base

Utility functions for oxDNA systems, strands and nucleotides.

base.py includes the classes: System, Strand, Nucleotide

class base.Nucleotide(cm_pos, a1, a3, base, btype=None, L=<mynumpy.mynumpy_core.array object>, v=<mynumpy.mynumpy_core.array object>, n3=-1)

Nucleotides compose Strands.

Parameters:
  • cm_pos – Center of mass position, e.g. [0, 0, 0]
  • a1 – Unit vector indicating orientation of backbone with respect to base, e.g. [1, 0, 0]
  • a3 – Unit vector indicating orientation (tilting) of base with respect to backbone, e.g. [0, 0, 1]
  • base –

    Identity of base, which must be designated with either numbers or letters (this is called type in the c++ code). Confusingly enough, this is similar to Particle.btype in oxDNA.

    Number: {0,1,2,3} or any number in between (-inf,-7) and (10, inf). To use specific sequences (or an alphabet large than four) one should start from the complementary pair 10 and -7. Complementary pairs are such that base_1 + base_2 = 3

    Letter: {A,G,T,C} (these will be translated to {0, 1, 3, 2}). These are set in the dictionaries: number_to_base, base_to_number

  • btype – Identity of base. Unused at the moment.
  • L – Angular velocity
  • v – Velocity
cm_pos

Position of the center of mass.

index

Index of the nucleotide.

pos_back

Position of the backbone centroid.

pos_base

Position of the base centroid.

pos_stack

Position of the stacking site centroid.

copy(disp=None, rot=None)

Returns a copy of the nucleotide, with optional translation and/or rotation.

Parameters:
  • disp – displacement vector to translate the copied nucleotide
  • rot – rotation matrix to rotate the copied nucleotide
distance(other, PBC=True, box=None)

Returns the distance to another nucleotide.

Parameters:
  • other – the other Nucleotide object
  • PBC – boolean. If true, considers periodic boundary conditions and returns the minimum image distance.
  • box – box dimensions in a numpy array
get_base()

Returns the base id. If the base is in [“A”, “G”, “C”, “T”, 0, 1, 2, 3], returns a string containing the letter of the base id. Otherwise, returns a string containing the number of the base id.

get_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.

rotate(R, origin=None)

Rotates the nucleotide.

Parameters:
  • R – rotation matrix to rotate the nucleotide
  • origin – the point around which the nucleotide rotates; defaults to be self.cm_pos
translate(disp)

Translates the nucleotide.

Parameters:disp – displacement vector to translate the nucleotide
class base.Strand

Strands are composed of Nucleotides. Access nucleotide objects of Strand strand1 by strand1._nucleotides[nucleotide_index]. Strands can be contained in a System.

N

Length of the strand (i.e. the number of nucleotides).

sequence

Sequence of the strand.

cm_pos

Center of mass of the strand.

index

Index of the strand.

add_nucleotide(n)

Adds a nucleotide to the strand.

Parameters:n – Nucleotide object to be added.
append(other)

Returns an extended strand which is formed by appending another strand to the current strand. Note that the current strand is not changed.

Parameters:other – the other Strand object
bring_in_box_nucleotides(box)

Brings nucleotides of the strand back into the box.

Parameters:box – box dimensions in a numpy array
copy()

Returns a copy of the strand.

get_slice(start=0, end=None)

Returns a slice of the strand.

Parameters:
  • start – starting point of the slice (default is 0)
  • end – ending point of the slice (default is end of strand)
make_circular(check_join_len=False)

Connect the ends of the strand to make it circular.

Parameters:check_join_len – boolean. If true, checks whether the ends of the strand are close enough.
make_noncircular()

Disconnect the ends of a circular strand.

overlaps_with(other, box)

Returns True if this strand overlaps with the other strand, False otherwise.

Parameters:
  • other – the other Strand object
  • box – box dimensions in a numpy array
rotate(R, origin=None)

Rotates the strand.

Parameters:
  • R – rotation matrix to rotate the system
  • origin – the point around which the strand rotates; defaults to be self.cm_pos (NB this does not exist at the moment, perhaps a bug)
set_cm_pos(new_pos)

Sets the center of mass of the strand to a new position by moving all the nucleotides.

Parameters:new_pos – new center of mass position
set_sequence(seq)

Sets the sequence of the strand.

Parameters:seq – either a string of letters (A,T,C,G), or a list of ints (0,1,2,3). Should have the same length as the strand.
translate(amount)

Translates the strand.

Parameters:amount – displacement vector to translate the strand
class base.System(box, time=0, E_pot=0, E_kin=0)

Object representing an oxDNA system. Contains strands. Access strand objects of System system1 by system1._strands[strand_index].

Parameters:
  • box – Box size of the system, e.g. box = [50, 50, 50]
  • time – Time of the system
  • E_pot – Potential energy
  • E_kin – Kinetic energy
N

Number of nucleotides in the system.

N_strands

Number of strands in the system.

E_pot

Potential energy

E_kin

Kinetic energy

E_tot

Total energy

add_strand(s, check_overlap=True)

Adds a Strand to the System. Returns True if non-overlapping, False otherwise.

Parameters:
  • s – Strand object to be added
  • check_overlap – boolean. If true, checks for overlap. Defaults to be true.
add_strands(ss, check_overlap=True)

Adds multiple Strands to the System. Returns True if non-overlapping, False otherwise.

Parameters:
  • ss – List of Strand objects to be added
  • check_overlap – boolean. If true, checks for overlap. Defaults to be true.
contains_overlaps()

Returns True if the system contains strand overlaps, False otherwise.

copy()

Returns a copy of the system.

get_nucleotide_list()

Returns a list of Nucleotide objects in the system.

get_reduced(according_to, bbox=None, check_overlap=False)

Returns a reduced copy of the system with only strands set to be visible in the visibility file.

Parameters:
  • according_to – path to visibility file
  • bbox – box size of the reduced system
  • check_overlap – boolean. If true, checks for strand overlap.
get_sequences()

Returns the sequence of the system as a list of lists containing strand sequences.

get_unique_seq()

Returns the unique sequences in the system.

join(other, box=None)

Returns a system formed by joining this system with another system.

Parameters:
  • other – the other System object
  • box – box size in a numpy array
map_nucleotides_to_strands()

Fills the nucl_id -> strand_id array self._nucleotide_to_strand

print_lorenzo_output(conf_name, top_name, visibility=None)

Outputs oxDNA configuration and topology files for the system.

Parameters:
  • conf_name – configuration file name
  • top_name – topology file name
  • visibility – path to visibility file (default is None - everything is visible)
rotate(amount, origin=None)

Rotates the system.

Parameters:
  • amount – rotation matrix
  • origin – the point around which the system rotates
set_visibility(arg=None)

Sets visibility according to a visibility file.

Parameters:arg – visibility file
translate(amount)

Translates the system.

Parameters:amount – displacement vector to translate the system