public float EVdW(int order, bool suppress)
{
VdW vdw0 = GetVdWParameter(0);
VdW vdw1 = GetVdWParameter(1);
float r = atoms.getDistance(this.a0, this.a1);
float r0 = (vdw0.r + vdw1.r) * 0.5f;
float v = Mathf.Sqrt(vdw0.v * vdw1.v);
//Amber type VdW
if (atoms.parameters.nonbonding.vType == 3)
{
if (order == 0)
{
return(v * (Mathf.Pow(r0 / r, 12f) - 2f * Mathf.Pow(r0 / r, 6f)));
}
else if (order == 1)
{
return(12f * v * (Mathf.Pow(r0 / r, 7f) * -Mathf.Pow(r0 / r, 13f)) / r0);
}
else if (order == 2)
{
return(12f * v * (13f * Mathf.Pow(r0 / r, 14f) - 7f * Mathf.Pow(r0 / r, 8f)) / (r0 * r0));
}
}
else
{
Debug.LogError(string.Format("VdW Nonbonding type {0} not available", atoms.parameters.nonbonding.vType));
}
return(0f);
}
//Find index of type equivalent VdW
//Return -1 if no type equivalent VdWs are in this parameters set
public int IndexVdW(VdW otherVdW)
{
for (int index = 0; index < vdws.Count; index++)
{
if (vdws[index].TypeEquivalent(otherVdW))
{
return(index);
}
}
return(-1);
}
public bool ContainsVdW(VdW otherVdW)
{
foreach (VdW thisVdW in vdws)
{
if (thisVdW.TypeEquivalent(otherVdW))
{
return(true);
}
}
return(false);
}
public void AddVdW(VdW newVdw)
{
foreach (VdW vdw in vdws)
{
if (vdw.TypeEquivalent(newVdw))
{
throw new System.Exception("VdW already exists in Parameters set");
}
}
vdws.Add(newVdw);
}
public Parameters ParametersFromFRCMODFile(string filename)
{
Parameters parameters = Instantiate <Parameters>(parametersPrefab);
string[] lines = FileIO.Readlines(filename);
int maxLines = lines.Length;
List <string> sections = new List <string> {
"MASS",
"BOND",
"ANGL",
"DIHE",
"IMPR",
"NONB",
"IPOL",
"CMAP",
"%"
};
string sectionName;
int sectionNum = 0;
int numSections = sections.Count;
string section = "";
lineNumber = 0;
string restOfLine;
string[] splitLine;
Stretch newStretchParam;
Bend newBendParam;
Torsion newTorsionParam;
ImproperTorsion newImproperTorsionParam;
VdW newVdWParam;
Torsion existingTorsionParam;
int existingTorsionNum;
bool torsionModified;
int offset;
while (lineNumber < maxLines)
{
line = lines [lineNumber];
if (line == "")
{
continue;
}
for (sectionNum = 0; sectionNum < numSections; sectionNum++)
{
sectionName = sections [sectionNum];
if (line.StartsWith(sectionName))
{
section = sectionName;
goto SKIP;
}
}
//Ignore MASS section
//Parse Bond
if (section == "BOND")
{
t0 = GetAmberFromString(line, 0);
t1 = GetAmberFromString(line, 3);
restOfLine = line.Substring(5, line.Length - 6);
splitLine = restOfLine.Split(new [] { " " }, System.StringSplitOptions.RemoveEmptyEntries);
keq = float.Parse(splitLine [0]);
req = float.Parse(splitLine [1]);
newStretchParam = new Stretch(t0, t1, req, keq);
parameters.stretches.Add(newStretchParam);
}
else if (section == "ANGL")
{
t0 = GetAmberFromString(line, 0);
t1 = GetAmberFromString(line, 3);
t2 = GetAmberFromString(line, 6);
restOfLine = line.Substring(8, line.Length - 9);
splitLine = restOfLine.Split(new [] { " " }, System.StringSplitOptions.RemoveEmptyEntries);
keq = float.Parse(splitLine [0]);
req = float.Parse(splitLine [1]);
newBendParam = new Bend(t0, t1, t2, req, keq);
parameters.bends.Add(newBendParam);
}
else if (section == "DIHE")
{
t0 = GetAmberFromString(line, 0);
t1 = GetAmberFromString(line, 3);
t2 = GetAmberFromString(line, 6);
t3 = GetAmberFromString(line, 9);
newTorsionParam = new Torsion(t0, t1, t2, t3);
restOfLine = line.Substring(11, line.Length - 12);
splitLine = restOfLine.Split(new [] { " " }, System.StringSplitOptions.RemoveEmptyEntries);
npaths = int.Parse(splitLine [0]);
v = float.Parse(splitLine [1]);
gamma = float.Parse(splitLine [2]);
periodicity = (int)Mathf.Abs(float.Parse(splitLine [3]));
//The same param can be defined on multiple lines
torsionModified = false;
for (existingTorsionNum = 0; existingTorsionNum < parameters.torsions.Count; existingTorsionNum++)
{
existingTorsionParam = parameters.torsions [existingTorsionNum];
if (existingTorsionParam.TypeEquivalent(newTorsionParam))
{
existingTorsionParam.Modify(periodicity, v, gamma);
torsionModified = true;
}
}
if (!torsionModified)
{
newTorsionParam.npaths = npaths;
if (periodicity == 1)
{
newTorsionParam.v0 = v;
newTorsionParam.gamma0 = gamma;
}
else if (periodicity == 2)
{
newTorsionParam.v1 = v;
newTorsionParam.gamma1 = gamma;
}
else if (periodicity == 3)
{
newTorsionParam.v2 = v;
newTorsionParam.gamma2 = gamma;
}
else if (periodicity == 4)
{
newTorsionParam.v3 = v;
newTorsionParam.gamma3 = gamma;
}
parameters.torsions.Add(newTorsionParam);
}
}
else if (section == "IMPR")
{
t0 = GetAmberFromString(line, 0);
t1 = GetAmberFromString(line, 3);
t2 = GetAmberFromString(line, 6);
t3 = GetAmberFromString(line, 9);
restOfLine = line.Substring(11, line.Length - 12);
splitLine = restOfLine.Split(new [] { " " }, System.StringSplitOptions.RemoveEmptyEntries);
offset = 1;
//Sometimes npaths is included here, even though ignored. Sometimes it's not.
if (splitLine [0].Contains("."))
{
offset = 0;
}
v = float.Parse(splitLine [offset]);
gamma = float.Parse(splitLine [offset + 1]);
periodicity = (int)Mathf.Abs(float.Parse(splitLine [offset + 2]));
newImproperTorsionParam = new ImproperTorsion(t0, t1, t2, t3, v, gamma, periodicity);
parameters.improperTorsions.Add(newImproperTorsionParam);
}
else if (section == "NONB")
{
splitLine = line.Split(new [] { " " }, System.StringSplitOptions.RemoveEmptyEntries);
t = splitLine [0];
radius = float.Parse(splitLine [1]);
v = float.Parse(splitLine [2]);
newVdWParam = new VdW(t, radius, v);
parameters.vdws.Add(newVdWParam);
}
SKIP:
;
}
return(parameters);
}
//This can be used to read parameters from gaussian input files as well
public IEnumerator ParametersFromPRMLines(string[] lines, Parameters parameters)
{
int vType;
int cType;
int vCutoff;
int cCutoff;
float vScale1;
float vScale2;
float vScale3;
float cScale1;
float cScale2;
float cScale3;
string t0;
string t1;
string t2;
string t3;
float req;
float keq;
float v;
float v0;
float v1;
float v2;
float v3;
float gamma;
float gamma0;
float gamma1;
float gamma2;
float gamma3;
int npaths;
int periodicity;
foreach (string line in lines)
{
string[] splitLine = line.Split(new [] { " " }, System.StringSplitOptions.RemoveEmptyEntries);
if (splitLine.Length == 0)
{
continue;
}
if (splitLine [0].ToUpper() == "NONBON")
{
vType = int.Parse(splitLine [1]);
cType = int.Parse(splitLine [2]);
vCutoff = int.Parse(splitLine [3]);
cCutoff = int.Parse(splitLine [4]);
vScale1 = float.Parse(splitLine [5]);
vScale2 = float.Parse(splitLine [6]);
vScale3 = float.Parse(splitLine [7]);
cScale1 = float.Parse(splitLine [8]);
cScale2 = float.Parse(splitLine [9]);
cScale3 = float.Parse(splitLine [10]);
parameters.SetNonBonding(vType, cType, vCutoff, cCutoff, vScale1, vScale2, vScale3, cScale1, cScale2, cScale3);
}
else if (splitLine [0].ToUpper().StartsWith("VDW"))
{
t0 = splitLine [1];
req = float.Parse(splitLine [2]);
v = float.Parse(splitLine [3]);
VdW stretch = new VdW(t0, req, v);
parameters.AddVdW(stretch);
}
else if (splitLine [0].ToUpper().StartsWith("HRMSTR"))
{
t0 = splitLine [1];
t1 = splitLine [2];
keq = float.Parse(splitLine [3]);
req = float.Parse(splitLine [4]);
Stretch stretch = new Stretch(t0, t1, req, keq);
parameters.AddStretch(stretch);
}
else if (splitLine [0].ToUpper().StartsWith("HRMBND"))
{
t0 = splitLine [1];
t1 = splitLine [2];
t2 = splitLine [3];
keq = float.Parse(splitLine [4]);
req = float.Parse(splitLine [5]);
Bend bend = new Bend(t0, t1, t2, req, keq);
parameters.AddBend(bend);
}
else if (splitLine [0].ToUpper().StartsWith("AMBTRS"))
{
t0 = splitLine [1];
t1 = splitLine [2];
t2 = splitLine [3];
t3 = splitLine [4];
gamma0 = float.Parse(splitLine [5]);
gamma1 = float.Parse(splitLine [6]);
gamma2 = float.Parse(splitLine [7]);
gamma3 = float.Parse(splitLine [8]);
v0 = float.Parse(splitLine [9]);
v1 = float.Parse(splitLine [10]);
v2 = float.Parse(splitLine [11]);
v3 = float.Parse(splitLine [12]);
npaths = (int)float.Parse(splitLine [13]);
Torsion torsion = new Torsion(t0, t1, t2, t3, v0, v1, v2, v3, gamma0, gamma1, gamma2, gamma3, npaths);
parameters.AddTorsion(torsion);
}
else if (splitLine [0].ToUpper().StartsWith("IMPTRS"))
{
t0 = splitLine [1];
t1 = splitLine [2];
t2 = splitLine [3];
t3 = splitLine [4];
v = float.Parse(splitLine [5]);;
gamma = float.Parse(splitLine [6]);
periodicity = (int)float.Parse(splitLine [7]);
ImproperTorsion improperTorsion = new ImproperTorsion(t0, t1, t2, t3, v, gamma, periodicity);
parameters.AddImproperTorsion(improperTorsion);
}
}
yield return(null);
}
public bool TypeEquivalent(VdW other)
{
return(this.t == other.t);
}
