blocks

package
v0.0.0-...-83155bb Latest Latest
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 Go to latest Published: Oct 24, 2015 License: GPL-3.0 Imports: 5 Imported by: 0

Documentation

Index

Constants

View Source 
const HASH_KEY_SEP = "_"

Variables

View Source 
var PROTONS_LIB = map[string]*atomInfo{
	"H":  &atomInfo{1, regexp.MustCompile(`^\d*H[A-Z0-9]*$`)},
	"LI": &atomInfo{3, regexp.MustCompile(`^LI[A-Z0-9]*$`)},
	"C":  &atomInfo{6, regexp.MustCompile(`^C[A-Z0-9]*$`)},
	"N":  &atomInfo{7, regexp.MustCompile(`^N[A-Z0-9]*$`)},
	"O":  &atomInfo{8, regexp.MustCompile(`^O[A-Z0-9]*$`)},
	"F":  &atomInfo{9, regexp.MustCompile(`^F[A-Z0-9]*$`)},
	"NA": &atomInfo{11, regexp.MustCompile(`^NA\d*$`)},
	"MG": &atomInfo{12, regexp.MustCompile(`^MG\d*$`)},
	"AL": &atomInfo{13, regexp.MustCompile(`^AL[A-Z0-9]*$`)},
	"P":  &atomInfo{15, regexp.MustCompile(`^P[A-Z0-9]*$`)},
	"S":  &atomInfo{16, regexp.MustCompile(`^S[A-Z0-9]*$`)},
	"CL": &atomInfo{17, regexp.MustCompile(`^CL\d*$`)},
	"K":  &atomInfo{19, regexp.MustCompile(`^K\d*$`)},
	"CA": &atomInfo{20, regexp.MustCompile(`^CA\d*$`)},
	"FE": &atomInfo{26, regexp.MustCompile(`^FE\d*$`)},
	"ZN": &atomInfo{30, regexp.MustCompile(`^ZN\d*$`)},
	"BR": &atomInfo{35, regexp.MustCompile(`^BR[A-Z0-9]*$`)},
	"RB": &atomInfo{37, regexp.MustCompile(`^RB[A-Z0-9]*$`)},
	"I":  &atomInfo{53, regexp.MustCompile(`^I[A-Z0-9]*$`)},
	"BA": &atomInfo{56, regexp.MustCompile(`^BA[A-Z0-9]*$`)},
}

Functions

func AtomNameToProtons 

func AtomNameToProtons(name1 string) (int, error)

Types

type ATSetting 

type ATSetting int64
const (
	AT_NULL       ATSetting = 1 << iota //
	AT_TYPE_CHM_1                       // Normal CHARMM ATOM
	AT_TYPE_GMX_1                       // Normal GROMACS ATOM
	AT_HAS_PROTONS_SET
	AT_HAS_MASS_SET
	AT_HAS_LJ_DISTANCE_SET
	AT_HAS_LJ_ENERGY_SET
	AT_HAS_LJ_DISTANCE_14_SET
	AT_HAS_LJ_ENERGY_14_SET
	AT_HAS_CHARGE_SET
	AT_HAS_PARTIAL_CHARGE_SET
	AT_HAS_RADIUS_SET
)

type Angle 

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

func NewAngle 

func NewAngle(atom1, atom2, atom3 *Atom) *Angle

func (*Angle) Atom1 

func (a *Angle) Atom1() *Atom

func (*Angle) Atom2 

func (a *Angle) Atom2() *Atom

func (*Angle) Atom3 

func (a *Angle) Atom3() *Atom

func (*Angle) Id 

func (a *Angle) Id() int64

func (*Angle) SetType 

func (a *Angle) SetType(at *AngleType)

func (*Angle) Type 

func (a *Angle) Type() *AngleType

type AngleType 

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

func NewAngleType 

func NewAngleType(at1, at2, at3 string, t NTSetting) *AngleType

func (*AngleType) AType1 

func (at *AngleType) AType1() string

func (*AngleType) AType2 

func (at *AngleType) AType2() string

func (*AngleType) AType3 

func (at *AngleType) AType3() string

func (*AngleType) ConvertTo 

func (at *AngleType) ConvertTo(to NTSetting) (*AngleType, error)

func (*AngleType) HasR13Set 

func (at *AngleType) HasR13Set() bool

func (*AngleType) HasThetaConstantSet 

func (at *AngleType) HasThetaConstantSet() bool

func (*AngleType) HasThetaSet 

func (at *AngleType) HasThetaSet() bool

func (*AngleType) HasUBConstantSet 

func (at *AngleType) HasUBConstantSet() bool

func (*AngleType) R13 

func (at *AngleType) R13() float64

func (*AngleType) SetR13 

func (at *AngleType) SetR13(th float64)

func (*AngleType) SetTheta 

func (at *AngleType) SetTheta(th float64)

func (*AngleType) SetThetaConstant 

func (at *AngleType) SetThetaConstant(th float64)

func (*AngleType) SetUBConstant 

func (at *AngleType) SetUBConstant(ub float64)

func (*AngleType) Setting 

func (at *AngleType) Setting() NTSetting

func (*AngleType) Theta 

func (at *AngleType) Theta() float64

func (*AngleType) ThetaConstant 

func (at *AngleType) ThetaConstant() float64

func (*AngleType) UBConstant 

func (at *AngleType) UBConstant() float64

type Atom 

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

func NewAtom 

func NewAtom(name string) *Atom

func (*Atom) AddCoord 

func (a *Atom) AddCoord(c [3]float64)

coords

func (*Atom) AltLoc 

func (a *Atom) AltLoc() string

func (*Atom) BFactor 

func (a *Atom) BFactor() float64

func (*Atom) Bonds 

func (a *Atom) Bonds() []*Bond

func (*Atom) Coords 

func (a *Atom) Coords() [][3]float64

func (*Atom) Fragment 

func (a *Atom) Fragment() *Fragment

func (*Atom) Id 

func (a *Atom) Id() int64

func (*Atom) IsHetero 

func (a *Atom) IsHetero() bool

func (*Atom) Name 

func (a *Atom) Name() string

func (*Atom) Occupancy 

func (a *Atom) Occupancy() float64

func (*Atom) Serial 

func (a *Atom) Serial() int64

func (*Atom) SetAltLoc 

func (a *Atom) SetAltLoc(v string)

func (*Atom) SetBFactor 

func (a *Atom) SetBFactor(v float64)

func (*Atom) SetFragment 

func (a *Atom) SetFragment(v *Fragment)

func (*Atom) SetHetero 

func (a *Atom) SetHetero(v bool)

func (*Atom) SetOccupancy 

func (a *Atom) SetOccupancy(v float64)

func (*Atom) SetSerial 

func (a *Atom) SetSerial(s int64)

func (*Atom) SetType 

func (a *Atom) SetType(v *AtomType)

func (*Atom) Type 

func (a *Atom) Type() *AtomType

type AtomType 

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

func NewAtomType 

func NewAtomType(label string, t ATSetting) *AtomType

func (*AtomType) Charge 

func (at *AtomType) Charge() int

func (*AtomType) ConvertTo 

func (at *AtomType) ConvertTo(to ATSetting) (*AtomType, error)

func (*AtomType) HasChargeSet 

func (at *AtomType) HasChargeSet() bool

func (*AtomType) HasLJDistance14Set 

func (at *AtomType) HasLJDistance14Set() bool

func (*AtomType) HasLJDistanceSet 

func (at *AtomType) HasLJDistanceSet() bool

func (*AtomType) HasLJEnergy14Set 

func (at *AtomType) HasLJEnergy14Set() bool

func (*AtomType) HasLJEnergySet 

func (at *AtomType) HasLJEnergySet() bool

func (*AtomType) HasMassSet 

func (at *AtomType) HasMassSet() bool

func (*AtomType) HasPartialChargeSet 

func (at *AtomType) HasPartialChargeSet() bool

func (*AtomType) HasProtonsSet 

func (at *AtomType) HasProtonsSet() bool

func (*AtomType) HasRadiusSet 

func (at *AtomType) HasRadiusSet() bool

func (*AtomType) LJDistance 

func (at *AtomType) LJDistance() float64

func (*AtomType) LJDistance14 

func (at *AtomType) LJDistance14() float64

func (*AtomType) LJEnergy 

func (at *AtomType) LJEnergy() float64

func (*AtomType) LJEnergy14 

func (at *AtomType) LJEnergy14() float64

func (*AtomType) Label 

func (at *AtomType) Label() string

func (*AtomType) Mass 

func (at *AtomType) Mass() float64

func (*AtomType) PartialCharge 

func (at *AtomType) PartialCharge() float64

func (*AtomType) Protons 

func (at *AtomType) Protons() int

func (*AtomType) Radius 

func (at *AtomType) Radius() float64

func (*AtomType) SetCharge 

func (at *AtomType) SetCharge(v int)

func (*AtomType) SetLJDistance 

func (at *AtomType) SetLJDistance(v float64)

func (*AtomType) SetLJDistance14 

func (at *AtomType) SetLJDistance14(v float64)

func (*AtomType) SetLJEnergy 

func (at *AtomType) SetLJEnergy(v float64)

func (*AtomType) SetLJEnergy14 

func (at *AtomType) SetLJEnergy14(v float64)

func (*AtomType) SetMass 

func (at *AtomType) SetMass(v float64)

func (*AtomType) SetPartialCharge 

func (at *AtomType) SetPartialCharge(v float64)

func (*AtomType) SetProtons 

func (at *AtomType) SetProtons(v int)

func (*AtomType) SetRadius 

func (at *AtomType) SetRadius(v float64)

func (*AtomType) Setting 

func (at *AtomType) Setting() ATSetting

type BTSetting 

type BTSetting int64
const (
	BT_NULL BTSetting = 1 << iota
	BT_ORDER_SINGLE
	BT_ORDER_DOUBLE
	BT_ORDER_TRIPLE
	BT_TYPE_GMX_1
	BT_TYPE_CHM_1
	BT_HAS_HARMONIC_CONSTANT_SET
	BT_HAS_HARMONIC_DISTANCE_SET
)

type Bond 

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

func NewBond 

func NewBond(atom1, atom2 *Atom) *Bond

func (*Bond) Atom1 

func (b *Bond) Atom1() *Atom

atoms

func (*Bond) Atom2 

func (b *Bond) Atom2() *Atom

func (*Bond) Id 

func (b *Bond) Id() int64

func (*Bond) SetType 

func (b *Bond) SetType(bt *BondType)

func (*Bond) Type 

func (b *Bond) Type() *BondType

type BondType 

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

func NewBondType 

func NewBondType(at1, at2 string, t BTSetting) *BondType

func (*BondType) AType1 

func (bt *BondType) AType1() string

func (*BondType) AType2 

func (bt *BondType) AType2() string

func (*BondType) ConvertTo 

func (bt *BondType) ConvertTo(to BTSetting) (*BondType, error)

func (*BondType) HarmonicConstant 

func (bt *BondType) HarmonicConstant() float64

func (*BondType) HarmonicDistance 

func (bt *BondType) HarmonicDistance() float64

func (*BondType) HasHarmonicConstantSet 

func (bt *BondType) HasHarmonicConstantSet() bool

func (*BondType) HasHarmonicDistanceSet 

func (bt *BondType) HasHarmonicDistanceSet() bool

func (*BondType) IsSingle 

func (bt *BondType) IsSingle() bool

func (*BondType) SetHarmonicConstant 

func (bt *BondType) SetHarmonicConstant(v float64)

func (*BondType) SetHarmonicDistance 

func (bt *BondType) SetHarmonicDistance(v float64)

func (*BondType) SetOrderSingle 

func (bt *BondType) SetOrderSingle()

func (*BondType) Setting 

func (bt *BondType) Setting() BTSetting

setting

type CMap 

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

func NewCMap 

func NewCMap(a1, a2, a3, a4, a5, a6, a7, a8 *Atom) *CMap

func (*CMap) Atom1 

func (c *CMap) Atom1() *Atom

func (*CMap) Atom2 

func (c *CMap) Atom2() *Atom

func (*CMap) Atom3 

func (c *CMap) Atom3() *Atom

func (*CMap) Atom4 

func (c *CMap) Atom4() *Atom

func (*CMap) Atom5 

func (c *CMap) Atom5() *Atom

func (*CMap) Atom6 

func (c *CMap) Atom6() *Atom

func (*CMap) Atom7 

func (c *CMap) Atom7() *Atom

func (*CMap) Atom8 

func (c *CMap) Atom8() *Atom

func (*CMap) SetType 

func (c *CMap) SetType(ct *CMapType)

func (*CMap) Type 

func (c *CMap) Type() *CMapType

type CMapType 

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

func NewCMapType 

func NewCMapType(at1, at2, at3, at4, at5, at6, at7, at8 string, t CTSetting) *CMapType

func (*CMapType) AType1 

func (ct *CMapType) AType1() string

func (*CMapType) AType2 

func (ct *CMapType) AType2() string

func (*CMapType) AType3 

func (ct *CMapType) AType3() string

func (*CMapType) AType4 

func (ct *CMapType) AType4() string

func (*CMapType) AType5 

func (ct *CMapType) AType5() string

func (*CMapType) AType6 

func (ct *CMapType) AType6() string

func (*CMapType) AType7 

func (ct *CMapType) AType7() string

func (*CMapType) AType8 

func (ct *CMapType) AType8() string

func (*CMapType) ConvertTo 

func (ct *CMapType) ConvertTo(to CTSetting) (*CMapType, error)

func (*CMapType) SetValues 

func (ct *CMapType) SetValues(vs []float64)

func (*CMapType) Setting 

func (ct *CMapType) Setting() CTSetting

func (*CMapType) Values 

func (ct *CMapType) Values() []float64

type CTSetting 

type CTSetting int64
const (
	CT_NULL CTSetting = 1 << iota
	CT_TYPE_CHM_1
	CT_TYPE_GMX_1
)

type Connection 

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

A Connection is made of two atoms.

func NewConnection 

func NewConnection(atom1, atom2 *Atom) *Connection

func (*Connection) Atom1 

func (c *Connection) Atom1() *Atom

func (*Connection) Atom2 

func (c *Connection) Atom2() *Atom

func (*Connection) Fragment1 

func (c *Connection) Fragment1() *Fragment

func (*Connection) Fragment2 

func (c *Connection) Fragment2() *Fragment

type DTSetting 

type DTSetting int64
const (
	DT_NULL       DTSetting = 1 << iota
	DT_TYPE_CHM_1           //
	DT_TYPE_GMX_1           // proper
	DT_TYPE_GMX_9           // prper muliple
	DT_HAS_PHI_SET
	DT_HAS_PHI_CONSTANT_SET
	DT_HAS_MULTIPLICITY_SET
)

type Dihedral 

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

func NewDihedral 

func NewDihedral(atom1, atom2, atom3, atom4 *Atom) *Dihedral

func (*Dihedral) Atom1 

func (d *Dihedral) Atom1() *Atom

func (*Dihedral) Atom2 

func (d *Dihedral) Atom2() *Atom

func (*Dihedral) Atom3 

func (d *Dihedral) Atom3() *Atom

func (*Dihedral) Atom4 

func (d *Dihedral) Atom4() *Atom

func (*Dihedral) Id 

func (d *Dihedral) Id() int64

func (*Dihedral) SetType 

func (d *Dihedral) SetType(dt *DihedralType)

func (*Dihedral) Type 

func (d *Dihedral) Type() *DihedralType

type DihedralType 

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

func NewDihedralType 

func NewDihedralType(at1, at2, at3, at4 string, t DTSetting) *DihedralType

func (*DihedralType) AType1 

func (dt *DihedralType) AType1() string

func (*DihedralType) AType2 

func (dt *DihedralType) AType2() string

func (*DihedralType) AType3 

func (dt *DihedralType) AType3() string

func (*DihedralType) AType4 

func (dt *DihedralType) AType4() string

func (*DihedralType) ConvertTo 

func (dt *DihedralType) ConvertTo(to DTSetting) (*DihedralType, error)

func (*DihedralType) HasMultiplicitySet 

func (dt *DihedralType) HasMultiplicitySet() bool

func (*DihedralType) HasPhiConstantSet 

func (dt *DihedralType) HasPhiConstantSet() bool

func (*DihedralType) HasPhiSet 

func (dt *DihedralType) HasPhiSet() bool

func (*DihedralType) Multiplicity 

func (dt *DihedralType) Multiplicity() int

func (*DihedralType) Phi 

func (dt *DihedralType) Phi() float64

func (*DihedralType) PhiConstant 

func (dt *DihedralType) PhiConstant() float64

func (*DihedralType) SetMultiplicity 

func (dt *DihedralType) SetMultiplicity(v int)

func (*DihedralType) SetPhi 

func (dt *DihedralType) SetPhi(v float64)

func (*DihedralType) SetPhiConstant 

func (dt *DihedralType) SetPhiConstant(v float64)

func (*DihedralType) Setting 

func (dt *DihedralType) Setting() DTSetting

type FFSetting 

type FFSetting int64
const (
	FF_TYPE_CHM FFSetting = 1 << iota
	FF_TYPE_GMX
	FF_TYPE_AMB
)

type ForceField 

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

func NewForceField 

func NewForceField(ft FFSetting) *ForceField

func (*ForceField) AddAngleType 

func (ff *ForceField) AddAngleType(at *AngleType)

func (*ForceField) AddAtomType 

func (ff *ForceField) AddAtomType(at *AtomType)

func (*ForceField) AddBondType 

func (ff *ForceField) AddBondType(bt *BondType)

func (*ForceField) AddCMapType 

func (ff *ForceField) AddCMapType(v *CMapType)

func (*ForceField) AddDihedralType 

func (ff *ForceField) AddDihedralType(dt *DihedralType)

func (*ForceField) AddFragment 

func (ff *ForceField) AddFragment(v *Fragment)

func (*ForceField) AddImproperType 

func (ff *ForceField) AddImproperType(it *ImproperType)

func (*ForceField) AddNonBondedType 

func (ff *ForceField) AddNonBondedType(nb *PairType)

func (*ForceField) AddOneFourType 

func (ff *ForceField) AddOneFourType(nb *PairType)

func (*ForceField) AngleType 

func (ff *ForceField) AngleType(key HashKey) *AngleType

func (*ForceField) AngleTypes 

func (ff *ForceField) AngleTypes() map[HashKey]*AngleType

func (*ForceField) AtomType 

func (ff *ForceField) AtomType(key HashKey) *AtomType

func (*ForceField) AtomTypes 

func (ff *ForceField) AtomTypes() map[HashKey]*AtomType

func (*ForceField) BondType 

func (ff *ForceField) BondType(key HashKey) *BondType

func (*ForceField) BondTypes 

func (ff *ForceField) BondTypes() map[HashKey]*BondType

func (*ForceField) CMapType 

func (ff *ForceField) CMapType(key HashKey) *CMapType

func (*ForceField) CMapTypes 

func (ff *ForceField) CMapTypes() map[HashKey]*CMapType

func (*ForceField) DihedralType 

func (ff *ForceField) DihedralType(key HashKey) *DihedralType

func (*ForceField) DihedralTypes 

func (ff *ForceField) DihedralTypes() map[HashKey]*DihedralType

func (*ForceField) Errors 

func (ff *ForceField) Errors() []error

func (*ForceField) Fragment 

func (ff *ForceField) Fragment(key HashKey) *Fragment

func (*ForceField) Fragments 

func (ff *ForceField) Fragments() map[HashKey]*Fragment

func (*ForceField) GMXSetup 

func (ff *ForceField) GMXSetup() *GMXSetup

func (*ForceField) ImproperType 

func (ff *ForceField) ImproperType(key HashKey) *ImproperType

func (*ForceField) ImproperTypes 

func (ff *ForceField) ImproperTypes() map[HashKey]*ImproperType

func (*ForceField) NonBondedType 

func (ff *ForceField) NonBondedType(key HashKey) *PairType

func (*ForceField) NonBondedTypes 

func (ff *ForceField) NonBondedTypes() map[HashKey]*PairType

func (*ForceField) OneFourType 

func (ff *ForceField) OneFourType(key HashKey) *PairType

func (*ForceField) OneFourTypes 

func (ff *ForceField) OneFourTypes() map[HashKey]*PairType

func (*ForceField) SetGMXSetup 

func (ff *ForceField) SetGMXSetup(g *GMXSetup)

func (*ForceField) Setting 

func (ff *ForceField) Setting() FFSetting

type Fragment 

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

func NewFragment 

func NewFragment(name string) *Fragment

func (*Fragment) AddAngle 

func (f *Fragment) AddAngle(a *Angle)

func (*Fragment) AddAtom 

func (f *Fragment) AddAtom(a *Atom)

func (*Fragment) AddBond 

func (f *Fragment) AddBond(b *Bond)

func (*Fragment) AddCMap 

func (f *Fragment) AddCMap(c *CMap)

func (*Fragment) AddDihedral 

func (f *Fragment) AddDihedral(d *Dihedral)

func (*Fragment) AddImproper 

func (f *Fragment) AddImproper(b *Improper)

func (*Fragment) Angles 

func (f *Fragment) Angles() []*Angle

func (*Fragment) Atoms 

func (f *Fragment) Atoms() []*Atom

func (*Fragment) Bonds 

func (f *Fragment) Bonds() []*Bond

func (*Fragment) CMaps 

func (f *Fragment) CMaps() []*CMap

func (*Fragment) Dihedrals 

func (f *Fragment) Dihedrals() []*Dihedral

func (*Fragment) HasLinkerNext 

func (f *Fragment) HasLinkerNext() bool

func (*Fragment) HasLinkerPrev 

func (f *Fragment) HasLinkerPrev() bool

func (*Fragment) Id 

func (f *Fragment) Id() int64

func (*Fragment) Impropers 

func (f *Fragment) Impropers() []*Improper

func (*Fragment) LinkerNext 

func (f *Fragment) LinkerNext() *Linker

func (*Fragment) LinkerPrev 

func (f *Fragment) LinkerPrev() *Linker

func (*Fragment) Name 

func (f *Fragment) Name() string

func (*Fragment) Serial 

func (f *Fragment) Serial() int64

func (*Fragment) SetLinkerNext 

func (f *Fragment) SetLinkerNext(l *Linker)

func (*Fragment) SetLinkerPrev 

func (f *Fragment) SetLinkerPrev(l *Linker)

func (*Fragment) SetSerial 

func (f *Fragment) SetSerial(s int64)

type GMXSetup 

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

func NewGMXSetup 

func NewGMXSetup(nbFunc, combRule int, genPairs bool, flj, fqq float64) *GMXSetup

func (*GMXSetup) CombinationRule 

func (g *GMXSetup) CombinationRule() int

func (*GMXSetup) FudgeLJ 

func (g *GMXSetup) FudgeLJ() float64

func (*GMXSetup) FudgeQQ 

func (g *GMXSetup) FudgeQQ() float64

func (*GMXSetup) GeneratePairs 

func (g *GMXSetup) GeneratePairs() bool

func (*GMXSetup) NbFunc 

func (g *GMXSetup) NbFunc() int

type HashKey 

type HashKey string

func GenerateHashKey 

func GenerateHashKey(v interface{}, hks HashKeySetting) HashKey

type HashKeySetting 

type HashKeySetting int64
const (
	HK_MODE_NORMAL HashKeySetting = 1 << iota
	HK_MODE_REVERSE_BOND
	HK_MODE_REVERSE_ANGLE
	HK_MODE_REVERSE_DIHEDRAL
	HK_MODE_SHORT_CMAP // 5 element cmap
)

type ITSetting 

type ITSetting int64
const (
	IT_NULL ITSetting = 1 << iota
	IT_TYPE_CHM_1
	IT_TYPE_GMX_2
	IT_HAS_PSI_SET
	IT_HAS_PSI_CONSTANT_SET
)

type Improper 

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

func NewImproper 

func NewImproper(atom1, atom2, atom3, atom4 *Atom) *Improper

func (*Improper) Atom1 

func (d *Improper) Atom1() *Atom

func (*Improper) Atom2 

func (d *Improper) Atom2() *Atom

func (*Improper) Atom3 

func (d *Improper) Atom3() *Atom

func (*Improper) Atom4 

func (d *Improper) Atom4() *Atom

func (*Improper) Id 

func (d *Improper) Id() int64

func (*Improper) SetType 

func (d *Improper) SetType(dt *ImproperType)

func (*Improper) Type 

func (d *Improper) Type() *ImproperType

type ImproperType 

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

func NewImproperType 

func NewImproperType(at1, at2, at3, at4 string, t ITSetting) *ImproperType

func (*ImproperType) AType1 

func (dt *ImproperType) AType1() string

func (*ImproperType) AType2 

func (dt *ImproperType) AType2() string

func (*ImproperType) AType3 

func (dt *ImproperType) AType3() string

func (*ImproperType) AType4 

func (dt *ImproperType) AType4() string

func (*ImproperType) ConvertTo 

func (dt *ImproperType) ConvertTo(to ITSetting) (*ImproperType, error)

func (*ImproperType) HasPsiConstantSet 

func (dt *ImproperType) HasPsiConstantSet() bool

func (*ImproperType) HasPsiSet 

func (dt *ImproperType) HasPsiSet() bool

func (*ImproperType) Psi 

func (dt *ImproperType) Psi() float64

func (*ImproperType) PsiConstant 

func (dt *ImproperType) PsiConstant() float64

func (*ImproperType) SetPsi 

func (dt *ImproperType) SetPsi(v float64)

func (*ImproperType) SetPsiConstant 

func (dt *ImproperType) SetPsiConstant(v float64)

func (*ImproperType) Setting 

func (dt *ImproperType) Setting() ITSetting
type Link struct {
	// contains filtered or unexported fields
}

A Link can have one or more Connection. 

func NewLink() *Link

func (*Link) AddConnection 

func (ln *Link) AddConnection(c *Connection)

func (*Link) Connections 

func (ln *Link) Connections() []*Connection

type Linker 

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

func NewLinker 

func NewLinker() *Linker

func (*Linker) Bond 

func (l *Linker) Bond() *Bond

func (*Linker) Fragment1 

func (l *Linker) Fragment1() *Fragment

func (*Linker) Fragment2 

func (l *Linker) Fragment2() *Fragment

func (*Linker) Improper 

func (l *Linker) Improper() *Improper

func (*Linker) SetBond 

func (l *Linker) SetBond(b *Bond)

func (*Linker) SetFragment1 

func (l *Linker) SetFragment1(frag1 *Fragment)

func (*Linker) SetFragment2 

func (l *Linker) SetFragment2(frag2 *Fragment)

func (*Linker) SetImproper 

func (l *Linker) SetImproper(m *Improper)

type NTSetting 

type NTSetting int64
const (
	NT_NULL       NTSetting = 1 << iota
	NT_TYPE_CHM_1           // UB
	NT_TYPE_GMX_1           // Harmonic
	NT_TYPE_GMX_5           // UB
	NT_HAS_THETA_CONSTANT_SET
	NT_HAS_THETA_SET
	NT_HAS_UB_CONSTANT_SET
	NT_HAS_R13_SET
)

type PTSetting 

type PTSetting int64
const (
	PT_NULL       PTSetting = 1 << iota
	PT_TYPE_CHM_1           // CHARMM NBFIX
	PT_TYPE_GMX_1           // equivalent to CHARMM NBFIX
	PT_HAS_LJ_DISTANCE_SET
	PT_HAS_LJ_ENERGY_SET
	PT_HAS_LJ_DISTANCE_14_SET
	PT_HAS_LJ_ENERGY_14_SET
)

type Pair 

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

func NewPair 

func NewPair(a1, a2 *Atom) *Pair

func (*Pair) Atom1 

func (p *Pair) Atom1() *Atom

func (*Pair) Atom2 

func (p *Pair) Atom2() *Atom

func (*Pair) SetType 

func (p *Pair) SetType(pt *PairType)

func (*Pair) Type 

func (p *Pair) Type() *PairType

type PairType 

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

PairType is used to describe custom parameters for non-bonding interactions

func NewPairType 

func NewPairType(at1, at2 string, t PTSetting) *PairType

func (*PairType) AType1 

func (pt *PairType) AType1() string

func (*PairType) AType2 

func (pt *PairType) AType2() string

func (*PairType) ConvertTo 

func (pt *PairType) ConvertTo(to PTSetting) (*PairType, error)

func (*PairType) HasLJDistance14Set 

func (pt *PairType) HasLJDistance14Set() bool

func (*PairType) HasLJDistanceSet 

func (pt *PairType) HasLJDistanceSet() bool

func (*PairType) HasLJEnergy14Set 

func (pt *PairType) HasLJEnergy14Set() bool

func (*PairType) HasLJEnergySet 

func (pt *PairType) HasLJEnergySet() bool

func (*PairType) LJDistance 

func (pt *PairType) LJDistance() float64

func (*PairType) LJDistance14 

func (pt *PairType) LJDistance14() float64

func (*PairType) LJEnergy 

func (pt *PairType) LJEnergy() float64

func (*PairType) LJEnergy14 

func (pt *PairType) LJEnergy14() float64

func (*PairType) SetLJDistance 

func (pt *PairType) SetLJDistance(v float64)

func (*PairType) SetLJDistance14 

func (pt *PairType) SetLJDistance14(v float64)

func (*PairType) SetLJEnergy 

func (pt *PairType) SetLJEnergy(v float64)

func (*PairType) SetLJEnergy14 

func (pt *PairType) SetLJEnergy14(v float64)

func (*PairType) Setting 

func (pt *PairType) Setting() PTSetting

type System 

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

func NewSystem 

func NewSystem() *System

func (*System) AddAngle 

func (s *System) AddAngle(a *Angle)

func (*System) AddAtom 

func (s *System) AddAtom(a *Atom)

func (*System) AddBond 

func (s *System) AddBond(b *Bond)

func (*System) AddDihedral 

func (s *System) AddDihedral(d *Dihedral)

func (*System) AddFragment 

func (s *System) AddFragment(f *Fragment)

func (*System) AddImproper 

func (s *System) AddImproper(b *Improper)

func (*System) Angles 

func (s *System) Angles() []*Angle

func (*System) Atoms 

func (s *System) Atoms() []*Atom

func (*System) Bonds 

func (s *System) Bonds() []*Bond

func (*System) Dihedrals 

func (s *System) Dihedrals() []*Dihedral

func (*System) Fragments 

func (s *System) Fragments() []*Fragment

func (*System) Id 

func (s *System) Id() int64

func (*System) Impropers 

func (s *System) Impropers() []*Improper

func (*System) String 

func (s *System) String() string

Source Files

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Path Synopsis
Package mol provides basic building blocks for molecular systems.
 Package mol provides basic building blocks for molecular systems.

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