Crate molar 

MolAR is a library for molecular modeling and analysis written in Rust with an emphasis on memory safety and performance. Molar is designed to simplify the analysis of molecular dynamics trajectories and to implement new analysis algorithms. Molar is intended to provide facilities, which are routinely used in all molecular analysis programs, namely input/output of popular file formats, powerful and flexible atom selections, geometry transformations, RMSD fitting and alignment, etc. MolAR is a logical successor of Pteros molecular modeling library, which is written in C++ and become hard to develop and maintain due to all C++ idiosyncrasies.

Re-exports

pub use crate::io::*;

Modules

io

IO handlers for different file formats and associated traits

prelude

Most useful public imports exposed to the users

voronoi_cell

2D Voronoi diagrams

Macros

bind

Convenience macro for binding several selections ar once

bind_mut

Convenience macro for binding several selections ar once mutably

Structs

AnalysisContext

Context passed to all frame processing methods

Atom

Information about the atom except its coordinates.

Dssp

DSSP secondary structure assignment result for a selection.

NdxFile

Representation of Gromacs index files

ParSplit

Collection of non-overlapping selections that could be mutated in parallel Selections don’t have access to shared fields such as box and bonds.

Particle

Holds immutable reference to Atom and Pos and particle id.

ParticleMut

Holds mutable reference to Atom and Pos and particle id.

PbcDims

Representation of periodic dimensions in 3D space.

PeriodicBox

Periodic box allowing working with periodicity and computing periodic distances and images.

Sasa

Solvent-Accessible Surface Area calculator backed by the pure-Rust PowerSASA algorithm.

SearchConnectivity

Contacts between atoms in the format of atom -> neib1 neib2 neib3...

SearchConnectivityIter

Iterator over SearchConnectivity entries

Sel

Selection index detached from any System. It is guaranteed to be non-empty.

SelBound

Read only selection that borrows its index Implements only read-only analysis traits

SelBoundMut

Read-write selection that borrows its index

SelOwnBound

Read only subsystem that owns its index Implements only read-only analysis traits

SelOwnBoundMut

Read-write bound subsystem having access to all fields of Topology and State

SelPar

Read-only subsystem for non-blocking parallel access to atoms and posisitons Doesn’t have access to shared fields such as box and bonds.

SelParMut

Read-write subsystem for non-blocking parallel access to atoms and posisitons Doesn’t have access to shared fields such as box and bonds.

SelectionExpr

A compiled selection expression that can be used to select atoms based on various criteria

State

State of molecular system including its coordinates, time stamp and periodic box.

System

System that stores Topology and State

Topology

Topology of the molecular system: atoms, bonds, molecules, etc.

TopologyStateSizesError

Error for different sizes of topology and state

TrajAnalysisArgs

Standard trajectory processing arguments

Enums

AnalysisError

Errors related to analysis task execution and trajectory processing

BuilderError

Errors related to builder sources

LipidOrderError

Errors related to computing lipid order parameter

MeasureError

Errors that can occur during measurements

NdxError

Errors related to reading and manipulating Gromacs index files

OrderType

Type of order parameter calculation

PeriodicBoxError

Errors related to periodic boxes and periodicity

SS

Secondary structure code assigned to a single residue.

SelectionError

Error related to creation of selections

StateError

Error type for missing optional state data (velocities or forces)

Constants

PBC_FULL

All dimentions are periodic

PBC_NONE

All dimentions are non-periodic

Traits

Analysis

Trait providing split and split_par for selections that have full particle access.

AnalysisTask

Analysis task trait. Should be implemented by user’s types.

AtomIterator

Convenience alias for iterator over atoms

AtomLike

AtomMutIterator

Convenience alias for mutable iterator over atoms

AtomMutProvider

Element trait providing mutable access to atoms.

AtomProvider

Element trait providing immutable access to atoms via index.

BondProvider

Element trait providing immutable access to bonds.

BoxMutProvider

Trait for providing mutable access to periodic box

BoxProvider

Trait for providing access to periodic box

DistanceSearchOutput

Trait for the results of distance seacrh

ForceIterator

Convenience alias for iterator over forces

ForceMutIterator

Convenience alias for mutable iterator over forces

ForceMutProvider

Element trait providing mutable access to forces.

ForceProvider

Element trait providing immutable access to forces via index.

IdPosIterator

Convenience alias for iterator over index-position pairs

IdPosMutIterator

Convenience alias for mutable iterator over index-position pairs

IndexIterator

Convenience alias for iterator over indices

IndexParProvider

Trait for parallel iteration over indexes

IndexProvider

Trait for selected indices

IndexSliceProvider

Trait for entities that contain continuous slices of indices (selections and such)

LenProvider

Trait for providing length of provided data

Measure

Unified trait for all measurement operations on selections.

Modify

Unified trait for all modification operations on selections.

MolProvider

Element trait providing immutable access to molecules.

ParticleIterMutProvider

Trait for providing mutable iteration over particles

ParticleIterProvider

Provides iteration over (id, atom, pos) particles

ParticleIterator

Convenience alias for iterator over particles

ParticleMutIterator

Convenience alias for mutable iterator over particles

ParticleParIterProvider

PosIterator

Convenience alias for iterator over positions

PosMutIterator

Convenience alias for mutable iterator over positions

PosMutProvider

Element trait providing mutable access to positions.

PosProvider

Element trait providing immutable access to positions via index.

Selectable

Trait for objects that support creating selections

SelectableBound

Trait for objects that support creating bound selections

SelectionDef

Trait for selection definitions. Implementors could be used as argumnets for selection creation methods.

SelectionLogic

Trait for logical operations in any (borrowed or own) bound selections

SystemMutProvider

Trait for things containing mut reference to System (mostly selections)

SystemProvider

Trait for things containing reference to System (mostly selections)

TimeMutProvider

Trait for setting simulation time

TimeProvider

Trait for getting time

TopLike

VelIterator

Convenience alias for iterator over velocities

VelMutIterator

Convenience alias for mutable iterator over velocities

VelMutProvider

Element trait providing mutable access to velocities.

VelProvider

Element trait providing immutable access to velocities via index.

Functions

distance_search_double

Performs distance search between two sets of points within a given cutoff distance

distance_search_double_pbc

Performs distance search between two sets of points within periodic boundary conditions

distance_search_double_vdw

Performs distance search between two sets of points using van der Waals radii

distance_search_double_vdw_pbc

Performs distance search between two sets of points using van der Waals radii with periodic boundaries

distance_search_single

Performs distance search within a single set of points

distance_search_single_pbc

Performs distance search within a single set of points with periodic boundaries

fit_transform

Computes the transformation that best fits sel1 onto sel2

fit_transform_at_origin

Like fit_transform but assumes both selections are centered at origin

fit_transform_matching

Computes the transformation that best fits sel1 onto sel2 taking into account only matching atoms. The sequences of atom names from both selections are aligned first with Needleman–Wunsch Global Alignment algorithm and then only the matching atoms are used to compute a fit transform

get_matching_atoms_by_name

greeting

Prints a welcome message for MolAR with package information and the specified tool name

rmsd

Calculates the Root Mean Square Deviation between two selections

rmsd_mw

Calculates the mass-weighted Root Mean Square Deviation between two selections

Type Aliases

AtomStr

Stack-allocated ASCII atom string (max 8 bytes, no heap allocation).

Force

Atom force (kJ/mol/nm)

Matrix3f

Convenience alias for 3x3 matrix

Pos

Atom position

SVec

Alias to sorted vector

Vector3f

Convenience alias for 3D vector

Vel

Atom velocity (nm/ps)