stf

Documentation

Index

• Constants
• 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 StfR
  • func New(name string) (*StfR, map[string]string, error)
  • func (S *StfR) Close()
  • func (S *StfR) Len() int
  • func (S *StfR) Next(c *v3.Matrix, box ...[]float64) error
  • func (D *StfR) NextConc(frames []*v3.Matrix) ([]chan *v3.Matrix, error)
  • func (S *StfR) Readable() bool
• type StfW
  • func NewWriter(name string, natoms int, header map[string]string, Opts ...*WriterOptions) (*StfW, error)
  • func (S *StfW) Close()
  • func (S *StfW) Len() int
  • func (S *StfW) WNext(coord *v3.Matrix, box ...[]float64) error
  • func (S *StfW) WNextDense(dcoord *mat.Dense) error
• type WriterOptions
  • func DefaultWriterOptions() *WriterOptions
  • func (O *WriterOptions) Fix()

Constants

const (
	TrajUnIniRead       = "Traj object uninitialized to read"
	TrajUnIniWrite      = "Traj object uninitialized to read"
	ReadError           = "Error reading frame"
	UnableToOpen        = "Unable to open file"
	SecurityCheckFailed = "Failed Security Check"
	NilCoordinates      = "Given nil coordinates"
	WrongFormat         = "Wrong format in the STF file or frame"
	NotEnoughSpace      = "Not enough space in passed blocks"
	EOF                 = "EOF"
)

Types

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 StfR

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

Read!

func New

func New(name string) (*StfR, map[string]string, error)

New opens a STF trajectory for reading, and returns a pointer to the handle, a map with the metadata (or nil, if no metadata is found) and error or nil.

func (*StfR) Close

func (S *StfR) Close()

Close closes the object, and marks it as unreadable

func (*StfR) Len

func (S *StfR) Len() int

Len returns the number of atoms in each frame of the trajectory.

func (*StfR) Next

func (S *StfR) Next(c *v3.Matrix, box ...[]float64) error

Next puts in the given matrix (c) the coordinates for the next frame of the trajectory and, if given, and the information is present, puts the box vector information in box Returns error if the operation is not successful. If the error is EOF, the end of the trajectory has been reached, not an actual error.

func (*StfR) NextConc

func (D *StfR) 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 (*StfR) Readable

func (S *StfR) Readable() bool

Readabe returns true if the handle is readable (if it is possible to call Next on it)

type StfW

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

Write!

func NewWriter

func NewWriter(name string, natoms int, header map[string]string, Opts ...*WriterOptions) (*StfW, error)

For zstandard (stf) compression levels are progressively slower but offering better compression as compressionLevel increases from 1 to 4 (other numbers will result in '1' or fastest compression). If the precision is specified in the header, that overwrites whatever is in the options.

func (*StfW) Close

func (S *StfW) Close()

func (*StfW) Len

func (S *StfW) Len() int

func (*StfW) WNext

func (S *StfW) WNext(coord *v3.Matrix, box ...[]float64) error

Writes a frame to the trajectory. Will panic if the trjectory is nil or closed.

func (*StfW) WNextDense

func (S *StfW) WNextDense(dcoord *mat.Dense) error

compatibility with Gonum

type WriterOptions

type WriterOptions struct {
	//	Precision        int //How many decimals for each coordinate, in Angstroms
	CompressionLevel int // 1: Fastest/Worst compression to 4: Slowest/Best compression
}

func DefaultWriterOptions

func DefaultWriterOptions() *WriterOptions

func (*WriterOptions) Fix

func (O *WriterOptions) Fix()