dcd

Documentation

Index

• Constants
• type DCDObj
  • func New(filename string) (*DCDObj, error)
  • func (D *DCDObj) Close()
  • func (D *DCDObj) Len() int
  • func (D *DCDObj) Next(keep *v3.Matrix, box ...[]float64) 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) Close()
  • 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)

New builds a new DCDObj object from a DCD trajectory file

func (*DCDObj) Close

func (D *DCDObj) Close()

Close Closes the trajectory, including the underlying file

func (*DCDObj) Len

func (D *DCDObj) Len() int

Len 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, box ...[]float64) 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

Readable returns true if the object is ready to be read from false otherwise. It doesnt guarantee that there is something to read.

type DCDWObj

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

Container for an Charmm/NAMD binary trajectory file. opened for writing

func NewWriter

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

New writer initializes a DCD trajectory for writing.

func (*DCDWObj) Close

func (D *DCDWObj) Close()

func (*DCDWObj) WNext

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

WNext rites 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

Critical returns true if the error is critical, false otherwise

func (Error) Decorate

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

Decorate Adds new information to the error

func (Error) Error

func (err Error) Error() string

func (Error) FileName

func (err Error) FileName() string

Filename returns the file to which the failing trajectory was associated

func (Error) Format

func (err Error) Format() string

Format returns the format of the file (always "dcd") associated to the error

type WB

type WB []byte

A writing buffer for DCD format

func (WB) Write

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

Writes w to the buffer