Welcome to drawNA’s documentation!

drawNA

drawNA.polygons

class drawNA.polygons.BoundaryPolygon(vertices: numpy.ndarray)

A BoundaryPolygon is a cyclic combination of 3 or more edges, which result in a closed Polygon

The first vertex on the starting edge = the last vertex on the final edge

property edges

Iterate over all vertices and return a list of Edge instances

plot2D(ax: matplotlib.axes._axes.Axes = None, fout: str = None, **kwargs)

Assumes that the shape is 2D and lies on the z=0 plane.

write_PLY(fout: str, comments: List[str] = [])

Writes the BoundaryPolygon to a ASCII PLY File.

class drawNA.polygons.Edge(vertex_1: list, vertex_2: list, edge_kind: int = 0)

An Edge is a combination of two vertices and stores geometric information about this connection

class drawNA.polygons.Vertex(*args, **kwargs)

Geometric point in space.

drawNA.readers

class drawNA.readers.LAMMPSDumpReader(fnames: List[str])

LAMMPS DumpFile reader designed specifically for LAMMPS simulations that have used the oxDNA or oxDNA2 forcefields, and have data/dump files configured as per the literature (i.e. not customised)

LAMMPSDumpReader subclasses LAMMPSDataReader and is also a subclass of Reader, which LAMMPSDataReader also subclasses. This architecture is slightly confusing but results in very concise code for this class

The reason for subclassing LAMMPSDataReader is because the configuration data file is needed to generate the bonds, which cannot be stored in a dump file.

drawNA.readers.quat_to_matrix(row: pandas.core.series.Series) → numpy.ndarray

Converts a pd.Series which has entries:

[[‘qw’, ‘qi’, ‘qj’, ‘qk’]]

from a quaternion to a matrix rotation and returns it as a np.ndarray.

drawNA.tools

class drawNA.tools.DNAEdge(vertex_1: numpy.ndarray, vertex_2: numpy.ndarray, theta: float = 0.0)

Abstract class that allows subclasses to generate oxDNA Strand instances along a vector.

property length

The length of the edge in oxdna units (i think)

node(node_3p: drawNA.tools.DNANode = None, node_5p: drawNA.tools.DNANode = None) → drawNA.tools.DNANode

Returns a DNANode for the opposite end of the DNANode provided in parameters

property nt_length

The length of the edge in units of nucleotides

property perp_vector

Perpendicular vector which lies in the xy plane

segments() → float

There are 2.5 segments in every unit of oxDNA distance.

Each segment represents a Nucleotide

property summary

Extended equivalent of self.__repr__

class drawNA.tools.DNANode(*args, **kwargs)

Abstract class for use with DNAEdge that helps to determine angles and vectors needed to generate stable structures.

property angle

Returns the angle between the two vectors leaving the Node in radians

property vector_3p

Vector entering/leaving the node from the 3’ direction

vector_3p and vector_5p follow on from each other which means that they cannot start/finish at the same point

property vector_5p

Vector leaving/entering the node from the 5’ direction

vector_3p and vector_5p follow on from each other which means that they cannot start/finish at the same point

drawNA.oxdna

drawNA.oxdna.nucleotide

Management and Storage of oxDNA nucleotides

class drawNA.oxdna.nucleotide.Nucleotide(base: str, pos_com: numpy.ndarray, a1: numpy.ndarray, a3: numpy.ndarray, v: numpy.ndarray = array([0.0, 0.0, 0.0]), L: numpy.ndarray = array([0.0, 0.0, 0.0]))

A Nucleotide is a single oxDNA particle that forms a DNA strand Can be added to a strand using StrandObject.add_nucleotide

Parameters

• - 'A' (base) –

• 'T' –

• or 'G' ('C') –

• - Center of mass position vector (pos_com) –

• - Unit vector indicating orientation of backbone with respect to base (a1) –

• - Unit vector indicating orientation (a3) –

• - Linear velocity vector (v) –

• - Angular velocity vector (L) –

Attributes/Properties:

_base - ‘A’, ‘T’, ‘C’ or ‘G’ _a1 - Unit vector indicating orientation of backbone with respect to base _a3 - Unit vector indicating orientation (tilting) of base with respect to backbone _v - Linear velocity vector _L - Angular velocity vector pos_com - centre of mass pos_back - backbone position pos_base - position of base pos_stack - stacking direction series - table entry for writing conf and top files

property lammps

Returns a list of Series containing the following information needed to write a LAMMPS configuration data file

make_5p(base: str, angle: float = 0.626, rise: float = 0.39) → drawNA.oxdna.nucleotide.Nucleotide

Returns a new Nucleotide in the 5’ direction. The angle used for rotating the a1 vector can be specified in radians.

Args:

base

standard string base

angle (0.626)

angle of a1 rotation around a3 axis in radians

rise (0.390)

difference in a3 direction between nucleotides

Returns:

A new Nucleotide generated to be in the preferred orientation in the 5’ direction

make_across() → drawNA.oxdna.nucleotide.Nucleotide

Returns:

A Nucleotide across (aka complementary)

property pos_back

Returns the position of the backbone site

property pos_back_rel

Returns the position of the backbone centroid relative to the centre of mass i.e. it will be a vector pointing from the c.o.m. to the backbone

property pos_base

Returns the position of the base site

property pos_stack

Returns the position the stacking site

property quaternion

Returns the quaternion used to create a LAMMPS configuration

Taken from https://github.com/lorenzo-rovigatti/tacoxDNA/src/libs/oxDNA_LAMMPS.py

property series

Writes a pd.Series object containing the information needed for writing a row in pd.DataFrame that will be used for writing to file.

drawNA.oxdna.strand

Storage and Management of oxDNA strands via the Strand class

class drawNA.oxdna.strand.Strand(nucleotides: list = None)

Collection of nucleotides in the 3’ -> 5’ direction Can be added to the system using SystemObject.add_strand

Parameters

nucleotides ([]) –

Attributes/Properties:

index - strand_id sequence - string sequence of bases nucleotides - list of Nucleotides dataframe - table of values for top and conf files copy - get a copy of a Strand instance

property bonds

Returns a dataframe containing the information needed to write the bonds section of a LAMMPS configuration data file

property dataframe

Returns a pd.Dataframe which can be used to write the information for both the configuration and topology files.

property lammps

Returns a list of DataFrames containing the following information needed to write a LAMMPS configuration data file

property nucleotides

Returns the list of nucleotides, and allocates the strand index to each nucleotide for its Nucleotide.series property.

drawNA.oxdna.system

oxDNA system class - contains tools to manage, read and write oxDNA simulation configurations.

class drawNA.oxdna.system.System(box: numpy.ndarray, time: int = 0, E_pot: float = 0.0, E_kin: float = 0.0)

oxDNA simulation system, a container for strands which are composed of nucleotides.

Parameters

• - the box size of the system (box) –

• - Time of the system (time) –

• - Potential energy (E_pot) –

• - Kinetic energy (E_kin) –

add_strand(addition: drawNA.oxdna.strand.Strand, index: int = None)

Method to add strand(s) to the system

Parameters

• - accepted as Strand objects or a List of Strands (addition) –

• index (default = None) –

• Strand inserted at location given (otherwise) –

add_strands(strand_obj: list = None, index: int = None)

Add multiple strands to the system. Use a list of strands with an index indicating where they start, or a dictionary where the key is an integer and the value is a strand.

strand_lists are added in reverse order to preserve original list order

strand_dicts are added in normal order to preserve dictionary keys

Parameters

• strand_obj (-) – list or dict of strands

• index (-) – index to start adding list

property bonds

Returns the total number of bonds in the system, used for writing LAMMPS configuration data files.

property lammps

Returns a DataFrame containing the information needed to write a LAMMPS configuration data file

write_LAMMPS(prefix: str = 'out', root: str = '.')

Writes lammps.*.conf which is a configuration data file needed to run a lammps simulation.

Parameters;

prefix (‘out’) : prefix to output file

write_oxDNA(prefix: str = 'out', root: str = '.')

Writes two files oxdna.*.conf and oxdna.*.top for the configuration file and topology file required to run a simulation using oxDNA

Parameters

prefix ('out') – prefix to output files

drawNA.oxdna.system.lammps_string(dataframe: pandas.core.frame.DataFrame) → str

Formats the dataframes needed for writing the lammps dataframe to the appropriate file format.

drawNA.oxdna.system.oxDNA_string(dataframe: pandas.core.frame.DataFrame) → str

Formats the dataframes needed for writing the topology and configuration dataframes to the appropriate file format

drawNA.oxdna.utils

drawNA.oxdna.utils.get_rotation_matrix(axis: numpy.ndarray, theta: float) → numpy.ndarray

Returns a rotation matrix for rotating an angle theta (rad) around an axis vector

drawNA.oxdna.utils.next_5p(position: numpy.ndarray, a1: numpy.ndarray, a3: numpy.ndarray, angle: float, rise: float)

Returns the pos_com for a new nucleotide in the 5’ direction

drawNA.oxdna.utils.round_to_multiple(n, mo=0.34, decimal_places=2)

Function rounds to the nearest multiple of value given Returns output to (default) 2 decimal places

Parameters

• --- value (n) –

• --- "multiple_of" is the value (mo) –

• want to round to a multiple of (we) –

• --- no. of decimals to return (decimal_places) –

drawNA.lattice

drawNA.lattice._lattice

drawNA.lattice._lattice.all_same(items) → bool

Checks if all elements of a list are equal

drawNA.lattice._lattice.modify_lattice_row(grid: numpy.ndarray, difference: numpy.ndarray, change_side: str = 'yes')

Modifies the lattice sites for a given row in the grid by adding or removing the number of sites equal to the value which is stored in difference for that row

Parameters

• --- (change_side) –

• --- –

• --- –

• can be given (arguments) –

• adjustments will only be made (where) –

• the prescribed side (on) –

e.g. a difference of -5 or +11, remove (1 -> 0) or add (0 -> 1) to the lattice row, respectively. Each removal/addition occurs on the opposite side of the lattice than the previous removal/addition

drawNA.lattice._lattice.side(row_no: int, R: bool = None)

Returns either ‘onlyleft’ or ‘onlyright’ depending on which row we are modifying, i.e. row0 will always be modified at its end so if R = True, then right is the end of row0, row1 will always be modified at the opposite side to row0

drawNA.lattice.edge

class drawNA.lattice.edge.LatticeEdge(vertex_1, vertex_2, **kwargs)

drawNA.lattice.node

class drawNA.lattice.node.LatticeNode(*args, **kwargs)

drawNA.lattice.route

class drawNA.lattice.route.LatticeRoute(nodes: List[drawNA.lattice.node.LatticeNode] = [])

Strand which follows the path defined by a set of LatticeNodes which are joined by LatticeEdges

add_node(addition: drawNA.lattice.node.LatticeNode, index: int = None, update: bool = False)

Method to add strand(s) to the system

Parameters

• - accepted as Strand objects or a List of Strands (addition) –

• index (default = None) –

• Strand inserted at location given (otherwise) –

add_nodes(node_obj: list = None, index: int = None)

Add multiple strands to the system. Use a list of strands with an index indicating where they start, or a dictionary where the key is an integer and the value is a strand.

strand_lists are added in reverse order to preserve original list order

strand_dicts are added in normal order to preserve dictionary keys

Parameters

• node_obj (-) – list or dict of strands

• index (-) – index to start adding list

update_strands()

Generate strands between 2D lattice nodes, then generate a single strand representing the route

drawNA.lattice.utils

drawNA.lattice.utils.find_closest(myList, myNumber)

Credit: https://stackoverflow.com/questions/12141150 Assumes myList is sorted. Returns closest value to myNumber.

If two numbers are equally close, return the smallest number.

drawNA.lattice.utils.find_crossover_locations(max_size: int = 30, bp_per_turn: float = 10.45, kind: str = 'half', origin: int = 0) → dict

Function which returns an array containing the best locations for half or whole turns of the DNA strand where the strand will stay in plane and have the least strain/stress build-up.

This is computed given the number of basepairs per turn & locations are given in no. of base pairs

Arguments: bp_per_turn - (default: 10.45) kind - either half turns or whole turns max_size - max no. of turns to base pairs to the list origin - what number crossovers start at, either 0 (python indexing) or 1

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