amberold

Documentation

Index

• Constants
• type CrdObj
  • func New(filename string, ats int, box bool) (*CrdObj, error)
  • func (C *CrdObj) Close()
  • func (C *CrdObj) Len() int
  • func (C *CrdObj) Next(keep *v3.Matrix, box ...[]float64) error
  • func (C *CrdObj) Readable() bool
• 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

Constants

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

Types

type CrdObj

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

Container for an old-Amber/pDynamo trajectory file.

func New

func New(filename string, ats int, box bool) (*CrdObj, error)

New creates a new Old Amber trajectory object from a file.

func (*CrdObj) Close

func (C *CrdObj) Close()

func (*CrdObj) Len

func (C *CrdObj) Len() int

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

func (*CrdObj) Next

func (C *CrdObj) 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. The box argument is never used.

func (*CrdObj) Readable

func (C *CrdObj) 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 Error

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

Error is the general structure for Crd 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