diff --git a/_sources/forces.md.txt b/_sources/forces.md.txt index cc4ee84ba..1b6358c39 100644 --- a/_sources/forces.md.txt +++ b/_sources/forces.md.txt @@ -205,11 +205,45 @@ The following snippet defines a plane that acts on the whole system and will not ```` +## Attraction plane + +This kind of external force implements an attraction plane that attracts particles towards the plane with a constant force component while constraining them to stay on one side using a repulsive force component (compare repulsion plane). +The repulsion is implemented as a harmonic interaction, but the stiffness can be made arbitrarily high to mimic a hard repulsion. +The attraction is implemented as a constant force defined as: stiffness * a, where a = 1 units of length. +Both attractive and repulsive component use the same stiffness value. + +A force of this kind is specified with `type = attraction_plane`. 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. +* `stiff = `: stiffness of the repulsion and strength of the attraction. +* `dir = ,,`: the vector normal to the plane: it should point towards the half-plane where the attraction is not acting. +* `position = `: defines the position of the plane along the direction identified by the plane normal. + +If direction is `dir`{math}`=(u,v,w)`, then the plane contains all the points {math}`(x,y,z)` that satisfy the equation: {math}`u x + v y + w z + {\rm position} = 0`. +Nucleotides with coordinates {math}`(x,y,z)` that satisfy {math}`u x + v y + w z + {\rm position} \ge 0` will feel a constant attraction force towards the plane equal to `stiff`. +Nucleotides with coordinates {math}`(x,y,z)` that satisfy {math}`u x + v y + w z + {\rm position} \lt 0` will feel a repulsion force equal to `stiff` \* *D*, where {math}`D = | ux + vy + wz + \mbox{position}| / \sqrt{u^2 + v^2 + w^2 }` is the distance of the nucleotide from the plane. + +````{admonition} Example + +The following snippet defines an attraction plane that acts on on all nucleotides, pulling them towards the YZ plane (x-direction at origin). +Particles with a positive x-coordinate are pulled towards the YZ plane by a constant force of 1 simulation unit \* x (48.6 pN \* x for DNA) +A restoring force proportional to 1 simulation unit \* x (48.6 pN \* x for DNA) is exerted on all particles with a negative x-coordinate, constraining them at the plane. + + { + type = attraction_plane + particle = -1 + stiff = 1.00 + dir = 1, 0, 0 + position = 0 + } + +```` + ## Repulsive sphere This force encloses particle(s) in a repulsive sphere. The repulsion force is harmonic. -A force of this kind is specified with `type = sphere`. The relevant keys are: +A force of this kind is specified with `type = sphere`. 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. * `stiff = `: stiffness of the repulsion. diff --git a/_sources/index.md.txt b/_sources/index.md.txt index 0c62c18d8..df59141be 100644 --- a/_sources/index.md.txt +++ b/_sources/index.md.txt @@ -1,15 +1,33 @@ # oxDNA -oxDNA is a simulation code that was initially conceived as an implementation of the coarse-grained DNA model introduced by [T. E. Ouldridge, J. P. K. Doye and A. A. Louis](http://dx.doi.org/10.1063/1.3552946). It has been since reworked and it is now an extensible simulation+analysis framework. +oxDNA is a simulation code that was initially conceived as an implementation of the coarse-grained DNA model introduced by [T. E. Ouldridge, J. P. K. Doye and A. A. Louis](http://dx.doi.org/10.1063/1.3552946). It has been since reworked and it is now an extensible simulation+analysis framework. The following nucleic-acid-related force fields are implemented: -oxDNA can perform both molecular dynamics (MD) and Monte Carlo (MC) simulations of the oxDNA and oxRNA models. MD simulations can be run on single CPUs or single CUDA-enabled GPUs, while MC simulations, which can only be run serially, can exploit the Virtual Move Monte Carlo algorithm to greatly speed-up equilibration and sampling, and Umbrella Sampling biasing to efficiently obtain free-energy profiles. The package also features a Forward-Flux Sampling interface to study the kinetics of rare events, and makes it possible to alter the behaviour of the systems by adding *external forces* that can be used, for instance, to pull on or apply torques to strands or confine nucleotides within semi-planes or spheres. +* [oxDNA1](https://pubs.aip.org/aip/jcp/article-abstract/137/13/135101/191221/Sequence-dependent-thermodynamics-of-a-coarse?redirectedFrom=fulltext) +* [oxDNA2](https://pubs.aip.org/aip/jcp/article-abstract/142/23/234901/193554/Introducing-improved-structural-properties-and?redirectedFrom=fulltext) +* [oxRNA](https://pubs.aip.org/aip/jcp/article-abstract/140/23/235102/73414/A-nucleotide-level-coarse-grained-model-of-RNA?redirectedFrom=fulltext) +* [oxNA](https://pubs.aip.org/aip/jcp/article/160/11/115101/3275728) -The package also includes `oxpy`, a Python library which makes it possible to control the behavior of the simulation using Python scripts. The repository contains examples that demonstrate how to leverage `oxpy` to write backends to run replica-exchange and well-tempered metadynamics simulations, which are popular techniques in modern molecular dynamics to improve sampling efficiency. +oxDNA can perform both molecular dynamics (MD) and Monte Carlo (MC) simulations of the oxDNA and oxRNA models. MD simulations can be run on single CPUs or single CUDA-enabled GPUs, while MC simulations, which can only be run serially, can exploit the Virtual Move Monte Carlo algorithm to greatly speed-up equilibration and sampling, and [Umbrella Sampling biasing](umbrella_sampling.md) to efficiently obtain free-energy profiles. The package also features a [Forward-Flux Sampling interface](ffs.md) to study the kinetics of rare events, and makes it possible to alter the behaviour of the systems by adding [*external forces*](forces.md) that can be used, for instance, to pull on or apply torques to strands or confine nucleotides within semi-planes or spheres. -The package can also be used to compute nucleic-acid-related quantities such as the energy due to hydrogen bonding or stacking, the distance between groups of nucleotides, the list of hydrogen-bonded nucleotides or of over-stretched bonds, and much more. The analysis can be performed while the simulation is running or on generated trajectory files. +The package also includes [the `oxpy` Python module](oxpy/index.md), which makes it possible to control the behavior of the simulation using Python scripts. The repository contains examples that demonstrate how to leverage `oxpy` to write backends to run replica-exchange and well-tempered metadynamics simulations, which are popular techniques in modern molecular dynamics to improve sampling efficiency. + +The package can be used to compute [nucleic-acid-related quantities](observables.md) such as the energy due to hydrogen bonding or stacking, the distance between groups of nucleotides, the list of hydrogen-bonded nucleotides or of over-stretched bonds, and much more. The analysis can be performed while the simulation is running or on generated trajectory files. The simulation engine is complemented by an updated version of `oxDNA_analysis_tools` (`oat`), a Python library aimed at facilitating the analysis of oxDNA/oxRNA trajectories. `Oat` provides numerous common simulation trajectory analysis tools including alignment, mean structures, subsetting trajectories, distances between nucleotides, interduplex angles, and comparisons in hydrogen bonding patterns between the trajectory and an idealized structure. +## Citing oxDNA + +[![DOI](https://joss.theoj.org/papers/10.21105/joss.04693/status.svg)](https://doi.org/10.21105/joss.04693) + +Please cite these publications for any work that uses the oxDNA simulation package: + +- for the code: + * [E. Poppleton et al., J. Open Source Softw. 8, 4693 (2023)](https://doi.org/10.21105/joss.04693) +- for the CUDA-powered code: + * [L. Rovigatti et al., J. Comput. Chem. 36, 1 (2015)](https://doi.org/10.1002/jcc.23763) +- for oxDNA analysis tools: + * [E. Poppleton et al., Nucleic Acids Research e72 (2020)](https://doi.org/10.1093/nar/gkab324) + ```{eval-rst} .. toctree:: :caption: Table of Contents diff --git a/_sources/install.md.txt b/_sources/install.md.txt index f848d193d..c5afb3e4b 100644 --- a/_sources/install.md.txt +++ b/_sources/install.md.txt @@ -26,7 +26,7 @@ make -j4 # compile oxDNA. The -jX make option makes it compile the code At the end of the compilation three executables (*oxDNA*, *DNAnalysis* and *confGenerator*) will be placed in the `build/bin` directory. -Compiling with Python bindings will also generate an `oxpy` package in the `build/oxpy` directory that can be imported in Python. Running `make install` will attempt to copy the package (as well as `oxDNA_analysis_tools`) to the `pip`'s module directory. The specific location will depend on your system's settings. We advise you to use [virtual environments](https://docs.python.org/3/tutorial/venv.html) (see *e.g.* [pipenv](https://docs.pipenv.org/)) to avoid conflicts with other packages and/or dependency and permission issues. +Compiling with Python bindings will also generate an `oxpy` package in the `build/oxpy` directory that can be imported in Python. Running `make install` will attempt to copy the package (as well as `oxDNA_analysis_tools`) to the `pip`'s module directory. The specific location will depend on your system's settings. We advise you to use [virtual environments](https://docs.python.org/3/tutorial/venv.html) (see *e.g.* [pipenv](https://docs.pipenv.org/) or [conda](https://conda.io/projects/conda/en/latest/user-guide/getting-started.html)) to avoid conflicts with other packages and/or dependency and permission issues. ### Updating a local copy diff --git a/_sources/oat/api.md.txt b/_sources/oat/api.md.txt index d294aeb35..3d0a64c3b 100644 --- a/_sources/oat/api.md.txt +++ b/_sources/oat/api.md.txt @@ -266,6 +266,7 @@ decimate(align_output, decimate_output, ncpus=5, start=200, stride=10) ``` ## File info + ```{eval-rst} .. toctree:: :maxdepth: 2 @@ -280,6 +281,22 @@ decimate(align_output, decimate_output, ncpus=5, start=200, stride=10) .. autofunction:: oxDNA_analysis_tools.file_info.file_info ``` +## Forces to dot-bracket + +```{eval-rst} +.. toctree:: + :maxdepth: 2 + +.. currentmodule:: oxDNA_analysis_tools + +.. autosummary:: + :nosignatures: + + oxDNA_analysis_tools.forces2db.forces2db + +.. autofunction:: oxDNA_analysis_tools.forces2db.forces2db +``` + ## Mean ```{eval-rst} @@ -346,6 +363,38 @@ decimate(align_output, decimate_output, ncpus=5, start=200, stride=10) .. autofunction:: oxDNA_analysis_tools.output_bonds.output_bonds ``` +## OxDNA to PDB + +```{eval-rst} +.. toctree:: + :maxdepth: 2 + +.. currentmodule:: oxDNA_analysis_tools + +.. autosummary:: + :nosignatures: + + oxDNA_analysis_tools.oxDNA_PDB.oxDNA_PDB + +.. autofunction:: oxDNA_analysis_tools.oxDNA_PDB.oxDNA_PDB +``` + +## Pairs to dot-bracket + +```{eval-rst} +.. toctree:: + :maxdepth: 2 + +.. currentmodule:: oxDNA_analysis_tools + +.. autosummary:: + :nosignatures: + + oxDNA_analysis_tools.pairs2db.pairs2db + +.. autofunction:: oxDNA_analysis_tools.pairs2db.pairs2db +``` + ## Principle component analysis ```{eval-rst} diff --git a/_sources/oat/cli.md.txt b/_sources/oat/cli.md.txt index 6df231e79..1dd56a186 100644 --- a/_sources/oat/cli.md.txt +++ b/_sources/oat/cli.md.txt @@ -133,6 +133,14 @@ :prog: oat file_info ``` +## Forces to dot-bracket +```{eval-rst} +.. argparse:: + :filename: ../analysis/src/oxDNA_analysis_tools/forces2db.py + :func: cli_parser + :prog: oat forces2db +``` + ## Forces to pairs ```{eval-rst} @@ -196,6 +204,14 @@ :prog: oat oxDNA_PDB ``` +## Pairs to dot-bracket +```{eval-rst} +.. argparse:: + :filename: ../analysis/src/oxDNA_analysis_tools/pairs2db.py + :func: cli_parser + :prog: oat pairs2db +``` + ## Principal component analysis ```{eval-rst} diff --git a/_sources/oat/forces.md.txt b/_sources/oat/forces.md.txt index 77f4a810b..5110d71ad 100644 --- a/_sources/oat/forces.md.txt +++ b/_sources/oat/forces.md.txt @@ -17,6 +17,7 @@ Python data structures for all forces defined by oxDNA oxDNA_analysis_tools.external_force_utils.forces.harmonic_trap oxDNA_analysis_tools.external_force_utils.forces.rotating_harmonic_trap oxDNA_analysis_tools.external_force_utils.forces.repulsion_plane + oxDNA_analysis_tools.external_force_utils.forces.attraction_plane oxDNA_analysis_tools.external_force_utils.forces.repulsion_sphere .. autofunction:: oxDNA_analysis_tools.external_force_utils.forces.mutual_trap @@ -24,6 +25,7 @@ Python data structures for all forces defined by oxDNA .. autofunction:: oxDNA_analysis_tools.external_force_utils.forces.harmonic_trap .. autofunction:: oxDNA_analysis_tools.external_force_utils.forces.rotating_harmonic_trap .. autofunction:: oxDNA_analysis_tools.external_force_utils.forces.repulsion_plane +.. autofunction:: oxDNA_analysis_tools.external_force_utils.forces.attraction_plane .. autofunction:: oxDNA_analysis_tools.external_force_utils.forces.repulsion_sphere ``` diff --git a/forces.html b/forces.html index 92c811701..0285eed03 100644 --- a/forces.html +++ b/forces.html @@ -62,6 +62,7 @@
  • Harmonic trap
  • Rotating harmonic trap
  • Repulsion plane
    • +
  • Attraction plane
  • Repulsive sphere
  • Yukawa sphere
  • type = com
    • @@ -303,6 +304,38 @@

    Repulsion plane +

    Attraction plane

    +

    This kind of external force implements an attraction plane that attracts particles towards the plane with a constant force component while constraining them to stay on one side using a repulsive force component (compare repulsion plane). +The repulsion is implemented as a harmonic interaction, but the stiffness can be made arbitrarily high to mimic a hard repulsion. +The attraction is implemented as a constant force defined as: stiffness * a, where a = 1 units of length. +Both attractive and repulsive component use the same stiffness value.

    +

    A force of this kind is specified with type = attraction_plane. 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.

      • +

    • stiff = <float>: stiffness of the repulsion and strength of the attraction.

      • +

    • dir = <float>,<float>,<float>: the vector normal to the plane: it should point towards the half-plane where the attraction is not acting.

      • +

    • position = <float>: defines the position of the plane along the direction identified by the plane normal.

      • +
    +

    If direction is dir\(=(u,v,w)\), then the plane contains all the points \((x,y,z)\) that satisfy the equation: \(u x + v y + w z + {\rm position} = 0\). +Nucleotides with coordinates \((x,y,z)\) that satisfy \(u x + v y + w z + {\rm position} \ge 0\) will feel a constant attraction force towards the plane equal to stiff. +Nucleotides with coordinates \((x,y,z)\) that satisfy \(u x + v y + w z + {\rm position} \lt 0\) will feel a repulsion force equal to stiff * D, where \(D = | ux + vy + wz + \mbox{position}| / \sqrt{u^2 + v^2 + w^2 }\) is the distance of the nucleotide from the plane.

    +
    +

    Example

    +

    The following snippet defines an attraction plane that acts on on all nucleotides, pulling them towards the YZ plane (x-direction at origin). +Particles with a positive x-coordinate are pulled towards the YZ plane by a constant force of 1 simulation unit * x (48.6 pN * x for DNA) +A restoring force proportional to 1 simulation unit * x (48.6 pN * x for DNA) is exerted on all particles with a negative x-coordinate, constraining them at the plane.

    +
    {
+type = attraction_plane
+particle = -1
+stiff = 1.00
+dir = 1, 0, 0
+position = 0
+}
+
    +
    +
    +

    Repulsive sphere

    This force encloses particle(s) in a repulsive sphere. The repulsion force is harmonic.

    diff --git a/genindex.html b/genindex.html index 38f7cc70a..384ab40cd 100644 --- a/genindex.html +++ b/genindex.html @@ -141,10 +141,10 @@

    A

  • align() (in module oxDNA_analysis_tools.align)
    • - - + - - + +
    Returns:
    +

    The average configuration and the distance matrix with all distances above the cutoff masked

    +
    +
    Return type:
    +

    Tuple[Configuration, np.ndarray]

    +
    -oxDNA_analysis_tools.multidimensional_scaling_mean.distance_deviations(traj_info: TrajInfo, top_info: TopInfo, masked_mean: ndarray, ncpus: int = 1) → ndarray
    +oxDNA_analysis_tools.multidimensional_scaling_mean.distance_deviations(traj_info: TrajInfo, top_info: TopInfo, masked_mean: ndarray, ncpus: int = 1) → ndarray

    Compute the deviations of the contact map from the mean.

    Parameters:
    @@ -984,6 +1059,12 @@

    Multidimensional scaling meanint) – (optional) Number of CPUs to use.

    +
    Returns:
    +

    The per-particle deviation from the mean distance map

    +
    +
    Return type:
    +

    np.ndarray

    +
    @@ -1018,7 +1099,72 @@

    Output bonds

    If visualize is True, the energies are saved as a mean-per-particle oxView file. If False, they are printed to the screen and None is returned.

    Return type:
    -

    energies (np.array)

    +

    np.ndarray or None

    +
    + + + +

    +
    +

    OxDNA to PDB

    +
    +
    + + + + + + +

    oxDNA_analysis_tools.oxDNA_PDB.oxDNA_PDB

    Convert an oxDNA file to a PDB file.

    +
    +
    +oxDNA_analysis_tools.oxDNA_PDB.oxDNA_PDB(conf: Configuration, system: System, out_basename: str, protein_pdb_files: List[str] = [], reverse: bool = False, hydrogen: bool = True, uniform_residue_names: bool = False, one_file_per_strand: bool = False, rmsf_file: str = '')
    +

    Convert an oxDNA file to a PDB file. Directly writes the file.

    +
    +
    Parameters:
    +
      +

    • top_file (str) – Filename of oxDNA topology

      • +

    • conf_file (str) – Filename of oxDNA configuration

      • +

    • out_basename (str) – Filename(-.pdb) to write out to

      • +

    • protein_pdb_files (List[str]) – Filenames of pdb files corresponding to proteins present in the oxDNA files. Default: []

      • +

    • reverse (bool) – Reverse nucleic acid strands from oxDNA files (If you want ‘correct’ PDB files from backwards oxDNA files). Default: False

      • +

    • hydrogen (bool) – Write hydrogens to output file (Probably false if, for example, exporting for GROMACS simulation). Default: True

      • +

    • uniform_residue_names (bool) – Don’t add ‘5’ and ‘3’ to the names of the terminal residues (True if, for example, exporting for GROMACS simulation). Default: False

      • +

    • one_strand_per_file (bool) – Split each strand into a separate PDB file (appends numbers to out_basename). Default: False

      • +

    • rmsf_file (str) – Write oxDNA (json-formatted from deviations) RMSFs into the b-factor field of the PDB file. Default: ‘’

      • +
    +
    +
    +
    + +
    +
    +

    Pairs to dot-bracket

    +
    +
    + + + + + + +

    oxDNA_analysis_tools.pairs2db.pairs2db

    Convert a dictionary of paired nucleotides to dot-bracket notation

    +
    +
    +oxDNA_analysis_tools.pairs2db.pairs2db(n_bases: int, pairs: Dict[int, int]) → str
    +

    Convert a dictionary of paired nucleotides to dot-bracket notation

    +
    +
    Parameters:
    +
      +

    • n_bases (int) – The total number of bases in the structure

      • +

    • pairs (dict[int, int]) – The IDs of paired nucleotides

      • +
    +
    +
    Returns:
    +

    The pairs as a dot-bracket string, including any nested bases

    +
    +
    Return type:
    +

    str

    @@ -1046,14 +1192,21 @@

    Principle component analysis
    -oxDNA_analysis_tools.pca.align_positions(centered_ref_coords: ndarray, coords: ndarray) → ndarray
    +oxDNA_analysis_tools.pca.align_positions(centered_ref_coords: ndarray, coords: ndarray) → ndarray

    Single-value decomposition-based alignment of configurations

    This one only considers positions, unlike the one in align which also handles the a vectors

    -
    -
    Parameters

    centered_ref_coords (np.array): reference coordinates, centered on [0, 0, 0] -coords (np.array): coordinates to be aligned

    +
    +
    Parameters:
    +
      +

    • centered_ref_coords (np.array) – reference coordinates, centered on [0, 0, 0]

      • +

    • coords (np.array) – coordinates to be aligned

      • +
    +
    +
    Returns:
    +

    Aligned coordinates for the given conf

    -
    Returns

    (np.array) : Aligned coordinates for the given conf

    +
    Return type:
    +

    np.ndarray

    @@ -1073,14 +1226,14 @@

    Principle component analysis

    The positions of each frame of the trajectory in principal component space.

    Return type:
    -

    coordinates (numpy.array)

    +

    np.ndarray

    -oxDNA_analysis_tools.pca.make_heatmap(covariance: ndarray)
    +oxDNA_analysis_tools.pca.make_heatmap(covariance: ndarray)

    Produces a heatmat plot of the covariance between every particle

    Parameters:
    @@ -1095,7 +1248,7 @@

    Principle component analysis
    -oxDNA_analysis_tools.pca.pca(traj_info: TrajInfo, top_info: TopInfo, mean_conf: Configuration, ncpus: int = 1) → Tuple[ndarray, ndarray, ndarray]
    +oxDNA_analysis_tools.pca.pca(traj_info: TrajInfo, top_info: TopInfo, mean_conf: Configuration, ncpus: int = 1) → Tuple[ndarray, ndarray, ndarray]

    Performs a PCA on a trajectory

    Parameters:
    @@ -1110,7 +1263,7 @@

    Principle component analysis

    The structures mapped to coordinate space, the eigenvalues and the eigenvectors

    Return type:
    -

    (np.ndarray, np.ndarray, np.ndarray)

    +

    Tuple[np.ndarray, np.ndarray, np.ndarray]

    @@ -1135,7 +1288,7 @@

    Persistence length
    -oxDNA_analysis_tools.persistence_length.persistence_length(traj_info: TrajInfo, inp_file: str, n1: int, n2: int, ncpus: int = 1) → Tuple[float, ndarray]
    +oxDNA_analysis_tools.persistence_length.persistence_length(traj_info: TrajInfo, inp_file: str, n1: int, n2: int, ncpus: int = 1) → Tuple[float, ndarray]

    Computes the persistence length of a bonded sequence of nucleotides.

    Note that while n1 and n2 must be on the same strand, there can be multiple distinct duplexes within the strand.

    Only paired nucleotides will be considered in the persistence length calculation

    @@ -1152,14 +1305,14 @@

    Persistence length

    Tuple containing the average contour length and correlations between each pair step

    Return type:
    -

    (Tuple[float, np.ndarray])

    +

    Tuple[float, np.ndarray]

    -oxDNA_analysis_tools.persistence_length.get_r(conf, nucid: int, pair_dict: Dict) → ndarray
    +oxDNA_analysis_tools.persistence_length.get_r(conf, nucid: int, pair_dict: Dict) → ndarray

    Returns a normalized vector pointing from base midpoint of the nucid-th base pair to the midpoint of the next base pair.

    Parameters:
    @@ -1172,14 +1325,14 @@

    Persistence length

    The vector pointing from the midpoint of nucid’s base pair to the +1 base pair.

    Return type:
    -

    (np.ndarray)

    +

    np.ndarray

    -oxDNA_analysis_tools.persistence_length.fit_PL(correlations: ndarray, plt_name: str) → float
    +oxDNA_analysis_tools.persistence_length.fit_PL(correlations: ndarray, plt_name: str) → float

    Fits persistence length from tangent vector correlations

    Parameters:
    @@ -1192,7 +1345,7 @@

    Persistence length

    Persistence length in nucleotides

    Return type:
    -

    (float)

    +

    float

    @@ -1242,18 +1395,21 @@

    Superimpose
    -oxDNA_analysis_tools.superimpose.superimpose(ref: Configuration, victims: List[str], indexes: List[int] = [])
    +oxDNA_analysis_tools.superimpose.superimpose(ref: Configuration, victims: List[str], indexes: ndarray = array([], shape=(1, 0), dtype=float64))

    Superimposes one or more structures sharing a topology to a reference structure

    Parameters:

    • ref (Configuration) – the reference configuration to superimpose to

    • victims (List[Configuration]) – the configurations to superimpose on the reference

      • -

    • indexes (List[int]) – the indexes of the particles to superimpose on the reference (default: all)

      • +

    • indexes (np.ndarray[int]) – the indexes of the particles to superimpose on the reference (default: all)

    Returns:
    -

    Aligned configurations (List[Configuration])

    +

    Aligned configurations

    +
    +
    Return type:
    +

    List[Configuration]

    diff --git a/oat/cli.html b/oat/cli.html index d10fc10cc..0b2da26f0 100644 --- a/oat/cli.html +++ b/oat/cli.html @@ -78,6 +78,7 @@
  • Duplex angle plotter
  • Duplex finder
  • File info
    • +
  • Forces to dot-bracket
  • Forces to pairs
  • Generate force
  • Mean
    • @@ -85,6 +86,7 @@
  • Multidimensional scaling mean
  • Output bonds
  • oxDNA -> PDB
    • +
  • Pairs to dot-bracket
  • Principal component analysis
  • Persistence Length
  • Plot energy
    • @@ -154,20 +156,20 @@

    Positional Arguments

    Named Arguments

    -
    -p
    +
    -p, --parallel

    (optional) How many cores to use

    -
    -i
    +
    -i, --index

    Align to only a subset of particles from a space-separated list in the provided file

    -
    -r
    +
    -r, --ref

    Align to a provided configuration instead of the first frame.

    -
    -c
    +
    -c, --nocenter

    Don’t center the output. Can avoid errors caused by small boxes.

    Default: False

    -
    -q
    +
    -q, --quiet

    Don’t print ‘INFO’ messages to stderr

    Default: False

    @@ -222,16 +224,16 @@

    Positional Arguments

    Named Arguments

    -
    -p
    +
    -p, --parallel

    (optional) How many cores to use

    -
    -o
    +
    -o, --output

    (optional) The name of the file to write the graph to

    -
    -d
    +
    -d, --data

    (optional) The name of the file to write the data to

    -
    -q
    +
    -q, --quiet

    Don’t print ‘INFO’ messages to stderr

    Default: False

    @@ -243,7 +245,7 @@

    Bond analysis
    usage: oat bond_analysis [-h] [-o output_file] [-t trajectory_plot]
-                         [-p num_cpus] [-q]
+                         [-d data_file] [-p num_cpus] [-q]
                          inputfile trajectory designed_pairs
    @@ -264,16 +266,19 @@

    Positional Arguments

    Named Arguments

    -
    -o
    +
    -o, --output

    Name of the file to save the output oxView overlay to

    -
    -t
    +
    -t, --plot

    Name of the file to save the trajecotry plot to

    -
    -p
    +
    -d, --data
    +

    If set, save the data used to make the plot to a json file.

    +
    +
    -p, --parallel

    (optional) How many cores to use

    -
    -q
    +
    -q, --quiet

    Don’t print ‘INFO’ messages to stderr

    Default: False

    @@ -302,16 +307,16 @@

    Positional Arguments

    Named Arguments

    -
    -p
    +
    -p, --parallel

    (optional) How many cores to use

    -o, --output

    The filename to save the centroid to

    -
    -i
    +
    -i, --index

    Alignment and RMSD based on a subset of particles given in a space-separated list in the provided file

    -
    -q
    +
    -q, --quiet

    Don’t print ‘INFO’ messages to stderr

    Default: False

    @@ -342,7 +347,7 @@

    Named Arguments

    Named Arguments

    -
    -g
    +
    -g, --plot

    Filename for the plot

    -
    -d
    +
    -d, --data

    The name of the file to save the contact map as a pickle.

    -
    -p
    +
    -p, --parallel

    (optional) How many cores to use

    -
    -q
    +
    -q, --quiet

    Don’t print ‘INFO’ messages to stderr

    Default: False

    @@ -425,22 +430,22 @@

    Positional Arguments

    Named Arguments

    -
    -p
    +
    -p, --parallel

    (optional) How many cores to use

    Default: 1

    -
    -s
    +
    -s, --start

    First conf to write to the output file.

    Default: 0

    -
    -e
    +
    -e, --stop

    Process up to this conf (exclusive). Accepts negative indexes.

    -
    -d
    +
    -d, --stride

    Write out every this many confs (default=10)

    Default: 10

    -
    -q
    +
    -q, --quiet

    Don’t print ‘INFO’ messages to stderr

    Default: False

    @@ -470,22 +475,22 @@

    Positional Arguments

    Named Arguments

    -
    -p
    +
    -p, --parallel

    (optional) How many cores to use

    -o, --output

    The filename to save the RMSF json file to

    -
    -i
    +
    -i, --index

    Compute mean structure of a subset of particles from a space-separated list in the provided file

    -
    -r
    +
    -r, --plot

    The name of the file to save the RMSD plot to.

    -
    -d
    +
    -d, --data

    The name of the file to save the RMSD data in json format.

    -
    -q
    +
    -q, --quiet

    Don’t print ‘INFO’ messages to stderr

    Default: False

    @@ -524,11 +529,11 @@

    Named Arguments

    Named Arguments

    -
    -p
    +
    -p, --parallel

    (optional) How many cores to use

    -o, --output

    name of the file to write the angle list to

    -
    -q
    +
    -q, --quiet

    Don’t print ‘INFO’ messages to stderr

    Default: False

    @@ -666,7 +671,38 @@

    Named Arguments +

    Forces to dot-bracket

    +

    Convert a force file to dot-bracket notation

    +

    +
    usage: oat forces2db [-h] [-o OUTPUT] [-q] topology force_file
+
    +
    +
    +

    Positional Arguments

    +
    +
    topology
    +

    Topology file for the structure

    +
    +
    force_file
    +

    The force file to generate the dot-bracket from

    +
    +
    +
    +
    +

    Named Arguments

    +
    +
    -o, --output
    +

    If set, print the dot-bracket to a file, otherwise to the screen

    +
    +
    -q, --quiet

    Don’t print ‘INFO’ messages to stderr

    Default: False

    @@ -694,7 +730,7 @@

    Named Arguments

    Named Arguments

    -
    -p
    +
    -p, --parallel

    (optional) How many cores to use

    -o, --output
    @@ -768,13 +804,13 @@

    Named Arguments

    Compress given configuration.

    -
    usage: oat minify [-h] [-p num_cpus] [-a] [-d D] [-q] trajectory outfile
+
    usage: oat minify [-h] [-p num_cpus] [-a] [-d DECIMALS] [-q]
+                  trajectory outfile
 
    
 
    
 
    
@@ -802,17 +839,17 @@ 
    Positional Arguments
 
    Named Arguments
    
 
    
-
    -p
    
+
    -p, --parallel
    
 
    (optional) How many cores to use
    
 
    
-
    -a
    
+
    -a, --no_a
    
 
    Discard a vectors.
    
 
    Default: False
    
 
    
-
    -d
    
+
    -d, --decimals
    
 
    Round positions and orientations to the specified number of digits.
    
 
    
-
    -q
    
+
    -q, --quiet
    
 
    Don’t print ‘INFO’ messages to stderr
    
 
    Default: False
    
 
    
@@ -845,10 +882,10 @@ 
    Named Arguments
 
    Named Arguments
    
 
    
-
    -v
    
+
    -v, --view
    
 
    if you want instead average per-particle energy as an oxView JSON
    
 
    
-
    -p
    
+
    -p, --parallel
    
 
    (optional) How many cores to use
    
 
    
 
    -u, --units
    
 
    (optional) The units of the energy (pNnm or oxDNA)
    
 
    
-
    -q
    
+
    -q, --quiet
    
 
    Don’t print ‘INFO’ messages to stderr
    
 
    Default: False
    
 
    
@@ -928,7 +965,7 @@ 
    Named Arguments
+
    Pairs to dot-bracket
    
+
    Convert a pair file to dot-bracket notation
    
+
    
+
    usage: oat pairs2db [-h] [-o OUTPUT] [-q] topology pair_file
+
    
+
    
+
    
+
    Positional Arguments
    
+
    
+
    topology
    
+
    Topology file for the structure
    
+
    
+
    pair_file
    
+
    The pair file to generate the dot-bracket from
    
+
    
+
    
+
    
+
    
+
    Named Arguments
    
+
    
+
    -o, --output
    
+
    If set, print the dot-bracket to a file, otherwise to the screen
    
+
    
+
    -q, --quiet
    
+
    Don’t print ‘INFO’ messages to stderr
    
+
    Default: False
    
+
    
+
    
+
    
+
    
 
    
 
    Principal component analysis
    
 
    Calculates a principal component analysis of nucleotide deviations over a trajectory
    
@@ -975,17 +1043,17 @@ 
    Positional Arguments
 
    Named Arguments
    
 
    
-
    -p
    
+
    -p, --parallel
    
 
    (optional) How many cores to use
    
 
    
-
    -c
    
+
    -c, --cluster
    
 
    Run the clusterer on each configuration’s position in PCA space?
    
 
    Default: False
    
 
    
-
    -n
    
+
    -n, --view_comps
    
 
    (optional) Print the first N components as oxView overlay files (defaults to 1)
    
 
    
-
    -q
    
+
    -q, --quiet
    
 
    Don’t print ‘INFO’ messages to stderr
    
 
    Default: False
    
 
    
@@ -1030,7 +1098,7 @@ 
    Named Arguments
    
 
    superimposes one or more structures sharing a topology to a reference structure
    
 
    
-
    usage: oat superimpose [-h] [-i index_file]
+
    usage: oat superimpose [-h] [-i index_files) [index_file(s ...]]
                        [-o output_names [output_names ...]] [-q]
                        reference victims [victims ...]
 
    
@@ -1132,13 +1200,13 @@ 
    Positional Arguments
 
    Named Arguments
    
 
    
-
    -i
    
-
    Align to only a subset of particles from a space-separated list in the provided file
    
+
    -i, --index
    
+
    Align to only a subset of particles from a space-separated list in the provided file. If 1 file provided, the indexing is applied to all structures. Otherwise an equal number of indexes and configurations must be provided.
    
 
    
-
    -o
    
+
    -o, --output
    
 
    The names of the output files (defaults to inputname_a.dat)
    
 
    
-
    -q
    
+
    -q, --quiet
    
 
    Don’t print ‘INFO’ messages to stderr
    
 
    Default: False
    
 
    
diff --git a/oat/forces.html b/oat/forces.html
index 3bb0ec34a..6fb33608a 100644
--- a/oat/forces.html
+++ b/oat/forces.html
@@ -129,7 +129,10 @@ 
    Forces
    oxDNA_analysis_tools.external_force_utils.forces.repulsion_plane
    
 
    A plane that forces the affected particle to stay on one side.
    
 
-
    oxDNA_analysis_tools.external_force_utils.forces.repulsion_sphere
    
+
    oxDNA_analysis_tools.external_force_utils.forces.attraction_plane
    
+
    A plane that pulls the affected particle towards it while staying on one side.
    
+
+
    oxDNA_analysis_tools.external_force_utils.forces.repulsion_sphere
    
 
    A sphere that encloses the particle
    
 
 
@@ -222,6 +225,22 @@ 
    Forces
 
    
 
+
    
+
    
+oxDNA_analysis_tools.external_force_utils.forces.attraction_plane(particle: int, stiff: float, direction: List[float], position: List[float]) → Dict
    
+
    A plane that pulls the affected particle towards it while staying on one side.
    
+
    
+
    Parameters:
    
+
      
+
    • particle (int) – the particle that the force acts upon.  -1 will act on whole system.
      • 
+
    • stiff (float) – the stiffness of the trap (force = stiff * distance below plane)
      • 
+
    • direction ([float, float, float]) – the normal vector to the plane
      • 
+
    • position ([float, float, float]) – position of the plane (plane is d0*x + d1*y + d2*z + position = 0)
      • 
+
    
+
    
+
    
+
    
+
 
    
 
    
 oxDNA_analysis_tools.external_force_utils.forces.repulsion_sphere(particle: int, center: List[float], stiff: float, r0: float, rate: float) → Dict
    
@@ -257,7 +276,7 @@ 
    Reader/Writer
 
    
-oxDNA_analysis_tools.external_force_utils.force_reader.read_force_file(file)
    
+oxDNA_analysis_tools.external_force_utils.force_reader.read_force_file(file: str) → List[Dict]
 
    Read a force file into a list of force dictionaries.
    
 
    
 
    Parameters:
    
@@ -274,7 +293,7 @@ 
    Reader/Writer
 
    
-oxDNA_analysis_tools.external_force_utils.force_reader.write_force_file(force_list, filename, mode='w')
    
+oxDNA_analysis_tools.external_force_utils.force_reader.write_force_file(force_list, filename, mode='w+')
 
    Write a list of forces out to a file.
    
 
    
 
    Parameters:
    
@@ -282,7 +301,7 @@ 
    Reader/Writerlist) – a list of force dictionaries
    
 
  • filename (str) – file to write out to
    • 
 
  • mode (<optional>) – the mode of the python open funciton.  Defaults to ‘w’
-change mode to ‘w+’ if you want to append instead of overwrite.
    • 
+change mode to ‘a’ if you want to append instead of overwrite.
    
 
 
    
 
    
diff --git a/oat/index.html b/oat/index.html
index 5db43c3e6..8eeb0f49f 100644
--- a/oat/index.html
+++ b/oat/index.html
@@ -142,6 +142,7 @@ 
    Command Line InterfaceDuplex angle plotter
 
  • Duplex finder
    • 
 
  • File info
    • 
+
  • Forces to dot-bracket
    • 
 
  • Forces to pairs
    • 
 
  • Generate force
    • 
 
  • Mean
    • 
@@ -149,6 +150,7 @@ 
    Command Line InterfaceMultidimensional scaling mean
 
  • Output bonds
    • 
 
  • oxDNA -> PDB
    • 
+
  • Pairs to dot-bracket
    • 
 
  • Principal component analysis
    • 
 
  • Persistence Length
    • 
 
  • Plot energy
    • 
@@ -192,10 +194,13 @@ 
    Top-level APIDuplex angle plotter
 
  • Duplex finder
    • 
 
  • File info
    • 
+
  • Forces to dot-bracket
    • 
 
  • Mean
    • 
 
  • Minify
    • 
 
  • Multidimensional scaling mean
    • 
 
  • Output bonds
    • 
+
  • OxDNA to PDB
    • 
+
  • Pairs to dot-bracket
    • 
 
  • Principle component analysis
    • 
 
  • Persistence length
    • 
 
  • Subset trajectory
    • 
diff --git a/oat/utils.html b/oat/utils.html
index a3669f6f8..1ece1b775 100644
--- a/oat/utils.html
+++ b/oat/utils.html
@@ -246,44 +246,44 @@ 
    Data structures
 
    
-class oxDNA_analysis_tools.UTILS.data_structures.Configuration(time: int, box: ndarray, energy: ndarray, positions: ndarray, a1s: ndarray, a3s: ndarray)
    
+class oxDNA_analysis_tools.UTILS.data_structures.Configuration(time: int, box: ndarray, energy: ndarray, positions: ndarray, a1s: ndarray, a3s: ndarray)
 
    Bases: object
    
 
    Dataclass/numpy representation for oxDNA configurations
    
 
    
 
    Parameters:
    
 
      
 
    • time (int) – The time step of the configuration
      • 
-
    • box (numpy.ndarray) – The box size for the simulation
      • 
-
    • energy (numpy.ndarray) – The potential, kinetic and total energy for the configuration
      • 
-
    • positions (numpy.ndarray) – The positions of the nucleotides
      • 
-
    • a1s (numpy.ndarray) – the orientations of the base pairing sites
      • 
-
    • a3s (numpy.ndarray) – the orientations of the stacking sites
      • 
+
    • box (numpy.ndarray) – The box size for the simulation
      • 
+
    • energy (numpy.ndarray) – The potential, kinetic and total energy for the configuration
      • 
+
    • positions (numpy.ndarray) – The positions of the nucleotides
      • 
+
    • a1s (numpy.ndarray) – the orientations of the base pairing sites
      • 
+
    • a3s (numpy.ndarray) – the orientations of the stacking sites
      • 
 
    
 
    
 
    
 
    
 
    
-a1s: ndarray
    
+a1s: ndarray
 
    
 
 
    
 
    
-a3s: ndarray
    
+a3s: ndarray
 
    
 
 
    
 
    
-box: ndarray
    
+box: ndarray
 
    
 
 
    
 
    
-energy: ndarray
    
+energy: ndarray
 
    
 
 
    
 
    
-positions: ndarray
    
+positions: ndarray
 
    
 
 
    
@@ -529,10 +529,7 @@ 
    Geometry utilitiesParameters:
 
      
 
    • particles (oxpy.config_info) – The positions/orientations of the particles
      • 
-
    • start1 (int) – Particle ID of the first particle in the first strand
      • 
-
    • end1 (int) – Particle ID of the last particle in the first strand
      • 
-
    • end2 (int) – Particle ID of the particle complimentary to start1
      • 
-
    • start2 (int) – Particle ID of the particle complimentary to end1
      • 
+
    • d (duplex_list) – A duplex_list object with members “start1”, “end1”, “end2”, “start2” containing integer values of the corresponding particle IDs.
      • 
 
    
 
    
 
    
@@ -546,10 +543,7 @@ 
    Geometry utilitiesParameters:
 
      
 
    • particles (oxpy.config_info) – The positions/orientations of the particles
      • 
-
    • start1 (int) – Particle ID of the first particle in the first strand
      • 
-
    • end1 (int) – Particle ID of the last particle in the first strand
      • 
-
    • end2 (int) – Particle ID of the particle complimentary to start1
      • 
-
    • start2 (int) – Particle ID of the particle complimentary to end1
      • 
+
    • d (duplex_list) – A duplex_list object with members “start1”, “end1”, “end2”, “start2” containing integer values of the corresponding particle IDs.
      • 
 
    
 
    
 
    
@@ -581,12 +575,12 @@ 
    iPython oxView plugin
 
    
 
    
-oxDNA_analysis_tools.UTILS.oxview.display_files(files_with_ext, inbox_settings=['Monomer', 'Origin'], oxview_src='https://sulcgroup.github.io/oxdna-viewer/')
    
+oxDNA_analysis_tools.UTILS.oxview.display_files(system_list, inbox_settings=['Monomer', 'Origin'], oxview_src='https://sulcgroup.github.io/oxdna-viewer/')
 
    Generate an iframe displaying the provided files in oxview
    
 
    
 
    Parameters:
    
 
      
-
    • files_with_ext (tuple) – a list of tuples (file_string, extension)
      • 
+
    • system_list (tuple) – a list of lists of tuples (file_string, extension)
      • 
 
    • inbox_settings (list[str]) – a list of strings, the inbox settings to use
      • 
 
    • oxview_src (str) – the url of the oxview source
      • 
 
    
@@ -599,18 +593,18 @@ 
    iPython oxView plugin
 
    
-oxDNA_analysis_tools.UTILS.oxview.from_path(*args: List[str], **kwargs)
    
+oxDNA_analysis_tools.UTILS.oxview.from_path(*args: List[str] | List[List[str]], **kwargs)
 
    Display oxview frame based on the string path provided
    
 
    
 
    Parameters:
    
 
      
-
    • args (List[str]) – contains the paths to the files
      • 
+
    • args (Union[List[str],List[List[str]]]) – contains the paths to the files or a list of lists of paths
      • 
 
    • kwargs (dict) – the properties to oxview defaults to = {“inbox_settings”:[“Monomer”, “Origin”], “oxview_src” : “https://sulcgroup.github.io/oxdna-viewer/”}
      • 
 
    
 
    
 
    
 
    
-
    Usage:
    raw(“conf.top”, “conf.dat”,**{“inbox_settings”:[“Monomer”, “Origin”]})
    
+
    Usage:
    from_path(“conf.top”, “conf.dat”,**{“inbox_settings”:[“Monomer”, “Origin”]})
    
 
    
 
    
 
    
@@ -927,7 +921,7 @@ 
    Rye reader
 
    
-oxDNA_analysis_tools.UTILS.RyeReader.inbox(conf: Configuration, center: bool = True, centerpoint: str | ndarray = 'bc') → 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.
    
diff --git a/objects.inv b/objects.inv
index 47d203808..c656985fd 100644
Binary files a/objects.inv and b/objects.inv differ
diff --git a/oxpy/modules/core/core.html b/oxpy/modules/core/core.html
index 0fb906b04..4d14c403d 100644
--- a/oxpy/modules/core/core.html
+++ b/oxpy/modules/core/core.html
@@ -506,7 +506,7 @@ 
    The core module
    The position of the site.
    
 
    
 
    Return type:
    
-
    numpy.ndarray
    
+
    numpy.ndarray
    
 
    
 
    
 
    
@@ -520,7 +520,7 @@ 
    The core module
    The position of the site.
    
 
 
    Return type:
    
-
    numpy.ndarray
    
+
    numpy.ndarray

    @@ -534,7 +534,7 @@

    The core module

    The position of the site.

    Return type:
    -

    numpy.ndarray

    +

    numpy.ndarray

    @@ -556,7 +556,7 @@

    The core module

    The position of the site.

    Return type:
    -

    numpy.ndarray

    +

    numpy.ndarray

    @@ -570,7 +570,7 @@

    The core module

    The position of the site.

    Return type:
    -

    numpy.ndarray

    +

    numpy.ndarray

    @@ -584,7 +584,7 @@

    The core module

    The position of the site.

    Return type:
    -

    numpy.ndarray

    +

    numpy.ndarray

    @@ -598,7 +598,7 @@

    The core module

    The position of the site.

    Return type:
    -

    numpy.ndarray

    +

    numpy.ndarray

    @@ -612,7 +612,7 @@

    The core module

    The position of the site.

    Return type:
    -

    numpy.ndarray

    +

    numpy.ndarray

    @@ -626,7 +626,7 @@

    The core module

    The position of the site.

    Return type:
    -

    numpy.ndarray

    +

    numpy.ndarray

    @@ -640,7 +640,7 @@

    The core module

    The position of the site.

    Return type:
    -

    numpy.ndarray

    +

    numpy.ndarray

    @@ -763,7 +763,7 @@

    The core modulepair_interaction() for additional details).

    Parameters:
    -

    r (numpy.ndarray) – The distance vector to be stored.

    +

    r (numpy.ndarray) – The distance vector to be stored.

    @@ -1005,7 +1005,7 @@

    The core module

    The absolute (unwrapped) position of the given particle.

    Return type:
    -

    numpy.ndarray

    +

    numpy.ndarray

    @@ -1042,7 +1042,7 @@

    The core module

    The distance vector connecting p to q.

    Return type:
    -

    numpy.ndarray

    +

    numpy.ndarray

    diff --git a/oxpy/modules/core/forces.html b/oxpy/modules/core/forces.html index feee25145..bdb1ea1b3 100644 --- a/oxpy/modules/core/forces.html +++ b/oxpy/modules/core/forces.html @@ -203,7 +203,7 @@

    The core.forces moduleParameters:

    • step (int) – The current time step.

      • -

    • pos (numpy.ndarray) – The position where the force should be computed.

      • +

    • pos (numpy.ndarray) – The position where the force should be computed.

    Returns:
    @@ -241,14 +241,14 @@

    The core.forces moduleParameters:

    • step (int) – The current time step.

      • -

    • pos (numpy.ndarray) – The position where the force should be computed.

      • +

    • pos (numpy.ndarray) – The position where the force should be computed.

    Returns:

    The computed force vector.

    Return type:
    -

    numpy.ndarray

    +

    numpy.ndarray

    diff --git a/searchindex.js b/searchindex.js index 07937dc14..49354d26e 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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"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 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"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 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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, 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"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 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