pdb

package
Version: v0.0.0-...-568057e Latest Latest
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Published: Nov 1, 2019 License: MIT Imports: 4 Imported by: 7

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Constants

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Variables

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Functions

This section is empty.

Types

type Atom

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

func ParseAtom(line string) *Atom

type Chain

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

type Connection

type Connection struct {
	Serial1 int
	Serial2 int
}

func ParseConnections

func ParseConnections(line string) []*Connection

type Helix

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

func ParseHelix(line string) *Helix

type Matrix

type Matrix [4][4]float64

type Model

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

func (*Model) RemoveChain

func (model *Model) RemoveChain(chainID string)

type Reader

type Reader struct {
	io.Reader
}

func NewReader

func NewReader(r io.Reader) *Reader

func (*Reader) Read

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

func (*Reader) ReadAll

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

type Residue

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

type ResidueType

type ResidueType int
const (
	ResidueTypeCoil ResidueType
	ResidueTypeHelix
	ResidueTypeStrand
)

type Strand

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

func ParseStrand(line string) *Strand

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