ribbon: github.com/fogleman/ribbon/pdb Index | Files

package pdb

import "github.com/fogleman/ribbon/pdb"

Index

Package Files

atom.go chain.go connection.go helix.go matrix.go model.go reader.go residue.go strand.go util.go

func ParseConnections Uses

func ParseConnections(line string) []*Connection

type Atom Uses

type Atom struct {
    Serial     int
    Name       string
    AltLoc     string
    ResName    string
    ChainID    string
    ResSeq     int
    ICode      string
    X, Y, Z    float64
    Occupancy  float64
    TempFactor float64
    Element    string
    Charge     string
}

func ParseAtom Uses

func ParseAtom(line string) *Atom

type Chain Uses

type Chain struct {
    ChainID  string
    Residues []*Residue
}

type Connection Uses

type Connection struct {
    Serial1 int
    Serial2 int
}

type Helix Uses

type Helix struct {
    Serial      int
    HelixID     string
    InitResName string
    InitChainID string
    InitSeqNum  int
    InitICode   string
    EndResName  string
    EndChainID  string
    EndSeqNum   int
    EndICode    string
    HelixClass  int // TODO: enum?
    Length      int
}

func ParseHelix Uses

func ParseHelix(line string) *Helix

type Matrix Uses

type Matrix [4][4]float64

type Model Uses

type Model struct {
    Atoms       []*Atom
    HetAtoms    []*Atom
    Connections []*Connection
    Helixes     []*Helix
    Strands     []*Strand
    BioMatrixes []Matrix
    SymMatrixes []Matrix
    Residues    []*Residue
    Chains      []*Chain
}

type Reader Uses

type Reader struct {
    io.Reader
}

func NewReader Uses

func NewReader(r io.Reader) *Reader

func (*Reader) Read Uses

func (r *Reader) Read() (*Model, error)

func (*Reader) ReadAll Uses

func (r *Reader) ReadAll() ([]*Model, error)

type Residue Uses

type Residue struct {
    ResName     string
    ChainID     string
    ResSeq      int
    Atoms       []*Atom
    AtomsByName map[string]*Atom
    Type        ResidueType
}

type ResidueType Uses

type ResidueType int
const (
    ResidueTypeCoil ResidueType
    ResidueTypeHelix
    ResidueTypeStrand
)

type Strand Uses

type Strand struct {
    Strand      int
    SheetID     string
    NumStrands  int
    InitResName string
    InitChainID string
    InitSeqNum  int
    InitICode   string
    EndResName  string
    EndChainID  string
    EndSeqNum   int
    EndICode    string
    Sense       int // TODO: enum?
    CurAtom     string
    CurResName  string
    CurChainId  string
    CurResSeq   int
    CurICode    string
    PrevAtom    string
    PrevResName string
    PrevChainId string
    PrevResSeq  int
    PrevICode   string
}

func ParseStrand Uses

func ParseStrand(line string) *Strand

Package pdb imports 4 packages (graph) and is imported by 2 packages. Updated 2017-03-16. Refresh now. Tools for package owners.