API Reference

exception slow_rotations.torsions.BadTorsionError

Bases: Exception

Exception raised when there is a problem with the user input torsion

class slow_rotations.torsions.LigandTorsionFinder(trajf, topf, ligcode, smiles, torsion_smarts=None)

Bases: TorsionFinder

Analyze torsions in the ligand of a system

convert_idx_to_sysidx(idx)

when ligand is not the only molecule in the system converts the ligand indices starting at 0 to indices that are relevant to the system

Parameters:

idx – int; index to be converted

Returns:

index of the atom within the context of the system

Return type:

int

export_pdb_from_traj(frame, opdb, sel='all')

exports the specified selection (sel) from the frame of interest as a pdb

Parameters:

  • frame – int; frame of trajectory

  • opdb – str; name of the output pdb

  • output (sel; str; MD Analysis selection language of what to)

Returns:

None

get_rdmol()

return RDKit Mol for the small molecule

Parameters:

None

Returns:

Mol

get_rdmol_by_frame(frame)

returns the conformation of the rdkit molecule in the specified frame

Parameters:

frame – int; frame of trajectory of interest

Returns:

Mol

get_torsions()

gets a list of all torsions

Parameters:

None

Returns:

list of torsions

Return type:

[[int, int, int, int]]

highlight_dihedral(dihedral, save_path=None)

highlights the dihedral of a protein sidechain

  • exports the protein residue as a single AA pdb

    • loads in the single protein into rdkit with and without Hs

    • compares the 2 to get atom orderings via MCS

make_torsion_img(torsion, angle_min=None, save_path=None)

create a matplot lib figure of scatter plot

Parameters:

  • torsion – [int, int, int, int]: torsions atom indices

  • angle_min – int; minimum angle of the histogram

  • save_path – str; path to save image to

Returns:

torsion state boundaries TransitionMatrixCounter: counts of transitions between states [str]: names of each state bool: True if torison has symmetry, False otherwise float: populations of each state

Return type:

[[float, float]]

make_torsion_img_no_shift(torsion, save_path=None)

create a matplot lib figure where the histogram is not shifted (bounds are -180 to 180)

Parameters:

  • torsion – [int, int, int, int]: torsions atom indices

  • save_path – str; path to save image to

Returns:

None

plot_dihedral_scatter(torsion, ax=None, angle_min=None, title=None, save_path=None)

create a matplot lib figure of scatter plot

Parameters:

  • torsion – [int, int, int, int]: torsions atom indices

  • ax – axis; matplotlib axis to use for plot

  • angle_min – int; minimum angle of the histogram

  • title – str; title of the figure

  • save_path – str; path to save image to

Returns:

None

class slow_rotations.torsions.ProteinTorsionFinder(trajf, topf, ligcode=None)

Bases: TorsionFinder

Class for running analysis on protein sidechain torsions

determine_chi_angle(torsion)

Determine which chi angle (1 to 8) a torsion belongs to in a residue.

Parameters:

torsion – [int,int,int,int]’’ list of 4 atom indices (integers)

Returns:

int from 1 to 8, or None if not found

Return type:

chi_number

determine_chi_x(torsion)
get_all_chi_x_torsions(sel=None, a_cutoff=5)
get_binding_residues(A_cutoff=5)

identify all residues within A_cutoff angstroms of the ligand

Parameters:

A_cutoff –

float Angstrom cutoff from binding mode

Returns:

[int]: list of interacting residue IDs

get_chi1_torsions(resids=None, a_cutoff=None)

identify the chi1 torsion atom indices of specified residue ids

get_chi_x_ags(x, resgrp)

returns a list of atom groups inolved in chi x anglebased on the residue group :param resgrp: ResidueGroup; MDAnalysis residue Group

Returns:

MDAnalysis atom group

Return type:

[AtomGroup]

get_chi_x_aid(x, resgrp)

returns a list of tuples of atom indices (aid)

Parameters:

  • x – int; chi angle (ex. 2 for chi2)

  • resgrp – ResidueGroup; residues of interest

Returns

[[int]]; atom indices for each chi X torsion of interest

get_chi_x_residues(x, sel=None, a_cutoff=5)

identify the chi torsion atom indices of specified residue indices at the specified chi angle

Parameters:

  • x – int; which chi up to chi8

  • sel – str; MDAnalysis selection language of residues of interest

  • a_cutoff – float; Angstrom cutoff from ligand

Returns:

atom indices of chi1 torsions

Return type:

[[int, int, int, int]]

get_chi_x_torsions(x, sel=None, a_cutoff=5)

returns a list of chi x torsions atom indices in the protein given the selection (sel) :param x: int; chi angle (ex. 2 for chi2) :param sel: str; MDAnalysis selection string for residues of interest :param a_cutoff: float; Angstrom cutoff

Returns

[[int]]; atom indices for each chi X torsion of interest

static get_intersection(list_of_sets)

returns a set that is an intersection of all the sets in the list

Parameters:

list_of_sets – [set]; list of sets to intersect

Returns:

set that represents the intersection

Return type:

set

get_residues_ags(resgrp)

given the residues in resgrp, create an atom group of all relevant atoms :param resgrp: ResidueGroup; MDAnalysis residue Group

Returns:

MDAnalysis atom group

Return type:

AtomGroup

highlight_dihedral(torsion, save_path=None)

highlights the dihedral of a protein sidechain * exports the protein residue as a single AA pdb * loads in the single protein into rdkit with and

without Hs

  • compares the 2 to get atom orderings via MCS

Parameters:

  • torsion – [int, int, int, int]; atom indices representing torsion of interest

  • save_path – str; path to save image

Returns:

None

make_torsion_img(torsion, angle_min=None, save_path=None)

create a matplot lib figure of scatter plot

Parameters:

  • torsion – [int, int, int, int]: torsions atom indices

  • angle_min – int; minimum angle of the histogram

  • save_path – str; path to save image to

Returns:

torsion state boundaries TransitionMatrixCounter: counts of transitions between states [str]: names of each state bool: True if torison has symmetry, False otherwise float: populations of each state

Return type:

[[float, float]]

save_traj_sel(sel, frames, save_path)

saves out the atoms selected in sel as a new file for the purpose of this program meant to save out a single amino acid as a pdb file

Parameters:

  • sel – str; selection string using MDAnalysis atom selection language

  • frames – (int,int); 2 membered tuple with the start and end (not inclusive) frame to save out [start, end)

  • save_path – str; path to save

Returns:

None

class slow_rotations.torsions.TorsionFinder(trajf, topf)

Bases: object

Base class for performing analysis on all relevant torsions in a system

static add_0_to_kde(X, score)

shifts torsion angles in histogram to specified angle. if no angle is specified, shifts angle to

Parameters:

  • angles – [float]; timeseries of angles

  • num_bins – int; num bins in the historgram

  • angle_min – int; force a minimum for the angles if specified otherwise

Returns:

converted index

Return type:

int

convert_idx_to_sysidx(idx)

converts the index to 0 based index within molecule to index of the entire system

Parameters:

idx – int; index to convert

Returns:

converted index

Return type:

int

static get_angle_shift_point(angles, num_bins=40)

finds a new angle minimum for histogram so no peaks are split If no bins exist without histogram entries, shifts to the bin with the lowest number of entries.

Parameters:

  • angles – [float]; angles timeseries

  • num_bins – int; number of bins to use for histogram of angles

Returns:

minimum angle for histogram

Return type:

int

get_bounds_gmm()
static get_bounds_knn(X, num_components, peaks, tolerance=40)

get the bounds based of each peak using k nearest neighbor algorithm

Parameters:

  • X – [[float]]; angles

  • num_components – int; nubmer of peaks

  • peaks – [float]; angle locations of peaks

  • tolerance – int; the largest gap in angles we can have before it is considered not in that peak

Returns:

angle bounds of each peak

Return type:

[[float, float]]

static get_bounds_mindist(X, scores, num_components, peaks, tolerance=50)

get the bounds based of each peak by assigning each score value to its closest peak

Parameters:

  • X – [[float]]; angles

  • scores – [float]; kernel density estimator score

  • num_components – int; nubmer of peaks

  • peaks – [float]; angle locations of peaks

  • tolerance – int; the largest gap in angles we can have before it is considered not in that peak

Returns:

angle bounds of each peak

Return type:

[[float, float]]

static get_closest_peak(angle, peaks)

calculate the closest peak for that angle

Parameters:

  • angle – float; angle to get closest peak for

  • peaks – [float]; angle locations of peaks

Returns:

index of peak in peaks that is the minimum

Return type:

int

static get_gmm(X, num_components, angle_min)

get gaussian mixture model representation the entire distribution

Parameters:

  • X – [[float]]; angles

  • angle_min – int; minimum angle

  • min_max – [[float, float]] bounds of the peaks

Returns:

gaussian mixture model object x: pdf: probability distribution function pdf_individual: probability distribution function of the individual peakd

Return type:

gmm

static get_individual_gmm(X, angle_min, min_max)

get gaussian mixture model representation of a single peak

Parameters:

  • X – [[float]]; angles

  • angle_min – int; minimum angle

  • min_max – [[float, float]] bounds of the peaks

Returns:

gaussian mixture model object x: pdf: probability distribution function pdf_individual: probability distribution function of the individual peak [float, float]: minimum and maximum used

Return type:

gmm

static get_kde(angles, num_bins=40, angle_min=None)

calculates the kernel density estimator

Parameters:

  • angles – [float]; timeseries of angles

  • num_bins – int; num bins in the historgram

  • angle_min – int; force a minimum for the angles if specified otherwise

Returns:

X angles [float]: kernel density estimator score int: minimum angle of the distribution

Return type:

[[float]]

static get_kde_num_peaks(X, scores, smoothing_window=30, peak_prominence=0.0001, peak_dist=30)

counts the number of peaks in the Kernel Density estimator

Parameters:

  • X – [[float]] angles

  • scores – [float] kernel density estimator score

  • smoothing_window – int width of window to average over

  • peak_prominence – float how prominent the peak must be in order to be counted

  • peak_dist – int minimum distance apart peaks must fall

Returns:

num_peaks peaks: [float] angle location of the peaks

Return type:

int

get_residue_from_torsion(torsion)

get the residue the torsion atom indices belong to :param torsion: [int, int, int, int] atom indices of atom involved in torsion

Returns:

MDAnalysis residue that torsion belongs to

Return type:

Residue

get_residue_name_from_torsion(torsion)
static get_statistical_inefficiency(angles, num_bins=40, angle_min=None)

calculates the statistical inefficiency of the angles timeseries

Parameters:

  • angles – [float]; timeseries of angles

  • num_bins – int; num bins in the historgram

  • angle_min – int; force a minimum for the angles if specified otherwise

Returns:

statisitcal inefficiency

Return type:

float

get_torsion_angles(torsion)

Gets timeseries of torsion angles

Parameters:

torsion – [int, int, int, int]; list of torsion atom indices

Returns:

angle timeseries

Return type:

np.array

get_torsion_name(torsion)

count the transitions in and out each state (matrix)

Parameters:

  • [float] – angles

  • range_of_states – [[float, float]]; bounds of the peaks

Returns:

string name of torsion based on residue + residue number and indices

Return type:

str

get_torsions()
make_torsion_img(torsion, angle_min=None, save_path=None)

create a image of all the torsion transitions

Parameters:

  • torsion – [int, int, int, int]; indices of the torsion of interest

  • angle_min – int; minimum angle of the histogram

  • save_path – str; path to save the image

Returns:

minimum angle fo the histogram

Return type:

int

mindist(X, num_components, peaks)
static plot_dihedral_histogram(angles, angle_min=None, pdf_individual=[], ax=None, title=None, num_bins=40, alpha=0.5, show=True, color=None, pdf_colors=[], save_path=None)
static plot_dihedral_scatter(angles, ax=None, angle_min=None, title=None, show=False, save_path=None)
plot_kde(torsion, smoothing_window=-1, angle_min=None, save_path=None)
static plot_transition_counts(transition_ctr, ax=None, colors=[])
static shift_torsion_angles(angles, num_bins=40, angle_min=None)

shifts torsion angles in histogram to specified angle. if no angle is specified, shifts angle to

Parameters:

  • angles – [float]; timeseries of angles

  • num_bins – int; num bins in the historgram

  • angle_min – int; force a minimum for the angles if specified otherwise

Returns:

minimum angle of histogram

Return type:

float

static state_populations(angles, range_of_states)

calculate the transitions between each state

Parameters:

  • [float] – angles

  • range_of_states – [[float, float]]; bounds of the peaks

Returns:

populations of each state

Return type:

[float]

static transition_counter(angles, range_of_states)

count the transitions in OR out of each state (less information than transition_matrix())

Parameters:

  • [float] – angles

  • range_of_states – [[float, float]]; bounds of the peaks

Returns:

TransitionCounter

static transition_matrix(angles, range_of_states)

count the transitions in and out each state (matrix)

Parameters:

  • [float] – angles

  • range_of_states – [[float, float]]; bounds of the peaks

Returns:

TransitionMatrixCounter

class slow_rotations.compare.LigandTorsionComparator(tf_list)

Bases: TorsionComparator

convert_torsion_indices(trajidx, torsion)

Converts torsion from first indexing system into indexing system of another trajectory

Parameters:

  • trajidx – int; index of the trajectory we are converting to

  • torsion – [int, int, int, int]; torsion in the indexing system of the first trjaectory, (torsions from get_torsions function)

Returns

[int, int, int, int]: torsion in the indexing system of the trajectory specified

plot_all_distributions(torsion, save_path=None, close=False)

creates a matplotlib plot of the distribution across all the trajectories passed as well as one for each individual trajectory for comparison to each other and the cumulative distribution :param torsion: [int, int, int, int]; torsion in the indexing system of the first trjaectory, (torsions from get_torsions function) :param save_path: str; path to save :param close: bool; close the figure when done

Returns:

torsion information for futher analysis

Return type:

dict

class slow_rotations.compare.ProteinTorsionComparator(tf_list, a_cutoff=5)

Bases: TorsionComparator

get_torsions()

gets all protein sidechain torsions in the system

Parameters:

None

Returns:

list of torsions

Return type:

[[int, int, int, int]]

plot_all_distributions(torsion, save_path=None, close=False)

creates a matplotlib plot of the distribution across all the trajectories passed as well as one for each individual trajectory for comparison to each other and the cumulative distribution :param torsion: [int, int, int, int]; torsion in the indexing system of the first trjaectory, (torsions from get_torsions function) :param save_path: str; path to save :param close: bool; close the figure when done

Returns:

torsion information for futher analysis

Return type:

dict

class slow_rotations.compare.TorsionComparator(tf_list)

Bases: object

convert_torsion_indices(trajidx, torsion)

Converts torsion from first indexing system into indexing system of another trajectory

Parameters:

  • trajidx – int; index of the trajectory we are converting to

  • torsion – [int, int, int, int]; torsion in the indexing system of the first trjaectory, (torsions from get_torsions function)

Returns

[int, int, int, int]: torsion in the indexing system of the trajectory specified

get_all_angles(torsion)

gathers all the angles across all timeseries for the torsion of interest :param torsion: [int, int, int, int]; torsion in the indexing system of the first trjaectory, (torsions from get_torsions function)

Returns:

timeseries of angles

Return type:

[float]

static get_angle_min(angles)

gets the minimum angle across all angles provided to shift histogram by such that no peaks are split :param angles: [float]; list of angless

Returns:

minimum angle

Return type:

int

get_cumulative_angles(torsion)

gets all angles of the torsion across all trajectors, shifted such that no peaks are split :param torsion: [int, int, int, int]; torsion in the indexing system of the first trjaectory, (torsions from get_torsions function)

Returns:

minimum angle [float]: shifted angles across all trajectories

Return type:

int

get_torsions()

Get all small molecule torsions using the indexing system first input LigandTorsionFinder

Parameters:

None

Returns:

list of torsions

Return type:

[[int, int, int, int]]

plot_cumulative_distribution(torsion, ax=None, save_path=None, close=False)

creates a matplotlib plot of the distribution across all the trajectories passed :param torsion: [int, int, int, int]; torsion in the indexing system of the first trjaectory, (torsions from get_torsions function) :param ax: axis; matplot lib axis to put the plot in :param save_path: str; path to save :param close: bool; close the figure when done

Returns:

angle minimum [float]: angle location of peaks [[float,float]]: bounds of peaks

Return type:

int

slow_rotations.analysis.check_states(torsionrepeat)

Checks the torsion for missing states

Args: torsionrepeat: TorsionRepeat

Returns:

list of states that are missing

Return type:

[int]

slow_rotations.analysis.check_transitions(torsionrepeat, min_transitions=10)

Checks the torsion for missing states

Args: torsionrepeat: TorsionRepeat min_transitions: int; minimum transitions that must be observed in and out of a state to be considered adequately sampled

Returns:

list of states that are missing

Return type:

[int]

slow_rotations.mappings.check_symmetry(mol, torsion)

Checks symmetry of central bond atoms in a torsion using RDKit.

Parameters:

  • mol – RDKit Mol

  • torsion – (int, int, int, int) - atom indices defining the torsion

Returns:

True if torsion has symmetry, False otherwise

Return type:

bool

slow_rotations.mappings.convert_dihedral(mapping, dihedral)

converts indices in dihedral based on the provided mapping

Parameters:

  • mapping – dict; mapping dihedral atoms

  • dihedral

Returns:

bool

slow_rotations.mappings.get_atom_by_index(mol, idx)

finds RDKit Atom objects of interest based on provided atom

Parameters:

  • mol – (Chem.Mol) RDKit Mol

  • idx – int; index of atom of interest

Returns:

RDKit Atom

Return type:

Chem.Atom

slow_rotations.mappings.map_mols(mol1, mol2)

Creates dictionary mapping of indices between atoms of mol1 and mol2

Parameters:

  • mol1 – RDKit Mol

  • mol2 – RDKit Mol

Returns:

{int: int}; dictionary mapping of indices {mol1: mol2}

Return type:

dict

slow_rotations.mappings.rd_map_mols(rdmol1, rdmol2)

Given 2 RDKit Mols, determines the mapping based on the MCS

Parameters:

  • rdmol1 – Chem.Mol

  • rdmol2 – Chem.Mol

Returns:

mapping of atoms

Return type:

dict

slow_rotations.mappings.torsions_equivalent(t1, t2)

checks if 2 torsions are equivalent

Parameters:

  • t1 – (int, int, int, int); indices of atoms in torsion of interest

  • t2 – (int, int, int, int); indices of atoms in torsion of interest

Returns:

bool

slow_rotations.pdb_writer.get_atom_type(atype)
slow_rotations.pdb_writer.make_standard_atmname(pmd_struct)

Converts third column pdb atom name from any atom name to atom type naming convention. In gmx to prevent forcefield issues, we rename ligand atom types either as lower case, or with extra characters to prevent clashes with protein and other forcefield naming conventions

Parameters:

pmd_struct – parmed structure

Returns:

parmed.structure

slow_rotations.pdb_writer.rename_lig_pdb_atoms(ilig_pdb, olig_pdb)

Renames small molecule/ligand PDB atoms to have standard naming conventions recognized by gromacs

Parameters:

  • ilig_pdb – str; input pdb file name

  • olig_pdb – str; output pdb file name

Returns:

None

slow_rotations.rdkit_wrapper.assign_bond_order_from_smiles(smiles, molfile)

Assigns the bond order of a rdkit molecule lacking proper bond information based on its smiles

Parameters:

  • smiles – str; smiles str representing the correct bond orders

  • molfile – str; pdb, sdf, or mol2 filename of molecule that lacks correct bond order information

Returns:

RDKit Mol with

Return type:

Chem.Mol

slow_rotations.rdkit_wrapper.get_index_convert(rdmol1, rdmol2)
slow_rotations.rdkit_wrapper.get_mapped_bonds(mol, mapped_atoms)

Finds RDKit bonds objects of interest based on mapped_atoms indices list

Parameters:

  • mol – (Chem.Mol) RDKit Mol

  • mapped_atoms – [int]; indices of atoms of interest

Returns:

list of RDKit bonds

Return type:

list

slow_rotations.rdkit_wrapper.get_mapped_heavy_atom_indices(mol, mapped_atoms)

Finds RDKit Atom objects of interest based on mapped_atoms indices list

Parameters:

  • mol – (Chem.Mol) RDKit Mol

  • mapped_atoms – [int]; indices of atoms of interest

Returns:

list of RDKit Atoms

Return type:

list

slow_rotations.rdkit_wrapper.get_rotatable_bonds(mol, torsion_smarts=None)

Finds rotatable bonds in a molecule.

BY DEFAULT Flags:

  • Standard rotatable bonds (R-C-C-R, etc.)

  • Terminal hetero torsions R-C-X-H (alcohols, amines, thiols)

Parameters:

mol (Chem.Mol) – RDKit molecule

Returns:

RDKit bond objects representing rotatable bonds

Return type:

list of Chem.Bond

slow_rotations.rdkit_wrapper.highlight_dihedral(mol, mol_wo_H, index_convert, dihedral, save_path=None)

Creates an image of the molecule with the dihedral of interest highlighted in red

Parameters:

  • mol – Chem.Mol; rdkit molecule

  • dihedral – (int, int, int, int); 4 consecutive atom indices that represent the torsion of interest

  • save_path – str; file path to save image to

Returns:

None

slow_rotations.rdkit_wrapper.load_rdmol_from_file(molfile, removeHs=False)

load molecule in molfile as an RDKit Mol

Parameters:

  • molfile – str; sdf or mol2 filename of small molecule

  • removeHs – bool; strip Hs from the rdkit molecule

Returns:

rdkit molecule

Return type:

Chem.Mol

slow_rotations.rdkit_wrapper.sanitize_rdmol(mol)

Checks and corrects the chemical structure of molecule. (Checks valence, aromaticity, kekulization, and stereochemistry)

Parameters:

mol – Chem.Mol; rdkit molecule

Returns:

santized rdkit molecule

Return type:

Chem.Mol

exception slow_rotations.utils.NoMoleculeError

Bases: Exception

exception slow_rotations.utils.NotImplementedError

Bases: Exception

slow_rotations.utils.warn(msg)