

compute_weight_fractions(self: pylimer_tools_cpp.Universe) → dict[int, float]

Compute the weight fractions of each atom type in the network.

If no masses are stored, assumes a mass of 1 for each atom.

If the total mass is 0., returns the total mass per atom type.

contract_vertices_along_bond_type(self: pylimer_tools_cpp.Universe, bond_type: int) → pylimer_tools_cpp.Universe

Merge vertices along a specific bond type.

May result in new self-loops; use simplify() to remove them.

Parameters:

bond_type – The bond type to contract along

count_atom_types(self: pylimer_tools_cpp.Universe) → dict[int, int]

Count how often each atom type is present.

Returns:

Dictionary mapping atom types to their counts

count_atoms_in_skin_distance(self: pylimer_tools_cpp.Universe, distances: list[float], unwrapped: bool = False) → list[int]

This is a function that may help you to compute the radial distribution function. It loops through all atoms and counts neighbors within specified distance ranges.

Parameters:

  • distances – The edges of the bins for distance counting

  • unwrapped – Whether to measure the distance in unwrapped coordinates or as PBC-corrected distance

Returns:

Array of counts for each distance bin

count_loop_lengths(self: pylimer_tools_cpp.Universe, max_length: int = -1) → dict[int, int]

Find all loops (below a specific length) and count the number of atoms involved in them. Returns the count, how many loops per length are found.

detect_angles(self: pylimer_tools_cpp.Universe) → dict[str, list[int]]

Detect angles in the network based on the current bonds. Return the result in the same format as get_angles(), but all angles that are detected in the network, rather than the ones already set. Note that the angle types are determined by hash_angle_type(), which serves angle types that should be mapped by you back to smaller numbers, before serving them again to add_angles(), if you want to have them written e.g. for LAMMPS.

Returns:

Dictionary with detected angle information

detect_dihedral_angles(self: pylimer_tools_cpp.Universe) → dict[str, list[int]]

Detect dihedral angles in the network based on the current bonds. Return the result in the same format as get_dihedral_angles(), but all dihedral angles that are detected in the network, rather than the ones already set. Note that the angle types are determined by hash_dihedral_angle_type(), which serves angle types that should be mapped by you back to smaller numbers, before serving them to add_dihedral_angles(), if you want to have them written e.g. for LAMMPS.

Returns:

Dictionary with detected dihedral angle information

determine_effective_functionality_per_type(self: pylimer_tools_cpp.Universe) → dict[int, float]

Find the average functionality of each atom type in the network.

Returns:

Dictionary mapping atom types to average functionality

determine_functionality_per_type(self: pylimer_tools_cpp.Universe) → dict[int, int]

Find the maximum functionality of each atom type in the network.

Returns:

Dictionary mapping atom types to maximum functionality

find_loops(self: pylimer_tools_cpp.Universe, crosslinker_type: int, max_length: int = -1, skip_self_loops: bool = False) → dict[int, list[list[pylimer_tools_cpp.Atom]]]

Decompose the Universe into loops. The primary index specifies the degree of the loop.

Caution

There are exponentially many paths between two crosslinkers of a network, and you may run out of memory when using this function, if your Universe/Network is lattice-like. You can use the max_length parameter to restrict the algorithm to only search for loops up to a certain length. Use a negative value to find all loops and paths.

find_minimal_order_loop_from(self: pylimer_tools_cpp.Universe, loop_start: int, loop_step1: int, max_length: int = -1, skip_self_loops: bool = False) → list[pylimer_tools_cpp.Atom]

Find the loops in the network starting with one connection.

Warning

There are exponentially many paths between two crosslinkers of a network, and you may run out of memory when using this function, if your Universe/Network is lattice-like. You can use the max_length parameter to restrict the algorithm to only search for loops up to a certain length. Use a negative value to find all loops and paths.

Parameters:

  • loop_start – The atom ID to start the search from

  • loop_step1 – The first step to take, i.e., the first bond to follow

  • max_length – The maximum length of the loop to find, or -1 for no limit

  • skip_self_loops – Whether to skip self-loops (i.e., loops that start and end at the same atom; only relevant if loop_start is equal to loop_step1)

Returns:

List of loops found

get_angles(self: pylimer_tools_cpp.Universe) → dict[str, list[int]]

Get all angles added to this network.

Returns a dict with three properties: ‘angle_from’, ‘angle_via’ and ‘angle_to’.

Note

The integer values returned refer to the atom IDs, not the vertex IDs. Use get_idx_by_atom_id() to translate them to vertex IDs.

Returns:

Dictionary with angle information

get_atom(self: pylimer_tools_cpp.Universe, atom_id: int) → pylimer_tools_cpp.Atom

Find an atom by its ID.

Parameters:

atom_id – The ID of the atom to find

Returns:

The atom with the specified ID

get_atom_by_vertex_id(self: pylimer_tools_cpp.Universe, vertex_id: int) → pylimer_tools_cpp.Atom

Find an atom by the ID of the vertex of the underlying graph.

Parameters:

vertex_id – The vertex ID to query

Returns:

The atom at the specified vertex

get_atom_id_by_vertex_idx(self: pylimer_tools_cpp.Universe, vertex_id: int) → int

Get the ID of the atom by the vertex ID of the underlying graph.

Parameters:

vertex_id – The vertex index in the underlying graph

Returns:

The atom ID corresponding to the vertex

get_atom_types(self: pylimer_tools_cpp.Universe) → list[int]

Get all types (each one for each atom) ordered by atom vertex ID.

Returns:

Vector of atom types in vertex order

get_atoms(self: pylimer_tools_cpp.Universe) → list[pylimer_tools_cpp.Atom]

Get all atoms in the universe.

Returns:

List of all atoms

get_atoms_by_degree(self: pylimer_tools_cpp.Universe, functionality: int) → list[pylimer_tools_cpp.Atom]

Get the atoms that have the specified number of bonds.

get_atoms_by_type(self: pylimer_tools_cpp.Universe, atom_type: int) → list[pylimer_tools_cpp.Atom]

Query all atoms by their type.

get_atoms_connected_to(self: pylimer_tools_cpp.Universe, atom: pylimer_tools_cpp.Atom) → list[pylimer_tools_cpp.Atom]

Get the atoms connected to a specified atom.

Internally uses get_atoms_connected_to().

Parameters:

atom – The atom to query connections for

Returns:

List of connected atoms

get_atoms_connected_to_vertex(self: pylimer_tools_cpp.Universe, vertex_idx: int) → list[pylimer_tools_cpp.Atom]

Get the atoms connected to a specified vertex ID.

Parameters:

vertex_idx – The vertex index to query

Returns:

List of connected atoms

get_bonds(self: pylimer_tools_cpp.Universe) → dict[str, list[int]]

Get all bonds. Returns a dict with three properties: ‘bond_from’, ‘bond_to’ and ‘bond_type’. The order is not necessarily related to any structural characteristic.

Returns:

Dictionary with bond information

get_box(self: pylimer_tools_cpp.Universe) → pylimer_tools_cpp.Box

Get the underlying bounding box object.

Returns:

The simulation box

get_chains_with_crosslinker(self: pylimer_tools_cpp.Universe, crosslinker_type: int) → list[pylimer_tools_cpp.Molecule]

Decompose the Universe into strands (molecules, which could be either chains, or even lonely atoms), without omitting the crosslinkers (as in get_molecules()). In turn, e.g. for a tetrafunctional crosslinker, it will be 4 times in the resulting molecules.

Note

Crosslinkers without bonds to non-crosslinkers are not returned (i.e., single crosslinkers, are not counted as strands).

Parameters:

crosslinker_type – The type of crosslinker atoms

Returns:

List of chains including crosslinkers

get_clusters(self: pylimer_tools_cpp.Universe) → list[pylimer_tools_cpp.Universe]

Get the components of the universe that are not connected to each other. Returns a list of Universe objects. Unconnected, free atoms/beads become their own Universe.

Returns:

List of disconnected Universe components

get_edge_ids_from(self: pylimer_tools_cpp.Universe, vertex_id: int) → list[int]

Get the edge IDs incident to a specific vertex.

Parameters:

vertex_id – The ID of the vertex to query

Returns:

List of edge IDs connected to the vertex

get_edge_ids_from_to(self: pylimer_tools_cpp.Universe, vertex_id_from: int, vertex_id_to: int) → list[int]

Get the edge IDs of all edges between two specific vertices.

Parameters:

  • vertex_id_from – The starting vertex ID

  • vertex_id_to – The ending vertex ID

Returns:

List of edge IDs connecting the two vertices

get_edges(self: pylimer_tools_cpp.Universe) → dict[str, list[int]]

Get all edges. Returns a dict with three properties: ‘edge_from’, ‘edge_to’ and ‘edge_type’. The order is not necessarily related to any structural characteristic.

Note

The integer values returned refer to the vertex IDs, not the atom IDs. Use get_atom_id_by_idx() to translate them to atom IDs, or get_bonds() to have that done for you.

Returns:

Dictionary with edge information

get_masses(self: pylimer_tools_cpp.Universe) → dict[int, float]

Get the mass of one atom per type.

Returns:

Dictionary mapping atom types to masses

get_molecules(self: pylimer_tools_cpp.Universe, atom_type_to_omit: int) → list[pylimer_tools_cpp.Molecule]

Decompose the Universe into molecules, which could be either chains, networks, or even lonely atoms.

Reduces the Universe to a list of molecules. Specify the crosslinker_type to an existing type ID, then those atoms will be omitted, and this function returns chains instead.

Parameters:

atom_type_to_omit – The type of atom to omit from the universe to end up with the desired molecules (e.g., the type of the crosslinkers).

Returns:

List of molecules

get_network_of_crosslinker(self: pylimer_tools_cpp.Universe, crosslinker_type: int) → pylimer_tools_cpp.Universe

Reduce the network to contain only crosslinkers, replacing all the strands with a single bond. Useful e.g. to reduce the memory usage and runtime of find_loops() or has_infinite_strand().

Further use simplify() to remove primary loops.

Parameters:

crosslinker_type – The type of crosslinker atoms

Returns:

Reduced network containing only crosslinkers

get_nr_of_angles(self: pylimer_tools_cpp.Universe) → int

Query the number of angles that have been added to this universe.

get_nr_of_atoms(self: pylimer_tools_cpp.Universe) → int

Query the number of atoms in this universe.

Returns:

Number of atoms

get_nr_of_bonds(self: pylimer_tools_cpp.Universe) → int

Query the number of bonds associated with this universe.

get_nr_of_bonds_of_atom(self: pylimer_tools_cpp.Universe, arg0: int) → int

Count the number of immediate neighbors of an atom, specified by its ID.

Parameters:

atom_id – The ID of the atom to query

Returns:

Number of bonds connected to the atom

get_nr_of_bonds_of_vertex(self: pylimer_tools_cpp.Universe, arg0: int) → int

Count the number of immediate neighbors of an atom, specified by its vertex ID.

Parameters:

vertex_id – The vertex ID of the atom to query

Returns:

Number of bonds connected to the vertex

get_nr_of_dihedral_angles(self: pylimer_tools_cpp.Universe) → int

Query the number of dihedral angles that have been added to this universe.

get_nr_of_edges_from_to(self: pylimer_tools_cpp.Universe, vertex_id_from: int, vertex_id_to: int, max_length: int = -1) → int

Get the number of edges in the shortest path between two specific vertices.

If max_length is provided and positive, it will only consider paths up to that length.

Parameters:

  • vertex_id_from – The starting vertex ID

  • vertex_id_to – The ending vertex ID

  • max_length – Maximum path length to consider (default: -1 for no limit)

Returns:

Number of edges in shortest path, or -1 if no path exists

get_timestep(self: pylimer_tools_cpp.Universe) → int

Query the timestep when this universe was captured.

get_vertex_degrees(self: pylimer_tools_cpp.Universe) → list[int]

Get the degree (functionality) of each vertex.

get_vertex_idx_by_atom_id(self: pylimer_tools_cpp.Universe, atom_id: int) → int

Get the vertex ID of the underlying graph for an atom with a specified ID.

Parameters:

atom_id – The atom ID to look up

Returns:

The vertex index corresponding to the atom

get_volume(self: pylimer_tools_cpp.Universe) → float

Query the volume of the underlying bounding box.

Returns:

The volume of the simulation box

has_infinite_strand(self: pylimer_tools_cpp.Universe, arg0: int, arg1: int) → bool

Check whether there is a strand (with crosslinker) in the universe that loops through periodic images without coming back.

Warning

There are exponentially many paths between two crosslinkers of a network, and you may run out of memory when using this function, if your Universe/Network is lattice-like.

Returns:

True if infinite strands are detected, False otherwise

hash_angle_type(self: pylimer_tools_cpp.Universe, angle_from: int, angle_via: int, angle_to: int) → int

Convert the three integers to one long number/hash. Used internally for duplicate detection.

Parameters:

  • angle_from – First atom ID in the angle

  • angle_via – Middle atom ID in the angle

  • angle_to – Last atom ID in the angle

Returns:

Hash value for the angle type

hash_dihedral_angle_type(self: pylimer_tools_cpp.Universe, angle_from: int, angle_via1: int, angle_via2: int, angle_to: int) → int

Convert the four integers to one long number/hash. Used internally for duplicate detection.

Parameters:

  • angle_from – First atom ID in the dihedral

  • angle_via1 – Second atom ID in the dihedral

  • angle_via2 – Third atom ID in the dihedral

  • angle_to – Fourth atom ID in the dihedral

Returns:

Hash value for the dihedral angle type

interpolate_edges(self: pylimer_tools_cpp.Universe, crosslinker_type: int, interpolation_factor: float) → list[tuple[int, int]]

Get more or less edges than currently present, interpolating between junctions.

Parameters:

  • crosslinker_type – The type of crosslinker atoms

  • interpolation_factor – Factor for edge interpolation

Returns:

Interpolated edge structure

remove_all_angles(self: pylimer_tools_cpp.Universe) → None

Remove all angles from the Universe. This will not remove the atoms or bonds, just the angles.

Warning

This will not remove dihedral angles, use remove_all_dihedral_angles() for that.

remove_all_dihedral_angles(self: pylimer_tools_cpp.Universe) → None

Remove all dihedral angles from the Universe. This will not remove the atoms or bonds, just the stored dihedral angles.

remove_atoms(self: pylimer_tools_cpp.Universe, atom_ids: list[int]) → None

Remove atoms and all associated bonds by their atom IDs.

Parameters:

atom_ids – Vector of atom IDs to remove

remove_bonds(self: pylimer_tools_cpp.Universe, bonds_from: list[int], bonds_to: list[int]) → None

Remove bonds by their connected atom IDs.

Parameters:

  • bonds_from – Vector of starting atom IDs

  • bonds_to – Vector of ending atom IDs

remove_bonds_by_type(self: pylimer_tools_cpp.Universe, bond_type: int) → None

Remove bonds with a specific type.

Parameters:

bond_type – The bond type to remove

replace_atom(self: pylimer_tools_cpp.Universe, atom_id: int, replacement_atom: pylimer_tools_cpp.Atom) → None

Replace the properties of an atom with the properties of another given atom.

Parameters:

  • atom_id – ID of the atom to replace

  • replacement_atom – The atom with new properties

replace_atom_type(self: pylimer_tools_cpp.Universe, atom_id: int, new_type: int) → None

Replace the type of an atom with another type.

Parameters:

  • atom_id – ID of the atom to modify

  • new_type – The new atom type

resample_velocities(self: pylimer_tools_cpp.Universe, mean: float, variance: float, seed: str = '', is_2d: bool = False) → None

Resample velocities for atoms in the universe.

Parameters:

  • mean – Mean velocity

  • variance – Velocity variance

  • seed – Random seed for velocity generation

  • is_2d – Whether to omit sampling the z direction

set_box(self: pylimer_tools_cpp.Universe, box: pylimer_tools_cpp.Box, rescale_atoms: bool = False) → None

Override the currently assigned box with the one specified.

Parameters:

  • box – The new box to assign

  • rescale_atoms – Whether to rescale atom positions

set_box_lengths(self: pylimer_tools_cpp.Universe, lx: float, ly: float, lz: float, rescale_atoms: bool = False) → None

Override the currently assigned box with one with the side lengths specified.

Parameters:

  • lx – Length in x direction

  • ly – Length in y direction

  • lz – Length in z direction

  • rescale_atoms – Whether to rescale atom positions

set_mass(self: pylimer_tools_cpp.Universe, atom_type: int, mass: float) → None

Set the mass for a specific atom type.

Parameters:

  • atom_type – The atom type to set mass for

  • mass – The mass value to assign

set_masses(self: pylimer_tools_cpp.Universe, mass_per_type: dict[int, float]) → None

Set the mass per type of atom.

Parameters:

mass_per_type – Map of atom types to their masses

set_timestep(self: pylimer_tools_cpp.Universe, timestep: int) → None

Set the timestep when this Universe was captured.

Parameters:

timestep – The timestep value

set_vertex_property(self: pylimer_tools_cpp.Universe, vertex_id: int, property_name: str, value: float) → None

Set a specific property for a specific vertex.

Parameters:

  • vertex_id – The vertex ID to modify

  • property_name – Name of the property to set

  • value – Value to assign to the property

simplify(self: pylimer_tools_cpp.Universe) → None

Remove self links and double bonds. This function is called automatically after adding bonds.

This operation cleans up the graph structure by removing redundant connections.