dcd

Documentation

Index

• Constants
• type DCDObj
  • func New(filename string) (*DCDObj, error)
  • func (D *DCDObj) Len() int
  • func (D *DCDObj) Next(keep *v3.Matrix) error
  • func (D *DCDObj) NextConc(frames []*v3.Matrix) ([]chan *v3.Matrix, error)
  • func (D *DCDObj) Readable() bool
• type DCDWObj
  • func NewWriter(filename string, natoms int) (*DCDWObj, error)
  • func (D *DCDWObj) WNext(towrite *v3.Matrix) error
• type Error
  • func (err Error) Critical() bool
  • func (E Error) Decorate(deco string) []string
  • func (err Error) Error() string
  • func (err Error) FileName() string
  • func (err Error) Format() string
• type WB
  • func (B WB) Write(w []byte) (int, error)

Constants

const (
	TrajUnIni           = "Traj object uninitialized to read"
	ReadError           = "Error reading frame"
	UnableToOpen        = "Unable to open file"
	SecurityCheckFailed = "FailedSecurityCheck"
	WrongFormat         = "Wrong format in the DCD file or frame"
	NotEnoughSpace      = "Not enough space in passed blocks"
	EOF                 = "EOF"
)

Types

type DCDObj

type DCDObj struct {
	// contains filtered or unexported fields
}

Container for an Charmm/NAMD binary trajectory file.

func New

func New(filename string) (*DCDObj, error)

func (*DCDObj) Len

func (D *DCDObj) Len() int

Natoms returns the number of atoms per frame in the XtcObj. XtcObj must be initialized. 0 means an uninitialized object.

func (*DCDObj) Next

func (D *DCDObj) Next(keep *v3.Matrix) error

Next Reads the next frame in a DcDObj that has been initialized for read With initread. If keep is true, returns a pointer to matrix.DenseMatrix With the coordinates read, otherwiser, it discards the coordinates and returns nil.

func (*DCDObj) NextConc

func (D *DCDObj) NextConc(frames []*v3.Matrix) ([]chan *v3.Matrix, error)

NextConc takes a slice of bools and reads as many frames as elements the list has form the trajectory. The frames are discarted if the corresponding elemetn of the slice * is false. The function returns a slice of channels through each of each of which * a *matrix.DenseMatrix will be transmited

func (*DCDObj) Readable

func (D *DCDObj) Readable() bool

Returns true if the object is ready to be read from false otherwise. It doesnt guarantee that there is something to read. true or false depending on whether D is ready to read snapshots from it.

type DCDWObj

type DCDWObj struct {
	// contains filtered or unexported fields
}

Container for an Charmm/NAMD binary trajectory file.

func NewWriter

func NewWriter(filename string, natoms int) (*DCDWObj, error)

Initializes a trajectory for writing. You need to provide _some_ estimate of the frames to be write here.

func (*DCDWObj) WNext

func (D *DCDWObj) WNext(towrite *v3.Matrix) error

Writes the next frame to the trajectory.

type Error

type Error struct {
	// contains filtered or unexported fields
}

Error is the general structure for DCD trajectory errors. It fullfills chem.Error and chem.TrajError

func (Error) Critical

func (err Error) Critical() bool

func (Error) Decorate

func (E Error) Decorate(deco string) []string

func (Error) Error

func (err Error) Error() string

func (Error) FileName

func (err Error) FileName() string

func (Error) Format

func (err Error) Format() string

type WB

type WB []byte

A writing buffer

func (WB) Write

func (B WB) Write(w []byte) (int, error)