public static Vector[] GetRotate(Vector[] coords, Vector cent, int[] block)
{
throw new Exception("this implementation is wrong. Use the following algorithm to get rotation modes for RTB.");
double[] io_mass = null;
if (HDebug.IsDebuggerAttached)
{
using (var temp = new HTempDirectory(@"K:\temp\", null))
{
temp.EnterTemp();
HFile.WriteAllText("rtbProjection.m", @"
function [P, xyz] = rtbProjection(xyz, mass)
% the approach is to find the inertia. compute the principal axes. and then use them to determine directly translation or rotation.
n = size(xyz, 1); % n: the number of atoms
if nargin == 1
mass = ones(n,1);
end
M = sum(mass);
% find the mass center.
m3 = repmat(mass, 1, 3);
center = sum (xyz.*m3)/M;
xyz = xyz - center(ones(n, 1), :);
mwX = sqrt (m3).*xyz;
inertia = sum(sum(mwX.^2))*eye(3) - mwX'*mwX;
[V,D] = eig(inertia);
tV = V'; % tV: transpose of V. Columns of V are principal axes.
for i=1:3
trans{i} = tV(ones(n,1)*i, :); % the 3 translations are along principal axes
end
P = zeros(n*3, 6);
for i=1:3
rotate{i} = cross(trans{i}, xyz);
temp = mat2vec(trans{i});
P(:,i) = temp/norm(temp);
temp = mat2vec(rotate{i});
P(:,i+3) = temp/norm(temp);
end
m3 = mat2vec(sqrt(m3));
P = repmat (m3(:),1,size(P,2)).*P;
% now normalize columns of P
P = P*diag(1./normMat(P,1));
function vec = mat2vec(mat)
% convert a matrix to a vector, extracting data *row-wise*.
vec = reshape(mat',1,prod(size(mat)));
");
Matlab.Execute("cd \'" + temp.dirinfo.FullName + "\'");
Matlab.PutMatrix("xyz", coords.ToMatrix(false));
Matlab.PutVector("mass", io_mass);
temp.QuitTemp();
}
}
HDebug.Assert(coords.Length == io_mass.Length);
Vector mwcenter = new double[3];
for (int i = 0; i < coords.Length; i++)
{
mwcenter += (coords[i] * io_mass[i]);
}
mwcenter /= io_mass.Sum();
Vector[] mwcoords = new Vector[coords.Length];
for (int i = 0; i < coords.Length; i++)
{
mwcoords[i] = (coords[i] - mwcenter) * io_mass[i];
}
Matrix mwPCA = new double[3, 3];
for (int i = 0; i < coords.Length; i++)
{
mwPCA += LinAlg.VVt(mwcoords[i], mwcoords[i]);
}
var V_D = LinAlg.Eig(mwPCA.ToArray());
var V = V_D.Item1;
Vector[] rotvecs = new Vector[3];
for (int i = 0; i < 3; i++)
{
Vector rotaxis = new double[] { V[0, i], V[1, i], V[2, i] };
Vector[] rotveci = new Vector[coords.Length];
for (int j = 0; j < coords.Length; j++)
{
rotveci[j] = LinAlg.CrossProd(rotaxis, mwcoords[i]);
}
rotvecs[i] = rotveci.ToVector().UnitVector();
}
if (HDebug.IsDebuggerAttached)
{
double dot01 = LinAlg.VtV(rotvecs[0], rotvecs[1]);
double dot02 = LinAlg.VtV(rotvecs[0], rotvecs[2]);
double dot12 = LinAlg.VtV(rotvecs[1], rotvecs[2]);
HDebug.Assert(Math.Abs(dot01) < 0.0000001);
HDebug.Assert(Math.Abs(dot02) < 0.0000001);
HDebug.Assert(Math.Abs(dot12) < 0.0000001);
}
return(rotvecs);
////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
/// from song: rtbProjection.m
////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
/// function [P, xyz] = rtbProjection(xyz, mass)
/// % the approach is to find the inertia. compute the principal axes. and then use them to determine directly translation or rotation.
///
/// n = size(xyz, 1); % n: the number of atoms
/// if nargin == 1
/// mass = ones(n,1);
/// end
///
/// M = sum(mass);
/// % find the mass center.
/// m3 = repmat(mass, 1, 3);
/// center = sum (xyz.*m3)/M;
/// xyz = xyz - center(ones(n, 1), :);
///
/// mwX = sqrt (m3).*xyz;
/// inertia = sum(sum(mwX.^2))*eye(3) - mwX'*mwX;
/// [V,D] = eig(inertia);
/// tV = V'; % tV: transpose of V. Columns of V are principal axes.
/// for i=1:3
/// trans{i} = tV(ones(n,1)*i, :); % the 3 translations are along principal axes
/// end
/// P = zeros(n*3, 6);
/// for i=1:3
/// rotate{i} = cross(trans{i}, xyz);
/// temp = mat2vec(trans{i});
/// P(:,i) = temp/norm(temp);
/// temp = mat2vec(rotate{i});
/// P(:,i+3) = temp/norm(temp);
/// end
/// m3 = mat2vec(sqrt(m3));
/// P = repmat (m3(:),1,size(P,2)).*P;
/// % now normalize columns of P
/// P = P*diag(1./normMat(P,1));
///
/// function vec = mat2vec(mat)
/// % convert a matrix to a vector, extracting data *row-wise*.
/// vec = reshape(mat',1,prod(size(mat)));
////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
/// rotx[t_ ] := { { 1,0,0,0},{ 0,Cos[t],-Sin[t],0},{ 0,Sin[t],Cos[t],0},{ 0,0,0,1} };
/// roty[t_ ] := { { Cos[t],0,Sin[t],0},{ 0,1,0,0},{ -Sin[t],0,Cos[t],0},{ 0,0,0,1} };
/// rotz[t_ ] := { { Cos[t],-Sin[t],0,0},{ Sin[t],Cos[t],0,0},{ 0,0,1,0},{ 0,0,0,1} };
/// tran[tx_, ty_, tz_] := { { 1,0,0,tx},{ 0,1,0,ty},{ 0,0,1,tz},{ 0,0,0,1} };
/// pt = Transpose[{{px,py,pz,1}}];
///
/// point : (px,py,pz)
/// center : (cx,cy,cz)
/// angle : t
///
/// tran[cx, cy, cz].rotx[t].tran[-cx, -cy, -cz].pt = {{px}, {cy - cy Cos[t] + py Cos[t] + cz Sin[t] - pz Sin[t]}, {cz - cz Cos[t] + pz Cos[t] - cy Sin[t] + py Sin[t]}, {1}}
/// tran[cx, cy, cz].roty[t].tran[-cx, -cy, -cz].pt = {{cx - cx Cos[t] + px Cos[t] - cz Sin[t] + pz Sin[t]}, {py}, {cz - cz Cos[t] + pz Cos[t] + cx Sin[t] - px Sin[t]}, {1}}
/// tran[cx, cy, cz].rotz[t].tran[-cx, -cy, -cz].pt = {{cx - cx Cos[t] + px Cos[t] + cy Sin[t] - py Sin[t]}, {cy - cy Cos[t] + py Cos[t] - cx Sin[t] + px Sin[t]}, {pz}, {1}}
///
/// D[tran[cx, cy, cz].rotx[t].tran[-cx, -cy, -cz].pt, t] = {{0}, {cz Cos[t] - pz Cos[t] + cy Sin[t] - py Sin[t]}, {-cy Cos[t] + py Cos[t] + cz Sin[t] - pz Sin[t]}, {0}}
/// D[tran[cx, cy, cz].roty[t].tran[-cx, -cy, -cz].pt, t] = {{-cz Cos[t] + pz Cos[t] + cx Sin[t] - px Sin[t]}, {0}, {cx Cos[t] - px Cos[t] + cz Sin[t] - pz Sin[t]}, {0}}
/// D[tran[cx, cy, cz].rotz[t].tran[-cx, -cy, -cz].pt, t] = {{cy Cos[t] - py Cos[t] + cx Sin[t] - px Sin[t]}, {-cx Cos[t] + px Cos[t] + cy Sin[t] - py Sin[t]}, {0}, {0}}
///
/// D[tran[cx,cy,cz].rotx[a].tran[-cx,-cy,-cz].pt,a]/.a->0 = {{0}, {cz - pz}, {-cy + py}, {0}}
/// D[tran[cx,cy,cz].roty[a].tran[-cx,-cy,-cz].pt,a]/.a->0 = {{-cz + pz}, {0}, {cx - px}, {0}}
/// D[tran[cx,cy,cz].rotz[a].tran[-cx,-cy,-cz].pt,a]/.a->0 = {{cy - py}, {-cx + px}, {0}, {0}}
/// rotx of atom (px,py,pz) with center (cx,cy,cz): {{0}, {cz - pz}, {-cy + py}, {0}} = { 0, cz - pz, -cy + py, 0 } => { 0, cz - pz, -cy + py }
/// rotx of atom (px,py,pz) with center (cx,cy,cz): {{-cz + pz}, {0}, {cx - px}, {0}} = { -cz + pz, 0, cx - px, 0 } => { -cz + pz, 0, cx - px }
/// rotx of atom (px,py,pz) with center (cx,cy,cz): {{cy - py}, {-cx + px}, {0}, {0}} = { cy - py, -cx + px, 0, 0 } => { cy - py, -cx + px, 0 }
///
int leng = coords.Length;
Vector[] rots;
{
Vector[] rotbyx = new Vector[leng];
Vector[] rotbyy = new Vector[leng];
Vector[] rotbyz = new Vector[leng];
double cx = cent[0];
double cy = cent[1];
double cz = cent[2];
for (int i = 0; i < leng; i++)
{
double px = coords[i][0];
double py = coords[i][1];
double pz = coords[i][2];
rotbyx[i] = new double[] { 0, cz - pz, -cy + py };
rotbyy[i] = new double[] { -cz + pz, 0, cx - px };
rotbyz[i] = new double[] { cy - py, -cx + px, 0 };
}
rots = new Vector[]
{
rotbyx.ToVector().UnitVector(),
rotbyy.ToVector().UnitVector(),
rotbyz.ToVector().UnitVector(),
};
}
if (HDebug.IsDebuggerAttached)
{
Vector[] rotbyx = new Vector[leng];
Vector[] rotbyy = new Vector[leng];
Vector[] rotbyz = new Vector[leng];
Vector zeros = new double[3];
for (int i = 0; i < leng; i++)
{
rotbyx[i] = rotbyy[i] = rotbyz[i] = zeros;
}
Vector rx = new double[3] {
1, 0, 0
};
Vector ry = new double[3] {
0, 1, 0
};
Vector rz = new double[3] {
0, 0, 1
};
Func <Vector, Vector, Vector> GetTangent = delegate(Vector pt, Vector axisdirect)
{
/// Magnitude of rotation tangent is proportional to the distance from the point to the axis.
/// Ex) when a point is in x-axis (r,0), rotating along z-axis by θ is: (r*sin(θ), 0)
///
/// |
/// | ^ sin(θ)
/// | |
/// -+-----------------r----------
///
Vector rot1 = cent;
Vector rot2 = cent + axisdirect;
double dist = Geometry.DistancePointLine(pt, rot1, rot2);
Vector tan = Geometry.RotateTangentUnit(pt, rot1, rot2) * dist;
return(tan);
};
IEnumerable <int> enumblock = block;
if (block != null)
{
enumblock = block;
}
else
{
enumblock = HEnum.HEnumCount(leng);
}
foreach (int i in enumblock)
{
Vector pt = coords[i];
rotbyx[i] = GetTangent(pt, rx);
rotbyy[i] = GetTangent(pt, ry);
rotbyz[i] = GetTangent(pt, rz);
}
Vector[] trots = new Vector[3]
{
rotbyx.ToVector().UnitVector(),
rotbyy.ToVector().UnitVector(),
rotbyz.ToVector().UnitVector(),
};
double test0 = LinAlg.VtV(rots[0], trots[0]);
double test1 = LinAlg.VtV(rots[1], trots[1]);
double test2 = LinAlg.VtV(rots[2], trots[2]);
HDebug.Assert(Math.Abs(test0 - 1) < 0.00000001);
HDebug.Assert(Math.Abs(test1 - 1) < 0.00000001);
HDebug.Assert(Math.Abs(test2 - 1) < 0.00000001);
}
return(rots);
}
/// https://www.charmmtutorial.org/index.php/Full_example
public static SPsfCrd Solvate
(IEnumerable <string> toplines
, IEnumerable <string> parlines
, IEnumerable <string> psflines_prot
, IEnumerable <string> crdlines_prot
, IEnumerable <string> crdlines_water
)
{
string tempbase = @"C:\temp\";
SPsfCrd psfcrd;
using (var temp = new HTempDirectory(tempbase, null))
{
temp.EnterTemp();
string topname = "top.rtf"; HFile.WriteAllLines(topname, toplines);
string parname = "par.prm"; HFile.WriteAllLines(parname, parlines);
string psfname_prot = "prot.psf"; HFile.WriteAllLines(psfname_prot, psflines_prot);
string crdname_prot = "prot.crd"; HFile.WriteAllLines(crdname_prot, crdlines_prot);
string crdname_water = "water.crd"; HFile.WriteAllLines(crdname_water, crdlines_water);
string psfname_protwater = "protwater.psf";
string crdname_protwater = "protwater.crd";
string conf_inp = @"* Run Segment Through CHARMM
*
! read topology and parameter files
read rtf card name $$topname$$
read para card name $$parname$$
! read the psf and coordinate file
read psf card name $$psfname_prot$$
read coor card name $$crdname_prot$$
! Read in water sequence
read sequence tip3 46656
! Generate new segment for the water
generate bwat noangle nodihedral
! Read the water PDB coordinates and append them to the protein
read coor card append name $$crdname_water$$
! Delete waters which overlap with protein
delete atom sort -
select .byres. (segid bwat .AND. type oh2 .and. -
((.not. (segid bwat .OR. hydrogen)) .around. 2.5)) end
! set headstr = rhdo with a crystal dimension of @greatervalue
set headstr = test xxx
! we want to do a quick-and-dirty minimization to remove bad contacts. Therefore, we should
! set up shake and the non-bond parameters again.
shake bonh param sele all end
nbond inbfrq -1 elec fswitch vdw vswitch cutnb 16. ctofnb 12. ctonnb 10.
mini sd nstep 100 nprint 1 tolgrd 100.0
! use Expanded I/O format
ioform extended
! since we've changed the structure by adding waters, we need to write out a new PSF
write psf card name $$psfname_protwater$$
* new_1cbn-18126-1-solv.psf
* solvation: @headstr
*
write coor card name $$crdname_protwater$$
* new_1cbn-18126-1-solv.crd
* solvation: @headstr
*
stop
".Replace("$$topname$$", topname)
.Replace("$$parname$$", parname)
.Replace("$$psfname_prot$$", psfname_prot)
.Replace("$$crdname_prot$$", crdname_prot)
.Replace("$$crdname_water$$", crdname_water)
.Replace("$$psfname_protwater$$", psfname_protwater)
.Replace("$$crdname_protwater$$", crdname_protwater)
;
HFile.WriteAllText("conf.inp", conf_inp);
System.Console.WriteLine("Run the following command at " + temp + " :");
System.Console.WriteLine(" $ charmm < conf.inp");
System.Console.WriteLine(" or $ mpd&");
System.Console.WriteLine(" $ mpirun -n 38 charmm_M < conf.inp");
System.Console.WriteLine("Then, copy " + psfname_protwater + " and " + crdname_protwater + " to " + temp);
while (true)
{
bool next = HConsole.ReadValue <bool>("Ready for next? ", false, null, false, true);
if (next)
{
if (HFile.ExistsAll(psfname_protwater, crdname_protwater))
{
string[] psflines_protwater = HFile.ReadAllLines(psfname_protwater);
string[] crdlines_protwater = HFile.ReadAllLines(crdname_protwater);
psfcrd = new SPsfCrd
{
psflines = psflines_protwater,
crdlines = crdlines_protwater,
};
break;
}
System.Console.WriteLine("DO, copy " + psfname_protwater + " and " + crdname_protwater + " to " + temp);
}
}
temp.QuitTemp();
}
return(psfcrd);
}
/// https://www.charmmtutorial.org/index.php/Full_example
public static string[] Hessian
(IEnumerable <string> toplines
, IEnumerable <string> parlines
, IEnumerable <string> psflines
, IEnumerable <string> crdlines
)
{
string tempbase = @"C:\temp\";
string[] mincrdlines;
using (var temp = new HTempDirectory(tempbase, null))
{
temp.EnterTemp();
string topname = "top.rtf"; HFile.WriteAllLines(topname, toplines);
string parname = "par.prm"; HFile.WriteAllLines(parname, parlines);
string psfname = "target.psf"; HFile.WriteAllLines(psfname, psflines);
string crdname = "target.crd"; HFile.WriteAllLines(crdname, crdlines);
string mincrdname = "target-minimized.crd";
string conf_inp = @"* Minimize PDB
* Minimize PDB
*
! read topology and parameter file
read rtf card name top.rtf
read param card name par.prm
! read the psf and coordinate file
read psf card name target.psf
read coor card name target.crd
! set up shake
shake bonh param sele all end
! set up electrostatics, since we're not using PME, set up switching
! electrostatics
nbond inbfrq -1 elec fswitch vdw vswitch cutnb 16. ctofnb 12. ctonnb 10.
energy
coor copy comp
! mini sd nstep 100
! mini abnr nstep 1000 nprint 10000 tolg 0.0000
! ! mini abnr nstep 1000 nprint 100 tolg 0.01
! ! mini abnr nstep 10000000 nprint 100 tolg 0.00
! ! mini abnr nstep 1000000 nprint 100 tolg 10.00 ! target-min-step1-tolg-10_00.crd
! ! mini abnr nstep 1000000 nprint 100 tolg 1.00 ! target-min-step2-tolg-1_00.crd
! ! mini abnr nstep 1000000 nprint 100 tolg 0.10
! ! mini sd nstep 10000 ! target-min-step3-sd10000.crd
! ! mini abnr nstep 1000000 nprint 100 tolg 0.01 ! target-min-step4-tolg-0_01.crd
! ! mini abnr nstep 10000 nprint 100 tolg 0.0001 ! target-min-step5-tolg-0_0001.crd
! ! mini abnr nstep 10000 nprint 100 tolg 0.000001 ! target-min-step6-tolg-0_000001.crd
! ! mini abnr nstep 10000 nprint 100 tolg 0.000000 ! target-min-step7-tolg-0_000000.crd
!
!
! coor rms
!
! ioform extended
!
! write coor card name target-minimized.crd
! * Initial minimization, no PME.
! *
! VIBRAN NMOD 20 ATOM FSWITCH rdie eps 4.0 VDW VSHIFT cutnb 13.0 ctofnb 12.0 CTONNB 8.0
!
! DIMB ITERations 500 TOLErance 0.04 PARDim 200 IUNMode 21 DWIN
!
! WRITe SECOnd-derivatives card
! BOMLEV -2
! VIBRAN
! DIAG ENTRopy
! VIBRan NMODes 500
! DIAG
! print norm vector dipole
!mini abnr nstep 100 nprint 100 tolg 0.000000 ! target-min-step7-tolg-0_000000.crd
BOMLEV -2
open unit 1 write form name " + " \"second.dat\" " + @"
REDUce CMPAct
vibran
!diag
write second card unit 1
close unit 1
!calc natom3 ?NATOM *3
!vibran nmode @natom3
!diag
!print norm
!bomlev - 2
!VIBRan NMOD 300
!DIAGonalize
!https://www.charmm.org/charmm/documentation/by-version/c42b1/params/doc/vibran/
stop
";
conf_inp = conf_inp.Replace("$$topname$$", topname)
.Replace("$$parname$$", parname)
.Replace("$$psfname$$", psfname)
.Replace("$$crdname$$", crdname)
.Replace("$$mincrdname$$", mincrdname)
;
HFile.WriteAllText("conf.inp", conf_inp);
System.Console.WriteLine("Run the following command at " + temp + " :");
System.Console.WriteLine(" $ charmm < conf.inp");
System.Console.WriteLine(" or $ mpd&");
System.Console.WriteLine(" $ mpirun -n 38 charmm_M < conf.inp");
System.Console.WriteLine("Then, copy second.dat to " + temp);
while (true)
{
bool next = HConsole.ReadValue <bool>("Ready for next? ", false, null, false, true);
if (next)
{
if (HFile.ExistsAll(mincrdname))
{
mincrdlines = HFile.ReadAllLines(mincrdname);
/// second.dat has the following format
///
/// num-atoms
/// pot-energy
/// atom1-xforce atom1-yforce atom1-zforce
/// atom2-xforce atom2-yforce atom2-zforce
/// ...
/// atomn-xforce atomn-yforce atomn-zforce
/// upper- or lower-diag elem 1
/// upper- or lower-diag elem 2
/// ....
/// upper- or lower-diag elem 3n*3n/2
/// atom1-xcoord atom1-ycoord atom1-zcoord
/// atom2-xcoord atom2-ycoord atom2-zcoord
/// ...
/// atomn-xcoord atomn-ycoord atomn-zcoord
///
break;
}
System.Console.WriteLine("DO, copy target.psf and target.crd to " + temp);
}
}
temp.QuitTemp();
}
return(mincrdlines);
}
public static ONewton Newton(string tinkerpath
, Tinker.Xyz xyz
, Tinker.Xyz.Atom.Format xyz_atoms_format
, Tinker.Prm prm
, string tempbase
, string copytemp // = null
, string param
//, string precondition // = "A" // Precondition via Auto/None/Diag/Block/SSOR/ICCG [A] : A
//, double gradCriterion // = 0.01 // Enter RMS Gradient per Atom Criterion [0.01] : 0.001
, IList <Tinker.Xyz.Atom> atomsToFix // = null
, bool pause // = false
, params string[] keys
)
{
if (HDebug.IsDebuggerAttached && atomsToFix != null)
{
Dictionary <int, Tinker.Xyz.Atom> xyzatoms = xyz.atoms.ToIdDictionary();
foreach (var atom in atomsToFix)
{
HDebug.Assert(object.ReferenceEquals(atom, xyzatoms[atom.Id]));
}
}
Tinker.Xyz minxyz;
string[] minlog;
using (var temp = new HTempDirectory(tempbase, copytemp))
{
temp.EnterTemp();
if (tinkerpath == null)
{
string resbase = "HTLib2.Bioinfo.HTLib2.Bioinfo.External.Tinker.Resources.tinker_6_2_06.";
HResource.CopyResourceTo <Tinker>(resbase + "newton.exe", "newton.exe");
tinkerpath = "newton.exe";
}
xyz.ToFile("prot.xyz", false);
prm.ToFile("prot.prm");
List <string> keylines = new List <string>(keys);
if (atomsToFix != null)
{
foreach (var atom in atomsToFix)
{
Vector coord = atom.Coord;
double force_constant = 10000; // force constant in kcal/Å2 for the harmonic restraint potential
string keyline = string.Format("RESTRAIN-POSITION {0} {1} {2} {3} {4}", atom.Id, coord[0], coord[1], coord[2], force_constant);
keylines.Add(keyline);
}
}
HFile.WriteAllLines("prot.key", keylines);
// Precondition via Auto/None/Diag/Block/SSOR/ICCG [A] : A
// Enter RMS Gradient per Atom Criterion [0.01] : 0.001
//bool pause = false;
string command = tinkerpath;
command += string.Format(" prot.xyz prot.prm");
command += string.Format(" -k prot.key");
command += string.Format(" {0}", param);
HProcess.StartAsBatchInConsole("newton.bat", pause
, "time /t >> prot.log"
, command //+" >> prot.log"
, "time /t >> prot.log"
);
HDebug.Assert(HFile.Exists("prot.xyz_2"));
HDebug.Assert(HFile.Exists("prot.xyz_3") == false);
minxyz = Tinker.Xyz.FromFile("prot.xyz_2", false, xyz_atoms_format);
minlog = HFile.ReadAllLines("prot.log");
temp.QuitTemp();
}
return(new ONewton
{
minxyz = minxyz,
minlog = minlog
});
}
/// https://www.charmmtutorial.org/index.php/Full_example
public static string[] MinimizeCrd
(IEnumerable <string> toplines
, IEnumerable <string> parlines
, IEnumerable <string> psflines
, IEnumerable <string> crdlines
, string conf_inp_mini
)
{
string tempbase = @"C:\temp\";
if (conf_inp_mini == null)
{
conf_inp_mini = @"
mini sd nstep 100
mini abnr nstep 1000 nprint 10000 tolg 0.0001
! mini abnr nstep 1000 nprint 100 tolg 0.01
! mini abnr nstep 10000000 nprint 100 tolg 0.00
! mini abnr nstep 1000000 nprint 100 tolg 10.00 ! target-min-step1-tolg-10_00.crd
! mini abnr nstep 1000000 nprint 100 tolg 1.00 ! target-min-step2-tolg-1_00.crd
! mini abnr nstep 1000000 nprint 100 tolg 0.10
! mini sd nstep 10000 ! target-min-step3-sd10000.crd
! mini abnr nstep 1000000 nprint 100 tolg 0.01 ! target-min-step4-tolg-0_01.crd
! mini abnr nstep 10000 nprint 100 tolg 0.0001 ! target-min-step5-tolg-0_0001.crd
! mini abnr nstep 10000 nprint 100 tolg 0.000001 ! target-min-step6-tolg-0_000001.crd
! mini abnr nstep 10000 nprint 100 tolg 0.000000 ! target-min-step7-tolg-0_000000.crd
";
}
string[] mincrdlines;
using (var temp = new HTempDirectory(tempbase, null))
{
temp.EnterTemp();
string topname = "top.rtf"; HFile.WriteAllLines(topname, toplines);
string parname = "par.prm"; HFile.WriteAllLines(parname, parlines);
string psfname = "target.psf"; HFile.WriteAllLines(psfname, psflines);
string crdname = "target.crd"; HFile.WriteAllLines(crdname, crdlines);
string mincrdname = "target-minimized.crd";
string conf_inp = @"* Minimize PDB
*
! read topology and parameter file
read rtf card name $$topname$$
read param card name $$parname$$
! read the psf and coordinate file
read psf card name $$psfname$$
read coor card name $$crdname$$
! set up shake
shake bonh param sele all end
! set up electrostatics, since we're not using PME, set up switching
! electrostatics
nbond inbfrq -1 elec fswitch vdw vswitch cutnb 16. ctofnb 12. ctonnb 10.
energy
coor copy comp
" + conf_inp_mini + @"
coor rms
ioform extended
write coor card name $$mincrdname$$
* Initial minimization, no PME.
*
stop
";
conf_inp = conf_inp.Replace("$$topname$$", topname)
.Replace("$$parname$$", parname)
.Replace("$$psfname$$", psfname)
.Replace("$$crdname$$", crdname)
.Replace("$$mincrdname$$", mincrdname)
;
HFile.WriteAllText("conf.inp", conf_inp);
System.Console.WriteLine("Run the following command at " + temp + " :");
System.Console.WriteLine(" $ charmm < conf.inp");
System.Console.WriteLine(" or $ mpd&");
System.Console.WriteLine(" $ mpirun -n 38 charmm_M < conf.inp");
System.Console.WriteLine("Then, copy target-minimized.crd to " + temp);
while (true)
{
bool next = HConsole.ReadValue <bool>("Ready for next? ", false, null, false, true);
if (next)
{
if (HFile.ExistsAll(mincrdname))
{
mincrdlines = HFile.ReadAllLines(mincrdname);
break;
}
System.Console.WriteLine("DO, copy target.psf and target.crd to " + temp);
}
}
temp.QuitTemp();
}
return(mincrdlines);
}
public static OMinimize Minimize(string minimizepath
, Tinker.Xyz xyz
, Tinker.Xyz.Atom.Format xyz_atoms_format
, Tinker.Prm prm
, string tempbase
, string copytemp // = null
, string param
, IList <Tinker.Xyz.Atom> atomsToFix // = null
, bool pause // = false
, params string[] keys
)
{
if (HDebug.IsDebuggerAttached && atomsToFix != null)
{
Dictionary <int, Tinker.Xyz.Atom> xyzatoms = xyz.atoms.ToIdDictionary();
foreach (var atom in atomsToFix)
{
HDebug.Assert(object.ReferenceEquals(atom, xyzatoms[atom.Id]));
}
}
Tinker.Xyz minxyz;
string[] minlog;
using (var temp = new HTempDirectory(tempbase, copytemp))
{
temp.EnterTemp();
xyz.ToFile("prot.xyz", false);
prm.ToFile("prot.prm");
List <string> keylines = new List <string>();
//if(grdmin != null)
//{
// string keyline = string.Format("GRDMIN {0}", grdmin.Value);
// keylines.Add(keyline);
//}
if (atomsToFix != null)
{
foreach (var atom in atomsToFix)
{
Vector coord = atom.Coord;
double force_constant = 10000; // force constant in kcal/Å2 for the harmonic restraint potential
string keyline = string.Format("RESTRAIN-POSITION {0} {1} {2} {3} {4}", atom.Id, coord[0], coord[1], coord[2], force_constant);
keylines.Add(keyline);
}
}
if (keys != null)
{
keylines.AddRange(keys);
}
HFile.WriteAllLines("prot.key", keylines);
// Enter RMS Gradient per Atom Criterion [0.01] :
string command = minimizepath;
command += " prot.xyz prot.prm";
command += " -k prot.key < param.txt";
HFile.WriteAllLines("param.txt", param.HSplit());
//command += string.Format(" >> prot.log");
HProcess.StartAsBatchInConsole("minimize.bat", pause
, "time /t >> prot.log"
, command
, "time /t >> prot.log"
);
HDebug.Assert(HFile.Exists("prot.xyz_2"));
HDebug.Assert(HFile.Exists("prot.xyz_3") == false);
minxyz = Tinker.Xyz.FromFile("prot.xyz_2", false, xyz.atoms_format);
minlog = HFile.ReadAllLines("prot.log");
temp.QuitTemp();
}
return(new OMinimize
{
minxyz = minxyz,
minlog = minlog
});
}
public static void SelfTest(string pdbname, string psfname, string prmname, string xyzname)
{
using (var temp = new HTempDirectory(@"C:\temp\", null))
{
temp.EnterTemp();
{
string resbase = "HTLib2.Bioinfo.HTLib2.Bioinfo.External.Tinker.Resources.selftest.";
HResource.CopyResourceTo <Tinker>(resbase + pdbname, pdbname);
HResource.CopyResourceTo <Tinker>(resbase + psfname, psfname);
HResource.CopyResourceTo <Tinker>(resbase + "par_all27_prot_lipid.inp", prmname);
if (xyzname != null)
{
HResource.CopyResourceTo <Tinker>(resbase + xyzname, xyzname);
}
HResource.CopyResourceTo <Tinker>(resbase + "charmm22.prm", "charmm22.prm");
{
var pdb = Pdb.FromFile(pdbname);
var psf = Namd.Psf.FromFile(psfname);
var prm = Namd.Prm.FromFile(prmname);
var xyz_prm = BuildFromNamd(pdb, psf, prm);
xyz_prm.Item1.ToFile("TinkFromNamd.xyz", false);
xyz_prm.Item2.ToFile("TinkFromNamd.prm");
}
if (xyzname != null)
{
var xyz0 = Xyz.FromFile("TinkFromNamd.xyz", false);
var prm0 = Prm.FromFile("TinkFromNamd.prm");
var grad0 = Run.Testgrad(xyz0, prm0, @"C:\temp\"
//, "VDWTERM NONE"
//, "CHARGETERM NONE"
//, "BONDTERM NONE"
//, "ANGLETERM NONE"
//, "UREYTERM NONE"
//, "IMPROPTERM NONE"
//, "TORSIONTERM NONE"
);
var forc0 = grad0.anlyts.GetForces(xyz0.atoms);
var xyz1 = Xyz.FromFile(xyzname, false);
var prm1 = Prm.FromFile("charmm22.prm");
var grad1 = Run.Testgrad(xyz1, prm1, @"C:\temp\"
//, "VDWTERM NONE"
//, "CHARGETERM NONE"
//, "BONDTERM NONE"
//, "ANGLETERM NONE"
//, "UREYTERM NONE"
//, "IMPROPTERM NONE"
//, "TORSIONTERM NONE"
);
var forc1 = grad1.anlyts.GetForces(xyz1.atoms);
{
KDTree.KDTree <object> kdtree = new KDTree.KDTree <object>(3);
var atoms0 = xyz0.atoms;
for (int i = 0; i < atoms0.Length; i++)
{
kdtree.insert(atoms0[i].Coord, i);
}
var atoms1 = xyz1.atoms;
int[] idx1to0 = new int[atoms1.Length];
for (int i1 = 0; i1 < atoms1.Length; i1++)
{
Vector coord1 = atoms1[i1].Coord;
int i0 = (int)kdtree.nearest(coord1);
Vector coord0 = atoms0[i0].Coord;
kdtree.delete(coord0);
idx1to0[i0] = i1;
}
atoms1 = atoms1.HSelectByIndex(idx1to0);
forc1 = forc1.HSelectByIndex(idx1to0);
}
Vector[] dforc = VectorBlock.PwSub(forc0, forc1).ToArray();
double[] dforcl = dforc.Dist();
double max_dforc = dforc.Dist().Max();
HDebug.Exception(max_dforc < 1); // 0.72682794387667848
{
double EB = Math.Abs(grad0.enrgCmpnt.EB - grad1.enrgCmpnt.EB); HDebug.Exception(EB < 0.1);
double EA = Math.Abs(grad0.enrgCmpnt.EA - grad1.enrgCmpnt.EA); HDebug.Exception(EA < 0.1);
double EBA = Math.Abs(grad0.enrgCmpnt.EBA - grad1.enrgCmpnt.EBA); HDebug.Exception(EBA < 0.1);
double EUB = Math.Abs(grad0.enrgCmpnt.EUB - grad1.enrgCmpnt.EUB); HDebug.Exception(EUB < 0.1);
double EAA = Math.Abs(grad0.enrgCmpnt.EAA - grad1.enrgCmpnt.EAA); HDebug.Exception(EAA < 0.1);
double EOPB = Math.Abs(grad0.enrgCmpnt.EOPB - grad1.enrgCmpnt.EOPB); HDebug.Exception(EOPB < 0.1);
double EOPD = Math.Abs(grad0.enrgCmpnt.EOPD - grad1.enrgCmpnt.EOPD); HDebug.Exception(EOPD < 0.1);
double EID = Math.Abs(grad0.enrgCmpnt.EID - grad1.enrgCmpnt.EID); HDebug.Exception(EID < 0.1); // 0.0019000000000000128 : N-terminus (and C-terminus) information is/are inconsistent betweeen namd-charmm and tink-charmm22
double EIT = Math.Abs(grad0.enrgCmpnt.EIT - grad1.enrgCmpnt.EIT); HDebug.Exception(EIT < 0.1);
double ET = Math.Abs(grad0.enrgCmpnt.ET - grad1.enrgCmpnt.ET); HDebug.Exception(ET < 0.5); // 0.33029999999999404 : N-terminus (and C-terminus) information is/are inconsistent betweeen namd-charmm and tink-charmm22
double EPT = Math.Abs(grad0.enrgCmpnt.EPT - grad1.enrgCmpnt.EPT); HDebug.Exception(EPT < 0.1);
double EBT = Math.Abs(grad0.enrgCmpnt.EBT - grad1.enrgCmpnt.EBT); HDebug.Exception(EBT < 0.1);
double ETT = Math.Abs(grad0.enrgCmpnt.ETT - grad1.enrgCmpnt.ETT); HDebug.Exception(ETT < 0.1);
double EV = Math.Abs(grad0.enrgCmpnt.EV - grad1.enrgCmpnt.EV); HDebug.Exception(EV < 0.1);
double EC = Math.Abs(grad0.enrgCmpnt.EC - grad1.enrgCmpnt.EC); HDebug.Exception(EC < 0.5); // 0.37830000000002428
double ECD = Math.Abs(grad0.enrgCmpnt.ECD - grad1.enrgCmpnt.ECD); HDebug.Exception(ECD < 0.1);
double ED = Math.Abs(grad0.enrgCmpnt.ED - grad1.enrgCmpnt.ED); HDebug.Exception(ED < 0.1);
double EM = Math.Abs(grad0.enrgCmpnt.EM - grad1.enrgCmpnt.EM); HDebug.Exception(EM < 0.1);
double EP = Math.Abs(grad0.enrgCmpnt.EP - grad1.enrgCmpnt.EP); HDebug.Exception(EP < 0.1);
double ER = Math.Abs(grad0.enrgCmpnt.ER - grad1.enrgCmpnt.ER); HDebug.Exception(ER < 0.1);
double ES = Math.Abs(grad0.enrgCmpnt.ES - grad1.enrgCmpnt.ES); HDebug.Exception(ES < 0.1);
double ELF = Math.Abs(grad0.enrgCmpnt.ELF - grad1.enrgCmpnt.ELF); HDebug.Exception(ELF < 0.1);
double EG = Math.Abs(grad0.enrgCmpnt.EG - grad1.enrgCmpnt.EG); HDebug.Exception(EG < 0.1);
double EX = Math.Abs(grad0.enrgCmpnt.EX - grad1.enrgCmpnt.EX); HDebug.Exception(EX < 0.1);
}
}
}
temp.QuitTemp();
}
//{
// //string pathbase = @"C:\Users\htna.IASTATE\svn\htnasvn_htna\Research.bioinfo.prog.NAMD\1A6G\New folder\";
// string pathbase = @"C:\Users\htna.IASTATE\svn\htnasvn_htna\Research.bioinfo.prog.NAMD\1A6G\";
// string toplbase = @"C:\Users\htna.IASTATE\svn\htnasvn_htna\Research.bioinfo.prog.NAMD\top_all27_prot_lipid\";
// var pdb = Pdb .FromFile(pathbase+"1A6G.psfgen.pdb");
// var psf = Namd.Psf.FromFile(pathbase+"1A6G.psfgen.psf");
// var prm = Namd.Prm.FromFile(toplbase+"par_all27_prot_na.prm");
//
// pdb = Pdb .FromFile(@"K:\Tim-8TIM,1TPH,1M6J\Tim-1M6J\1M6J.psfgen.pdb");
// psf = Namd.Psf.FromFile(@"K:\Tim-8TIM,1TPH,1M6J\Tim-1M6J\1M6J.psfgen.psf");
// prm = Namd.Prm.FromFile(@"K:\Tim-8TIM,1TPH,1M6J\Tim-1M6J\par_all27_prot_lipid.inp");
// var xyz_prm = BuildFromNamd(pdb, psf, prm);
// xyz_prm.Item1.ToFile(@"C:\temp\TinkFromNamd.xyz", false);
// xyz_prm.Item2.ToFile(@"C:\temp\TinkFromNamd.prm");
//}
}
public static SPsfCrd BuildPsfCrd
(IEnumerable <string> toplines
, IEnumerable <string> parlines
, IEnumerable <string> pdblines
)
{
string tempbase = @"C:\temp\";
SPsfCrd psfcrd;
using (var temp = new HTempDirectory(tempbase, null))
{
temp.EnterTemp();
string topname = "top.rtf"; HFile.WriteAllLines(topname, toplines);
string parname = "par.prm"; HFile.WriteAllLines(parname, parlines);
string tgtname = "target"; HFile.WriteAllLines(tgtname + ".pdb", pdblines);
string Setup_inp = @"* Run Segment Through CHARMM
*
! read topology and parameter files
read rtf card name $$topname$$
read para card name $$parname$$
! Read sequence from the PDB coordinate file
open unit 1 card read name $$tgtname$$.pdb
read sequ pdb unit 1
! now generate the PSF and also the IC table (SETU keyword)
generate setu a-pro first NTER last CTER
rewind unit 1
! set bomlev to -1 to avois sying on lack of hydrogen coordinates
bomlev -1
read coor pdb unit 1
! them put bomlev back up to 0
bomlev 0
close unit 1
! prints out number of atoms that still have undefined coordinates.
define test select segid a-pro .and. ( .not. hydrogen ) .and. ( .not. init ) show end
ic para
ic fill preserve
ic build
hbuild sele all end
! write out the protein structure file (psf) and
! the coordinate file in pdb and crd format.
write psf card name $$tgtname$$.psf
* PSF
*
write coor card name $$tgtname$$.crd
* Coords
*
stop
"
.Replace("$$topname$$", topname)
.Replace("$$parname$$", parname)
.Replace("$$tgtname$$", tgtname);
HFile.WriteAllText("Setup.inp", Setup_inp);
System.Console.WriteLine("Run the following command at " + temp + " :");
System.Console.WriteLine(" $ charmm < Setup.inp");
System.Console.WriteLine(" or $ mpd&");
System.Console.WriteLine(" $ mpirun -n 38 charmm_M < Setup.inp");
System.Console.WriteLine("Then, copy target.psf and target.crd to " + temp);
while (true)
{
bool next = HConsole.ReadValue <bool>("Ready for next? ", false, null, false, true);
if (next)
{
if (HFile.ExistsAll("target.crd", "target.psf"))
{
string[] crdlines = HFile.ReadAllLines("target.crd");
string[] psflines = HFile.ReadAllLines("target.psf");
psfcrd = new SPsfCrd
{
crdlines = crdlines,
psflines = psflines,
};
break;
}
System.Console.WriteLine("DO, copy target.psf and target.crd to " + temp);
}
}
temp.QuitTemp();
}
return(psfcrd);
}
public static CPsfgenExt PsfgenExt
(IList <Tuple <string, string, Pdb.IAtom[]> > lstSegFileAtoms
, string[] toplines
, string[] parlines
, Pdb alignto
, string[] psfgen_lines
, IList <string> minimize_conf_lines = null
, HOptions options = null
)
{
if (options == null)
{
options = new HOptions((string)null);
}
string tempbase = @"C:\temp\";
string psfgen_workdir = null;
string topname = "prot.top";
string parname = "prot.par";
List <string> psf_lines = null;
List <string> pdb_lines = null;
using (var temp = new HTempDirectory(tempbase, null))
{
temp.EnterTemp();
HFile.WriteAllLines(topname, toplines);
HFile.WriteAllLines(parname, parlines);
if ((HFile.Exists("prot.pdb") == false) || (HFile.Exists("prot.psf") == false))
{
var psfgen = Namd.RunPsfgen
(lstSegFileAtoms, tempbase, null, "2.10"
, new string[] { topname }
, new string[] {}
, topname
, psfgen_lines: psfgen_lines
, psfgen_workdir: psfgen_workdir
, options: options
);
psf_lines = psfgen.psf_lines;
pdb_lines = psfgen.pdb_lines;
if (alignto != null)
{
HDebug.Exception("check!!!");
////////////////////////////
Pdb prot = Pdb.FromLines(pdb_lines);
prot = PsfgenExt_AlignTo(prot, alignto);
pdb_lines = prot.ToLines().ToList();
}
HFile.WriteAllLines("prot.pdb", pdb_lines);
HFile.WriteAllLines("prot.psf", psf_lines);
}
if (options.Contains("nomin") == false)
{
if ((HFile.Exists("protmin.coor") == false) || (HFile.Exists("protmin.pdb") == false))
{
List <string> psfgen_pdb_lines = System.IO.File.ReadLines("prot.pdb").ToList();
List <string> psfgen_psf_lines = System.IO.File.ReadLines("prot.psf").ToList();
List <string> prm_lines = System.IO.File.ReadLines(parname).ToList();
string Namd2_opt = null;
if (options.HSelectStartsWith("minimize option:").Length >= 1)
{
Namd2_opt = options.HSelectStartsWith("minimize option:").First().Replace("minimize option:", "");
}
var minpdb = Namd.Run.Namd2
(psfgen_pdb_lines
, psfgen_psf_lines
, prm_lines
, tempbase
, "2.10"
, ((Namd2_opt == null) ? "+p3" : Namd2_opt)
, conf_lines: minimize_conf_lines
);
HFile.WriteAllLines("protmin.coor", minpdb.coor_lines);
Pdb prot0 = Pdb.FromLines(psfgen_pdb_lines);
Pdb prot1 = Pdb.FromLines(minpdb.coor_lines);
HDebug.Exception(prot0.atoms.Length == prot1.atoms.Length);
HDebug.Exception(prot0.elements.Length == prot1.elements.Length);
// update conformation to minimized conformation
for (int i = 0; i < prot0.elements.Length; i++)
{
if (prot0.elements[i].GetType() != prot1.elements[i].GetType())
{
throw new HException("prot0.elements[i].GetType() != prot1.elements[i].GetType()");
}
if ((prot0.elements[i] is Pdb.IAtom) == false)
{
continue;
}
Pdb.IAtom iatom0 = prot0.elements[i] as Pdb.IAtom;
Pdb.IAtom iatom1 = prot1.elements[i] as Pdb.IAtom;
Vector coord0 = iatom0.coord;
Vector coord1 = iatom1.coord;
double dist = (coord0 - coord1).Dist;
if (iatom0.occupancy != 0)
{
if (dist != 0)
{
throw new HException("iatom0.coord - iatom1.coord != 0");
}
}
if (dist != 0)
{
if (iatom0 is Pdb.Atom)
{
string nline0 = (iatom0 as Pdb.Atom).GetUpdatedLine(coord1);
Pdb.Atom natom0 = Pdb.Atom.FromString(nline0);
prot0.elements[i] = natom0;
continue;
}
if (iatom0 is Pdb.Hetatm)
{
string nline0 = (iatom0 as Pdb.Hetatm).GetUpdatedLine(coord1);
Pdb.Hetatm natom0 = Pdb.Hetatm.FromString(nline0);
prot0.elements[i] = natom0;
continue;
}
}
}
if ((prot0.elements[0] is Pdb.Remark) && (prot1.elements[0] is Pdb.Remark))
{
prot0.elements[0] = Pdb.Remark.FromString(prot1.elements[0].line);
}
prot0.ToFile("protmin.pdb");
pdb_lines = System.IO.File.ReadLines("protmin.pdb").ToList();
}
}
//{
// Pdb confpdb = GetConfPdb(options);
// var psf = Namd.Psf.FromFile("prot.psf");
// var prm = Namd.Prm.FromFile(parname);
// List<string> log = new List<string>();
// Universe univ = Universe.BuilderNamd.Build(psf, prm, confpdb, true, new TextLogger(log));
// return univ;
//}
temp.QuitTemp();
}
return(new CPsfgenExt
{
psflines = psf_lines,
pdblines = pdb_lines,
});
}
