Functions

read_dcd(filename::String;
         frame_indices::Union{Vector, OrdinalRange, Colon, Nothing} = nothing,
         step::Union{Int, Nothing} = nothing)
::Trajectory

Return Trajectory object which filled coordinates, nframe, natom fields. If you set frame_indices, only specified frame is read. If you set step, every step frame is read. You can't specify both frame_indices and step at the same time.

write_dcd(filename::String, trj::Trajectory;
          save_step::Integer = 1, total_step::Integer = trj.nframe,
          unit_num::Integer  = 1,  time_step::Real = 1.0f0)

Write coordinates, nframe and natom information of trj to dcd file, named filename. dcd file contain other information - save interval step, unit(chain) number in the system, total step and time step of original trajectory -, and if you do not specify these parameter, these are filled with default value.

read_pdb(filename::AbstractString; model = :unspecified)::Trajectory

Return Trajectory object which filled all field. If you set :AA to model field, this function set the mass of particle based on atomname field. If you set :CA to model field, this function only read CA atom and set the mass of particcle mase on resname field.

write_pdb(filename::AbstractString, trj::Trajectory;
          tempfactor::Union{RealT, Nothing} = nothing) where RealT <: Real

Write coordinates, resname, resid, atomname, atomid to filename based on trj. If you set Real value to tempfactor, all tempfactor will be field with that value.

read_xyz(filename::AbstractString)::Trajectory

Return Trajectory object which filled coordinates, nframe, natom fields.

write_xyz(filename:AbstractString, trj::Trajectory)

Write coordinates, nframe and natom information of trj to xyz file, named filename.

get_frame(frame_idx::Int64, trajectory::Trajectory)
::Frame

Return Frame object which correspond to framd_idx frame from trajectory.

get_atom(query::Int64, trajectory::Trajectory)
::Vector{Atom}

Return Vector of queryth Atom object from trajectory.

get_atom(query::Int64, frame::Frame)
::Atom

Return queryth Atom object from frame.

clip_trajectory(query::Union{Integer, Vector{IntT}, OrdinalRange}, trj::Trajectory;
                query_key::Symbol = :frame)
::Trajecotory where IntT <: Integer

Clip a part of trajectory you specified. Expected query key is one of the following

• :frame : in this case, query specify the frame index.
• :atom : in this case, query specify the atom index.

geometric_center_of_mass(coordinates::Vector{Coordinate};
                         atom_indices::Union{Vector, OrdinalRange, Colon} = :)
::Coordinate

Calculate the geometric center of mass of Coordinate vector for specified atom indices.

For trajectory case, geometric center of mass is calculated by center_of_mass method with geometric flag.

center_of_mass(coordinates::Vector{Coordiante}, mass_vec{Real};
               atom_indices::Union{Vector, OrdinalRange, Colon} = :)
::Coordinate{RealT}

Calculate the (non-geometric) center of mass of Coordinate vector for specified atom indices. You have to pass mass information vector which have same length to coordinates vector.

center_of_mass(query::Trajectory;
               frame_indices::Union{Vector, OrdinalRange, Colon} = :,
               atom_indices::Union{Vector, OrdinalRange, Colon} = :,
               geometric::Bool = false)
::Vector{Coordinate{Real}}

Calculate the center of mass of trajectory for specified frame and atom indices. If you set geometric is true, this function calculate geometric center of mass.

move_pbc_center(coordinates::Vector{Coordinate},
                new_center::Coordinate, box_size::Coordinate)
                )::Vector{Coordinate}

Fix coordinate to consistent with new box center and box size. Box size should match to original periodic boundary box size.

radius_of_gyration(trj::Trajectory;
                   frame_indices::Union{Vector, OrdinalRange, Colon} = :,
                   atom_indices ::Union{Vector, OrdinalRange, Colon} = :,
                   geometric::Bool = false)
::Vector{Real}

Calculate radius of gyration over the trajectory. If you set geometric is true, this function calculate radius of gyration without mass info.

pair_length_matrix(corrds1::Vector{Coordinate}, coords2::Vector{Coordinate})
::Matrix{Real}

Calculate distance matrix for all combination between coords1 and coord2. The row of returned matrix coresspond to coords1, and the column correspond to coords2.

pair_length_matrix(trj::Trajectory;
                   frame_indices::Union{Vector, OrdinalRange, Colon}       = :,
                   first_atom_indices::Union{Vector, OrdinalRange, Colon}  = :,
                   second_atom_indices::Union{Vector, OrdinalRange, Colon} = atom_indices1)
::Vector{Matrix{Coordinate}}

Calculate distance matrix for all combination between first_atom_indices and second_atom_indices. This cauculation apply to each frame of trajectory and the result matrices are stored in Vector. The target frame can be restricted by pass indeces vector or range to frame_indices.

 pair_length_matrix_pbc(corrds1::Vector{Coordinate}, coords2::Vector{Coordinate},
                        box_size::Coordinate)
::Matrix{Real}

Calculate distance matrix for all combination between coords1 and coord2 considering periodic boundary condition. The box size information used for calculation is specified by box_size argument. The row of returned matrix coresspond to coords1, and the column correspond to coords2.

pair_length_matrix_pbc(trj::Trajectory, box_size::Coordinate;
                       frame_indices::Union{Vector, OrdinalRange, Colon}       = :,
                       first_atom_indices::Union{Vector, OrdinalRange, Colon}  = :,
                       second_atom_indices::Union{Vector, OrdinalRange, Colon} = atom_indices1)
::Vector{Matrix{Coordinate}}

Calculate distance matrix for all combinations between first_atom_indices and second_atom_indices considering periodic boundary condition. The box size information used for calculation is specified by box_size argument. This cauculation apply to each frame of trajectory and the result matrices are stored in Vector. The target frame can be restricted by pass indeces vector or range to frame_indices.

contact_bool_matrix(threshold::Real, trj::Trajectory;
                    frame_indices::Union{Array, OrdinalRange, Colon}       = :,
                    first_atom_indices::Union{Array, OrdinalRange, Colon}  = :,
                    second_atom_indices::Union{Array, OrdinalRange, Colon} = first_atom_indices)
::Vector{Matrix{Bool}}

Judge contact is formed or not. If the distance between two coordinate is shorter than threshold, contact is considered to be formed. In returned vector of matrices, each matrix correspond to contact matrix of each frame. You can specify the target frames or atoms by frame_indices, first_atom_indices or second_atom_indices. When you specify the target atoms, the row of matrices corresponds to firstatomindices and column of matrices corresponds to secondatomindices.

contact_bool_matrix_pbc(threshold::Real, trj::Trajectory, box_size::Coordinate;
                        frame_indices::Union{Array, OrdinalRange, Colon}       = :,
                        first_atom_indices::Union{Array, OrdinalRange, Colon}  = :,
                        second_atom_indices::Union{Array, OrdinalRange, Colon} = first_atom_indices)
::Vector{Matrix{Bool}}

Judge contact is formed or not considering periodic boundary condition. If the distance between two coordinate is shorter than threshold, contact is considered to be formed. In returned vector of matrices, each matrix correspond to contact matrix of each frame. The box size information used for calculation is specified box_size argument. You can specify the target frames or atoms by frame_indices, first_atom_indices or second_atom_indices. When you specify the target atoms, the row of matrices corresponds to firstatomindices and column of matrices corresponds to secondatomindices.

contact_probability_matrix(threshold::Real, trj::Trajectory;
                           frame_indices::Union{Vector, OrdinalRange, Colon}       = :,
                           first_atom_indices::Union{Vector, OrdinalRange, Colon}  = :,
                           second_atom_indices::Union{Vector, OrdinalRange, Colon} = first_atom_indices)
::Matrix{Real}

Calculate contact formation probability over the trajectory. If the distance between two coordinate is shorter than threshold, contact is considered to be formed. You can specify the target frames or atoms by frame_indices, first_atom_indices or second_atom_indices. When you specify the target atoms, the row of matrices corresponds to firstatomindices and column of matrices corresponds to secondatomindices.

fix_pbc(coordinates::Vector{Coordinate}, groupid_vec::Vector{Integer},
box_size::Coordinate{<:Real};
x::Bool = true, y::Bool = true, z::Bool = true)::Vector{Coordinate}

Fix the atom group splited by periodic boundary box. This group is defined by groupid_vec which contain each particles group id. For example, if your system have 3 atom, and atom 1 and 2 are group 1, and atom 3 is group 2, this groupid_vec is [1, 1, 2]. If the group over the boundary of the box, the atoms in the group which separated from first atom of that move to the position where the atom locate without periodic boundary condition. You can specify the axies which applied fixing by x,y and option. If you set z = false, only x and y coordinate fixed and z don't change.

fix_pbc(trj::Trajectory, groupid_vec::Vector{Integer},
box_size::Coordinate;
x::Bool = true, y::Bool = true, z::Bool = true)::Trajectory

Fix residues splited by periodic boundary condition. This is more specific version of fix_pbc function for trajectory handling. For example, if your system have 3 atom, and atom 1 and 2 are group 1, and atom 3 is group 2, this groupid_vec is [1, 1, 2]. If the group over the boundary of the box, the atoms in the group which more than half a box away from the first atom of that move to the position where the atom locate without periodic boundary condition. You can specify the axies which applied fixing by x,y and option. If you set z = false, only x and y coordinate fixed and z don't change.

sasa(coordinates::Vector{Coordinate}, radiuses::Vector{Real},
     solvent_radius::RealT = 1.4,     MCtrial_num::Integer = 1000
     seed::Integer         = undef)::Vector{Real}

Calculate Solvent Accessible Surface Area(SASA) for each particle. The length of radiuses should match to the number of particles in coordinates. The default value of solvent radius, 1.4, corresponds to water case 1.4 Å. MCtrial means MonteCarlo trial num for calculate the solvent accessible area of each particle. For each particle, this function generate the point MCtrial times on the solvent accessible surface and count the number of non-overlapping dots with other particle.

atom_mass(name::AbstractString)
::Float32

Return mass of the name atom. The kind of each atom is judged by PDB format atom names rule. https://cdn.rcsb.org/wwpdb/docs/documentation/file-format/PDBformat1992.pdf

residue_mass(name::AbstractString)
::Float32

Return mass of the name residue. The kind of each residue is judged by amino acid 3-letter abbreviation.

distance_pdc(first_atom::Coordinate,  second_atom::Coordinate,
             box_size::Coordinate)
::Real

Calculate distance first_atom and second_atom considering periodic boundary condition. The box size information used calculatin is specified by box_size argument.

pair_length_matrix_parallel(trj::Trajectory;
                            frame_indices::Union{Vector, OrdinalRange, Colon}       = :,
                            first_atom_indices::Union{Vector, OrdinalRange, Colon}  = :,
                            second_atom_indices::Union{Vector, OrdinalRange, Colon} = atom_indices1)
::Vector{Matrix{Coordinate}}

Multi-threads version of pairlengthmatrix. If you set available threads number to Threads.nthreads(), this function would faster than non-parallel version.

contact_bool_matrix_parallel(threshold::Real, trj::Trajectory;
                             frame_indices::Union{Vector, OrdinalRange, Colon}       = :,
                             first_atom_indices::Union{Vector, OrdinalRange, Colon}  = :,
                             second_atom_indices::Union{Vector, OrdinalRange, Colon} = first_atom_indices)
::Vector{Matrix{Bool}}

Multi-threads version of contactboolmatrix. If you set available threads number to Threads.nthreads(), this function would faster than non-parallel version.

contact_probability_matrix_parallel(threshold::Real, trj::Trajectory;
                                    frame_indices::Union{Vector, OrdinalRange, Colon}       = :,
                                    first_atom_indices::Union{Vector, OrdinalRange, Colon}  = :,
                                    second_atom_indices::Union{Vector, OrdinalRange, Colon} = first_atom_indices)
::Matrix{Real}

Multi-threads version of contactprobabilitymatrix. If you set available threads number to Threads.nthreads(), this function would faster than non-parallel version.