/// <summary>
/// build base unit cell of a crystal from atom coordinates from XML file,
/// symmetry operators for the space group
/// </summary>
/// <param name="crystalXmlFile">our own crystal XML file</param>
public Dictionary <string, AtomInfo[]> BuildCrystal(string crystalXmlFile)
{
// read data from crystal xml file
EntryCrystal thisEntryCrystal;
XmlSerializer xmlSerializer = new XmlSerializer(typeof(EntryCrystal));
FileStream xmlFileStream = new FileStream(crystalXmlFile, FileMode.Open);
thisEntryCrystal = (EntryCrystal)xmlSerializer.Deserialize(xmlFileStream);
crystal1 = thisEntryCrystal.crystal1;
xmlFileStream.Close();
if (AppSettings.symOps == null)
{
AppSettings.LoadSymOps();
}
if (crystal1.spaceGroup == "-")
{
crystal1.spaceGroup = "P 1";
}
SymOpMatrix[] symOpMatrices = AppSettings.symOps.FindSpaceGroup(crystal1.spaceGroup);
if (symOpMatrices == null)
{
throw new Exception("No symmetry operators provided for this entry " + crystalXmlFile);
}
cartn2fractMatrix = thisEntryCrystal.scaleCat.ScaleMatrix;
fract2cartnMatrix = cartn2fractMatrix.Inverse();
//ChainAtoms[] chainAtomsList = thisEntryCrystal.atomCat.ChainAtomList;
ChainAtoms[] chainAtomsList = new ChainAtoms [thisEntryCrystal.atomCat.ChainAtomList.Length];
switch (atomType.ToUpper())
{
case "CA":
chainAtomsList = thisEntryCrystal.atomCat.CalphaAtomList();
// clear the whole atom list,free memory
thisEntryCrystal.atomCat.ChainAtomList = null;
break;
case "CB":
chainAtomsList = thisEntryCrystal.atomCat.CbetaAtomList();
// clear the whole atom list, free memory
thisEntryCrystal.atomCat.ChainAtomList = null;
break;
case "CA_CB":
chainAtomsList = thisEntryCrystal.atomCat.CalphaCbetaAtomList();
// clear the whole atom list, free memory
thisEntryCrystal.atomCat.ChainAtomList = null;
break;
case "ALL":
chainAtomsList = thisEntryCrystal.atomCat.ChainAtomList;
break;
default:
break;
}
Dictionary <string, AtomInfo[]> crystalChainsHash = BuildCrystalBySymOps(chainAtomsList, symOpMatrices);
return(crystalChainsHash);
}
/// <summary>
/// build crystal from the xml serialization object and full symmetry operators
/// </summary>
/// <param name="thisEntryCrystal"></param>
/// <param name="symOpStrings"></param>
/// <param name="fullSymOpStrings"></param>
/// <returns></returns>
public Dictionary <string, AtomInfo[]> BuildPdbBu(EntryCrystal thisEntryCrystal, string[] symOpStrings, string[] fullSymOpStrings)
{
SymOperator symOp = new SymOperator();
CrystalInfo crystal1 = thisEntryCrystal.crystal1;
Dictionary <string, AtomInfo[]> crystalChainsHash = new Dictionary <string, AtomInfo[]>();
base.cartn2fractMatrix = thisEntryCrystal.scaleCat.ScaleMatrix;
base.fract2cartnMatrix = cartn2fractMatrix.Inverse();
AtomInfo[] transformedAtoms = null;
SymOpMatrix symOpMatrix = null;
//ChainAtoms[] chainAtomsList = thisEntryCrystal.atomCat.ChainAtomList;
ChainAtoms[] chainAtomsList = thisEntryCrystal.atomCat.ChainAtomList;
for (int i = 0; i < symOpStrings.Length; i++)
{
if (crystalChainsHash.ContainsKey(symOpStrings[i]))
{
continue;
}
string chainId = symOpStrings[i].Substring(0, symOpStrings[i].IndexOf("_"));
string symOpString = symOpStrings[i].Substring(symOpStrings[i].IndexOf("_") + 1,
symOpStrings[i].Length - symOpStrings[i].IndexOf("_") - 1);
int asymCount = 0;
for (asymCount = 0; asymCount < chainAtomsList.Length; asymCount++)
{
string asymChain = chainAtomsList[asymCount].AsymChain;
if (asymChain == chainId)
{
break;
}
}
if (symOpString == origSymOpString)
{
crystalChainsHash.Add(symOpStrings[i], chainAtomsList[asymCount].CartnAtoms);
continue;
}
// get the symmetry operator matrix
if (IsFullSymOpStringAMatrix(fullSymOpStrings[i]))
{
symOpMatrix = GetSymMatrixFromMatrixString(fullSymOpStrings[i]);
transformedAtoms = TransformChainByCartesianSymOp
(chainAtomsList[asymCount].CartnAtoms, symOpMatrix);
}
else
{
symOpMatrix = symOp.GetSymMatrix(fullSymOpStrings[i], symOpStrings[i]);
transformedAtoms = TransformChainBySpecificSymOp(chainAtomsList[asymCount].CartnAtoms, symOpMatrix);
}
crystalChainsHash.Add(symOpStrings[i], transformedAtoms);
}
return(crystalChainsHash);
}
public void SetCartn2fractMatrix(string xmlFile)
{
// read data from crystal xml file
EntryCrystal thisEntryCrystal;
XmlSerializer xmlSerializer = new XmlSerializer(typeof(EntryCrystal));
FileStream xmlFileStream = new FileStream(xmlFile, FileMode.Open);
thisEntryCrystal = (EntryCrystal)xmlSerializer.Deserialize(xmlFileStream);
crystal1 = thisEntryCrystal.crystal1;
xmlFileStream.Close();
cartn2fractMatrix = thisEntryCrystal.scaleCat.ScaleMatrix;
fract2cartnMatrix = cartn2fractMatrix.Inverse();
}
/// <summary>
/// calculate and transfer all chains based on the input symmetry strings
/// </summary>
/// <param name="thisEntryCrystal"></param>
/// <param name="symmetryStrings">digits: 2_565</param>
/// <returns></returns>
public Dictionary <string, AtomInfo[]> BuildCrystalWithAllChains(EntryCrystal thisEntryCrystal, string[] symmetryStrings)
{
SymOperator symOp = new SymOperator();
crystal1 = thisEntryCrystal.crystal1;
if (AppSettings.symOps == null)
{
AppSettings.LoadSymOps();
}
if (crystal1.spaceGroup == "-")
{
crystal1.spaceGroup = "P 1";
}
SymOpMatrix[] sgSymOpMatrices = AppSettings.symOps.FindSpaceGroup(crystal1.spaceGroup);
Dictionary <string, AtomInfo[]> crystalChainsHash = new Dictionary <string, AtomInfo[]>();
cartn2fractMatrix = thisEntryCrystal.scaleCat.ScaleMatrix;
fract2cartnMatrix = cartn2fractMatrix.Inverse();
ChainAtoms[] chainAtomsList = thisEntryCrystal.atomCat.ChainAtomList;
string symOpString = "";
for (int i = 0; i < symmetryStrings.Length; i++)
{
for (int asymCount = 0; asymCount < chainAtomsList.Length; asymCount++)
{
string asymChain = chainAtomsList[asymCount].AsymChain;
symOpString = asymChain + "_" + symmetryStrings[i];
if (crystalChainsHash.ContainsKey(symOpString))
{
continue;
}
if (symmetryStrings[i] == origSymOpString)
{
crystalChainsHash.Add(symOpString, chainAtomsList[asymCount].CartnAtoms);
continue;
}
SymOpMatrix symOpMatrix = symOp.GetSymmetryMatrixFromSymmetryString(sgSymOpMatrices, symmetryStrings[i]);
AtomInfo[] transformedAtoms = TransformChainBySpecificSymOp(chainAtomsList[asymCount].CartnAtoms, symOpMatrix);
crystalChainsHash.Add(symOpString, transformedAtoms);
}
}
return(crystalChainsHash);
}
/// <summary>
/// build base unit cell of a crystal from atom coordinates from XML file,
/// symmetry operators for the space group
/// </summary>
/// <param name="crystalXmlFile">our own crystal XML file</param>
public int[] BuildCrystal(string crystalXmlFile, ref Dictionary <string, AtomInfo[]> crystalChainsHash)
{
// read data from crystal xml file
EntryCrystal thisEntryCrystal;
XmlSerializer xmlSerializer = new XmlSerializer(typeof(EntryCrystal));
FileStream xmlFileStream = new FileStream(crystalXmlFile, FileMode.Open);
thisEntryCrystal = (EntryCrystal)xmlSerializer.Deserialize(xmlFileStream);
crystal1 = thisEntryCrystal.crystal1;
xmlFileStream.Close();
/* if (thisEntryCrystal.atomCat.IsOnlyCalphaChains())
* {
* throw new Exception("The crystal structure " + thisEntryCrystal.PdbId + " contains only Calpha atoms for at least of one chain. Skip it.");
* }*/
int[] maxSteps = BuildCrystal(thisEntryCrystal, ref crystalChainsHash);
return(maxSteps);
}
/// <summary>
/// build crystal from the xml serialization object and full symmetry operators
/// </summary>
/// <param name="thisEntryCrystal"></param>
/// <param name="symOpStrings"></param>
/// <param name="fullSymOpStrings"></param>
/// <returns></returns>
public Dictionary <string, AtomInfo[]> BuildCrystal(EntryCrystal thisEntryCrystal, string[] symOpStrings, string[] fullSymOpStrings)
{
SymOperator symOp = new SymOperator();
crystal1 = thisEntryCrystal.crystal1;
Dictionary <string, AtomInfo[]> crystalChainsHash = new Dictionary <string, AtomInfo[]>();
cartn2fractMatrix = thisEntryCrystal.scaleCat.ScaleMatrix;
fract2cartnMatrix = cartn2fractMatrix.Inverse();
//ChainAtoms[] chainAtomsList = thisEntryCrystal.atomCat.ChainAtomList;
ChainAtoms[] chainAtomsList = new ChainAtoms [thisEntryCrystal.atomCat.ChainAtomList.Length];
switch (atomType)
{
case "CA":
chainAtomsList = thisEntryCrystal.atomCat.CalphaAtomList();
// clear the whole atom list,free memory
thisEntryCrystal.atomCat.ChainAtomList = null;
break;
case "CB":
chainAtomsList = thisEntryCrystal.atomCat.CbetaAtomList();
// clear the whole atom list, free memory
thisEntryCrystal.atomCat.ChainAtomList = null;
break;
case "CA_CB":
chainAtomsList = thisEntryCrystal.atomCat.CalphaCbetaAtomList();
// clear the whole atom list, free memory
thisEntryCrystal.atomCat.ChainAtomList = null;
break;
case "ALL":
chainAtomsList = thisEntryCrystal.atomCat.ChainAtomList;
break;
default:
break;
}
for (int i = 0; i < symOpStrings.Length; i++)
{
if (crystalChainsHash.ContainsKey(symOpStrings[i]))
{
continue;
}
string chainId = symOpStrings[i].Substring(0, symOpStrings[i].IndexOf("_"));
string symOpString = symOpStrings[i].Substring(symOpStrings[i].IndexOf("_") + 1,
symOpStrings[i].Length - symOpStrings[i].IndexOf("_") - 1);
int asymCount = 0;
for (asymCount = 0; asymCount < chainAtomsList.Length; asymCount++)
{
string asymChain = chainAtomsList[asymCount].AsymChain;
if (asymChain == chainId)
{
break;
}
}
if (symOpString == origSymOpString)
{
crystalChainsHash.Add(symOpStrings[i], chainAtomsList[asymCount].CartnAtoms);
continue;
}
SymOpMatrix symOpMatrix = symOp.GetSymMatrix(fullSymOpStrings[i], symOpStrings[i]);
AtomInfo[] transformedAtoms = TransformChainBySpecificSymOp(chainAtomsList[asymCount].CartnAtoms, symOpMatrix);
crystalChainsHash.Add(symOpStrings[i], transformedAtoms);
}
return(crystalChainsHash);
}
/// <summary>
/// build base unit cell of a crystal from atom coordinates from XML file,
/// using symmetry operations provided as parameters
/// </summary>
/// <param name="crystalXmlFile">our own crystal XML file</param>
/// <param name="symOpStrings">specified symmetry operators</param>
public Dictionary <string, AtomInfo[]> BuildCrystal(string crystalXmlFile, string[] symOpStrings)
{
SymOperator symOp = new SymOperator();
// read data from crystal xml file
EntryCrystal thisEntryCrystal;
XmlSerializer xmlSerializer = new XmlSerializer(typeof(EntryCrystal));
FileStream xmlFileStream = new FileStream(crystalXmlFile, FileMode.Open);
thisEntryCrystal = (EntryCrystal)xmlSerializer.Deserialize(xmlFileStream);
crystal1 = thisEntryCrystal.crystal1;
xmlFileStream.Close();
Dictionary <string, AtomInfo[]> crystalChainsHash = new Dictionary <string, AtomInfo[]>();
if (AppSettings.symOps == null)
{
AppSettings.LoadSymOps();
}
if (crystal1.spaceGroup == "-" || crystal1.spaceGroup == "")
{
crystal1.spaceGroup = "P 1";
}
SymOpMatrix[] sgSymOpMatrices = AppSettings.symOps.FindSpaceGroup(crystal1.spaceGroup);
if (sgSymOpMatrices == null)
{
throw new Exception("No symmetry operators provided for this entry " + crystalXmlFile);
}
cartn2fractMatrix = thisEntryCrystal.scaleCat.ScaleMatrix;
fract2cartnMatrix = cartn2fractMatrix.Inverse();
// ChainAtoms[] chainAtomsList = thisEntryCrystal.atomCat.ChainAtomList;
ChainAtoms[] chainAtomsList = new ChainAtoms [thisEntryCrystal.atomCat.ChainAtomList.Length];
switch (atomType)
{
case "CA":
chainAtomsList = thisEntryCrystal.atomCat.CalphaAtomList();
// clear the whole atom list,free memory
thisEntryCrystal.atomCat.ChainAtomList = null;
break;
case "CB":
chainAtomsList = thisEntryCrystal.atomCat.CbetaAtomList();
// clear the whole atom list, free memory
thisEntryCrystal.atomCat.ChainAtomList = null;
break;
case "CA_CB":
chainAtomsList = thisEntryCrystal.atomCat.CalphaCbetaAtomList();
// clear the whole atom list, free memory
thisEntryCrystal.atomCat.ChainAtomList = null;
break;
case "ALL":
chainAtomsList = thisEntryCrystal.atomCat.ChainAtomList;
break;
default:
break;
}
// just in case, something is messed up. It should not happen often.
// may hide some bugs
// add on Feb. 20, 2009
bool chainFound = false;
for (int i = 0; i < symOpStrings.Length; i++)
{
string chainId = symOpStrings[i].Substring(0, symOpStrings[i].IndexOf("_"));
string symOpString = symOpStrings[i].Substring(symOpStrings[i].IndexOf("_") + 1,
symOpStrings[i].Length - symOpStrings[i].IndexOf("_") - 1);
int asymCount = 0;
chainFound = false;
for (asymCount = 0; asymCount < chainAtomsList.Length; asymCount++)
{
string asymChain = chainAtomsList[asymCount].AsymChain;
if (asymChain == chainId)
{
chainFound = true;
break;
}
}
if (!chainFound)
{
continue;
}
if (symOpString == origSymOpString)
{
crystalChainsHash.Add(symOpStrings[i], chainAtomsList[asymCount].CartnAtoms);
continue;
}
try
{
SymOpMatrix symOpMatrix = symOp.GetSymmetryMatrixFromSymmetryString(sgSymOpMatrices, symOpString);
AtomInfo[] transformedAtoms = TransformChainBySpecificSymOp(chainAtomsList[asymCount].CartnAtoms, symOpMatrix);
crystalChainsHash.Add(symOpStrings[i], transformedAtoms);
}
catch
{
continue;
}
}
return(crystalChainsHash);
}
