func main() {
var prmtopFilename, rstFilename, outFilename string
var stride int
var savePreprocessed bool
flag.StringVar(&prmtopFilename, "p", "prmtop", "Prmtop filename (required)")
flag.StringVar(&rstFilename, "c", "", "Inpcrd/rst filename")
flag.IntVar(&stride, "s", 1, "Frame stride; 1 = don't skip any")
flag.StringVar(&outFilename, "o", "energies.bin", "Energy decomposition output filename")
flag.BoolVar(&savePreprocessed, "e", false, "Save prmtop preprocessed output (use with -c)")
flag.Parse()
trjFilenames := flag.Args()
mol := amber.LoadSystem(prmtopFilename)
if mol == nil {
return
}
fmt.Println("Number of atoms:", mol.NumAtoms())
fmt.Println("Number of residues:", mol.NumResidues())
hasBox := false
fmt.Print("Periodic box in prmtop: ")
if mol.GetInt("POINTERS", amber.IFBOX) > 0 {
hasBox = true
fmt.Println("Yes")
} else {
fmt.Println("No")
}
// Set up nonbonded parameters. We load them here so we don't have to keep
// doing it later
var params NonbondedParamsCache
params.Ntypes = mol.GetInt("POINTERS", amber.NTYPES)
params.NBIndices = amber.VectorAsIntArray(mol.Blocks["NONBONDED_PARM_INDEX"]) // ICO
params.AtomTypeIndices = amber.VectorAsIntArray(mol.Blocks["ATOM_TYPE_INDEX"]) // IAC
params.LJ12 = amber.VectorAsFloat32Array(mol.Blocks["LENNARD_JONES_ACOEF"]) // CN1
params.LJ6 = amber.VectorAsFloat32Array(mol.Blocks["LENNARD_JONES_BCOEF"]) // CN2
params.Charges = amber.VectorAsFloat32Array(mol.Blocks["CHARGE"])
// If we were given a single snapshot, just do that one
if rstFilename != "" || savePreprocessed {
var request EnergyCalcRequest
if rstFilename != "" {
fmt.Printf("Calculating energies for single snapshot %s.\n", rstFilename)
mol.LoadRst(rstFilename)
request.Coords = mol.Coords[0]
}
request.NBParams = params
request.Molecule = mol
// Lookup table for bond types so we don't calculate electrostatics
// and such between bonded atoms
request.BondType = makeBondTypeTable(mol)
request.ResidueMap = makeResidueMap(mol)
request.Decomp = make([]float64, mol.NumResidues()*mol.NumResidues())
// Dump the preprocessed info to a file so a C version of this program can easily load and parse it
if savePreprocessed {
outFile, _ := os.OpenFile("solute.top.tom", os.O_WRONLY|os.O_CREATE|os.O_TRUNC, 0644)
defer outFile.Close()
WriteInt32(outFile, mol.NumAtoms())
WriteInt32(outFile, mol.NumResidues())
WriteInt32(outFile, params.Ntypes)
WriteInt32Array(outFile, params.NBIndices)
WriteInt32Array(outFile, params.AtomTypeIndices)
WriteFloat32Array(outFile, params.LJ12)
WriteFloat32Array(outFile, params.LJ6)
WriteFloat32Array(outFile, params.Charges)
WriteInt8Array(outFile, request.BondType)
WriteInt32Array(outFile, request.ResidueMap)
if hasBox {
WriteInt32(outFile, 1)
} else {
WriteInt32(outFile, 0)
}
fmt.Println("Wrote preprocessed prmtop data. Done!")
os.Exit(0)
}
fmt.Println("Electrostatic energy:", Electro(&request), "kcal/mol")
fmt.Println("van der Waals energy:", LennardJones(&request), "kcal/mol")
fmt.Println(amber.Status())
amber.DumpFloat64MatrixAsText(request.Decomp, mol.NumResidues(), "decomp.txt")
fmt.Println("Saved decomposition matrix to decomp.txt")
} else if len(trjFilenames) > 0 {
fmt.Println("Frame stride:", stride)
// Lookup table for bond types so we don't calculate nonbonded energies
// between bonded atoms
bondType := makeBondTypeTable(mol)
residueMap := makeResidueMap(mol)
ch := make(chan int)
decompCh := make(chan []float64, 32)
// This goroutine will be fed the decomposition matrices made by the energy functions
fmt.Println("Writing residue decomposition matrices to", outFilename)
go decompProcessor(outFilename, mol.NumResidues(), decompCh, ch)
numAtoms := mol.NumAtoms()
fileId := 0
trj, err := openTrj(trjFilenames[fileId])
if err != nil {
return
}
numKids := 0
frame := 0
strideCountdown := stride
for {
// If there was an error reading the next frame, move on to the next trajectory file
coords, err := amber.GetNextFrameFromTrajectory(trj, numAtoms, hasBox)
if err != nil {
fileId++
if fileId >= len(trjFilenames) {
break
}
trj, err = openTrj(trjFilenames[fileId])
if err != nil {
fmt.Println("Error opening", trjFilenames[fileId])
break
}
coords, err = amber.GetNextFrameFromTrajectory(trj, numAtoms, hasBox)
if err != nil {
fmt.Printf("Trajectory file %s doesn't have even one valid frame\n", trjFilenames[fileId])
break
}
}
frame++
// Only actually process the frames indicated by stride
strideCountdown--
if strideCountdown == 0 {
strideCountdown = stride
go calcSingleTrjFrame(mol, params, coords, frame, bondType, residueMap, decompCh, ch)
numKids++
}
}
if false {
for i := 0; i < numKids; i++ {
<-ch
}
}
decompCh <- nil
<-ch // Wait for decompProcessor to finish
}
}
func main() {
var prmtopFilename, rstFilename, outFilename string
var stride int
var savePreprocessed bool
flag.StringVar(&prmtopFilename, "p", "prmtop", "Prmtop filename (required)")
flag.StringVar(&rstFilename, "c", "", "Inpcrd/rst filename")
flag.IntVar(&stride, "s", 1, "Frame stride; 1 = don't skip any")
flag.StringVar(&outFilename, "o", "energies.bin", "Energy decomposition output filename")
flag.BoolVar(&savePreprocessed, "e", false, "Save prmtop preprocessed output (use with -c)")
flag.Parse()
mol := amber.LoadSystem(prmtopFilename)
if mol == nil {
return
}
fmt.Println("Number of atoms:", mol.NumAtoms())
fmt.Println("Number of residues:", mol.NumResidues())
hasBox := false
fmt.Print("Periodic box in prmtop: ")
if mol.GetInt("POINTERS", amber.IFBOX) > 0 {
hasBox = true
fmt.Println("Yes")
} else {
fmt.Println("No")
}
// Set up nonbonded parameters. We load them here so we don't have to keep
// doing it later
var params NonbondedParamsCache
params.Ntypes = mol.GetInt("POINTERS", amber.NTYPES)
params.NBIndices = amber.VectorAsIntArray(mol.Blocks["NONBONDED_PARM_INDEX"]) // ICO
params.AtomTypeIndices = amber.VectorAsIntArray(mol.Blocks["ATOM_TYPE_INDEX"]) // IAC
params.LJ12 = amber.VectorAsFloat32Array(mol.Blocks["LENNARD_JONES_ACOEF"]) // CN1
params.LJ6 = amber.VectorAsFloat32Array(mol.Blocks["LENNARD_JONES_BCOEF"]) // CN2
params.Charges = amber.VectorAsFloat32Array(mol.Blocks["CHARGE"])
var request EnergyCalcRequest
request.NBParams = params
request.Molecule = mol
// Lookup table for bond types so we don't calculate electrostatics
// and such between bonded atoms
request.BondType = makeBondTypeTable(mol)
request.ResidueMap = makeResidueMap(mol)
request.Decomp = make([]float64, mol.NumResidues()*mol.NumResidues())
// Dump the preprocessed info to a file so a C version of this program can easily load and parse it
outFile, _ := os.OpenFile("solute.top.tom", os.O_WRONLY|os.O_CREATE|os.O_TRUNC, 0644)
defer outFile.Close()
WriteInt32(outFile, mol.NumAtoms())
WriteInt32(outFile, mol.NumResidues())
WriteInt32(outFile, params.Ntypes)
WriteInt32Array(outFile, params.NBIndices)
WriteInt32Array(outFile, params.AtomTypeIndices)
WriteFloat32Array(outFile, params.LJ12)
WriteFloat32Array(outFile, params.LJ6)
WriteFloat32Array(outFile, params.Charges)
WriteInt8Array(outFile, request.BondType)
WriteInt32Array(outFile, request.ResidueMap)
if hasBox {
WriteInt32(outFile, 1)
} else {
WriteInt32(outFile, 0)
}
fmt.Println("Wrote preprocessed prmtop data. Done!")
os.Exit(0)
}