README
¶
Documentation
¶
Overview ¶
Package xyz implements access to read and write xyz content.
References:
http://openbabel.org/wiki/XYZ_%28format%29
Index ¶
Examples ¶
Constants ¶
This section is empty.
Variables ¶
View Source
var ( // ErrElementSymbol occurs when the symbol is unrecognized. ErrElementSymbol = errors.New("xyz: elements atomic symbol is unrecognized") // ErrElementNumber occurs when the given atomic number is out of range. ErrElementNumber = errors.New("xyz: elements atomic number is out of range") )
View Source
var ( // ErrInvalidMolecule is returned when the given molecule input isn't valid. ErrInvalidMolecule = errors.New("xyz: input is not a valid molecule") )
Functions ¶
This section is empty.
Types ¶
type Decoder ¶
type Decoder struct {
// contains filtered or unexported fields
}
Decoder reads and decodes lists of molecules.
Example ¶
package main
import (
"bytes"
"fmt"
"github.com/larzconwell/xyz"
"io"
)
func main() {
buf := bytes.NewBufferString(`5
Methane molecule
C 0.000000 0.000000 0.000000
H 0.000000 0.000000 1.089000
H 1.026719 0.000000 -0.363000
H -0.513360 -0.889165 -0.363000
H -0.513360 0.889165 -0.363000
3
Water molecule
O 0.00000 0.00000 0.00000
H 0.75700 0.58600 0.00000
H -0.75700 0.58600 0.00000`)
decoder := xyz.NewDecoder(buf)
for {
molecule, err := decoder.Decode()
if err == io.EOF {
break
}
if err != nil {
panic(err)
}
fmt.Println(molecule.Comment)
for _, atom := range molecule.Atoms {
fmt.Println(atom.Element, atom.X, atom.Y, atom.Z)
}
}
}
Output:
func NewDecoder ¶
NewDecoder returns a decoder reading from the given reader.
The decoder is buffered and may read data beyond the molecule data requests.
type Element ¶
type Element int
Element is a single elements atomic number.
func ParseElement ¶
ParseElement parses the element from a slice of bytes. It recognizes both atomic numbers and atomic symbols.
type Encoder ¶
type Encoder struct {
// contains filtered or unexported fields
}
Encoder writes and encodes lists of molecules.
Example ¶
package main
import (
"bytes"
"github.com/larzconwell/xyz"
"io"
"os"
)
func main() {
molecule := &xyz.Molecule{
Comment: "Water molecule",
Atoms: []*xyz.Atom{
{8, 0.00000, 0.00000, 0.00000},
{1, 0.75700, 0.58600, 0.00000},
{1, -0.075700, 0.58600, 0.00000},
},
}
var buf bytes.Buffer
encoder := xyz.NewEncoder(&buf)
err := encoder.Encode(molecule)
if err != nil {
panic(err)
}
io.Copy(os.Stdout, &buf)
}
Output:
func NewEncoder ¶
NewEncoder creates an encoder writing to writer.
Source Files
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