From 263f4650508bc80e40b63795b3f1bb34c676f4ac Mon Sep 17 00:00:00 2001 From: CI workflow Date: Fri, 31 May 2024 08:55:09 +0000 Subject: [PATCH] Update documentation --- _sources/forces.md.txt | 29 +++++++++++++++++++++++++++++ _sources/observables.md.txt | 5 +++++ forces.html | 30 ++++++++++++++++++++++++++++++ index.html | 1 + oat/api.html | 2 +- oat/cli.html | 8 ++++++-- oat/utils.html | 7 +++++-- observables.html | 5 +++++ searchindex.js | 2 +- 9 files changed, 83 insertions(+), 6 deletions(-) diff --git a/_sources/forces.md.txt b/_sources/forces.md.txt index dd7e38515..cc4ee84ba 100644 --- a/_sources/forces.md.txt +++ b/_sources/forces.md.txt @@ -232,6 +232,35 @@ The following snippet defines a repulsive sphere that acts on the first 50 nucle ```` +## Yukawa sphere + +This force encloses particle(s) in a sphere that interacts through a purely repulsive [WCA](http://www.sklogwiki.org/SklogWiki/index.php/Weeks-Chandler-Andersen_reference_system_model) potential complemented by a Yukawa potential of the form {math}`A \exp(-r / \lambda)`, where {math}`A` is the interaction strength (which can be either positive or negative), {math}`r` is the distance between a particle and the sphere surface, {math}`\lambda` is the Debye length. The relevant keys are: + +* `particle = `: comma-separated list of indices of particles to apply the force to. A value of `-1` or `all` applies it to all particles. Entries separated by a dash "-" get expanded in a list of all the particles on a same strand comprised between the two indices. For instance, `particle = 1,2,5-7` applies the force to 1,2,5,6,7 if 5 and 7 are on the same strand. +* `radius = `: radius of the sphere. +* `debye_A = `: Strength the Yukawa interaction. +* `debye_length = `: Debye length of the Yukawa interaction. +* `WCA_epsilon = `: strength of the WCA repulsion, defaults to `1`. +* `WCA_sigma = `: diameter of the WCA repulsion, defaults to `1`. +* `WCA_n = `: exponent of the WCA repulsion, defaults to `6`. +* `[cutoff = ]`: cutoff of the interaction, defaults to four times the Debye length. +* `[center = ,,]`: centre of the sphere, defaults to `0,0,0`. + +````{admonition} Example + +The following snippet defines a Yukawa sphere that acts on all nucleotides, confining them within a sphere of radius 5 centred in {math}`(0, 0, 10)`. The WCA parameters are set to their defaults, while the Debye length and strength are `5` and `-10`, respectively. + + { + type = yukawa_sphere + radius = 5 + center = 0,0,10 + debye_length = 5 + debye_A = -10 + particle = all + } + +```` + ## `type = com` stiff = diff --git a/_sources/observables.md.txt b/_sources/observables.md.txt index 8cbcd0a3c..0edf2f73b 100644 --- a/_sources/observables.md.txt +++ b/_sources/observables.md.txt @@ -86,6 +86,11 @@ The following options are supported by all observabes: * `[id = ]`: a unique identifier that can be used to refer to this specific observable (see *e.g.* {meth}`~oxpy.core.ConfigInfo.get_observable_by_id`). * `[update_every = ]`: the number of time steps every which the observable is updated (but no output is printed). Note that this is supported only by some observables. +The following options are supported by some observables, but we plan to extend their usage: + +* `[general_format = ]`: print output numbers with the `printf`'s `%g` type field (see *e.g.* [here](https://stackoverflow.com/a/54162153/5140209) for details). Defaults to `false`. +* `[precision = ]`: number of significant digits after decimal with which numbers should be printed. Defaults to 6. + ## Simulation time Print the current simulation time as the number of steps or as molecular-dynamics time. diff --git a/forces.html b/forces.html index 23ecd6424..92c811701 100644 --- a/forces.html +++ b/forces.html @@ -63,6 +63,7 @@
  • Rotating harmonic trap
  • Repulsion plane
  • Repulsive sphere
    • +
  • Yukawa sphere
  • type = com
  • type = LJ_wall
  • type = sawtooth
    • @@ -328,6 +329,35 @@

    Repulsive sphere +

    Yukawa sphere

    +

    This force encloses particle(s) in a sphere that interacts through a purely repulsive WCA potential complemented by a Yukawa potential of the form \(A \exp(-r / \lambda)\), where \(A\) is the interaction strength (which can be either positive or negative), \(r\) is the distance between a particle and the sphere surface, \(\lambda\) is the Debye length. The relevant keys are:

    +
      +

    • particle = <int>: comma-separated list of indices of particles to apply the force to. A value of -1 or all applies it to all particles. Entries separated by a dash “-” get expanded in a list of all the particles on a same strand comprised between the two indices. For instance, particle = 1,2,5-7 applies the force to 1,2,5,6,7 if 5 and 7 are on the same strand.

      • +

    • radius = <float>: radius of the sphere.

      • +

    • debye_A = <float>: Strength the Yukawa interaction.

      • +

    • debye_length = <float>: Debye length of the Yukawa interaction.

      • +

    • WCA_epsilon = <float>: strength of the WCA repulsion, defaults to 1.

      • +

    • WCA_sigma = <float>: diameter of the WCA repulsion, defaults to 1.

      • +

    • WCA_n = <int>: exponent of the WCA repulsion, defaults to 6.

      • +

    • [cutoff = <float>]: cutoff of the interaction, defaults to four times the Debye length.

      • +

    • [center = <float>,<float>,<float>]: centre of the sphere, defaults to 0,0,0.

      • +
    +
    +

    Example

    +

    The following snippet defines a Yukawa sphere that acts on all nucleotides, confining them within a sphere of radius 5 centred in \((0, 0, 10)\). The WCA parameters are set to their defaults, while the Debye length and strength are 5 and -10, respectively.

    +
    {
+type = yukawa_sphere
+radius = 5
+center = 0,0,10
+debye_length = 5
+debye_A = -10
+particle = all
+}
+
    +
    +
    +

    type = com

    stiff = <float>
diff --git a/index.html b/index.html
index fc1fbd32d..b0ac1d4be 100644
--- a/index.html
+++ b/index.html
@@ -164,6 +164,7 @@ 
    oxDNA
 
  • Rotating harmonic trap
    • 
 
  • Repulsion plane
    • 
 
  • Repulsive sphere
    • 
+
  • Yukawa sphere
    • 
 
  • type = com
    • 
 
  • type = LJ_wall
    • 
 
  • type = sawtooth
    • 
diff --git a/oat/api.html b/oat/api.html
index f5746148f..cdbf3d3e5 100644
--- a/oat/api.html
+++ b/oat/api.html
@@ -222,7 +222,7 @@ 
    Backbone flexibility
 
    
 
    
-oxDNA_analysis_tools.backbone_flexibility.backbone_flexibility(traj_info: TrajInfo, top_info: TopInfo, system: System, ncpus=1) → Tuple[array]
    
+oxDNA_analysis_tools.backbone_flexibility.backbone_flexibility(traj_info: TrajInfo, top_info: TopInfo, system: System, ncpus=1) → Tuple[ndarray, ndarray]
 
    Calculate backbone flexibility of a trajectory.
    
 
    
 
    Parameters:
    
diff --git a/oat/cli.html b/oat/cli.html
index 1dc2ef447..d10fc10cc 100644
--- a/oat/cli.html
+++ b/oat/cli.html
@@ -897,8 +897,8 @@ 
    Named Arguments
    
 
    Convert oxDNA files to PDB.  This converter can handle oxDNANM protein simulation files.
    
 
    
-
    usage: oat oxDNA_PDB [-h] [-o OUTPUT] [-d OUTPUT_DIRECTION] [-H] [-u] [-1]
-                     [-r RMSF_BFACTOR]
+
    usage: oat oxDNA_PDB [-h] [-o OUTPUT] [-d OUTPUT_DIRECTION] [-q] [-H] [-u]
+                     [-1] [-r RMSF_BFACTOR]
                      topology configuration direction [pdbfiles ...]
 
    
 
    
@@ -928,6 +928,10 @@ 
    Named Arguments
 
    
-oxDNA_analysis_tools.UTILS.RyeReader.inbox(conf: Configuration, center=False) → Configuration
    
+oxDNA_analysis_tools.UTILS.RyeReader.inbox(conf: Configuration, center: bool = True, centerpoint: str | ndarray = 'bc') → Configuration
 
    Modify the positions attribute such that all positions are inside the box.
    
+
    For cohesive structures, you almost always want center=True.
+For diffuse simulations, you probably want center=False.
    
 
    
 
    Parameters:
    
 
      
 
    • conf (Configuration) – The configuration to inbox
      • 
-
    • center (bool) – If True, center the configuration on the box
      • 
+
    • center (bool) – If True, center the configuration in the box (default True)
      • 
+
    • centerpoint (str|np.ndarray) – If ‘bc’, center in the box, if array, center on the array (default ‘bc’)
      • 
 
    
 
    
 
    Returns:
    
diff --git a/observables.html b/observables.html
index 0277ee2b3..a7020ae95 100644
--- a/observables.html
+++ b/observables.html
@@ -200,6 +200,11 @@ 
    Common options[id = <string>]: a unique identifier that can be used to refer to this specific observable (see e.g. get_observable_by_id()).
    
 
  • [update_every = <int>]: the number of time steps every which the observable is updated (but no output is printed). Note that this is supported only by some observables.
    • 
 
+
    The following options are supported by some observables, but we plan to extend their usage:
    
+
      
+
    • [general_format = <bool>]: print output numbers with the printf’s %g type field (see e.g. here for details). Defaults to false.
      • 
+
    • [precision = <int>]: number of significant digits after decimal with which numbers should be printed. Defaults to 6.
      • 
+

    Simulation time

    diff --git a/searchindex.js b/searchindex.js index 8c93bab5c..4125b2919 100644 --- a/searchindex.js +++ b/searchindex.js @@ -1 +1 @@ -Search.setIndex({"docnames": ["configurations", "events", "ffs", "forces", "index", "input", "install", "oat/api", "oat/cli", "oat/forces", "oat/index", "oat/utils", "observables", "oxpy/extending/forces", "oxpy/extending/observables", "oxpy/index", "oxpy/modules/analysis", "oxpy/modules/core/core", "oxpy/modules/core/forces", "oxpy/modules/core/observables", "oxpy/modules/utils", "performance", "relaxation", "scaling", "umbrella_sampling", "usage"], "filenames": ["configurations.md", "events.md", "ffs.md", "forces.md", "index.md", "input.md", "install.md", "oat/api.md", "oat/cli.md", "oat/forces.md", "oat/index.md", "oat/utils.md", "observables.md", "oxpy/extending/forces.md", "oxpy/extending/observables.md", "oxpy/index.md", "oxpy/modules/analysis.md", "oxpy/modules/core/core.md", "oxpy/modules/core/forces.md", "oxpy/modules/core/observables.md", 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"writing-observables-in-python"]], "Oxpy": [[15, "oxpy"]], "An example of a simple simulation": [[15, "an-example-of-a-simple-simulation"]], "An example of a simple analysis": [[15, "an-example-of-a-simple-analysis"]], "Library API": [[15, "library-api"]], "Exceptions": [[15, "exceptions"]], "Extending Oxpy": [[15, "extending-oxpy"]], "The analysis module": [[16, "the-analysis-module"]], "The core module": [[17, "the-core-module"]], "The core.forces module": [[18, "the-core-forces-module"]], "The core.observables module": [[19, "the-core-observables-module"]], "The utils module": [[20, "the-utils-module"]], "Improving performance": [[21, "improving-performance"]], "Molecular dynamics": [[21, "molecular-dynamics"]], "GPU simulations": [[21, "gpu-simulations"]], "Monte Carlo": [[21, "monte-carlo"]], "Relaxing initial configurations": [[22, "relaxing-initial-configurations"]], "First stage: Monte Carlo relaxation": [[22, "first-stage-monte-carlo-relaxation"]], "Second stage: molecular 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oxdna_analysis_tools.pca)": [[7, "oxDNA_analysis_tools.pca.align_positions"]], "anm_parameterize() (in module oxdna_analysis_tools.anm_parameterize)": [[7, "oxDNA_analysis_tools.anm_parameterize.anm_parameterize"]], "axis (oxdna_analysis_tools.duplex_finder.duplex attribute)": [[7, "oxDNA_analysis_tools.duplex_finder.Duplex.axis"]], "backbone_flexibility() (in module oxdna_analysis_tools.backbone_flexibility)": [[7, "oxDNA_analysis_tools.backbone_flexibility.backbone_flexibility"]], "bond_analysis() (in module oxdna_analysis_tools.bond_analysis)": [[7, "oxDNA_analysis_tools.bond_analysis.bond_analysis"]], "centroid() (in module oxdna_analysis_tools.centroid)": [[7, "oxDNA_analysis_tools.centroid.centroid"]], "check() (in module oxdna_analysis_tools.config)": [[7, "oxDNA_analysis_tools.config.check"]], "contact_map() (in module oxdna_analysis_tools.contact_map)": [[7, "oxDNA_analysis_tools.contact_map.contact_map"]], "db_to_forcelist() (in module oxdna_analysis_tools.db_to_force)": [[7, "oxDNA_analysis_tools.db_to_force.db_to_forcelist"]], "decimate() (in module oxdna_analysis_tools.decimate)": [[7, "oxDNA_analysis_tools.decimate.decimate"]], "deviations() (in module oxdna_analysis_tools.deviations)": [[7, "oxDNA_analysis_tools.deviations.deviations"]], "distance() (in module oxdna_analysis_tools.distance)": [[7, "oxDNA_analysis_tools.distance.distance"]], "distance_deviations() (in module oxdna_analysis_tools.multidimensional_scaling_mean)": [[7, "oxDNA_analysis_tools.multidimensional_scaling_mean.distance_deviations"]], "duplex_finder() (in module oxdna_analysis_tools.duplex_finder)": [[7, "oxDNA_analysis_tools.duplex_finder.duplex_finder"]], "end1 (oxdna_analysis_tools.duplex_finder.duplex attribute)": [[7, "oxDNA_analysis_tools.duplex_finder.Duplex.end1"]], "end2 (oxdna_analysis_tools.duplex_finder.duplex attribute)": [[7, "oxDNA_analysis_tools.duplex_finder.Duplex.end2"]], "file_info() (in module oxdna_analysis_tools.file_info)": [[7, "oxDNA_analysis_tools.file_info.file_info"]], "find_duplex() (in module oxdna_analysis_tools.duplex_finder)": [[7, "oxDNA_analysis_tools.duplex_finder.find_duplex"]], "fit_pl() (in module oxdna_analysis_tools.persistence_length)": [[7, "oxDNA_analysis_tools.persistence_length.fit_PL"]], "get_angle_between() (in module oxdna_analysis_tools.duplex_angle_plotter)": [[7, "oxDNA_analysis_tools.duplex_angle_plotter.get_angle_between"]], "get_centroid() (in module oxdna_analysis_tools.clustering)": [[7, "oxDNA_analysis_tools.clustering.get_centroid"]], "get_chunk_size() (in module oxdna_analysis_tools.config)": [[7, "oxDNA_analysis_tools.config.get_chunk_size"]], "get_r() (in module oxdna_analysis_tools.persistence_length)": [[7, "oxDNA_analysis_tools.persistence_length.get_r"]], "index (oxdna_analysis_tools.duplex_finder.duplex attribute)": [[7, "oxDNA_analysis_tools.duplex_finder.Duplex.index"]], "make_heatmap() (in module oxdna_analysis_tools.pca)": [[7, "oxDNA_analysis_tools.pca.make_heatmap"]], "map_confs_to_pcs() (in module oxdna_analysis_tools.pca)": [[7, "oxDNA_analysis_tools.pca.map_confs_to_pcs"]], "mean() (in module oxdna_analysis_tools.mean)": [[7, "oxDNA_analysis_tools.mean.mean"]], "min_image() (in module oxdna_analysis_tools.distance)": [[7, "oxDNA_analysis_tools.distance.min_image"]], "minify() (in module oxdna_analysis_tools.minify)": [[7, "oxDNA_analysis_tools.minify.minify"]], "multidimensional_scaling_mean() (in module oxdna_analysis_tools.multidimensional_scaling_mean)": [[7, "oxDNA_analysis_tools.multidimensional_scaling_mean.multidimensional_scaling_mean"]], "output() (in module oxdna_analysis_tools.deviations)": [[7, "oxDNA_analysis_tools.deviations.output"]], "output_bonds() (in module oxdna_analysis_tools.output_bonds)": [[7, "oxDNA_analysis_tools.output_bonds.output_bonds"]], "parse_dot_bracket() (in module oxdna_analysis_tools.db_to_force)": [[7, "oxDNA_analysis_tools.db_to_force.parse_dot_bracket"]], "pca() (in module oxdna_analysis_tools.pca)": [[7, "oxDNA_analysis_tools.pca.pca"]], "perform_dbscan() (in module oxdna_analysis_tools.clustering)": [[7, "oxDNA_analysis_tools.clustering.perform_DBSCAN"]], "persistence_length() (in module oxdna_analysis_tools.persistence_length)": [[7, "oxDNA_analysis_tools.persistence_length.persistence_length"]], "pos (oxdna_analysis_tools.duplex_finder.duplex attribute)": [[7, "oxDNA_analysis_tools.duplex_finder.Duplex.pos"]], "set_chunk_size() (in module oxdna_analysis_tools.config)": [[7, "oxDNA_analysis_tools.config.set_chunk_size"]], "split_trajectory() (in module oxdna_analysis_tools.clustering)": [[7, "oxDNA_analysis_tools.clustering.split_trajectory"]], "start1 (oxdna_analysis_tools.duplex_finder.duplex attribute)": [[7, "oxDNA_analysis_tools.duplex_finder.Duplex.start1"]], "start2 (oxdna_analysis_tools.duplex_finder.duplex attribute)": [[7, "oxDNA_analysis_tools.duplex_finder.Duplex.start2"]], "subset() (in module oxdna_analysis_tools.subset_trajectory)": [[7, "oxDNA_analysis_tools.subset_trajectory.subset"]], "superimpose() (in module oxdna_analysis_tools.superimpose)": [[7, "oxDNA_analysis_tools.superimpose.superimpose"]], "svd_align() (in module oxdna_analysis_tools.align)": [[7, "oxDNA_analysis_tools.align.svd_align"]], "time (oxdna_analysis_tools.duplex_finder.duplex attribute)": [[7, "oxDNA_analysis_tools.duplex_finder.Duplex.time"]], "vectorized_min_image() (in module oxdna_analysis_tools.distance)": [[7, "oxDNA_analysis_tools.distance.vectorized_min_image"]], "harmonic_trap() (in module oxdna_analysis_tools.external_force_utils.forces)": [[9, "oxDNA_analysis_tools.external_force_utils.forces.harmonic_trap"]], "mutual_trap() (in module oxdna_analysis_tools.external_force_utils.forces)": [[9, "oxDNA_analysis_tools.external_force_utils.forces.mutual_trap"]], "read_force_file() (in module oxdna_analysis_tools.external_force_utils.force_reader)": [[9, 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"subset-trajectory"]], "Superimpose": [[7, "superimpose"], [8, "superimpose"]], "OAT command line documentation": [[8, "oat-command-line-documentation"]], "Positional Arguments": [[8, "Positional Arguments"], [8, "Positional Arguments"], [8, "Positional Arguments"], [8, "Positional Arguments"], [8, "Positional Arguments"], [8, "Positional Arguments"], [8, "Positional Arguments"], [8, "Positional Arguments"], [8, "Positional Arguments"], [8, "Positional Arguments"], [8, "Positional Arguments"], [8, "Positional Arguments"], [8, "Positional Arguments"], [8, "Positional Arguments"], [8, "Positional Arguments"], [8, "Positional Arguments"], [8, "Positional Arguments"], [8, "Positional Arguments"], [8, "Positional Arguments"], [8, "Positional Arguments"], [8, "Positional Arguments"], [8, "Positional Arguments"], [8, "Positional Arguments"], [8, "Positional Arguments"]], "Named Arguments": [[8, "Named Arguments"], [8, "Named Arguments"], [8, "Named Arguments"], [8, "Named Arguments"], [8, 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[[10, "oxdna-analysis-tools"]], "Command Line Interface": [[10, "command-line-interface"]], "Scripting interface": [[10, "scripting-interface"]], "Top-level API": [[10, "top-level-api"]], "Utility API": [[10, "utility-api"]], "Forces API": [[10, "forces-api"]], "Analysis notebooks": [[10, "analysis-notebooks"]], "Citation": [[10, "citation"]], "OAT utilities documentation": [[11, "oat-utilities-documentation"]], "Data structures": [[11, "data-structures"]], "Geometry utilities": [[11, "geometry-utilities"]], "iPython oxView plugin": [[11, "ipython-oxview-plugin"]], "Multiprocesser": [[11, "multiprocesser"]], "Rye reader": [[11, "rye-reader"]], "External observable file": [[12, "external-observable-file"]], "Simulation time": [[12, "simulation-time"]], "Total potential energy": [[12, "total-potential-energy"]], "Hydrogen-bonding energy": [[12, "hydrogen-bonding-energy"]], "Hydrogen bonds": [[12, "hydrogen-bonds"]], "Position of a single nucleotide": [[12, "position-of-a-single-nucleotide"]], "Forces and torques due to pair interactions": [[12, "forces-and-torques-due-to-pair-interactions"]], "Distance between two (sets of) particles": [[12, "distance-between-two-sets-of-particles"]], "Distance between all pairs of particles": [[12, "distance-between-all-pairs-of-particles"]], "Interaction energy between pairs of particles": [[12, "interaction-energy-between-pairs-of-particles"]], "Stretched bonds": [[12, "stretched-bonds"]], "Energy associated to the external forces": [[12, "energy-associated-to-the-external-forces"]], "External force acting on particle(s)": [[12, "external-force-acting-on-particle-s"]], "Configuration": [[12, "configuration"]], "Pressure": [[12, "pressure"]], "Stress autocorrelation": [[12, "stress-autocorrelation"]], "Pitch": [[12, "pitch"]], "Coaxial-stacking-related quantities": [[12, "coaxial-stacking-related-quantities"]], "Structure factor": [[12, "structure-factor"]], "Density profile": [[12, "density-profile"]], "Radial distribution function": [[12, "radial-distribution-function"]], "Vector angle": [[12, "vector-angle"]], "Writhe": [[12, "writhe"]], "TEP contacts": [[12, "tep-contacts"]], "Modifying external forces at runtime": [[13, "modifying-external-forces-at-runtime"]], "Writing observables in Python": [[14, "writing-observables-in-python"]], "Oxpy": [[15, "oxpy"]], "An example of a simple simulation": [[15, "an-example-of-a-simple-simulation"]], "An example of a simple analysis": [[15, "an-example-of-a-simple-analysis"]], "Library API": [[15, "library-api"]], "Exceptions": [[15, "exceptions"]], "Extending Oxpy": [[15, "extending-oxpy"]], "The analysis module": [[16, "the-analysis-module"]], "The core module": [[17, "the-core-module"]], "The core.forces module": [[18, "the-core-forces-module"]], "The core.observables module": [[19, "the-core-observables-module"]], "The utils module": [[20, "the-utils-module"]], "Improving performance": [[21, "improving-performance"]], "Molecular dynamics": [[21, "molecular-dynamics"]], "GPU simulations": [[21, "gpu-simulations"]], "Monte Carlo": [[21, "monte-carlo"]], "Relaxing initial configurations": [[22, "relaxing-initial-configurations"]], "First stage: Monte Carlo relaxation": [[22, "first-stage-monte-carlo-relaxation"]], "Second stage: molecular dynamics relaxation": [[22, "second-stage-molecular-dynamics-relaxation"]], "Efficient GPU usage": [[23, "efficient-gpu-usage"]], "Simulation performance on GPU classes": [[23, "simulation-performance-on-gpu-classes"]], "Increasing simulation throughput with multi-process service": [[23, "increasing-simulation-throughput-with-multi-process-service"]], "Umbrella sampling": [[24, "umbrella-sampling"]], "Setting the order parameters and weights": [[24, "setting-the-order-parameters-and-weights"]], "Data evaluation and estimation of the melting temperature": [[24, "data-evaluation-and-estimation-of-the-melting-temperature"]], "Usage": [[25, "usage"]], "DNAnalysis": [[25, "dnanalysis"]], "confGenerator": [[25, "confgenerator"]]}, "indexentries": {"duplex (class in oxdna_analysis_tools.duplex_finder)": [[7, "oxDNA_analysis_tools.duplex_finder.Duplex"]], "align() (in module oxdna_analysis_tools.align)": [[7, "oxDNA_analysis_tools.align.align"]], "align_positions() (in module oxdna_analysis_tools.pca)": [[7, "oxDNA_analysis_tools.pca.align_positions"]], "anm_parameterize() (in module oxdna_analysis_tools.anm_parameterize)": [[7, "oxDNA_analysis_tools.anm_parameterize.anm_parameterize"]], "axis (oxdna_analysis_tools.duplex_finder.duplex attribute)": [[7, "oxDNA_analysis_tools.duplex_finder.Duplex.axis"]], "backbone_flexibility() (in module oxdna_analysis_tools.backbone_flexibility)": [[7, "oxDNA_analysis_tools.backbone_flexibility.backbone_flexibility"]], "bond_analysis() (in module oxdna_analysis_tools.bond_analysis)": [[7, "oxDNA_analysis_tools.bond_analysis.bond_analysis"]], "centroid() (in module oxdna_analysis_tools.centroid)": [[7, "oxDNA_analysis_tools.centroid.centroid"]], "check() (in module oxdna_analysis_tools.config)": [[7, "oxDNA_analysis_tools.config.check"]], "contact_map() (in module oxdna_analysis_tools.contact_map)": [[7, "oxDNA_analysis_tools.contact_map.contact_map"]], "db_to_forcelist() (in module oxdna_analysis_tools.db_to_force)": [[7, "oxDNA_analysis_tools.db_to_force.db_to_forcelist"]], "decimate() (in module oxdna_analysis_tools.decimate)": [[7, "oxDNA_analysis_tools.decimate.decimate"]], "deviations() (in module oxdna_analysis_tools.deviations)": [[7, "oxDNA_analysis_tools.deviations.deviations"]], "distance() (in module oxdna_analysis_tools.distance)": [[7, "oxDNA_analysis_tools.distance.distance"]], "distance_deviations() (in module oxdna_analysis_tools.multidimensional_scaling_mean)": [[7, "oxDNA_analysis_tools.multidimensional_scaling_mean.distance_deviations"]], "duplex_finder() (in module oxdna_analysis_tools.duplex_finder)": [[7, "oxDNA_analysis_tools.duplex_finder.duplex_finder"]], "end1 (oxdna_analysis_tools.duplex_finder.duplex attribute)": [[7, "oxDNA_analysis_tools.duplex_finder.Duplex.end1"]], "end2 (oxdna_analysis_tools.duplex_finder.duplex attribute)": [[7, "oxDNA_analysis_tools.duplex_finder.Duplex.end2"]], "file_info() (in module oxdna_analysis_tools.file_info)": [[7, "oxDNA_analysis_tools.file_info.file_info"]], "find_duplex() (in module oxdna_analysis_tools.duplex_finder)": [[7, "oxDNA_analysis_tools.duplex_finder.find_duplex"]], "fit_pl() (in module oxdna_analysis_tools.persistence_length)": [[7, "oxDNA_analysis_tools.persistence_length.fit_PL"]], "get_angle_between() (in module oxdna_analysis_tools.duplex_angle_plotter)": [[7, "oxDNA_analysis_tools.duplex_angle_plotter.get_angle_between"]], "get_centroid() (in module oxdna_analysis_tools.clustering)": [[7, "oxDNA_analysis_tools.clustering.get_centroid"]], "get_chunk_size() (in module oxdna_analysis_tools.config)": [[7, "oxDNA_analysis_tools.config.get_chunk_size"]], "get_r() (in module oxdna_analysis_tools.persistence_length)": [[7, "oxDNA_analysis_tools.persistence_length.get_r"]], "index (oxdna_analysis_tools.duplex_finder.duplex attribute)": [[7, "oxDNA_analysis_tools.duplex_finder.Duplex.index"]], "make_heatmap() (in module oxdna_analysis_tools.pca)": [[7, "oxDNA_analysis_tools.pca.make_heatmap"]], "map_confs_to_pcs() (in module oxdna_analysis_tools.pca)": [[7, "oxDNA_analysis_tools.pca.map_confs_to_pcs"]], "mean() (in module oxdna_analysis_tools.mean)": [[7, "oxDNA_analysis_tools.mean.mean"]], "min_image() (in module oxdna_analysis_tools.distance)": [[7, "oxDNA_analysis_tools.distance.min_image"]], "minify() (in module oxdna_analysis_tools.minify)": [[7, "oxDNA_analysis_tools.minify.minify"]], "multidimensional_scaling_mean() (in module oxdna_analysis_tools.multidimensional_scaling_mean)": [[7, "oxDNA_analysis_tools.multidimensional_scaling_mean.multidimensional_scaling_mean"]], "output() (in module oxdna_analysis_tools.deviations)": [[7, "oxDNA_analysis_tools.deviations.output"]], "output_bonds() (in module oxdna_analysis_tools.output_bonds)": [[7, "oxDNA_analysis_tools.output_bonds.output_bonds"]], "parse_dot_bracket() (in module oxdna_analysis_tools.db_to_force)": [[7, "oxDNA_analysis_tools.db_to_force.parse_dot_bracket"]], "pca() (in module oxdna_analysis_tools.pca)": [[7, "oxDNA_analysis_tools.pca.pca"]], "perform_dbscan() (in module oxdna_analysis_tools.clustering)": [[7, "oxDNA_analysis_tools.clustering.perform_DBSCAN"]], "persistence_length() (in module oxdna_analysis_tools.persistence_length)": [[7, "oxDNA_analysis_tools.persistence_length.persistence_length"]], "pos (oxdna_analysis_tools.duplex_finder.duplex attribute)": [[7, "oxDNA_analysis_tools.duplex_finder.Duplex.pos"]], "set_chunk_size() (in module oxdna_analysis_tools.config)": [[7, "oxDNA_analysis_tools.config.set_chunk_size"]], "split_trajectory() (in module oxdna_analysis_tools.clustering)": [[7, "oxDNA_analysis_tools.clustering.split_trajectory"]], "start1 (oxdna_analysis_tools.duplex_finder.duplex attribute)": [[7, "oxDNA_analysis_tools.duplex_finder.Duplex.start1"]], "start2 (oxdna_analysis_tools.duplex_finder.duplex attribute)": [[7, "oxDNA_analysis_tools.duplex_finder.Duplex.start2"]], "subset() (in module oxdna_analysis_tools.subset_trajectory)": [[7, "oxDNA_analysis_tools.subset_trajectory.subset"]], "superimpose() (in module oxdna_analysis_tools.superimpose)": [[7, "oxDNA_analysis_tools.superimpose.superimpose"]], "svd_align() (in module oxdna_analysis_tools.align)": [[7, "oxDNA_analysis_tools.align.svd_align"]], "time (oxdna_analysis_tools.duplex_finder.duplex attribute)": [[7, "oxDNA_analysis_tools.duplex_finder.Duplex.time"]], "vectorized_min_image() (in module oxdna_analysis_tools.distance)": [[7, "oxDNA_analysis_tools.distance.vectorized_min_image"]], "harmonic_trap() (in module oxdna_analysis_tools.external_force_utils.forces)": [[9, "oxDNA_analysis_tools.external_force_utils.forces.harmonic_trap"]], "mutual_trap() (in module oxdna_analysis_tools.external_force_utils.forces)": [[9, "oxDNA_analysis_tools.external_force_utils.forces.mutual_trap"]], "read_force_file() (in module oxdna_analysis_tools.external_force_utils.force_reader)": [[9, "oxDNA_analysis_tools.external_force_utils.force_reader.read_force_file"]], "repulsion_plane() (in module oxdna_analysis_tools.external_force_utils.forces)": [[9, "oxDNA_analysis_tools.external_force_utils.forces.repulsion_plane"]], "repulsion_sphere() (in module oxdna_analysis_tools.external_force_utils.forces)": [[9, "oxDNA_analysis_tools.external_force_utils.forces.repulsion_sphere"]], "rotating_harmonic_trap() (in module oxdna_analysis_tools.external_force_utils.forces)": [[9, "oxDNA_analysis_tools.external_force_utils.forces.rotating_harmonic_trap"]], "string() (in module oxdna_analysis_tools.external_force_utils.forces)": [[9, "oxDNA_analysis_tools.external_force_utils.forces.string"]], "write_force_file() (in module oxdna_analysis_tools.external_force_utils.force_reader)": [[9, "oxDNA_analysis_tools.external_force_utils.force_reader.write_force_file"]], "chunk (class in oxdna_analysis_tools.utils.data_structures)": [[11, "oxDNA_analysis_tools.UTILS.data_structures.Chunk"]], "chunker() (in module oxdna_analysis_tools.utils.ryereader)": [[11, "oxDNA_analysis_tools.UTILS.RyeReader.Chunker"]], "confinfo (class in oxdna_analysis_tools.utils.data_structures)": [[11, "oxDNA_analysis_tools.UTILS.data_structures.ConfInfo"]], "configuration (class in oxdna_analysis_tools.utils.data_structures)": [[11, "oxDNA_analysis_tools.UTILS.data_structures.Configuration"]], "monomer (class in oxdna_analysis_tools.utils.data_structures)": [[11, "oxDNA_analysis_tools.UTILS.data_structures.Monomer"]], "strand (class in oxdna_analysis_tools.utils.data_structures)": [[11, "oxDNA_analysis_tools.UTILS.data_structures.Strand"]], "system (class in oxdna_analysis_tools.utils.data_structures)": [[11, "oxDNA_analysis_tools.UTILS.data_structures.System"]], "topinfo (class in oxdna_analysis_tools.utils.data_structures)": [[11, "oxDNA_analysis_tools.UTILS.data_structures.TopInfo"]], "trajinfo (class in oxdna_analysis_tools.utils.data_structures)": [[11, "oxDNA_analysis_tools.UTILS.data_structures.TrajInfo"]], "__from_old (oxdna_analysis_tools.utils.data_structures.strand attribute)": [[11, "oxDNA_analysis_tools.UTILS.data_structures.Strand.__from_old"]], "a1s (oxdna_analysis_tools.utils.data_structures.configuration attribute)": [[11, "oxDNA_analysis_tools.UTILS.data_structures.Configuration.a1s"]], "a3s (oxdna_analysis_tools.utils.data_structures.configuration attribute)": [[11, "oxDNA_analysis_tools.UTILS.data_structures.Configuration.a3s"]], "append() (oxdna_analysis_tools.utils.data_structures.system method)": [[11, "oxDNA_analysis_tools.UTILS.data_structures.System.append"]], "block (oxdna_analysis_tools.utils.data_structures.chunk attribute)": [[11, "oxDNA_analysis_tools.UTILS.data_structures.Chunk.block"]], "box (oxdna_analysis_tools.utils.data_structures.configuration attribute)": [[11, "oxDNA_analysis_tools.UTILS.data_structures.Configuration.box"]], "btype (oxdna_analysis_tools.utils.data_structures.monomer attribute)": [[11, "oxDNA_analysis_tools.UTILS.data_structures.Monomer.btype"]], "circular (oxdna_analysis_tools.utils.data_structures.strand attribute)": [[11, "oxDNA_analysis_tools.UTILS.data_structures.Strand.circular"]], "conf_to_str() (in module oxdna_analysis_tools.utils.ryereader)": [[11, "oxDNA_analysis_tools.UTILS.RyeReader.conf_to_str"]], "describe() (in module oxdna_analysis_tools.utils.ryereader)": [[11, "oxDNA_analysis_tools.UTILS.RyeReader.describe"]], "display_files() (in module oxdna_analysis_tools.utils.oxview)": [[11, "oxDNA_analysis_tools.UTILS.oxview.display_files"]], "energy (oxdna_analysis_tools.utils.data_structures.configuration attribute)": [[11, "oxDNA_analysis_tools.UTILS.data_structures.Configuration.energy"]], "file_size (oxdna_analysis_tools.utils.data_structures.chunk attribute)": [[11, "oxDNA_analysis_tools.UTILS.data_structures.Chunk.file_size"]], "fit_plane() (in module oxdna_analysis_tools.utils.geom)": [[11, "oxDNA_analysis_tools.UTILS.geom.fit_plane"]], "flro_patchy_conf() (in module oxdna_analysis_tools.utils.oxview)": [[11, "oxDNA_analysis_tools.UTILS.oxview.flro_patchy_conf"]], "from_path() (in module oxdna_analysis_tools.utils.oxview)": [[11, "oxDNA_analysis_tools.UTILS.oxview.from_path"]], "get_dna_axis() (in module oxdna_analysis_tools.utils.geom)": [[11, "oxDNA_analysis_tools.UTILS.geom.get_DNA_axis"]], "get_rna_axis() (in module oxdna_analysis_tools.utils.geom)": [[11, "oxDNA_analysis_tools.UTILS.geom.get_RNA_axis"]], "get_confs() (in module oxdna_analysis_tools.utils.ryereader)": [[11, "oxDNA_analysis_tools.UTILS.RyeReader.get_confs"]], "get_input_parameter() (in module oxdna_analysis_tools.utils.ryereader)": [[11, "oxDNA_analysis_tools.UTILS.RyeReader.get_input_parameter"]], "get_kwdata() (oxdna_analysis_tools.utils.data_structures.strand method)": [[11, "oxDNA_analysis_tools.UTILS.data_structures.Strand.get_kwdata"]], "get_length() (oxdna_analysis_tools.utils.data_structures.strand method)": [[11, "oxDNA_analysis_tools.UTILS.data_structures.Strand.get_length"]], "get_sequence() (oxdna_analysis_tools.utils.data_structures.strand method)": [[11, "oxDNA_analysis_tools.UTILS.data_structures.Strand.get_sequence"]], "get_top_info() (in module oxdna_analysis_tools.utils.ryereader)": [[11, "oxDNA_analysis_tools.UTILS.RyeReader.get_top_info"]], "get_top_info_from_traj() (in module oxdna_analysis_tools.utils.ryereader)": [[11, "oxDNA_analysis_tools.UTILS.RyeReader.get_top_info_from_traj"]], "get_top_string() (in module oxdna_analysis_tools.utils.ryereader)": [[11, "oxDNA_analysis_tools.UTILS.RyeReader.get_top_string"]], "get_traj_info() (in module oxdna_analysis_tools.utils.ryereader)": [[11, "oxDNA_analysis_tools.UTILS.RyeReader.get_traj_info"]], "id (oxdna_analysis_tools.utils.data_structures.confinfo attribute)": [[11, "oxDNA_analysis_tools.UTILS.data_structures.ConfInfo.id"]], "id (oxdna_analysis_tools.utils.data_structures.monomer attribute)": [[11, "oxDNA_analysis_tools.UTILS.data_structures.Monomer.id"]], "id (oxdna_analysis_tools.utils.data_structures.strand attribute)": [[11, "oxDNA_analysis_tools.UTILS.data_structures.Strand.id"]], "idxs (oxdna_analysis_tools.utils.data_structures.trajinfo attribute)": [[11, "oxDNA_analysis_tools.UTILS.data_structures.TrajInfo.idxs"]], "inbox() (in module oxdna_analysis_tools.utils.ryereader)": [[11, "oxDNA_analysis_tools.UTILS.RyeReader.inbox"]], "incl_v (oxdna_analysis_tools.utils.data_structures.trajinfo attribute)": [[11, "oxDNA_analysis_tools.UTILS.data_structures.TrajInfo.incl_v"]], "is_circular() (oxdna_analysis_tools.utils.data_structures.strand method)": [[11, "oxDNA_analysis_tools.UTILS.data_structures.Strand.is_circular"]], "is_last (oxdna_analysis_tools.utils.data_structures.chunk attribute)": [[11, "oxDNA_analysis_tools.UTILS.data_structures.Chunk.is_last"]], "is_old() (oxdna_analysis_tools.utils.data_structures.strand method)": [[11, "oxDNA_analysis_tools.UTILS.data_structures.Strand.is_old"]], "linear_read() (in module oxdna_analysis_tools.utils.ryereader)": [[11, "oxDNA_analysis_tools.UTILS.RyeReader.linear_read"]], "loro_patchy_conf() (in module oxdna_analysis_tools.utils.oxview)": [[11, "oxDNA_analysis_tools.UTILS.oxview.loro_patchy_conf"]], "monomers (oxdna_analysis_tools.utils.data_structures.strand attribute)": [[11, "oxDNA_analysis_tools.UTILS.data_structures.Strand.monomers"]], "n3 (oxdna_analysis_tools.utils.data_structures.monomer attribute)": [[11, "oxDNA_analysis_tools.UTILS.data_structures.Monomer.n3"]], "n5 (oxdna_analysis_tools.utils.data_structures.monomer attribute)": [[11, 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