public Nonbonded FindNonbonded(string type0, ITextLogger logger)
{
if (_FindNonbonded.ContainsKey(type0) == false)
{
Nonbonded found = null;
foreach (Nonbonded nonbonded in nonbondeds)
{
if (nonbonded.types[0] == type0)
{
if (found != null)
{
bool writelog = ((found.epsilon != nonbonded.epsilon) ||
(found.Rmin2 != nonbonded.Rmin2) ||
(found.eps_14 != nonbonded.eps_14) ||
(found.Rmin2_14 != nonbonded.Rmin2_14));
if (writelog)
{
logger.Log(string.Format("Nonbonded params of {0}-(eps {1}, rmin2 {2}, esp_14 {3}, rmin2_14 {4}) is replaced to ({5}, {6}, {7}, {8})",
type0, found.epsilon, found.Rmin2, found.eps_14, found.Rmin2_14,
nonbonded.epsilon, nonbonded.Rmin2, nonbonded.eps_14, nonbonded.Rmin2_14));
}
}
found = nonbonded;
}
}
HDebug.Assert(found != null);
HDebug.AssertIf(double.IsNaN(found.Rmin2) == false, found.Rmin2 > 0);
HDebug.AssertIf(double.IsNaN(found.Rmin2_14) == false, found.Rmin2_14 > 0);
_FindNonbonded.Add(type0, found);
}
return(_FindNonbonded[type0]);
}
public static Nonbonded FromString(string line, ITextLogger logger)
{
Element elem = Element.FromString(line, 1, 6);
//Debug.Assert(0 == elem.parms[0]); // "FE 0.010000 0.000000 0.650000" happens
if (!(0 == elem.parms[0]))
{
logger.Log(string.Format("Warning: Nonbonded params ({0}): 1st parameter should be in general == 0", line));
}
double epsilon = elem.parms[1];
double Rmin2 = elem.parms[2]; //Debug.Assert(Rmin2 > 0);
if (!(Rmin2 > 0))
{
logger.Log(string.Format("Error : Nonbonded params ({0}): 3rd parameter (Rmin2) must be '> 0'", line));
}
double eps_14 = double.NaN;
double Rmin2_14 = double.NaN;
if (elem.parms.Length > 3)
{
HDebug.Assert(0 == elem.parms[3]);
eps_14 = elem.parms[4];
Rmin2_14 = elem.parms[5]; //Debug.Assert(Rmin2_14 > 0);
if (!(Rmin2_14 > 0))
{
logger.Log(string.Format("Error : Nonbonded params ({0}): 6th parameter (Rmin2_14) must be '> 0'", line));
}
}
Nonbonded nonbonded = new Nonbonded(line, elem.types, epsilon, Rmin2, eps_14, Rmin2_14);
return(nonbonded);
}
public static Prm FromFileXPlor(string filepath, ITextLogger logger)
{
List <string> lines = new List <string>(System.IO.File.ReadAllLines(filepath));
RemoveComments(ref lines);
string[] keywards = CollectKeywards(lines);
List <Bond> bonds = new List <Bond>();
List <Angle> angles = new List <Angle>();
List <Dihedral> dihedrals = new List <Dihedral>();
List <Improper> impropers = new List <Improper>();
List <Nonbonded> nonbondeds = new List <Nonbonded>();
for (int i = 0; i < lines.Count; i++)
{
string line = lines[i];
string keyward = line.Split(separator, StringSplitOptions.RemoveEmptyEntries).First().ToUpper();
line = line.Substring(keyward.Length);
switch (keyward)
{
case "REMARK": break;
case "SET": break;
case "BOND": bonds.Add(Bond.FromString(line, logger)); break;
case "ANGLE": angles.Add(Angle.FromString(line, logger)); break;
case "DIHE": dihedrals.Add(Dihedral.FromString(line, logger)); break;
case "IMPR": impropers.Add(Improper.FromString(line, logger)); break;
case "{*": break; // comment
case "NONBONDED": nonbondeds.Add(Nonbonded.FromStringXPlor(line, logger)); break;
default:
HDebug.Assert(false);
break;
}
}
Prm prm = new Prm();
prm.bonds = bonds.ToArray();
prm.angles = angles.ToArray();
prm.dihedrals = dihedrals.ToArray();
prm.impropers = impropers.ToArray();
prm.nonbondeds = nonbondeds.ToArray();
return(prm);
}
public static Nonbonded FromStringXPlor(string line, ITextLogger logger)
{
Element elem = Element.FromString(line, 1, 4);
double epsilon = elem.parms[0];
double Rmin2 = elem.parms[1]; //Debug.Assert(Rmin2 > 0);
if (!(Rmin2 > 0))
{
logger.Log(string.Format("Error : Nonbonded params ({0}): 3rd parameter (Rmin2) must be '> 0'", line));
}
double eps_14 = elem.parms[2];
double Rmin2_14 = elem.parms[3]; //Debug.Assert(Rmin2_14 > 0);
if (!(Rmin2_14 > 0))
{
logger.Log(string.Format("Error : Nonbonded params ({0}): 4th parameter (Rmin2_14) must be '> 0'", line));
}
Nonbonded nonbonded = new Nonbonded(line, elem.types, epsilon, Rmin2, eps_14, Rmin2_14);
return(nonbonded);
}
public static Nonbonded[] FromFileXXX_CollectNonbondeds(List <string> lines, ITextLogger logger)
{
RemoveComments(ref lines);
HDebug.Assert(lines[0].Split(separator).First().ToUpper() == "NONBONDED");
List <Nonbonded> nonbondeds = new List <Nonbonded>();
bool skip = false;
foreach (string line in lines)
{
if (line.Split(separator).First().ToUpper() == "NONBONDED")
{
skip = true; continue;
}
if (skip)
{
skip = false; continue;
}
nonbondeds.Add(Nonbonded.FromString(line, logger));
}
return(nonbondeds.ToArray());
}
