Forgi

https://viennarna.github.io/forgi/
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Forgi is a Python library for manipulating and analyzing RNA secondary structures with tools for...
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### Install forgi from source directory

Source: https://viennarna.github.io/forgi/download

Installs the forgi package from a local source directory using pip. This method is recommended over directly invoking setup.py.

```Shell
pip install --upgrade path/to/forgi/directory
```

--------------------------------

### Get version string

Source: https://viennarna.github.io/forgi/apidoc/forgi.utilities

Retrieves the version string of the forgi package. If installed from GitHub, it uses 'git describe' to get the version. Otherwise, it attempts to get the commit hash directly.

```Python
forgi.utilities.stuff.get_version_string()
```

--------------------------------

### Install forgi with all optional dependencies from PyPI

Source: https://viennarna.github.io/forgi/download

Installs or upgrades the forgi package along with all its optional dependencies from PyPI. This is useful for enabling all features of forgi.

```Shell
pip install --upgrade forgi[all]
```

--------------------------------

### Install forgi with visualization dependencies

Source: https://viennarna.github.io/forgi/download

Installs forgi with specific optional dependencies for visualization, such as matplotlib. This is required for functions in forgi.threedee.visual, forgi.visual, and forgi.projection.

```Shell
pip install forgi[forgi.visual]
```

--------------------------------

### Install forgi with development dependencies

Source: https://viennarna.github.io/forgi/download

Installs forgi with development dependencies, including Cython. This is typically not needed for regular use as forgi includes pre-generated C-code.

```Shell
pip install forgi[development]
```

--------------------------------

### Install forgi from PyPI

Source: https://viennarna.github.io/forgi/download

Installs or upgrades the forgi package from the Python Package Index (PyPI). This command ensures you have the latest stable version of forgi.

```Shell
pip install --upgrade forgi
```

--------------------------------

### Install forgi with PDBeChem dependencies

Source: https://viennarna.github.io/forgi/download

Installs forgi with the beautifulsoup4 dependency, which is needed for fetching information about modified residues in PDB files.

```Shell
pip install forgi[pdbechem]
```

--------------------------------

### Get Forgi Version String

Source: https://viennarna.github.io/forgi/_modules/forgi/utilities/stuff

Retrieves the version string for the forgi library. It prioritizes version information from Git tags if installed from a repository, otherwise falls back to the package's defined version.

```Python
from builtins import next
from builtins import range
import itertools as it
import contextlib
import random
import shutil
import tempfile as tf
import collections as col
import sys
import subprocess

import logging
log = logging.getLogger(__name__)

import forgi
import forgi.utilities.debug as cud
from .exceptions import GraphConstructionError


bracket_left = "([{<ABCDEFGHIJKLMNOPQRSTUVWXYZ"
bracket_right = ")]}>abcdefghijklmnopqrstuvwxyz"



[docs]
def get_version_string():
    """
    If installed from github, print the version obtained by `git describe`
    On my local machine, when run within a git directory, get the commit
    hash directly using `git describe`
    """
    try:
        # Installed with setup.py from a gitrepo
        label = "forgi {}".format(forgi.__complete_version__)
    except:
        try:
            # On my local machine, run from git directory.
            repo = subprocess.check_output(
                ["git", "rev-parse", "--show-toplevel"]).decode('ascii')
            if "forgi" not in repo:
                raise OSError("")
            label = subprocess.check_output(
                ["git", "describe", "--dirty"]).decode('ascii')
            label = "forgi {}".format(label)
        except OSError:
            # In production, use the version variable
            label = "forgi {}".format(forgi.__version__)
    return label
```

--------------------------------

### Get Version String

Source: https://viennarna.github.io/forgi/genindex

Returns the version string of the Forgi library. This function is located in the stuff module.

```Python
from forgi.utilities.stuff import get_version_string
```

--------------------------------

### Get Flanking Handles for Bulge Fitting

Source: https://viennarna.github.io/forgi/_modules/forgi/graph/bulge_graph

Gets the indices of residues for fitting bulge regions, used for aligning fitted regions against handles. It returns original chain residues and flanking residues relative to the flanking region start.

```Python
    def get_flanking_handles(self, bulge_name, side=0):
        """
        Get the indices of the residues for fitting bulge regions.

        So if there is a loop like so (between residues 7 and 16)::

          (((...))))
          7890123456
            ^   ^

        Then residues 9 and 13 will be used as the handles against which
        to align the fitted region.

        In the fitted region, the residues (2,6) will be the ones that will
        be aligned to the handles.

        :return: (orig_chain_res1, orig_chain_res1, flanking_res1, flanking_res2)
        """
        f1 = self.get_flanking_region(bulge_name, side)
        c = self.connections(bulge_name)

        if bulge_name[0] == 'h':
            s1 = self.defines[c[0]]
            ab = [s1[1], s1[2]]
            return (ab[0], ab[1], ab[0] - f1[0], ab[1] - f1[0])

        s1 = self.defines[c[0]]
        s2 = self.defines[c[1]]

        if bulge_name[0] == 'm':
            sides = self.get_multiloop_side(bulge_name)
            ab = [s1[sides[0]], s2[sides[1]]]
            ab.sort()

            return (ab[0], ab[1], ab[0] - f1[0], ab[1] - f1[0])

        if bulge_name[0] == 'i':
            if side == 0:
                ab = [s1[1], s2[0]]
            else:
                ab = [s2[3], s1[2]]

            return (ab[0], ab[1], ab[0] - f1[0], ab[1] - f1[0])

        # probably still have to include the 5' and 3' regions, but that
        # will come a little later
        return None
```

--------------------------------

### Get Stem Coordinates String

Source: https://viennarna.github.io/forgi/_modules/forgi/threedee/model/coarse_grain

Generates a string representation of stem start and end coordinates in a specific format. It excludes bulge coordinates as they are redundant.

```Python
def _get_coord_str(self):
    '''
    Place the start and end coordinates of each stem into a string.

    The format is:

        coord s1 x1 y1 z1 x2 y2 z2

    Where s1 is the name of the stem, (x1,y1,z1) and (x2,y2,z2) are
    the two endpoints of the stem.

    :return: A string containing the coordinates for all of the stems.
    '''

    out_str = ''
    for key in self.coords.keys():
        if key[0] in ["m", "i"]:
            # Bulge coordinates are redundant. They can be deduced from the stem coordinates.
            continue
        [p, n] = self.coords[key]
        out_str += ("coord {k} {x[0]:.16f} {x[1]:.16f} {x[2]:.16f} "
                    "{y[0]:.16f} {y[1]:.16f} {y[2]:.16f}".format(k=key, x=p, y=n))
        out_str += '\n'
    return out_str
```

--------------------------------

### Generate PyMOL Intro String

Source: https://viennarna.github.io/forgi/_modules/forgi/threedee/visual/pymol

Generates the introductory lines for a PyMOL script, importing necessary modules like 'pymol.cgo', 'pymol', and 'pymol.vfont'.

```python
def pymol_intro_string(self):
        s = "from pymol.cgo import *" + '\n'
        s += "from pymol import cmd" + '\n'
        s += "from pymol.vfont import plain" + '\n'
        return s
```

--------------------------------

### Get Condensed Element String Representation

Source: https://viennarna.github.io/forgi/graph_tutorial

This example demonstrates using `rnaConvert.py` to obtain a condensed string representation of an RNA secondary structure, mapping nucleotide positions to element types like stems and hairpin loops.

```Shell
$ python examples/rnaConvert.py examples/input/1y26_ss.dotbracket -T element_string
```

--------------------------------

### Get Bulge Angle Statistics

Source: https://viennarna.github.io/forgi/_modules/forgi/threedee/model/coarse_grain

Retrieves the angle statistics for a given bulge, describing the relative orientation of the two stems it connects. It handles a special 'start' case and calls a core function for the actual calculation. An assertion verifies that the angle statistics are consistent when calculated in reverse.

```Python
def get_bulge_angle_stats(self, bulge):
        '''
        Return the angle stats for a particular bulge. These stats describe
        the relative orientation of the two stems that it connects.

        :param bulge: The name of the bulge.
        :param connections: The two stems that are connected by it.
        :return: The angle statistics in one direction and angle statistics in
                 the other direction
        '''
        if bulge == 'start':
            return (ftms.AngleStat(), ftms.AngleStat())

        angle_stat1 = self.get_bulge_angle_stats_core(bulge, True)
        angle_stat2 = self.get_bulge_angle_stats_core(bulge, False)
        # If we go into the reverse direction, the first vector of the element basis is inverted.
        # and thus also the last one (cross product of first and second)
        # for k,v in angle_stat2.vres.items():
        #    angle_stat2.vres[k]= v*[-1,1,-1]
        assert round(angle_stat1.get_angle(), 5) == round(angle_stat2.get_angle(
        ), 5), ("{}!={}".format(angle_stat1.get_angle(), angle_stat2.get_angle()))
        return (angle_stat1, angle_stat2)
```

--------------------------------

### Generate PyMOL Introduction String

Source: https://viennarna.github.io/forgi/genindex

Generates an introductory command string for PyMOL sessions. This method belongs to the PymolPrinter class in the forgi.threedee.visual.pymol module.

```Python
from forgi.threedee.visual.pymol import PymolPrinter

# Assuming 'printer' is an instance of PymolPrinter
# intro_command = printer.pymol_intro_string()
```

--------------------------------

### Iterate Elements Along Backbone

Source: https://viennarna.github.io/forgi/_modules/forgi/graph/bulge_graph

Yields coarse-grained elements along the RNA backbone, starting from a specified nucleotide position. Stems are yielded twice, and interior loops may be yielded once or twice. Handles 0-length multiloop segments correctly. Requires methods to get nodes from residue numbers and flanking nucleotides.

```Python
def iter_elements_along_backbone(self, startpos=1):
        """
        Iterate all coarse grained elements along the backbone.

        Note that stems are yielded twice (for forward and backward strand).
        Interior loops may be yielded twice or once (if one side has no nucleotide)

        0-length multiloop-segments are correctly yielded.

        :param startpos: The nucleotide position at which to start
        :yields: Coarse grained element names, like "s0", "i0"
        """
        nuc = startpos
        try:
            node = self.get_node_from_residue_num(nuc)
        except:
            assert len(self.defines) == 0
            raise StopIteration("Empty Graph")
        while True:
            log.debug("Yielding node %s with edges %s", node, self.edges[node])
            yield node
            if node[0] in "si":  # The strand matters
                if node[0] == "s":
                    strand = self.get_stem_edge(node, nuc)
                    if strand == 0:  # forward
                        nuc = self.flanking_nuc_at_stem_side(node, 1)
                    else:
                        nuc = self.flanking_nuc_at_stem_side(node, 3)
                else:
                    f1, f2, f3, f4 = sorted(self.flanking_nucleotides(node))
                    if f1 < nuc < f2:
                        nuc = f2
                    elif f3 < nuc < f4:
                        nuc = f4
                    else:
                        assert False
                try:
                    next_node = self.get_node_from_residue_num(nuc)
                except LookupError:
                    raise StopIteration("End of chain reached")
                else:
                    # We need to make sure there is no 0-length multiloop between the two stems.
                    intersect = self.edges[node] & self.edges[next_node]
                    for el in intersect:
                        if el[0] == "m" and self.defines[el] == []:

```

--------------------------------

### Initialize LineSegmentStorage

Source: https://viennarna.github.io/forgi/_modules/forgi/threedee/model/linecloud

Constructor for LineSegmentStorage. It initializes the parent class, creates a mapping from index to element name, and sets up an extended on_change handler.

```Python
class LineSegmentStorage(CoordinateStorage):
    _coords_per_key = 2

    def __init__(self, *args, **kwargs):
        super(LineSegmentStorage, self).__init__(*args, **kwargs)
        self._i_to_elem = {i: elem for elem, i in self._elem_names.items()}
        self.is_centered = False
        self.on_change = self._extended_on_change(self.on_change)
```

--------------------------------

### Configure PDB annotation tool

Source: https://viennarna.github.io/forgi/download

Configures the tool used for PDB file annotation. You can either run the forgi_config.py script or use a command-line option when running forgi scripts.

```Shell
forgi_config.py
```

```Shell
forgi_config.py --pdb-annotation-tool DSSR
```

```Shell
forgi_config.py --pdb-annotation-tool MC-Annotate
```

--------------------------------

### Observed Dictionary and Command Line Utilities in Forgi

Source: https://viennarna.github.io/forgi/genindex

Includes an observed dictionary class for tracking changes and utilities for opening files for output.

```Python
observedDict
open_for_out()
```

--------------------------------

### Open File for Writing with Force Option

Source: https://viennarna.github.io/forgi/_modules/forgi/utilities/commandline_utils

This context manager opens a file for writing. It includes an option to force overwriting an existing file or raise an IOError if the file exists and force is not enabled. It handles closing the file properly.

```Python
import contextlib
import os
import sys

@contextlib.contextmanager
def open_for_out(filename=None, force=False):
    """From http://stackoverflow.com/a/17603000/5069869"""
    if filename and filename != '-':
        if not force and os.path.isfile(filename):
            raise IOError(
                "Cannot create file {}. File exists.".format(filename))
        fh = open(filename, 'w')
    else:
        fh = sys.stdout
    try:
        yield fh
    finally:
        if fh is not sys.stdout:
            fh.close()
```

--------------------------------

### Python SeqidList Initialization

Source: https://viennarna.github.io/forgi/_modules/forgi/graph/sequence

Initializes a SeqidList with a sequence of residue IDs, creating a lookup dictionary for efficient access. It includes error handling for duplicate sequence IDs.

```Python
class SeqidList(SequenceABC):
    def __init__(self, arg):
        self._list = list(arg)
        self._lookup = {resid: i for i, resid in enumerate(self._list)}
        if len(self._lookup) != len(self._list):
            # duplicate seqids
            c = Counter(self._list)
            for k, amount in c.most_common():
                if amount > 1:
                    log.error("Seq_id %s  occurs %s times!", k, amount)
                else:
                    break
            if c.most_common()[0][1] == 1:
                raise ValueError("len %{} ({}) != ({}) len {}".format(
                                            self._lookup, len(self._lookup),
                                            len(self._list), self._list))
            raise ValueError(
                "Duplicate Seq_id encountered: {}".format(c.most_common()[0][0]))

    def __getitem__(self, i):
        return self._list[i]

    def __len__(self):

```

--------------------------------

### Sort Points Along a Line (Python)

Source: https://viennarna.github.io/forgi/_modules/forgi/threedee/utilities/vector

Sorts a list of points based on their distance from a specified start point along a line defined by the start and end points. The start and end points are also included in the sorted list.

```Python
def sortAlongLine(start, end, points):
    """
    Sort all points in points along the line from start to end.

    :param start: A point
    :param end: A point
    :param points: A list of points

    :returns: A list containing start, end and all elements of points, sorted by the distance from start
    """
    # print start, end, points
    s_points = points + [start, end]
    s_points.sort(key=lambda x: vec_distance(x, start))
    return s_points

```

--------------------------------

### Rosetta Constraints File Format

Source: https://viennarna.github.io/forgi/graph_tutorial

An example output format for a Rosetta rna_denovo constraint file, generated from an RNA dot-bracket sequence, indicating paired nucleotide positions.

```Text
STEM PAIR 42 60
STEM PAIR 43 59
STEM PAIR 44 58
STEM PAIR 45 57
STEM PAIR 46 56
STEM PAIR 47 55
STEM PAIR 13 33
STEM PAIR 14 32
STEM PAIR 15 31
STEM PAIR 16 30
STEM PAIR 17 29
STEM PAIR 18 28
STEM PAIR 19 27
STEM PAIR 1 71
STEM PAIR 2 70
STEM PAIR 3 69
STEM PAIR 4 68
STEM PAIR 5 67
STEM PAIR 6 66
STEM PAIR 7 65
STEM PAIR 8 64
STEM PAIR 9 63
```

--------------------------------

### Try Starting Points with Heuristics

Source: https://viennarna.github.io/forgi/_modules/forgi/projection/hausdorff

This function appears to be part of a larger optimization process. It calculates the longest diameter of a reference image and then iterates through a set of starting points (projection directions). For each starting point, it generates a projection and potentially applies heuristics based on the image diameter and scale. It tracks heuristics usage and best scores.

```Python
def _try_startpoints(ref_img, scale, cg, start_points, starting_rotations,
                     starting_offsets, local_maxiter, virtual_atoms, use_heuristic, distance, verbose):
    # Longest extention in the image
    longest_distance_image = get_longest_img_diameter(ref_img, scale)
    if longest_distance_image == 0:
        raise ValueError("Reference image probably empty")

    # We count, how often certain heuristics kicked in
    la_heur = 0
    no_heur = 0
    score_heur = 0
    # 
    dpi = len(ref_img)
    best_score = float('inf')
    decrease = float("inf")
    for i, project_dir in enumerate(start_points):
        sys.stdout.write("{:2.0%}\r".format(i / len(start_points)))  # Progress
        sys.stdout.flush()
        proj = fhp.Projection2D(cg, from_polar([1] + list(project_dir)),
                                project_virtual_atoms=virtual_atoms)

        if use_heuristic:
            # 4 pixels is arbitrary heuristic
            if abs(proj.longest_axis - longest_distance_image) > 6 * scale / dpi:

```

--------------------------------

### Calculate Stem Length

Source: https://viennarna.github.io/forgi/_modules/forgi/graph/bulge_graph

Calculates the length of a stem based on its defined start and end points. The length is determined by the difference between the end and start indices plus one.

```Python
def stem_length(self, key):
        d = self.defines[key]
        length = 0

        for i in range(0, len(d), 2):
            length += d[i + 1] - d[i] + 1

        return length
```

--------------------------------

### RNA Loading and Structure Utilities in Forgi

Source: https://viennarna.github.io/forgi/genindex

Utilities for loading RNA data, including loading from command line arguments and loading structural information from PDB files.

```Python
load_rna()
load_structure()
```

--------------------------------

### Bresenham Line Rasterization

Source: https://viennarna.github.io/forgi/apidoc/forgi.projection

Rasterizes a line from a start point to an end point onto a grid with a grid-width of 1. It takes start and end coordinates as input and returns a list of integer (x,y) tuples representing the rasterized line.

```Python
forgi.projection.projection2d.bresenham(_start_, _end_)
```

--------------------------------

### Developer Representation of Object

Source: https://viennarna.github.io/forgi/_modules/forgi/threedee/model/linecloud

Returns a developer-friendly string representation of the object, including its type, memory address, and a concise summary of its contents.

```Python
def __repr__(self):
    return "<{} object at {} with {}>".format(type(self).__name__, hex(id(self)), str(self).replace("\n", "; "))
```

--------------------------------

### Calculate Clockwise Angle

Source: https://viennarna.github.io/forgi/_modules/forgi/threedee/utilities/my_math

Determines the amount of clockwise rotation needed to move from a starting angle (a1) to a target angle (a2). If the target angle is less than the starting angle, it adds 2 * pi to the target angle to ensure a positive clockwise rotation. This is useful in applications involving circular motion or angular measurements.

```Python
import math



[docs]def clock_angle(a1, a2):
    '''
    The amount one needs to rotate from angle a1
    to angle a2 in a clockwise direction. I.e.
    increasing a1 until it reaches a2.

    @param a1: The first angle.
    @param a2: The second angle.
    '''
    if a2 < a1:
        a2 += 2. * math.pi
    return a2 - a1
```

--------------------------------

### Generate Graphviz Visualization from Dot-Bracket

Source: https://viennarna.github.io/forgi/graph_tutorial

This snippet illustrates converting an RNA secondary structure from dot-bracket format to a format suitable for Graphviz's `neato` program, generating a PNG image of the structure's graph representation.

```Shell
python examples/rnaConvert.py examples/input/1y26_ss.dotbracket -T neato | neato -Tpng -o 1y26_neato.png
```

--------------------------------

### Initialize ClusteredAngleStats

Source: https://viennarna.github.io/forgi/_modules/forgi/threedee/model/stats

Initializes the ClusteredAngleStats class by parsing a clustered angle statistics file. It reads the file line by line, identifying cluster definitions and individual angle statistics, and stores them in a dictionary. Dependencies include the AngleStat class and the collections.defaultdict.

```Python
class ClusteredAngleStats(object):
    def __init__(self, filename):
        """
        A collection of clustered angle_stats. Whenever stats for a certain key are retrieved,
        only one (randomly choosen) representative per cluster is returned.

        Requires a clustered angle stats file (created by fess/scripts/cluster_stats.py).
        The file should look like this:

        '
        # Cluster 0 for (1, 1, -1):
        angle RS_1788_S_000008_A 1 1 1.520877 1.837257 -1.380352 11.237569 0.867246 2.057771 1 19 19 30 30 UCG CAA
        # Cluster 1 for (1, 1, -1):
        angle RS_1140_S_000002_A 1 1 1.563667 1.869580 -0.967966 16.241881 0.896602 2.177000 -1 13 13 24 24 ACG CUU
        angle RS_1183_S_000008_A 1 1 1.533551 1.914482 -1.108396 15.780723 0.829850 2.255556 -1 4 4 46 46 UAG CAG
        '

        :param filename: The filename of the clustered angle stats file.
        """
        #: A dict `(dim1, dim2, ang_type)` : list of lists.
        #: Each value is a list of clusters, and each cluster is a list.
        self._stats_dict = c.defaultdict(list)
        lastkey = None
        with open(filename) as f:
            for line in f:
                if line.startswith('# Cluster'):
                    fields = line.split()
                    dim1 = int(fields[4].lstrip("(").rstrip(","))
                    dim2 = int(fields[5].rstrip(","))
                    ang_type = int(fields[6].rstrip("): "))
                    self._stats_dict[(dim1, dim2, ang_type)].append([])
                    lastkey = (dim1, dim2, ang_type)
                elif line.startswith('#'):
                    continue
                else:
                    angle_stat = AngleStat()
                    angle_stat.parse_line(line)
                    # I don't know what this does, I just copied the following 2 lines from
                    # Peter's code in get_angle_stats
                    if len(angle_stat.define) > 0 and angle_stat.define[0] == 1:
                        continue

                    assert lastkey == (angle_stat.dim1, angle_stat.dim2, angle_stat.ang_type) or lastkey == (
                        angle_stat.dim2, angle_stat.dim1, -angle_stat.ang_type)
                    self._stats_dict[lastkey][-1].append(angle_stat)
```

--------------------------------

### Get Sequence Property

Source: https://viennarna.github.io/forgi/_modules/forgi/graph/bulge_graph

A property that returns the RNA sequence itself.

```Python
@property
def seq(self):
    return self._seq
```

--------------------------------

### Experimental Modules ftm.ensemble, ftm.ensemble2, ftu.dssr

Source: https://viennarna.github.io/forgi/changelog

The modules `ftm.ensemble`, `ftm.ensemble2`, and `ftu.dssr` are now included but marked as EXPERIMENTAL.

```Python
# No specific code snippet provided, modules are experimental.
```

--------------------------------

### Get Sequence Length Property

Source: https://viennarna.github.io/forgi/_modules/forgi/graph/bulge_graph

A property that returns the length of the RNA sequence.

```Python
@property
def seq_length(self):
    return len(self.seq)
```

--------------------------------

### Get Some Leaf-Leaf Distances in Projection2D

Source: https://viennarna.github.io/forgi/apidoc/forgi.projection

Retrieves a subset of distances between leaf nodes in the projection.

```Python
def get_some_leaf_leaf_distances(self):
    """Get a list of distances between any pair of leaf nodes. The distances are measured in direct line, not along the path
    """
    pass
```

--------------------------------

### Initialize ConformationStats

Source: https://viennarna.github.io/forgi/_modules/forgi/threedee/model/stats

Initializes the ConformationStats class, loading various statistical data for RNA conformations. It can either load raw angle statistics or pre-clustered angle statistics, along with stem, five-prime, three-prime, and loop statistics. Dependencies include get_angle_stats, ClusteredAngleStats, get_stem_stats, get_fiveprime_stats, get_threeprime_stats, and get_loop_stats.

```Python
class ConformationStats(object):
    def __init__(self, stats_file, clustered_angle_stats_file=None):
        if clustered_angle_stats_file is None:
            self.angle_stats = get_angle_stats(stats_file, refresh=True)
        else:
            self.angle_stats = ClusteredAngleStats(clustered_angle_stats_file)
        self.stem_stats = get_stem_stats(stats_file, refresh=True)
        self.fiveprime_stats = get_fiveprime_stats(stats_file, refresh=True)
        self.threeprime_stats = get_threeprime_stats(stats_file, refresh=True)
        self.loop_stats = get_loop_stats(stats_file, refresh=True)

        self.constrained_stats = c.defaultdict(list)
```

--------------------------------

### Main Execution Block

Source: https://viennarna.github.io/forgi/_modules/forgi/threedee/utilities/modified_res

This block configures logging, prints a header indicating the script's execution, and creates a dictionary of residue information from PDB files specified as command-line arguments. It also adds common ions to the dictionary and prints the resulting dictionary.

```python
if __name__ == "__main__":
    logging.basicConfig(level=logging.INFO)
    print("# Created by `python {}`".format(" ".join(sys.argv)))
    print("RESIDUE_DICT = ", end="")
    d = dict_from_pdbs(sys.argv[1:])
    for ion in ["MG", "NA", "K", "CL"]:
        if ion not in d:
            d[ion] = None
    pprint({k: v for k, v in d.items() if v is not None})
```

--------------------------------

### Get Vector Centroid

Source: https://viennarna.github.io/forgi/genindex

Calculates the centroid of a given vector. This utility is part of the vector module.

```Python
from forgi.threedee.utilities.vector import get_vector_centroid
```

--------------------------------

### Timing Orthonormal Basis Creation

Source: https://viennarna.github.io/forgi/_modules/forgi/threedee/utilities/vector

Compares the performance of two methods for creating orthonormal bases (`create_orthonormal_basis1` and `create_orthonormal_basis`). It times the execution of each method with 100,000 repetitions and prints the results.

```Python
def time_cob1():
    vec1 = get_random_vector()
    vec2 = get_random_vector()

    basis = create_orthonormal_basis1(vec1, vec2)

def time_cob2():
    vec1 = get_random_vector()
    vec2 = get_random_vector()

    basis = create_orthonormal_basis(vec1, vec2)

def time_cob():
    t1 = timeit.Timer("time_cob1()", "from forgi.threedee.utilities.vector import time_cob1")
    t2 = timeit.Timer("time_cob2()", "from forgi.threedee.utilities.vector import time_cob2")

    print "1: ", t1.repeat(number=100000) #prints [3.045403003692627, 3.0388529300689697, 3.0359420776367188]
    print "2: ", t2.repeat(number=100000) #prints [2.7473390102386475, 2.74338698387146, 2.731964111328125]
```

--------------------------------

### Get Twist Parameters

Source: https://viennarna.github.io/forgi/genindex

Retrieves twist parameters for a given angle statistic. This is a method of the AngleStat class.

```Python
twist_params()
```

--------------------------------

### Initialize PymolPrinter for RNA Visualization

Source: https://viennarna.github.io/forgi/_modules/forgi/threedee/visual/pymol

The `PymolPrinter` class is initialized with various attributes to control RNA visualization in PyMOL. These attributes include settings for displaying virtual residues, rainbow coloring, basis vectors, sidechain atoms, and colors for different RNA features like stems and loops.

```Python
class PymolPrinter(object):
    def __init__(self):
        self.display_virtual_residues = False
        self.rainbow = False
        self.basis = None
        self.visualize_three_and_five_prime = True
        self.encompassing_stems = False
        self.state = 2
        self.virtual_atoms = False
        self.sidechain_atoms = False
        self.override_color = None
        self.element_specific_colors = None
        self.print_text = True
        self.add_longrange = False
        self.add_loops = True
        self.max_stem_distances = 0
        self.add_letters = False
        self.draw_axes = False
        self.draw_segments = True
        self.movie = False
        self.stem_color = 'green'
        self.multiloop_color = 'red'
        self.prev_obj_name = ''     # The name of the previously created
        # object which needs to be hidden
        # when creating a movie
        self.only_elements = None
        self.cylinder_width = 1.0
        self.show_twists = True
        self.plotters = []
        self.show_bounding_boxes = False
```

--------------------------------

### Get Total Length of CoarseGrainRNA

Source: https://viennarna.github.io/forgi/genindex

Returns the total length of the CoarseGrainRNA model. This is a method of the CoarseGrainRNA class.

```Python
total_length()
```

--------------------------------

### Get Position Parameters

Source: https://viennarna.github.io/forgi/genindex

Retrieves position-related parameters for an AngleStat object. This method is part of the forgi.threedee.model.stats module.

```Python
from forgi.threedee.model.stats import AngleStat

# Assuming 'angle_stat' is an instance of AngleStat
# params = angle_stat.position_params()
```

--------------------------------

### Get All Define Strings

Source: https://viennarna.github.io/forgi/_modules/forgi/graph/bulge_graph

Converts all 'defines' into a formatted string. Each define entry follows the format: 'define [name] [start_res1] [end_res1] [start_res2] [end_res2]'. The defines are sorted before formatting.

```Python
def _get_define_str(self):
        """
        Convert the defines into a string.

        Format:

        define [name] [start_res1] [end_res1] [start_res2] [end_res2]
        """
        defines_str = ''

        # a method for sorting the defines
        def define_sorter(k):

```

--------------------------------

### String Representation of Object

Source: https://viennarna.github.io/forgi/_modules/forgi/threedee/model/linecloud

Provides a human-readable string representation of the coordinate storage object, listing elements and their associated coordinate values.

```Python
def __str__(self):
    lines = []
    for elem in self._elem_names:
        lines.append("{}: ".format(elem) + ",  ".join(str(val)
                                                      for val in self[elem]))
    return("\n".join(lines))
```

--------------------------------

### Get Twist Parameter

Source: https://viennarna.github.io/forgi/genindex

Retrieves the parameter related to the twist of structural components. This function is in the graph_pdb utilities.

```Python
from forgi.threedee.utilities.graph_pdb import get_twist_parameter
```

--------------------------------

### Get Twist Angle

Source: https://viennarna.github.io/forgi/genindex

Calculates the twist angle between structural elements. This utility is part of the graph_pdb module.

```Python
from forgi.threedee.utilities.graph_pdb import get_twist_angle
```

--------------------------------

### GNU General Public License v3

Source: https://viennarna.github.io/forgi/license_link

The GNU General Public License (GPL) version 3 provides a legal framework for software freedom. It allows users to freely use, study, share, and modify the software, with the condition that any derivative works are also distributed under the same license. This ensures that the software remains free for all subsequent users.

```text
GNU GENERAL PUBLIC LICENSE
Version 3, 29 June 2007

Copyright (C) 2007 Free Software Foundation, Inc. <https://fsf.org/>
Everyone is permitted to copy and distribute verbatim copies
of this license document, but changing it is not allowed.

                        Preamble

  The GNU General Public License is a free, copyleft license for
software and other kinds of works.

  The licenses for most software and other practical works are designed
to take away your freedom to share and change the works.  By contrast,
the GNU General Public License is intended to guarantee your freedom to
share and change all versions of a program--to make sure it remains free
software for all its users.  We, the Free Software Foundation, use the
GNU General Public License for most of our software; it applies also to
any other work released this way by its authors.  You can apply it to
your programs, too.

  When we speak of free software, we are referring to freedom, not
price.  Our General Public Licenses are designed to make sure that you
have the freedom to distribute copies of free software (and charge for
them if you wish), that you receive source code or can get it if you
want it, that you can change the software or use pieces of it in new
free programs, and that you know you can do these things.

  To protect your rights, we need to prevent others from denying you
these rights or asking you to surrender the rights.  Therefore, you have
certain responsibilities if you distribute copies of the software, or if
you modify it: responsibilities to respect the freedom of others.

  For example, if you distribute copies of such a program, whether
gratis or for a fee, you must pass on to the recipients the same
freedoms that you received.  You must make sure that they, too, receive
or can get the source code.  And you must show them these terms so they
know their rights.

  Developers that use the GNU GPL protect your rights with two steps:
(1) assert copyright on the software, and (2) offer you this License
giving you legal permission to copy, distribute and/or modify it.

  For the developers' and authors' protection, the GPL clearly explains
that there is no warranty for this free software.  For both users' and
authors' sake, the GPL requires that modified versions be marked as
changed, so that their problems will not be attributed erroneously to
authors of previous versions.

  Some devices are designed to deny users access to install or run
modified versions of the software inside them, although the manufacturer
can do so.  This is fundamentally incompatible with the aim of
protecting users' freedom to change the software.  The systematic
pattern of such abuse occurs in the area of products for individuals to
use, which is precisely where it is most unacceptable.  Therefore, we
have designed this version of the GPL to prohibit the practice for those
products.  If such problems arise substantially in other domains, we
stand ready to extend this provision to those domains in future versions
of the GPL, as needed to protect the freedom of users.

  Finally, every program is threatened constantly by software patents.
States should not allow patents to restrict development and use of
software on general-purpose computers, but in those that do, we wish to
avoid the special danger that patents applied to a free program could
make it effectively proprietary.  To prevent this, the GPL assures that
patents cannot be used to render the program non-free.

  The precise terms and conditions for copying, distribution and
modification follow.

                       TERMS AND CONDITIONS

  0. Definitions.

  "This License" refers to version 3 of the GNU General Public License.

  "Copyright" also means copyright-like laws that apply to other kinds of
works, such as semiconductor masks.

  "The Program" refers to any copyrightable work licensed under this
License.  Each licensee is addressed as "you".  "Licensees"
and "recipients" may be individuals or organizations.

  To "modify" a work means to copy from or adapt all or part of the work
in a fashion requiring copyright permission, other than the making of an
exact copy.  The resulting work is called a "modified version" of the
earlier work or a work "based on" the earlier work.

  A "covered work" means either the unmodified Program or a work based
on the Program.

  To "propagate" a work means to do anything with it that, without
permission, would make you directly or secondarily liable for
infringement under applicable copyright law, except executing it on a
computer or modifying a private copy.  Propagation includes copying,
distribution (with or without modification), making available to the
public, and in some countries other activities as well.

  To "convey" a work means any kind of propagation that enables other
parties to make or receive copies.  Mere interaction with a user through
```

--------------------------------

### Get Centroid (Forgi)

Source: https://viennarna.github.io/forgi/genindex

Calculates the centroid of a structural element in an RNA. This function is part of the forgi.threedee.utilities.graph_pdb module.

```Python
get_centroid()
```

--------------------------------

### Create RNA Input Parser

Source: https://viennarna.github.io/forgi/_modules/forgi/utilities/commandline_utils

Generates an argument parser for handling RNA input files. It supports various file formats like PDB, forgi cg, forgi bg, FASTA, and dot-bracket strings. Options for controlling stem dissolution, PDB-specific parsing (pseudoknots, chains, secondary structure), and logging verbosity are included.

```Python
from __future__ import print_function

import sys
import argparse
import logging
import os.path
import contextlib
import warnings
import textwrap

import numpy as np

from .exceptions import GraphConstructionError
from logging_exceptions import log_to_exception
import logging_exceptions


import forgi.graph.bulge_graph as fgb
import forgi.threedee.model.coarse_grain as ftmc

log = logging.getLogger(__name__)




class WrongFileFormat(ValueError):
    """
    Error raised if the input file has the wrong file format or the file format could not be detected.
    """




def get_rna_input_parser(helptext, nargs=1, rna_type="any", enable_logging=True, parser_kwargs={}):
    parser = argparse.ArgumentParser(description=helptext, **parser_kwargs)
    if nargs == 1:
        helptext = "One file containing an RNA.\n"
    elif isinstance(nargs, int) and nargs > 1:
        helptext = "{:d} files containing one RNA each.\n".format(nargs)
    elif nargs == "+":
        helptext = "One or more files containing one or more RNAs each.\n"
    else:
        raise ValueError(
            "get_parser_any_cgsg does not support nargs={}".format(nargs))

    if rna_type != "only_cg":
        fileformats = ["pdb files"]
    else:
        fileformats = []
    if rna_type != "pdb":
        fileformats.append("forgi cg files")
        if rna_type != "3d" and rna_type != "only_cg":
            fileformats.append("forgi bg files")
            fileformats.append("fasta files")
    if rna_type == "any":
        fileformats.append("dotbracketfiles")
    n = len(fileformats)
    helptext += "\n".join(textwrap.wrap(
        "Supported Filetypes are: {}".format(", ".join(fileformats)), 55))
    if rna_type == "any":
        helptext += ("Alternatively you can supply a dotbracket-string\n "
                     "(containing only the characters '.()[]{}&') from the commandline.\n")
    parser.add_argument("rna", nargs=nargs, type=str, help=helptext)
    parser.add_argument("--keep-length-one-stems", action="store_true",
                        help="For all input formats except forgi bg/cg files,\n" 
                             "this controlls whether stems of length one are \n" 
                             "dissolved to unpaired regions (default) \n" 
                             "or kept (if this option is present).\n" 
                             "In  the case of input in forgi-format,\n" 
                             "the RNA from the file is not modified.")
    if rna_type != "only_cg":
        pdb_input_group = parser.add_argument_group("Options for loading of PDB files",
                                                    description="These options only take effect, " 
                                                    "if the input RNA is in pdb file format.")
        pdb_input_group.add_argument("--pseudoknots", action="store_true",
                                     help="Allow pseudoknots when extracting the structure\n" 
                                          "from PDB files.")
        pdb_input_group.add_argument("--chains", type=str,
                                     help="When reading pdb-files: Only extract the given chain(s). Comma-seperated")
        pdb_input_group.add_argument("--pdb-secondary-structure", type=str, default="",
                                     help="When reading a single chain from a pdb-files: \nEnforce the secondary structure given as dotbracket\n string. (This only works, if --chain is given!)")
        pdb_input_group.add_argument("--pdb-annotation-tool", type=str, default=None,
                                     help="What program to use for detecting basepairs in PDB/ MMCIF structures." 
                                     " This commandline option overrides the value in the config file (if present)." 
                                     "If this is not present and no config-file is given, we try to detect the installed programs.")
        pdb_input_group.add_argument("--pdb-allow-www-query", action="store_true",
                                     help="Usually, if modified residues/ ligand with an unknown 3-letter code are encountered in PDB files, " 
                                          "they are removed from the chain and a log message of severity INFO is issued. " 
                                          "With this option, we first try to query the PDBeChem database for the 3-letter code, to " 
                                          "see whether or not it is a modified residue that can be converted to its standard parent " 
                                          " and should be part of the chain.")

    if enable_logging:
        verbosity_group = parser.add_argument_group(
            "Control verbosity of logging output")
        logging_exceptions.update_parser(verbosity_group)
    return parser




def cgs_from_args(args, rna_type="any", enable_logging=True,
                  return_filenames=False, skip_errors=False):
    """

```
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