//EulerRotateAbout uses Euler angles to rotate the coordinates in coordsorig around by angle
//radians around the axis given by the vector axis. It returns the rotated coordsorig,
//since the original is not affected. It seems more clunky than the RotateAbout, which uses Clifford algebra.
//I leave it for benchmark, mostly, and might remove it later. There is no test for this function!
func EulerRotateAbout(coordsorig, ax1, ax2 *v3.Matrix, angle float64) (*v3.Matrix, error) {
r, _ := coordsorig.Dims()
coords := v3.Zeros(r)
translation := v3.Zeros(ax1.NVecs())
translation.Copy(ax1)
axis := v3.Zeros(ax2.NVecs())
axis.Sub(ax2, ax1) //now it became the rotation axis
f := func() { coords.SubVec(coordsorig, translation) }
if err := gnMaybe(gnPanicker(f)); err != nil {
return nil, CError{err.Error(), []string{"v3.Matrix.Subvec", "EulerRotateAbout"}}
}
Zswitch := RotatorToNewZ(axis)
coords.Mul(coords, Zswitch) //rotated
Zrot, err := RotatorAroundZ(angle)
if err != nil {
return nil, errDecorate(err, "EulerRotateAbout")
}
// Zsr, _ := Zswitch.Dims()
// RevZ := v3.Zeros(Zsr)
RevZ, err := gnInverse(Zswitch)
if err != nil {
return nil, errDecorate(err, "EulerRotateAbout")
}
coords.Mul(coords, Zrot) //rotated
coords.Mul(coords, RevZ)
coords.AddVec(coords, translation)
return coords, nil
}
func EncodeCoords(coords *v3.Matrix, enc *json.Encoder) *Error {
c := new(Coords)
t := make([]float64, 3, 3)
for i := 0; i < coords.NVecs(); i++ {
c.Coords = coords.Row(t, i)
if err := enc.Encode(c); err != nil {
return NewError("postprocess", "chemjson.EncodeCoords", err)
}
}
return nil
}
//SelCone, Given a set of cartesian points in sellist, obtains a vector "plane" normal to the best plane passing through the points.
//It selects atoms from the set A that are inside a cone in the direction of "plane" that starts from the geometric center of the cartesian points,
//and has an angle of angle (radians), up to a distance distance. The cone is approximated by a set of radius-increasing cilinders with height thickness.
//If one starts from one given point, 2 cgnOnes, one in each direction, are possible. If whatcone is 0, both cgnOnes are considered.
//if whatcone<0, only the cone opposite to the plane vector direction. If whatcone>0, only the cone in the plane vector direction.
//the 'initial' argument allows the construction of a truncate cone with a radius of initial.
func SelCone(B, selection *v3.Matrix, angle, distance, thickness, initial float64, whatcone int) []int {
A := v3.Zeros(B.NVecs())
A.Copy(B) //We will be altering the input so its better to work with a copy.
ar, _ := A.Dims()
selected := make([]int, 0, 3)
neverselected := make([]int, 0, 30000) //waters that are too far to ever be selected
nevercutoff := distance / math.Cos(angle) //cutoff to be added to neverselected
A, _, err := MassCenter(A, selection, nil) //Centrate A in the geometric center of the selection, Its easier for the following calculations
if err != nil {
panic(PanicMsg(err.Error()))
}
selection, _, _ = MassCenter(selection, selection, nil) //Centrate the selection as well
plane, err := BestPlane(selection, nil) //I have NO idea which direction will this vector point. We might need its negative.
if err != nil {
panic(PanicMsg(err.Error()))
}
for i := thickness / 2; i <= distance; i += thickness {
maxdist := math.Tan(angle)*i + initial //this should give me the radius of the cone at this point
for j := 0; j < ar; j++ {
if isInInt(selected, j) || isInInt(neverselected, j) { //we dont scan things that we have already selected, or are too far
continue
}
atom := A.VecView(j)
proj := Projection(atom, plane)
norm := proj.Norm(0)
//Now at what side of the plane is the atom?
angle := Angle(atom, plane)
if whatcone > 0 {
if angle > math.Pi/2 {
continue
}
} else if whatcone < 0 {
if angle < math.Pi/2 {
continue
}
}
if norm > i+(thickness/2.0) || norm < (i-thickness/2.0) {
continue
}
proj.Sub(proj, atom)
projnorm := proj.Norm(0)
if projnorm <= maxdist {
selected = append(selected, j)
}
if projnorm >= nevercutoff {
neverselected = append(neverselected, j)
}
}
}
return selected
}
//XYZStringWrite writes the mol Ref and the Coord coordinates in an XYZ-formatted string.
func XYZStringWrite(Coords *v3.Matrix, mol Atomer) (string, error) {
var out string
if mol.Len() != Coords.NVecs() {
return "", CError{"Ref and Coords dont have the same number of atoms", []string{"XYZStringWrite"}}
}
c := make([]float64, 3, 3)
out = fmt.Sprintf("%-4d\n\n", mol.Len())
//towrite := Coords.Arrays() //An array of array with the data in the matrix
for i := 0; i < mol.Len(); i++ {
//c := towrite[i] //coordinates for the corresponding atoms
c = Coords.Row(c, i)
temp := fmt.Sprintf("%-2s %12.6f%12.6f%12.6f \n", mol.Atom(i).Symbol, c[0], c[1], c[2])
out = strings.Join([]string{out, temp}, "")
}
return out, nil
}
//RMSD returns the RSMD (root of the mean square deviation) for the sets of cartesian
//coordinates in test and template.
func RMSD(test, template *v3.Matrix) (float64, error) {
//This is a VERY naive implementation.
tmr, tmc := template.Dims()
tsr, tsc := test.Dims()
if tmr != tsr || tmc != 3 || tsc != 3 {
return 0, fmt.Errorf("Ill formed matrices for RMSD calculation")
}
tr := tmr
ctempla := v3.Zeros(template.NVecs())
ctempla.Copy(template)
//the maybe thing might not be needed since we check the dimensions before.
f := func() { ctempla.Sub(ctempla, test) }
if err := gnMaybe(gnPanicker(f)); err != nil {
return 0, CError{err.Error(), []string{"v3.Matrix.Sub", "RMSD"}}
}
var RMSD float64
for i := 0; i < template.NVecs(); i++ {
temp := ctempla.VecView(i)
RMSD += math.Pow(temp.Norm(0), 2)
}
RMSD = RMSD / float64(tr)
RMSD = math.Sqrt(RMSD)
return RMSD, nil
}
//XYZStringWrite writes the mol Ref and the Coord coordinates in an XYZ-formatted string.
func XYZWrite(out io.Writer, Coords *v3.Matrix, mol Atomer) error {
iowriterError := func(err error) error {
return CError{"Failed to write in io.Writer" + err.Error(), []string{"io.Writer.Write", "XYZWrite"}}
}
if mol.Len() != Coords.NVecs() {
return CError{"Ref and Coords dont have the same number of atoms", []string{"XYZWrite"}}
}
c := make([]float64, 3, 3)
_, err := out.Write([]byte(fmt.Sprintf("%-4d\n\n", mol.Len())))
if err != nil {
return iowriterError(err)
}
//towrite := Coords.Arrays() //An array of array with the data in the matrix
for i := 0; i < mol.Len(); i++ {
//c := towrite[i] //coordinates for the corresponding atoms
c = Coords.Row(c, i)
temp := fmt.Sprintf("%-2s %12.6f%12.6f%12.6f \n", mol.Atom(i).Symbol, c[0], c[1], c[2])
_, err := out.Write([]byte(temp))
if err != nil {
return iowriterError(err)
}
}
return nil
}
//RotateAbout about rotates the coordinates in coordsorig around by angle radians around the axis
//given by the vector axis. It returns the rotated coordsorig, since the original is not affected.
//Uses Clifford algebra.
func RotateAbout(coordsorig, ax1, ax2 *v3.Matrix, angle float64) (*v3.Matrix, error) {
coordsLen := coordsorig.NVecs()
coords := v3.Zeros(coordsLen)
translation := v3.Zeros(ax1.NVecs())
translation.Copy(ax1)
axis := v3.Zeros(ax2.NVecs())
axis.Sub(ax2, ax1) // the rotation axis
f := func() { coords.SubVec(coordsorig, translation) }
if err := gnMaybe(gnPanicker(f)); err != nil {
return nil, CError{err.Error(), []string{"v3.Matrix.SubVec", "RotateAbout"}}
}
Rot := v3.Zeros(coordsLen)
Rot = Rotate(coords, Rot, axis, angle)
g := func() { Rot.AddVec(Rot, translation) }
if err := gnMaybe(gnPanicker(g)); err != nil {
return nil, CError{err.Error(), []string{"v3.Matrix.AddVec", "RotateAbout"}}
}
return Rot, nil
}
func main() {
//This is the part that collects all the data from PyMOL, with all the proper error checking.
stdin := bufio.NewReader(os.Stdin)
options, err := chemjson.DecodeOptions(stdin)
if err != nil {
fmt.Fprint(os.Stderr, err.Marshal())
log.Fatal(err)
}
mainName := options.SelNames[0]
if len(options.AtomsPerSel) > 1 {
for _, v := range options.SelNames[1:] {
mainName = mainName + "__" + v //inefficient but there should never be THAT many selections.
}
}
dielectric := options.FloatOptions[0][0]
charge := options.IntOptions[0][0]
multi := options.IntOptions[0][1]
qmprogram := options.StringOptions[0][0]
method := options.StringOptions[0][1]
calctype := options.StringOptions[0][2]
var osidemol *chem.Topology
var osidecoords, sidecoords *v3.Matrix
var sidelist, sidefrozen []int
selindex := 0
total := 0
selections := len(options.AtomsPerSel)
if options.BoolOptions[0][0] { //sidechain selections exist
sidecoords, osidecoords, osidemol, sidelist, sidefrozen = SideChains(stdin, options)
selections--
total += osidemol.Len()
selindex++
}
fmt.Fprint(os.Stderr, selections)
obbmol := make([]*chem.Topology, selections, selections)
obbcoords := make([]*v3.Matrix, selections, selections)
bbcoords := make([]*v3.Matrix, selections, selections)
bblist := make([][]int, selections, selections)
bbfrozen := make([][]int, selections, selections)
for i := 0; i < selections; i++ {
bbcoords[i], obbcoords[i], obbmol[i], bblist[i], bbfrozen[i] = BackBone(stdin, options, selindex)
total += obbmol[i].Len()
selindex++
fmt.Fprint(os.Stderr, "chetumanga")
}
//Now we put the juit together
bigC := v3.Zeros(total)
bigA := chem.NewTopology([]*chem.Atom{}, 0, 0)
bigFroz := make([]int, 0, total)
setoffset := 0
if options.BoolOptions[0][0] {
bigC.SetMatrix(0, 0, osidecoords)
setoffset += osidecoords.NVecs()
bigA = chem.MergeAtomers(bigA, osidemol)
// bigA = osidemol
bigFroz = append(bigFroz, sidefrozen...)
}
for k, v := range obbcoords {
bigC.SetMatrix(setoffset, 0, v)
bigA = chem.MergeAtomers(bigA, obbmol[k])
tmpfroz := SliceOffset(bbfrozen[k], setoffset)
bigFroz = append(bigFroz, tmpfroz...)
setoffset += v.NVecs()
}
bigA.SetCharge(charge)
bigA.SetMulti(multi)
chem.PDBFileWrite(mainName+"toOPT.pdb", bigC, bigA, nil) /////////////////////////////////////
chem.XYZFileWrite(mainName+"toOPT.xyz", bigC, bigA) /////////////////////////////////////
//Ok, we have now one big matrix and one big atom set, now the optimization
calc := new(qm.Calc)
if calctype == "Optimization" {
calc.Optimize = true
}
calc.RI = true //some options, including this one, are meaningless for MOPAC
calc.CConstraints = bigFroz
calc.Dielectric = dielectric
calc.SCFTightness = 1
calc.Dispersion = "D3"
calc.Method = "TPSS"
if method == "Cheap" {
calc.BSSE = "gcp"
if qmprogram == "ORCA" {
calc.Method = "HF-3c"
calc.RI = false
} else if qmprogram == "MOPAC2012" {
calc.Method = "PM6-D3H4 NOMM MOZYME"
} else {
calc.Basis = "def2-SVP"
}
} else {
calc.Basis = "def2-TZVP"
}
//We will use the default methods and basis sets of each program. In the case of MOPAC, that is currently PM6-D3H4.
var QM qm.Handle
switch qmprogram {
case "ORCA":
orca := qm.NewOrcaHandle()
orca.SetnCPU(runtime.NumCPU())
QM = qm.Handle(orca)
case "TURBOMOLE":
QM = qm.Handle(qm.NewTMHandle())
case "NWCHEM":
QM = qm.Handle(qm.NewNWChemHandle())
calc.SCFConvHelp = 1
default:
QM = qm.Handle(qm.NewMopacHandle())
}
QM.SetName(mainName)
QM.BuildInput(bigC, bigA, calc)
fmt.Fprint(os.Stderr, options.BoolOptions)
if options.BoolOptions[0][2] {
return //Dry run
}
if err2 := QM.Run(true); err != nil {
log.Fatal(err2.Error())
}
//Now we ran the calculation, we must retrive the geometry and divide the coordinates among the original selections.
var newBigC *v3.Matrix
info := new(chemjson.Info) //Contains the return info
var err2 error
if calc.Optimize {
newBigC, err2 = QM.OptimizedGeometry(bigA)
if err2 != nil {
log.Fatal(err2.Error())
}
if qmprogram == "NWCHEM" { //NWchem translates/rotates the system before optimizing so we need to superimpose with the original geometry in order for them to match.
newBigC, err2 = chem.Super(newBigC, bigC, bigFroz, bigFroz)
if err2 != nil {
log.Fatal(err2.Error())
}
}
info.Molecules = len(options.AtomsPerSel)
geooffset := 0
if options.BoolOptions[0][0] {
tmp := newBigC.View(geooffset, 0, len(sidelist), 3) //This is likely to change when we agree on a change for the gonum API!!!!
sidecoords.SetVecs(tmp, sidelist)
info.FramesPerMolecule = []int{1}
info.AtomsPerMolecule = []int{sidecoords.NVecs()}
//I DO NOT understand why the next line is += len(sidelist)-1 instead of len(sidelist), but it works. If a bug appears
//take a look at this line, and the equivalent in the for loop that follows.
geooffset += (len(sidelist) - 1)
}
for k, v := range bbcoords {
//Take a look here in case of bugs.
tmp := newBigC.View(geooffset, 0, len(bblist[k]), 3) //This is likely to change when we agree on a change for the gonum API!!!!
v.SetVecs(tmp, bblist[k])
info.FramesPerMolecule = append(info.FramesPerMolecule, 1)
info.AtomsPerMolecule = append(info.AtomsPerMolecule, v.NVecs())
geooffset += (len(bblist[k]) - 1)
}
// for k,v:=range(bbcoords){
// chem.XYZWrite(fmt.Sprintf("opti%d.xyz",k), , newcoords)
// }
} else {
//nothing here, the else part will get deleted after tests
}
energy, err2 := QM.Energy()
if err2 != nil {
log.Fatal(err2.Error())
}
//Start transfering data back
info.Energies = []float64{energy}
if err2 := info.Send(os.Stdout); err2 != nil {
fmt.Fprint(os.Stderr, err2)
log.Fatal(err2)
}
// fmt.Fprint(os.Stdout,mar)
// fmt.Fprint(os.Stdout,"\n")
// A loop again to transmit the info.
if options.BoolOptions[0][0] {
if err := chemjson.SendMolecule(nil, []*v3.Matrix{sidecoords}, nil, nil, os.Stdout); err2 != nil {
fmt.Fprint(os.Stderr, err)
log.Fatal(err)
}
}
for _, v := range bbcoords {
fmt.Fprintln(os.Stderr, "BB transmit!", v.NVecs())
if err := chemjson.SendMolecule(nil, []*v3.Matrix{v}, nil, nil, os.Stdout); err2 != nil {
fmt.Fprint(os.Stderr, err)
log.Fatal(err)
}
}
}