oxDNA
Table of Contents
Installation
Usage
Input file
Configuration and topology files
Relaxing initial configurations
Improving performance
Efficient GPU usage
External forces
Observables
Umbrella sampling
Forward Flux Sampling
Events
oxDNA Analysis Tools
Oxpy
oxDNA
Index
Index
_
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A
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B
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C
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D
|
E
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F
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G
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H
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I
|
K
|
L
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M
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N
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O
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P
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R
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S
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T
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U
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V
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W
_
_from_old (oxDNA_analysis_tools.UTILS.data_structures.Strand attribute)
A
a1 (oxDNA_analysis_tools.UTILS.data_structures.Monomer attribute)
a1s (oxDNA_analysis_tools.UTILS.data_structures.Configuration attribute)
(oxpy.core.FlattenedConfigInfo property)
a3 (oxDNA_analysis_tools.UTILS.data_structures.Monomer attribute)
a3s (oxDNA_analysis_tools.UTILS.data_structures.Configuration attribute)
(oxpy.core.FlattenedConfigInfo property)
add_output() (oxpy.core.OxpyManager method)
align() (in module oxDNA_analysis_tools.align)
align_positions() (in module oxDNA_analysis_tools.pca)
analyse() (oxpy.core.analysis.AnalysisBackend method)
AnalysisBackend (class in oxpy.core.analysis)
anm_parameterize() (in module oxDNA_analysis_tools.anm_parameterize)
append() (oxDNA_analysis_tools.UTILS.data_structures.Strand method)
(oxDNA_analysis_tools.UTILS.data_structures.System method)
as_RepulsiveSphere() (oxpy.core.forces.BaseForce method)
attraction_plane() (in module oxDNA_analysis_tools.external_force_utils.forces)
axis (oxDNA_analysis_tools.duplex_finder.Duplex attribute)
B
backbone_flexibility() (in module oxDNA_analysis_tools.backbone_flexibility)
backbone_site() (oxpy.core.DNANucleotide method)
(oxpy.core.RNANucleotide method)
base_site() (oxpy.core.DNANucleotide method)
(oxpy.core.RNANucleotide method)
BaseBox (class in oxpy.core)
BaseForce (class in oxpy.core.forces)
BaseInteraction (class in oxpy.core)
BaseObservable (class in oxpy.core.observables)
BaseParticle (class in oxpy.core)
bbvector3_site() (oxpy.core.RNANucleotide method)
bbvector5_site() (oxpy.core.RNANucleotide method)
begin_energy_computation() (oxpy.core.BaseInteraction method)
block (oxDNA_analysis_tools.UTILS.data_structures.Chunk attribute)
bond_analysis() (in module oxDNA_analysis_tools.bond_analysis)
box (oxDNA_analysis_tools.UTILS.data_structures.Configuration attribute)
(oxpy.core.ConfigInfo property)
box_sides (oxpy.core.BaseBox property)
(oxpy.core.ConfigInfo property)
btype (oxDNA_analysis_tools.UTILS.data_structures.Monomer attribute)
(oxpy.core.BaseParticle property)
C
Celsius_to_oxDNA() (in module oxpy.utils)
center (oxpy.core.forces.RepulsiveSphere property)
centroid() (in module oxDNA_analysis_tools.centroid)
check() (in module oxDNA_analysis_tools.config)
Chunk (class in oxDNA_analysis_tools.UTILS.data_structures)
Chunker() (in module oxDNA_analysis_tools.UTILS.RyeReader)
circular (oxDNA_analysis_tools.UTILS.data_structures.Strand attribute)
,
[1]
conf_step (oxpy.core.analysis.AnalysisBackend property)
conf_to_str() (in module oxDNA_analysis_tools.UTILS.RyeReader)
config_info (oxpy.core.observables.BaseObservable property)
config_info() (oxpy.core.analysis.AnalysisBackend method)
(oxpy.core.OxpyManager method)
ConfigInfo (class in oxpy.core)
Configuration (class in oxDNA_analysis_tools.UTILS.data_structures)
ConfInfo (class in oxDNA_analysis_tools.UTILS.data_structures)
contact_map() (in module oxDNA_analysis_tools.contact_map)
Context (class in oxpy.core)
current_step (oxpy.core.ConfigInfo property)
(oxpy.core.OxpyManager property)
D
db_to_forcelist() (in module oxDNA_analysis_tools.db_to_force)
decimate() (in module oxDNA_analysis_tools.decimate)
describe() (in module oxDNA_analysis_tools.UTILS.RyeReader)
deviations() (in module oxDNA_analysis_tools.deviations)
dir (oxpy.core.forces.MovingTrap property)
display_files() (in module oxDNA_analysis_tools.UTILS.oxview)
distance() (in module oxDNA_analysis_tools.distance)
distance_deviations() (in module oxDNA_analysis_tools.multidimensional_scaling_mean)
DNANucleotide (class in oxpy.core)
done() (oxpy.core.analysis.AnalysisBackend method)
Duplex (class in oxDNA_analysis_tools.duplex_finder)
duplex_finder() (in module oxDNA_analysis_tools.duplex_finder)
E
end1 (oxDNA_analysis_tools.duplex_finder.Duplex attribute)
end2 (oxDNA_analysis_tools.duplex_finder.Duplex attribute)
energy (oxDNA_analysis_tools.UTILS.data_structures.Configuration attribute)
ext_potential (oxpy.core.BaseParticle property)
F
file_info() (in module oxDNA_analysis_tools.file_info)
file_size (oxDNA_analysis_tools.UTILS.data_structures.Chunk attribute)
find_duplex() (in module oxDNA_analysis_tools.duplex_finder)
fit_PL() (in module oxDNA_analysis_tools.persistence_length)
fit_plane() (in module oxDNA_analysis_tools.UTILS.geom)
flattened_conf (oxpy.core.analysis.AnalysisBackend property)
(oxpy.core.ConfigInfo property)
FlattenedConfigInfo (class in oxpy.core)
FlattenedVectorArray (class in oxpy.core)
flro_patchy_conf() (in module oxDNA_analysis_tools.UTILS.oxview)
force (oxpy.core.BaseParticle property)
forces (oxpy.core.ConfigInfo property)
forces2db() (in module oxDNA_analysis_tools.forces2db)
from_path() (in module oxDNA_analysis_tools.UTILS.oxview)
G
generate_default_input() (in module oxpy.utils)
get_abs_pos() (oxpy.core.BaseBox method)
get_angle_between() (in module oxDNA_analysis_tools.duplex_angle_plotter)
get_bool() (oxpy.core.InputFile method)
get_centroid() (in module oxDNA_analysis_tools.clustering)
get_chunk_size() (in module oxDNA_analysis_tools.config)
get_confs() (in module oxDNA_analysis_tools.UTILS.RyeReader)
get_DNA_axis() (in module oxDNA_analysis_tools.UTILS.geom)
get_force_by_id() (oxpy.core.ConfigInfo method)
get_input_parameter() (in module oxDNA_analysis_tools.UTILS.RyeReader)
get_kwdata() (oxDNA_analysis_tools.UTILS.data_structures.Strand method)
get_length() (oxDNA_analysis_tools.UTILS.data_structures.Strand method)
get_observable_by_id() (oxpy.core.ConfigInfo method)
get_output_string() (oxpy.core.observables.BaseObservable method)
get_r() (in module oxDNA_analysis_tools.persistence_length)
get_RNA_axis() (in module oxDNA_analysis_tools.UTILS.geom)
get_sequence() (oxDNA_analysis_tools.UTILS.data_structures.Strand method)
get_settings() (oxpy.core.BaseBox method)
(oxpy.core.observables.BaseObservable method)
get_top_info() (in module oxDNA_analysis_tools.UTILS.RyeReader)
get_top_info_from_traj() (in module oxDNA_analysis_tools.UTILS.RyeReader)
get_top_string() (in module oxDNA_analysis_tools.UTILS.RyeReader)
get_traj_info() (in module oxDNA_analysis_tools.UTILS.RyeReader)
group_name (oxpy.core.forces.BaseForce property)
H
harmonic_trap() (in module oxDNA_analysis_tools.external_force_utils.forces)
has_custom_stress_tensor() (oxpy.core.BaseInteraction method)
hb_list() (oxpy.core.observables.HBList method)
HBList (class in oxpy.core.observables)
I
id (oxDNA_analysis_tools.UTILS.data_structures.ConfInfo attribute)
(oxDNA_analysis_tools.UTILS.data_structures.Monomer attribute)
(oxDNA_analysis_tools.UTILS.data_structures.Strand attribute)
,
[1]
(oxpy.core.forces.BaseForce property)
(oxpy.core.Molecule property)
(oxpy.core.observables.BaseObservable property)
idxs (oxDNA_analysis_tools.UTILS.data_structures.TrajInfo attribute)
inbox() (in module oxDNA_analysis_tools.UTILS.RyeReader)
incl_v (oxDNA_analysis_tools.UTILS.data_structures.TrajInfo attribute)
index (oxDNA_analysis_tools.duplex_finder.Duplex attribute)
(oxpy.core.BaseParticle property)
init() (oxpy.core.BaseBox method)
(oxpy.core.forces.BaseForce method)
(oxpy.core.observables.BaseObservable method)
(oxpy.core.OxpyManager method)
init_from_filename() (oxpy.core.InputFile method)
InputFile (class in oxpy.core)
int_centers (oxpy.core.BaseParticle property)
interaction (oxpy.core.ConfigInfo property)
is_bonded() (oxpy.core.BaseParticle method)
is_circular() (oxDNA_analysis_tools.UTILS.data_structures.Strand method)
is_last (oxDNA_analysis_tools.UTILS.data_structures.Chunk attribute)
is_old() (oxDNA_analysis_tools.UTILS.data_structures.Strand method)
K
Kelvin_to_oxDNA() (in module oxpy.utils)
keys() (oxpy.core.InputFile method)
L
L (oxpy.core.BaseParticle property)
linear_read() (in module oxDNA_analysis_tools.UTILS.RyeReader)
load_options() (oxpy.core.OxpyManager method)
loro_patchy_conf() (in module oxDNA_analysis_tools.UTILS.oxview)
LT2DCOMTrap (class in oxpy.core.forces)
LTCOMTrap (class in oxpy.core.forces)
M
make_heatmap() (in module oxDNA_analysis_tools.pca)
map_confs_to_pcs() (in module oxDNA_analysis_tools.pca)
mean() (in module oxDNA_analysis_tools.mean)
min_image() (in module oxDNA_analysis_tools.distance)
(oxpy.core.BaseBox method)
minify() (in module oxDNA_analysis_tools.minify)
Molecule (class in oxpy.core)
molecules() (oxpy.core.ConfigInfo method)
Monomer (class in oxDNA_analysis_tools.UTILS.data_structures)
monomers (oxDNA_analysis_tools.UTILS.data_structures.Strand attribute)
,
[1]
MovingTrap (class in oxpy.core.forces)
multidimensional_scaling_mean() (in module oxDNA_analysis_tools.multidimensional_scaling_mean)
mutual_trap() (in module oxDNA_analysis_tools.external_force_utils.forces)
N
N() (oxpy.core.ConfigInfo method)
n3 (oxDNA_analysis_tools.UTILS.data_structures.Monomer attribute)
(oxpy.core.BaseParticle property)
n5 (oxDNA_analysis_tools.UTILS.data_structures.Monomer attribute)
(oxpy.core.BaseParticle property)
nbases (oxDNA_analysis_tools.UTILS.data_structures.TopInfo attribute)
nconfs (oxDNA_analysis_tools.UTILS.data_structures.TrajInfo attribute)
notify() (oxpy.core.ConfigInfo method)
O
oat_multiprocesser() (in module oxDNA_analysis_tools.UTILS.oat_multiprocesser)
observables (oxpy.core.ConfigInfo property)
offset (oxDNA_analysis_tools.UTILS.data_structures.Chunk attribute)
(oxDNA_analysis_tools.UTILS.data_structures.ConfInfo attribute)
orientation (oxpy.core.BaseParticle property)
output() (in module oxDNA_analysis_tools.deviations)
output_bonds() (in module oxDNA_analysis_tools.output_bonds)
oxdna_conf() (in module oxDNA_analysis_tools.UTILS.oxview)
oxDNA_PDB() (in module oxDNA_analysis_tools.oxDNA_PDB)
OxpyManager (class in oxpy.core)
P
pair (oxDNA_analysis_tools.UTILS.data_structures.Monomer attribute)
pair_interaction() (oxpy.core.BaseInteraction method)
pair_interaction_bonded() (oxpy.core.BaseInteraction method)
pair_interaction_nonbonded() (oxpy.core.BaseInteraction method)
pair_interaction_term() (oxpy.core.BaseInteraction method)
pairs2db() (in module oxDNA_analysis_tools.pairs2db)
parse_dot_bracket() (in module oxDNA_analysis_tools.db_to_force)
particles (oxpy.core.analysis.AnalysisBackend property)
(oxpy.core.Molecule property)
particles() (oxpy.core.ConfigInfo method)
path (oxDNA_analysis_tools.UTILS.data_structures.TopInfo attribute)
(oxDNA_analysis_tools.UTILS.data_structures.TrajInfo attribute)
pca() (in module oxDNA_analysis_tools.pca)
PDB_oxDNA() (in module oxDNA_analysis_tools.PDB_oxDNA)
perform_DBSCAN() (in module oxDNA_analysis_tools.clustering)
persistence_length() (in module oxDNA_analysis_tools.persistence_length)
pos (oxDNA_analysis_tools.duplex_finder.Duplex attribute)
(oxDNA_analysis_tools.UTILS.data_structures.Monomer attribute)
(oxpy.core.BaseParticle property)
pos0 (oxpy.core.forces.BaseForce property)
(oxpy.core.forces.MovingTrap property)
positions (oxDNA_analysis_tools.UTILS.data_structures.Configuration attribute)
(oxpy.core.FlattenedConfigInfo property)
potential() (oxpy.core.forces.BaseForce method)
potential_grid (oxpy.core.forces.LT2DCOMTrap property)
(oxpy.core.forces.LTCOMTrap property)
print_configuration() (oxpy.core.OxpyManager method)
print_timings() (oxpy.core.OxpyManager method)
R
r0 (oxpy.core.forces.RepulsiveSphere property)
r_ext (oxpy.core.forces.RepulsiveSphere property)
rate (oxpy.core.forces.BaseForce property)
(oxpy.core.forces.MovingTrap property)
(oxpy.core.forces.RepulsiveSphere property)
read_force_file() (in module oxDNA_analysis_tools.external_force_utils.force_reader)
read_next_configuration() (oxpy.core.analysis.AnalysisBackend method)
remove_output() (oxpy.core.OxpyManager method)
repulsion_plane() (in module oxDNA_analysis_tools.external_force_utils.forces)
repulsion_sphere() (in module oxDNA_analysis_tools.external_force_utils.forces)
RepulsiveSphere (class in oxpy.core.forces)
RNANucleotide (class in oxpy.core)
rotating_harmonic_trap() (in module oxDNA_analysis_tools.external_force_utils.forces)
run() (oxpy.core.OxpyManager method)
run_complete() (oxpy.core.OxpyManager method)
S
set_chunk_size() (in module oxDNA_analysis_tools.config)
set_computed_r() (oxpy.core.BaseInteraction method)
set_old() (oxDNA_analysis_tools.UTILS.data_structures.Strand method)
set_sequence() (oxDNA_analysis_tools.UTILS.data_structures.Strand method)
size (oxDNA_analysis_tools.UTILS.data_structures.ConfInfo attribute)
split_trajectory() (in module oxDNA_analysis_tools.clustering)
sqr_min_image_distance() (oxpy.core.BaseBox method)
stack3_site() (oxpy.core.RNANucleotide method)
stack5_site() (oxpy.core.RNANucleotide method)
stacking_site() (oxpy.core.DNANucleotide method)
(oxpy.core.RNANucleotide method)
start1 (oxDNA_analysis_tools.duplex_finder.Duplex attribute)
start2 (oxDNA_analysis_tools.duplex_finder.Duplex attribute)
steps_run() (oxpy.core.OxpyManager method)
stiff (oxpy.core.forces.BaseForce property)
(oxpy.core.forces.MovingTrap property)
Strand (class in oxDNA_analysis_tools.UTILS.data_structures)
strand (oxDNA_analysis_tools.UTILS.data_structures.Monomer attribute)
strand_describe() (in module oxDNA_analysis_tools.UTILS.RyeReader)
strand_id (oxpy.core.BaseParticle property)
strands (oxDNA_analysis_tools.UTILS.data_structures.System attribute)
string() (in module oxDNA_analysis_tools.external_force_utils.forces)
subscribe() (oxpy.core.ConfigInfo method)
subset() (in module oxDNA_analysis_tools.subset_trajectory)
superimpose() (in module oxDNA_analysis_tools.superimpose)
svd_align() (in module oxDNA_analysis_tools.align)
System (class in oxDNA_analysis_tools.UTILS.data_structures)
system_energy() (oxpy.core.OxpyManager method)
T
temperature (oxpy.core.ConfigInfo property)
time (oxDNA_analysis_tools.duplex_finder.Duplex attribute)
(oxDNA_analysis_tools.UTILS.data_structures.Configuration attribute)
top_file (oxDNA_analysis_tools.UTILS.data_structures.System attribute)
TopInfo (class in oxDNA_analysis_tools.UTILS.data_structures)
topology_id (oxpy.core.Molecule property)
torque (oxpy.core.BaseParticle property)
TrajInfo (class in oxDNA_analysis_tools.UTILS.data_structures)
type (oxDNA_analysis_tools.UTILS.data_structures.Strand attribute)
,
[1]
(oxpy.core.BaseParticle property)
(oxpy.core.forces.BaseForce property)
types (oxpy.core.FlattenedConfigInfo property)
U
update_CPU_data_structures() (oxpy.core.OxpyManager method)
update_temperature() (oxpy.core.OxpyManager method)
V
V (oxpy.core.BaseBox property)
value() (oxpy.core.forces.BaseForce method)
vectorized_min_image() (in module oxDNA_analysis_tools.distance)
vel (oxpy.core.BaseParticle property)
W
write_conf() (in module oxDNA_analysis_tools.UTILS.RyeReader)
write_force_file() (in module oxDNA_analysis_tools.external_force_utils.force_reader)