chem

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Versions in this module

v0

v0.7.1

Apr 3, 2024

v0.7.0

Feb 18, 2024

Changes in this version

+ const KBkJ

+ const RkJ

+ func BondedPathsFunc(at *Atom, targetIndex int, f func(*Bond) bool, options ...*BondedOptions) [][]int

+ func DihedralRama(a, b, c, d *v3.Matrix) float64

+ func MassCenterMem(in, oref, ret *v3.Matrix, massS ...*mat.Dense) (*v3.Matrix, error)

+ func MemPerAtomRMSD(test, templa, ctest, ctempla, tmp *v3.Matrix, indexes ...[]int) ([]float64, error)

type Atom

+ MolName string

+ MolName1 byte

+ func (N *Atom) SetIndex(i int)

type Bond

+ Energy float64

type Molecule

+ func (M *Molecule) Close()

type RamaSet

+ MolName string

v0.6.3

Nov 2, 2021

Changes in this version

+ func BondedPaths(at *Atom, targetIndex int, options ...*BondedOptions) [][]int

+ func InWhichRing(at *Atom, rings []*Ring) int

type Atom

+ Bonds []*Bond

+ func (N *Atom) Index() int

+ type Bond struct

+ At1 *Atom

+ At2 *Atom

+ Dist float64

+ Index int

+ Order float64

+ func (B *Bond) Cross(origin *Atom) *Atom

+ func (b *Bond) Remove() error

+ type BondedOptions struct

+ OnlyShortest bool

type Molecule

+ XYZFileData []string

+ type Ring struct

+ Atoms []int

+ func FindRings(coords *v3.Matrix, mol Atomer) []*Ring

+ func (R *Ring) AddHs(mol Atomer)

+ func (R *Ring) IsIn(index int) bool

+ func (R *Ring) Planarity(coord *v3.Matrix) float64

+ func (R *Ring) Size() int

type Topology

+ func (T *Topology) AssignBonds(coord *v3.Matrix) error

+ func (T *Topology) FillIndexes()

+ func (T *Topology) FillMasses()

+ func (T *Topology) FillVdw()

v0.6.1

Mar 8, 2021

v0.6.0

Mar 6, 2021

Changes in this version

+ const KB

+ const NA

+ const R

+ func ConcMolRDF(traj ConcTraj, mol *Molecule, refindexes []int, residues []string, ...) ([]float64, []float64, error)

+ func DihedralAlt(a, b, c, d *v3.Matrix) float64

+ func FrameUMolCRDF(coord *v3.Matrix, mol Atomer, refindexes []int, residues []string, ...) []float64

+ func GroFileWrite(outname string, Coords []*v3.Matrix, mol Atomer) error

+ func GroSnapWrite(coords *v3.Matrix, mol Atomer, out io.Writer) error

+ func Improper(a, b, c, d *v3.Matrix) float64

+ func ImproperAlt(a, b, c, d *v3.Matrix) float64

+ func MolRDF(traj Traj, mol Atomer, refindexes []int, residues []string, step, end float64, ...) ([]float64, []float64, error)

+ func MolShortestDist(test, ref *v3.Matrix) float64

+ func NegateIndexes(indexes []int, length int) []int

+ func XYZFileAsTraj(xyzname string) (*Molecule, *XYZTraj, error)

+ type MolDistList []*molDist

+ func DistRank(coord *v3.Matrix, mol Atomer, refindexes []int, residues []string, ...) MolDistList

+ func (M MolDistList) AtomIDs(mol Atomer) []int

+ func (M MolDistList) Data() ([]int, []float64)

+ func (M MolDistList) Distance(i int) float64

+ func (M MolDistList) Distances() []float64

+ func (M MolDistList) Len() int

+ func (M MolDistList) Less(i, j int) bool

+ func (M MolDistList) Merge(list ...MolDistList)

+ func (M MolDistList) MolID(i int) int

+ func (M MolDistList) MolIDs() []int

+ func (M MolDistList) String() string

+ func (M MolDistList) Swap(i, j int)

type Molecule

+ func GroFileRead(groname string) (*Molecule, error)

type Topology

+ func BackboneCGize(coord *v3.Matrix, mol Atomer, top bool) (*v3.Matrix, *Topology, error)

+ type XYZTraj struct

+ func (X *XYZTraj) Len() int

+ func (X *XYZTraj) Next(coords *v3.Matrix) error

+ func (X *XYZTraj) Readable() bool

v0.5.0

Mar 27, 2020

Changes in this version

+ const A2Bohr

+ const Bohr2A

+ const CHDist

+ const Deg2Rad

+ const EV2Kcal

+ const ErrAtomOutOfRange

+ const ErrCliffordRotation

+ const ErrInconsistentData

+ const ErrNilAtom

+ const ErrNilAtoms

+ const ErrNilData

+ const ErrNilFrame

+ const ErrNilMatrix

+ const ErrNotXx3Matrix

+ const H2Kcal

+ const KJ2Kcal

+ const Kcal2EV

+ const Kcal2H

+ const Kcal2KJ

+ const Rad2Deg

+ func Angle(v1, v2 *v3.Matrix) float64

+ func AntiProjection(test, ref *v3.Matrix) *v3.Matrix

+ func BestPlane(coords *v3.Matrix, mol ...Masser) (*v3.Matrix, error)

+ func BestPlaneP(evecs *v3.Matrix) (*v3.Matrix, error)

+ func CenterOfMass(geometry *v3.Matrix, massS ...*mat.Dense) (*v3.Matrix, error)

+ func Corrupted(X Traj, R Atomer) error

+ func CutAlphaRef(r Atomer, chain []string, list []int) []int

+ func CutBackRef(r Atomer, chains []string, list [][]int) ([]int, error)

+ func CutBetaRef(r Atomer, chain []string, list []int) []int

+ func Dihedral(a, b, c, d *v3.Matrix) float64

+ func EasyShape(coords *v3.Matrix, epsilon float64, mol ...Masser) (float64, float64, error)

+ func EulerRotateAbout(coordsorig, ax1, ax2 *v3.Matrix, angle float64) (*v3.Matrix, error)

+ func FixGromacsPDB(mol Atomer)

+ func FixNumbering(r Atomer)

+ func MakeWater(a1, a2 *v3.Matrix, distance, angle float64, oxygen bool) *v3.Matrix

+ func MassCenter(in, oref *v3.Matrix, massS ...*mat.Dense) (*v3.Matrix, *v3.Matrix, error)

+ func MemRMSD(test, templa, tmp *v3.Matrix, indexes ...[]int) (float64, error)

+ func MolIDNameChain2Index(mol Atomer, molID int, name, chain string) (int, error)

+ func Molecules2Atoms(mol Atomer, residues []int, chains []string) []int

+ func MomentTensor(A *v3.Matrix, massslice ...[]float64) (*v3.Matrix, error)

+ func MultiPDBWrite(out io.Writer, Coords []*v3.Matrix, mol Atomer, Bfactors [][]float64) error

+ func OnesMass(lenght int) *v3.Matrix

+ func PDBFileWrite(pdbname string, coords *v3.Matrix, mol Atomer, Bfactors []float64) error

+ func PDBStringWrite(coords *v3.Matrix, mol Atomer, bfact []float64) (string, error)

+ func PDBWrite(out io.Writer, coords *v3.Matrix, mol Atomer, bfact []float64) error

+ func Projection(test, ref *v3.Matrix) *v3.Matrix

+ func RMSD(test, templa *v3.Matrix, indexes ...[]int) (float64, error)

+ func RamaCalc(M *v3.Matrix, dihedrals []RamaSet) ([][]float64, error)

+ func RhoShapeIndexes(rhos []float64) (float64, float64, error)

+ func Rhos(momentTensor *v3.Matrix, epsilon ...float64) ([]float64, error)

+ func Rotate(Target, Res, axis *v3.Matrix, angle float64) *v3.Matrix

+ func RotateAbout(coordsorig, ax1, ax2 *v3.Matrix, angle float64) (*v3.Matrix, error)

+ func RotateP(...)

+ func RotateSer(Target, ToRot, axis *v3.Matrix, angle float64) *v3.Matrix

+ func RotateSerP(...)

+ func RotatorAroundZ(gamma float64) (*v3.Matrix, error)

+ func RotatorAroundZToNewY(newy *v3.Matrix) (*v3.Matrix, error)

+ func RotatorToNewZ(newz *v3.Matrix) *v3.Matrix

+ func RotatorTranslatorToSuper(test, templa *v3.Matrix) (*v3.Matrix, *v3.Matrix, *v3.Matrix, *v3.Matrix, error)

+ func ScaleBond(C, H *v3.Matrix, bond float64)

+ func ScaleBonds(coords *v3.Matrix, mol Atomer, n1, n2 string, finallenght float64)

+ func SelCone(B, selection *v3.Matrix, angle, distance, thickness, initial float64, ...) []int

+ func Super(test, templa *v3.Matrix, indexes ...[]int) (*v3.Matrix, error)

+ func TagAtomsByName(r Atomer, name string, list []int) int

+ func XYZFileWrite(xyzname string, Coords *v3.Matrix, mol Atomer) error

+ func XYZStringWrite(Coords *v3.Matrix, mol Atomer) (string, error)

+ func XYZWrite(out io.Writer, Coords *v3.Matrix, mol Atomer) error

+ type Atom struct

+ Chain string

+ Char16 byte

+ Charge float64

+ Het bool

+ ID int

+ Mass float64

+ MolID int

+ Molname string

+ Molname1 byte

+ Name string

+ Occupancy float64

+ Symbol string

+ Tag int

+ Vdw float64

+ func (N *Atom) Copy(A *Atom)

+ type AtomMultiCharger interface

+ Charge func() int

+ Multi func() int

+ type Atomer interface

+ Atom func(i int) *Atom

+ Len func() int

+ type CError struct

+ func (err CError) Decorate(dec string) []string

+ func (err CError) Error() string

+ type ConcTraj interface

+ Len func() int

+ NextConc func(frames []*v3.Matrix) ([]chan *v3.Matrix, error)

+ Readable func() bool

+ type Error interface

+ Decorate func(string) []string

+ Error func() string

+ type LastFrameError interface

+ NormalLastFrameTermination func()

+ type Masser interface

+ Masses func() ([]float64, error)

+ type Molecule struct

+ Bfactors [][]float64

+ Coords []*v3.Matrix

+ func NewMolecule(coords []*v3.Matrix, ats Atomer, bfactors [][]float64) (*Molecule, error)

+ func PDBFileRead(pdbname string, read_additional bool) (*Molecule, error)

+ func PDBRead(pdb io.Reader, read_additional bool) (*Molecule, error)

+ func Reduce(mol Atomer, coords *v3.Matrix, build int, report *os.File, executable string) (*Molecule, error)

+ func XYZFileRead(xyzname string) (*Molecule, error)

+ func XYZRead(xyzp io.Reader) (*Molecule, error)

+ func (M *Molecule) AddFrame(newframe *v3.Matrix)

+ func (M *Molecule) AddManyFrames(newframes []*v3.Matrix)

+ func (M *Molecule) Coord(atom, frame int) *v3.Matrix

+ func (M *Molecule) Copy(A *Molecule)

+ func (M *Molecule) Corrupted() error

+ func (M *Molecule) Current() int

+ func (M *Molecule) Del(i int) error

+ func (M *Molecule) DelCoord(i int) error

+ func (M *Molecule) InitRead() error

+ func (M *Molecule) Less(i, j int) bool

+ func (M *Molecule) NFrames() int

+ func (M *Molecule) Next(V *v3.Matrix) error

+ func (M *Molecule) NextConc(frames []bool) ([]chan *v3.Matrix, error)

+ func (M *Molecule) Readable() bool

+ func (M *Molecule) SetCurrent(i int)

+ func (M *Molecule) Swap(i, j int)

+ type PanicMsg string

+ func (v PanicMsg) Error() string

+ type RamaSet struct

+ C int

+ Ca int

+ Cprev int

+ MolID int

+ Molname string

+ N int

+ Npost int

+ func RamaList(M Atomer, chains string, resran []int) ([]RamaSet, error)

+ func RamaResidueFilter(dihedrals []RamaSet, filterdata []string, shouldBePresent bool) ([]RamaSet, []int)

+ type Topology struct

+ Atoms []*Atom

+ func MergeAtomers(A, B Atomer) *Topology

+ func NewTopology(charge, multi int, ats ...[]*Atom) *Topology

+ func (R *Topology) SomeAtoms(T Atomer, atomlist []int)

+ func (R *Topology) SomeAtomsSafe(T Atomer, atomlist []int) error

+ func (T *Topology) AppendAtom(at *Atom)

+ func (T *Topology) Atom(i int) *Atom

+ func (T *Topology) Charge() int

+ func (T *Topology) CopyAtoms(A Atomer)

+ func (T *Topology) DelAtom(i int)

+ func (T *Topology) Len() int

+ func (T *Topology) Masses() ([]float64, error)

+ func (T *Topology) Multi() int

+ func (T *Topology) ResetIDs()

+ func (T *Topology) SetAtom(i int, at *Atom)

+ func (T *Topology) SetCharge(i int)

+ func (T *Topology) SetMulti(i int)

+ type Traj interface

+ Len func() int

+ Next func(output *v3.Matrix) error

+ Readable func() bool

+ type TrajError interface

+ Critical func() bool

+ FileName func() string

+ Format func() string

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