Versions in this module Expand all Collapse all v0 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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