public IEnumerator AtomsFromMol2File(string path, Atoms atoms, Atom atomPrefab)
{
atoms.globalSettings = globalSettings;
atoms.setSourceFile(path);
atoms.name = Path.GetFileName(path);
gc = Instantiate <GaussianCalculator> (GameObject.FindObjectOfType <PrefabManager>().gaussianCalculatorPrefab, atoms.transform);
atoms.gaussianCalculator = gc;
int index = 0;
Vector3 position = new Vector3();
List <Data.AmberToElement> amberToElementList = data.amberToElementData;
Data.AmberToElement amberToElement;
int amberToElementNum;
List <int[]> connectionList = new List <int[]> ();
int a0;
int a1;
int bondOrder;
bool readAtoms = false;
bool readConnectivity = false;
string[] lines = FileIO.Readlines(path);
string[] splitLine;
int lineNumber;
string line;
for (lineNumber = 0; lineNumber < lines.Length; lineNumber++)
{
line = lines [lineNumber];
if (line.StartsWith("@<TRIPOS>"))
{
readAtoms = line.Contains("ATOM");
//readConnectivity = line.Contains("BOND");
}
else if (readAtoms)
{
splitLine = line.Split(new [] { " " }, System.StringSplitOptions.RemoveEmptyEntries);
Atom atom = Instantiate <Atom> (atomPrefab);
//Atom types
atom.pdbName = splitLine [1];
atom.amberName = splitLine [5];
for (amberToElementNum = 0; amberToElementNum < amberToElementList.Count; amberToElementNum++)
{
amberToElement = amberToElementList [amberToElementNum];
if (amberToElement.amberName == atom.amberName)
{
atom.element = amberToElement.element;
atom.formalCharge = amberToElement.formalCharge;
}
}
//Position
position.x = float.Parse(splitLine [2]);
position.y = float.Parse(splitLine [3]);
position.z = float.Parse(splitLine [4]);
atom.transform.position = position;
//Residue
atom.residueNumber = int.Parse(splitLine [6]);
atom.residueName = splitLine [7];
if (splitLine.Length > 8)
{
atom.partialCharge = float.Parse(splitLine [8]);
}
atom.index = index;
atoms.AddAtom(atom);
//atom.resolution = globalSettings.ballResolution;
//atom.transform.SetParent(atoms.atomsHolder.transform);
//atoms.atomList.Add (atom);
index++;
}
else if (readConnectivity)
{
splitLine = line.Split(new [] { " " }, System.StringSplitOptions.RemoveEmptyEntries);
a0 = int.Parse(splitLine [1]) - 1;
a1 = int.Parse(splitLine [2]) - 1;
bondOrder = int.Parse(splitLine [3]);
connectionList.Add(new int[3] {
a0, a1, bondOrder
});
}
if (lineNumber % globalSettings.maxLinesToYield == 0)
{
yield return(new WaitForSeconds(0.1f));
}
}
atoms.graph.SetAtoms(atoms);
gc.SetAtoms(atoms);
foreach (int[] connectionPair in connectionList)
{
atoms.graph.Connect(connectionPair [0], connectionPair [1], (double)connectionPair [2]);
}
}
public IEnumerator AtomsFromGaussianInput(string path, Atoms atoms, Atom atomPrefab)
{
atoms.globalSettings = globalSettings;
atoms.setSourceFile(path);
atoms.name = Path.GetFileName(path);
gc = Instantiate <GaussianCalculator> (GameObject.FindObjectOfType <PrefabManager>().gaussianCalculatorPrefab, atoms.transform);
atoms.gaussianCalculator = gc;
int index = 0;
int lineNumber = 0;
string line;
string[] lines = FileIO.Readlines(path, "!");
string[] stringArray;
int stringArrayIndex;
int maxLines = lines.Length;
//Link 0 commands
while (lineNumber < maxLines)
{
line = lines [lineNumber].Trim();
if (line.StartsWith("#"))
{
break;
}
else if (line.ToUpper().StartsWith("%CHK"))
{
gc.checkpointPath = GetValueFromPair(line);
}
else if (line.ToUpper().StartsWith("%OLDCHK"))
{
gc.oldCheckpointPath = GetValueFromPair(line);
}
else if (line.ToUpper().StartsWith("%MEM"))
{
gc.jobMemoryMB = GetMemoryMB(GetValueFromPair(line));
}
else if (line.ToUpper().StartsWith("%NPROC"))
{
gc.nProcessors = int.Parse(GetValueFromPair(line));
}
else if (line.ToUpper().StartsWith("%KJOB"))
{
stringArray = line.Split(new [] { " " }, System.StringSplitOptions.RemoveEmptyEntries);
gc.killJobLink = stringArray [1];
if (stringArray.Length > 2)
{
gc.killJobAfter = int.Parse(stringArray [2]);
}
else
{
gc.killJobAfter = 1;
}
}
lineNumber++;
}
List <string> keywordsList = new List <string> ();
string keywordItem;
//Keywords
while (lineNumber < maxLines)
{
line = lines [lineNumber].Trim();
if (line == "")
{
break;
}
stringArray = line.Split(new [] { " " }, System.StringSplitOptions.RemoveEmptyEntries);
for (stringArrayIndex = 0; stringArrayIndex < stringArray.Length; stringArrayIndex++)
{
keywordsList.Add(stringArray [stringArrayIndex].ToLower());
}
lineNumber++;
}
//Parse keywords - only one line so don't need to worry about optimisation
for (stringArrayIndex = 0; stringArrayIndex < keywordsList.Count; stringArrayIndex++)
{
keywordItem = keywordsList [stringArrayIndex];
//Print level
if (keywordItem.StartsWith("#"))
{
gc.gaussianPrintLevel = keywordItem.Replace("#", "");
//Method
}
else if (keywordItem.StartsWith("oniom"))
{
string oniomMethodsStr = GetStringInParentheses(keywordItem);
string oniomOptionsStr = GetStringInParentheses(GetValueFromPair(keywordItem, checkEnclosed: true));
string[] oniomOptions = oniomOptionsStr.Split(new [] { "," }, System.StringSplitOptions.RemoveEmptyEntries);
foreach (string oniomOption in oniomOptions)
{
gc.oniomOptions.Add(oniomOption);
}
string[] methods = oniomMethodsStr.Split(new [] { ":" }, System.StringSplitOptions.RemoveEmptyEntries);
string[] highMBO = GetMethodFromString(methods [0]);
gc.layers.AddLayer(highMBO [0], highMBO [1], highMBO [2], 'H');
if (methods.Length == 2)
{
string[] lowMBO = GetMethodFromString(methods [1]);
gc.layers.AddLayer(lowMBO [0], lowMBO [1], lowMBO [2], 'L');
}
else if (methods.Length == 3)
{
string[] mediumMBO = GetMethodFromString(methods [1]);
gc.layers.AddLayer(mediumMBO [0], mediumMBO [1], mediumMBO [2], 'M');
string[] lowMBO = GetMethodFromString(methods [2]);
gc.layers.AddLayer(lowMBO [0], lowMBO [1], lowMBO [2], 'L');
}
}
else if (keywordItem.StartsWith("guess"))
{
string guessOptionsStr = GetStringInParentheses(GetValueFromPair(keywordItem, checkEnclosed: true));
string[] guessOptions = guessOptionsStr.Split(new [] { "," }, System.StringSplitOptions.RemoveEmptyEntries);
foreach (string guessOption in guessOptions)
{
gc.guessOptions.Add(guessOption);
}
}
else if (keywordItem.StartsWith("geom"))
{
string geomOptionsStr = GetStringInParentheses(GetValueFromPair(keywordItem, checkEnclosed: true));
string[] geomOptions = geomOptionsStr.Split(new [] { "," }, System.StringSplitOptions.RemoveEmptyEntries);
foreach (string geomOption in geomOptions)
{
gc.geomOptions.Add(geomOption);
}
}
else
{
foreach (string methodName in data.gaussianMethods)
{
if (keywordItem.StartsWith(methodName))
{
string[] highMBO = GetMethodFromString(keywordItem);
gc.layers.AddLayer(highMBO [0], highMBO [1], highMBO [2], 'H');
break;
}
}
}
}
//Title
List <string> titleLines = new List <string>();
if (!gc.geomOptions.Contains("allcheck"))
{
while (lineNumber < maxLines)
{
line = lines [lineNumber].Trim();
if (line != "")
{
titleLines.Add(line);
}
else if (titleLines.Count != 0)
{
break;
}
lineNumber++;
}
}
gc.title = string.Join("\n", titleLines.ToArray());
//Layer Charge/Multiplicity
if (!gc.geomOptions.Contains("allcheck"))
{
while (lineNumber < maxLines)
{
line = lines [lineNumber].Trim();
if (line != "")
{
string[] cmStr = line.Split(new [] { " " }, System.StringSplitOptions.RemoveEmptyEntries);
int numLayersSpecified = cmStr.Length / 2;
for (int layerIndex = 0; layerIndex < numLayersSpecified; layerIndex++)
{
gc.layers.SetLayerCharge(gc.layers.layerNames[layerIndex], int.Parse(cmStr [2 * layerIndex]));
gc.layers.SetLayerMultiplicity(gc.layers.layerNames[layerIndex], int.Parse(cmStr [2 * layerIndex + 1]));
}
lineNumber++;
break;
}
lineNumber++;
}
}
System.Text.StringBuilder sb = new System.Text.StringBuilder();
int charNum = 0;
int phase = 0;
char lineChar;
int pdbOption = 0;
string linkType = "";
int linkIndex = 0;
Vector3 position = new Vector3();
List <int> highAtoms = new List <int>();
List <int> mediumAtoms = new List <int>();
List <int> lowAtoms = new List <int>();
//Atoms - AtomFromGaussianInputLine should be optimised
if (!(gc.geomOptions.Contains("allcheck") && gc.geomOptions.Contains("check") && gc.geomOptions.Contains("checkpoint")))
{
while (lineNumber < maxLines)
{
line = lines [lineNumber].Trim();
if (line == "")
{
lineNumber++;
break;
}
Atom atom = Instantiate <Atom> (atomPrefab);
atom.index = index;
charNum = 0;
phase = (int)atomPhase.ELEMENT;
sb.Length = 0;
while (charNum <= line.Length)
{
if (charNum == line.Length)
{
lineChar = ' ';
}
else
{
lineChar = line [charNum];
}
//Read element
if (phase == (int)atomPhase.ELEMENT)
{
if (lineChar == '-')
{
phase = (int)atomPhase.AMBER_NAME;
}
else if (lineChar == '(')
{
phase = (int)atomPhase.PDB;
}
else if (lineChar == ' ')
{
phase = (int)atomPhase.FROZEN;
}
else
{
sb.Append(lineChar);
charNum++;
continue;
}
atom.element = sb.ToString();
sb.Length = 0;
}
else if (phase == (int)atomPhase.AMBER_NAME)
{
if (lineChar == '-')
{
phase = (int)atomPhase.PARTIAL_CHARGE;
}
else if (lineChar == '(')
{
phase = (int)atomPhase.PDB;
}
else if (lineChar == ' ')
{
phase = (int)atomPhase.FROZEN;
}
else
{
sb.Append(lineChar);
charNum++;
continue;
}
atom.amberName = sb.ToString();
sb.Length = 0;
}
else if (phase == (int)atomPhase.PARTIAL_CHARGE)
{
if (lineChar == '(')
{
phase = (int)atomPhase.PDB;
}
else if (lineChar == ' ')
{
phase = (int)atomPhase.FROZEN;
}
else
{
sb.Append(lineChar);
charNum++;
continue;
}
if (sb.Length > 0)
{
atom.partialCharge = float.Parse(sb.ToString());
}
sb.Length = 0;
}
else if (phase == (int)atomPhase.PDB)
{
if (lineChar == '=')
{
phase = (int)atomPhase.PDB_VALUE;
}
else if (lineChar == ')')
{
phase = (int)atomPhase.FROZEN;
}
else if (sb.Length == 5)
{
if (sb.ToString().ToUpper() == "PDBNA")
{
pdbOption = (int)pdbOptions.PDBNAME;
}
if (sb.ToString().ToUpper() == "RESNA")
{
pdbOption = (int)pdbOptions.RESNAME;
}
if (sb.ToString().ToUpper() == "RESNU")
{
pdbOption = (int)pdbOptions.RESNUM;
}
}
else
{
sb.Append(lineChar);
charNum++;
continue;
}
sb.Length = 0;
}
else if (phase == (int)atomPhase.PDB_VALUE)
{
if (lineChar == ',')
{
if (pdbOption == (int)pdbOptions.PDBNAME)
{
atom.pdbName = sb.ToString();
}
else if (pdbOption == (int)pdbOptions.RESNAME)
{
atom.residueName = sb.ToString();
}
else if (pdbOption == (int)pdbOptions.RESNUM)
{
atom.residueNumber = int.Parse(ToNumber(sb.ToString()));
}
phase = (int)atomPhase.PDB;
}
else if (lineChar == ')')
{
if (pdbOption == (int)pdbOptions.PDBNAME)
{
atom.pdbName = sb.ToString();
}
else if (pdbOption == (int)pdbOptions.RESNAME)
{
atom.residueName = sb.ToString();
}
else if (pdbOption == (int)pdbOptions.RESNUM)
{
atom.residueNumber = int.Parse(ToNumber(sb.ToString()));
}
phase = (int)atomPhase.FROZEN;
}
else
{
sb.Append(lineChar);
charNum++;
continue;
}
sb.Length = 0;
//Frozen is optional, so this could be the X coordinate
}
else if (phase == (int)atomPhase.FROZEN)
{
if (lineChar == ' ')
{
if (sb.Length == 0)
{
;
}
else if (sb.Length == 1)
{
atom.frozen = int.Parse(sb.ToString());
phase = (int)atomPhase.X;
}
else
{
position.x = float.Parse(sb.ToString());
phase = (int)atomPhase.Y;
}
}
else
{
sb.Append(lineChar);
charNum++;
continue;
}
sb.Length = 0;
charNum++;
continue;
}
else if (phase == (int)atomPhase.X)
{
if (lineChar == ' ')
{
if (sb.Length == 0)
{
;
}
else
{
position.x = float.Parse(sb.ToString());
phase = (int)atomPhase.Y;
}
}
else
{
sb.Append(lineChar);
charNum++;
continue;
}
sb.Length = 0;
charNum++;
continue;
}
else if (phase == (int)atomPhase.Y)
{
if (lineChar == ' ')
{
if (sb.Length == 0)
{
;
}
else
{
position.y = float.Parse(sb.ToString());
phase = (int)atomPhase.Z;
}
}
else
{
sb.Append(lineChar);
charNum++;
continue;
}
sb.Length = 0;
charNum++;
continue;
}
else if (phase == (int)atomPhase.Z)
{
if (lineChar == ' ')
{
if (sb.Length == 0)
{
;
}
else
{
position.z = float.Parse(sb.ToString());
atom.transform.position = position;
phase = (int)atomPhase.LAYER_NAME;
}
}
else
{
sb.Append(lineChar);
charNum++;
continue;
}
sb.Length = 0;
charNum++;
continue;
}
else if (phase == (int)atomPhase.LAYER_NAME)
{
if (lineChar == ' ')
{
if (sb.Length == 0)
{
;
}
else
{
if (sb[0] == 'H')
{
highAtoms.Add(index);
}
else if (sb[0] == 'M')
{
mediumAtoms.Add(index);
}
else if (sb[0] == 'L')
{
lowAtoms.Add(index);
}
phase = (int)atomPhase.LINK;
}
}
else
{
sb.Append(lineChar);
charNum++;
continue;
}
sb.Length = 0;
charNum++;
continue;
}
else if (phase == (int)atomPhase.LINK)
{
if (lineChar == ' ')
{
if (sb.Length == 0)
{
;
}
else
{
linkType = sb.ToString();
phase = (int)atomPhase.LINK_INDEX;
}
}
else if (lineChar == '-')
{
sb.Length = 0;
}
else
{
sb.Append(lineChar);
charNum++;
continue;
}
sb.Length = 0;
charNum++;
continue;
}
else if (phase == (int)atomPhase.LINK_INDEX)
{
if (lineChar == ' ')
{
if (sb.Length == 0)
{
;
}
else
{
linkIndex = int.Parse(sb.ToString());
gc.layers.AddLink(index, linkIndex, linkType);
charNum++;
continue;
}
}
else
{
sb.Append(lineChar);
charNum++;
continue;
}
sb.Length = 0;
charNum++;
continue;
}
charNum++;
}
atoms.AddAtom(atom);
index++;
lineNumber++;
if (lineNumber % globalSettings.maxLinesToYield == 0)
{
yield return(null);
}
}
}
gc.SetAtoms(atoms);
gc.layers.SetHighAtoms(highAtoms);
gc.layers.SetMediumAtoms(mediumAtoms);
gc.layers.SetLowAtoms(lowAtoms);
//Connectivity
atoms.graph.SetAtoms(atoms);
if (gc.geomOptions.Contains("connectivity"))
{
string[] splitConn;
int connectionNum;
int numConnections;
int connectionIndex0;
int connectionIndex1;
double bondOrder;
while (lineNumber < maxLines)
{
line = lines [lineNumber].Trim();
if (line == "")
{
break;
}
splitConn = line.Split(new [] { " " }, System.StringSplitOptions.RemoveEmptyEntries);
connectionIndex0 = int.Parse(splitConn [0]) - 1;
numConnections = (splitConn.Length - 1) / 2;
for (connectionNum = 0; connectionNum < numConnections; connectionNum++)
{
connectionIndex1 = int.Parse(splitConn [connectionNum * 2 + 1]) - 1;
bondOrder = double.Parse(splitConn [connectionNum * 2 + 2]);
atoms.graph.Connect(connectionIndex0, connectionIndex1, bondOrder);
}
lineNumber++;
if (lineNumber % globalSettings.maxLinesToYield == 0)
{
yield return(new WaitForSeconds(0.1f));
}
}
}
//Parameters
List <string> parameterLines = new List <string>();
while (lineNumber < maxLines)
{
line = lines [lineNumber].Trim();
parameterLines.Add(line);
lineNumber++;
}
IEnumerator iEnumerator = prmReader.ParametersFromPRMLines(parameterLines.ToArray(), atoms.graph.parameters);
while (iEnumerator.MoveNext())
{
}
atoms.graph.parameters.transform.parent = atoms.transform;
}
public IEnumerator AtomsFromPQRFile(string path, Atoms atoms, Atom atomPrefab)
{
atoms.globalSettings = globalSettings;
atoms.setSourceFile(path);
atoms.name = Path.GetFileName(path);
gc = Instantiate <GaussianCalculator> (GameObject.FindObjectOfType <PrefabManager>().gaussianCalculatorPrefab, atoms.transform);
atoms.gaussianCalculator = gc;
int index = 0;
int residueNumber;
int offset;
Vector3 position;
string[] splitLine;
List <int> highAtoms = new List <int>();
List <int> lowAtoms = new List <int>();
string[] lines = FileIO.Readlines(path, "#");
for (lineNumber = 0; lineNumber < lines.Length; lineNumber++)
{
line = lines [lineNumber];
if ((line.StartsWith("ATOM") || line.StartsWith("HETATM")))
{
Atom atom = Instantiate(atomPrefab, atoms.atomsHolder.transform);
splitLine = line.Split(new [] { " " }, System.StringSplitOptions.RemoveEmptyEntries);
//PDB
atom.pdbName = line.Substring(12, 4).Trim();
//Element
if (data.pdbToElementDict.ContainsKey(atom.pdbName.ToUpper()))
{
atom.element = data.pdbToElementDict [atom.pdbName];
}
else
{
atom.element = atom.pdbName.Substring(0, 1);
}
//Residue
atom.residueName = splitLine[3];
if (line.StartsWith("HETATM") && !(atom.residueName == "WAT" || atom.residueName == "HOH"))
{
highAtoms.Add(index);
}
else
{
lowAtoms.Add(index);
}
//Chain ID is optional in PQR, but can also merge with residue number
residueNumber = 0;
offset = 0;
if (!int.TryParse(splitLine [4], out residueNumber))
{
if (splitLine [4].Length == 1)
{
offset = 1;
atom.chainID = splitLine [4];
residueNumber = int.Parse(splitLine [5]);
}
else
{
atom.chainID = splitLine [4].Substring(0, 1);
residueNumber = int.Parse(splitLine [4].Substring(1));
}
}
atom.residueNumber = residueNumber;
//Position
position = new Vector3();
position.x = float.Parse(splitLine[5 + offset]);
position.y = float.Parse(splitLine[6 + offset]);
position.z = float.Parse(splitLine[7 + offset]);
atom.transform.position = position;
atom.partialCharge = float.Parse(splitLine[8 + offset]);
atom.vdwRadius = float.Parse(splitLine[9 + offset]);
atom.index = index;
atoms.AddAtom(atom);
//atom.resolution = globalSettings.ballResolution;
//atom.transform.SetParent(atoms.atomsHolder.transform);
//atoms.atomList.Add (atom);
index++;
}
if (lineNumber % globalSettings.maxLinesToYield == 0)
{
yield return(new WaitForSeconds(0.1f));
}
}
atoms.graph.SetAtoms(atoms);
gc.SetAtoms(atoms);
gc.layers.SetLowAtoms(lowAtoms);
gc.layers.SetHighAtoms(highAtoms);
yield return(null);
}
public IEnumerator AtomsFromPDBFile(string path, Atoms atoms, Atom atomPrefab, string alternateLocationID = "A")
{
atoms.globalSettings = globalSettings;
atoms.setSourceFile(path);
atoms.name = Path.GetFileName(path);
gc = Instantiate <GaussianCalculator> (GameObject.FindObjectOfType <PrefabManager>().gaussianCalculatorPrefab, atoms.transform);
atoms.gaussianCalculator = gc;
string element;
Vector3 position;
string chargeStr;
List <int> highAtoms = new List <int>();
List <int> lowAtoms = new List <int>();
int index = 0;
string[] lines = FileIO.Readlines(path, "#");
for (lineNumber = 0; lineNumber < lines.Length; lineNumber++)
{
line = lines [lineNumber];
if (
(
line.StartsWith("ATOM") ||
line.StartsWith("HETATM")
) && (
line [16].ToString() == " " ||
line [16].ToString() == alternateLocationID
))
{
Atom atom = Instantiate(atomPrefab, atoms.atomsHolder.transform);
element = line.Substring(76, 2).Trim();
//PDB
atom.pdbName = line.Substring(12, 4).Trim();
//Use PDB to get Atom
if (element == string.Empty)
{
//If 12th column is a letter, it is a metal
if (char.IsLetter(line [12]))
{
element = line.Substring(12, 2).Trim();
atom.element = ToAlpha(element);
}
else
{
element = line.Substring(12, 4).Trim();
atom.element = ToAlpha(element) [0].ToString();
}
}
else
{
if (element.Length > 1)
{
atom.element = element.Substring(0, 1).ToUpper() + element.Substring(1).ToLower();
}
else
{
atom.element = element;
}
}
//Residue
atom.residueName = line.Substring(17, 3).Trim();
atom.residueNumber = int.Parse(line.Substring(22, 4).Trim());
atom.chainID = line [21].ToString();
if (line.StartsWith("HETATM") && !(atom.residueName == "WAT" || atom.residueName == "HOH"))
{
highAtoms.Add(index);
}
else
{
lowAtoms.Add(index);
}
//Position
position = new Vector3();
position.x = float.Parse(line.Substring(30, 8));
position.y = float.Parse(line.Substring(38, 8));
position.z = float.Parse(line.Substring(46, 8));
atom.transform.position = position;
chargeStr = line [79].ToString();
if (chargeStr != " ")
{
if (line [78].ToString() == "-")
{
atom.formalCharge = -int.Parse(chargeStr);
}
else
{
atom.formalCharge = int.Parse(chargeStr);
}
}
atom.index = index;
atoms.AddAtom(atom);
index++;
}
if (lineNumber % globalSettings.maxLinesToYield == 0)
{
yield return(new WaitForSeconds(0.1f));
}
}
atoms.graph.SetAtoms(atoms);
gc.SetAtoms(atoms);
gc.layers.SetLowAtoms(lowAtoms);
gc.layers.SetHighAtoms(highAtoms);
yield return(null);
}