//This is a very inefficient way to get the residue IDs. I am kind of hoping that
//the QM optimization will allways take longer than this function.
func GetResidueIds(mol chem.Atomer) ([]int, []string) {
residues := make([]int, 0, int(mol.Len()/10))
chains := make([]string, 0, int(mol.Len()/10))
for i := 0; i < mol.Len(); i++ {
curr := mol.Atom(i)
if !scu.IsInInt(curr.MolID, residues) {
residues = append(residues, curr.MolID)
chains = append(chains, curr.Chain)
}
}
return residues, chains
}
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, errj := chemjson.DecodeOptions(stdin)
if errj != nil {
fmt.Fprint(os.Stderr, errj.Marshal())
log.Fatal(errj)
}
mols := make([]*chem.Topology, 0, len(options.SelNames))
coordset := make([]*v3.Matrix, 0, len(options.SelNames))
for k, _ := range options.SelNames {
mol, coords, errj := chemjson.DecodeMolecule(stdin, options.AtomsPerSel[k], 1)
if errj != nil {
fmt.Fprint(os.Stderr, errj.Marshal())
log.Fatal(errj)
}
mols = append(mols, mol)
coordset = append(coordset, coords[0])
}
//The program itself
ramadata := make([][][]float64, 0, 0)
var HLS [][]int
var HL []int
for k, mol := range mols {
fmt.Println("len in go", mol.Len(), coordset[k].NVecs()) //////
HL = []int{}
oldres1 := mol.Atom(0).MolID + 1 //the residues should be contiguous!!!
chem.FixNumbering(mol)
ramalist, errj := chemplot.RamaList(mol, "ABC DEFGHI", []int{0, -1}) ////
if errj != nil {
log.Fatal(errj)
}
ramalist2, index := chemplot.RamaResidueFilter(ramalist, options.StringOptions[0], false)
rama, errj := chemplot.RamaCalc(coordset[k], ramalist2)
if errj != nil {
log.Fatal(errj)
}
ramadata = append(ramadata, rama)
var i int
if options.IntOptions != nil && options.IntOptions[0] != nil {
for i = 0; i < len(ramalist); i++ {
fmt.Println(i, i+oldres1, index[i], options.IntOptions[0])
if index[i] != -1 && scu.IsInInt(i+oldres1, options.IntOptions[0]) {
HL = append(HL, index[i])
fmt.Println("NAME:", ramalist[index[i]].Molname)
}
}
HLS = append(HLS, HL)
}
}
name := append(options.SelNames, "Rama")
var err error
if len(ramadata) == 1 {
err = chemplot.RamaPlot(ramadata[0], HL, "Ramachandran plot", strings.Join(name, "_"))
} else {
err = chemplot.RamaPlotParts(ramadata, HLS, "Ramachandran plot", strings.Join(name, "_"))
}
if err != nil {
fmt.Fprint(os.Stderr, chemjson.NewError("process", "main", err).Marshal())
}
}
