/// <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>
///
/// </summary>
/// <param name="xmlFile"></param>
/// <param name="chainMatrixHash"></param>
/// <returns></returns>
public Dictionary<string, AtomInfo[]> BuildOneBuAssembly(string xmlFile, Dictionary<string, List<SymOpMatrix>> chainMatrixHash, string type)
{
Dictionary<string, AtomInfo[]> chainCoordHash = new Dictionary<string, AtomInfo[]>();
// 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);
xmlFileStream.Close();
ChainAtoms[] chainAtomsList = thisEntryCrystal.atomCat.ChainAtomList;
ChainAtoms thisChain = null;
foreach (string asymChain in chainMatrixHash.Keys)
{
thisChain = null; // fixed on June 30, 2010
foreach (ChainAtoms chain in chainAtomsList)
{
if (chain.AsymChain == asymChain)
{
thisChain = chain;
break;
}
}
if (thisChain == null)
{
continue;
}
string chainSymOpString = "";
foreach (SymOpMatrix symMatrix in chainMatrixHash[asymChain])
{
if (symMatrix.symmetryString == "-" || symMatrix.symmetryString == "")
{
chainSymOpString = asymChain + "_" + symMatrix.symmetryOpNum + "_-";
}
else
{
chainSymOpString = asymChain + "_" + symMatrix.symmetryString;
if (type == "pisa")
{
if (symMatrix.symmetryOpNum != "" && symMatrix.symmetryOpNum != "0")
{
chainSymOpString += ("(" + symMatrix.symmetryOpNum + ")"); // those non-ncs operator (same symmetry string)
}
}
}
if (! chainCoordHash.ContainsKey(chainSymOpString))
{
AtomInfo[] atoms = BuildOneChain(thisChain, symMatrix);
chainCoordHash.Add(chainSymOpString, atoms);
}
}
}
return chainCoordHash;
}
public ChainAtoms(ChainAtoms extChain)
{
this.asymChain = extChain.AsymChain;
this.entityId = extChain.entityId;
this.polymerType = extChain.PolymerType;
this.cartnAtoms = new List <AtomInfo> ();
foreach (AtomInfo atom in extChain.CartnAtoms)
{
this.cartnAtoms.Add((AtomInfo)atom.Clone());
}
}
public int[] BuildCrystal(EntryCrystal thisEntryCrystal, ref Dictionary <string, AtomInfo[]> crystalChainsHash)
{
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 " + thisEntryCrystal.PdbId);
}
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;
}
crystalChainsHash = BuildCrystalBySymOps(chainAtomsList, symOpMatrices);
int[] maxSteps = TranslateUnitCell(ref crystalChainsHash);
return(maxSteps);
}
/// <summary>
///
/// </summary>
/// <param name="xmlFile"></param>
/// <param name="chainMatrixHash"></param>
/// <returns></returns>
public Dictionary<string, AtomInfo[]> BuildOneBuAssembly(EntryCrystal thisEntryCrystal, Dictionary<string, List<SymOpMatrix>> chainMatrixHash, string type)
{
Dictionary<string, AtomInfo[]> chainCoordHash = new Dictionary<string,AtomInfo[]> ();
ChainAtoms[] chainAtomsList = thisEntryCrystal.atomCat.ChainAtomList;
ChainAtoms thisChain = null;
foreach (string asymChain in chainMatrixHash.Keys)
{
thisChain = null; // fixed on June 30, 2010
foreach (ChainAtoms chain in chainAtomsList)
{
if (chain.AsymChain == asymChain)
{
thisChain = chain;
break;
}
}
if (thisChain == null)
{
continue;
}
string chainSymOpString = "";
foreach (SymOpMatrix symMatrix in chainMatrixHash[asymChain])
{
if (symMatrix.symmetryString == "-" || symMatrix.symmetryString == "")
{
chainSymOpString = asymChain + "_" + symMatrix.symmetryOpNum + "_-";
}
else
{
chainSymOpString = asymChain + "_" + symMatrix.symmetryString;
if (type == "pisa")
{
if (symMatrix.symmetryOpNum != "" && symMatrix.symmetryOpNum != "0")
{
chainSymOpString += ("(" + symMatrix.symmetryOpNum + ")"); // for those non-NCS operator (same symmetry string)
}
}
}
if (!chainCoordHash.ContainsKey(chainSymOpString))
{
AtomInfo[] atoms = BuildOneChain(thisChain, symMatrix);
chainCoordHash.Add(chainSymOpString, atoms);
}
}
}
return chainCoordHash;
}
/// <summary>
/// chains and their backbone atoms
/// </summary>
public ChainAtoms[] BackboneAtomList()
{
ChainAtoms[] backboneChainList = new ChainAtoms [chainAtomsList.Count];
for (int i = 0; i < chainAtomsList.Count; i++)
{
ChainAtoms backboneChainAtoms = new ChainAtoms();
backboneChainAtoms.CartnAtoms = ((ChainAtoms)chainAtomsList[i]).BackboneAtoms();
backboneChainAtoms.AsymChain = ((ChainAtoms)chainAtomsList[i]).AsymChain;
backboneChainAtoms.EntityID = ((ChainAtoms)chainAtomsList[i]).EntityID;
backboneChainAtoms.PolymerType = ((ChainAtoms)chainAtomsList[i]).PolymerType;
backboneChainList[i] = backboneChainAtoms;
}
return(backboneChainList);
}
/// <summary>
/// chains and their Calpha and Cbeta atoms
/// </summary>
/// <returns></returns>
public ChainAtoms[] CalphaCbetaAtomList()
{
ChainAtoms[] calphaCbetaChainList = new ChainAtoms [chainAtomsList.Count];
for (int i = 0; i < chainAtomsList.Count; i++)
{
ChainAtoms chainCalphaCbetaAtoms = new ChainAtoms();
chainCalphaCbetaAtoms.CartnAtoms = ((ChainAtoms)chainAtomsList[i]).CalphaCbetaAtoms();
chainCalphaCbetaAtoms.AsymChain = ((ChainAtoms)chainAtomsList[i]).AsymChain;
chainCalphaCbetaAtoms.EntityID = ((ChainAtoms)chainAtomsList[i]).EntityID;
chainCalphaCbetaAtoms.PolymerType = ((ChainAtoms)chainAtomsList[i]).PolymerType;
calphaCbetaChainList[i] = chainCalphaCbetaAtoms;
}
return(calphaCbetaChainList);
}
/// <summary>
/// transform one chain
/// </summary>
/// <param name="chain"></param>
/// <param name="symMatrix"></param>
/// <returns></returns>
public AtomInfo[] BuildOneChain(ChainAtoms chain, SymOpMatrix symMatrix)
{
if (symMatrix.symmetryString == "1_555")
{
return chain.CartnAtoms;
}
AtomInfo[] transformedAtoms = new AtomInfo[chain.CartnAtoms.Length];
int i = 0;
foreach (AtomInfo atom in chain.CartnAtoms)
{
AtomInfo transformedAtom = atom.TransformAtom(symMatrix);
transformedAtoms[i] = transformedAtom;
i++;
}
return transformedAtoms;
}
/// <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);
}
/// <summary>
/// build asymmetric unit from NCS
/// </summary>
/// <param name="thisEntryCrystal"></param>
/// <returns></returns>
// public void BuildAsymUnitFromNcs (ref EntryCrystal thisEntryCrystal, string[] origAsymChains, out bool asuChanged)
public void BuildAsymUnitFromNcs(ref EntryCrystal thisEntryCrystal, out bool asuChanged)
{
asuChanged = false;
// chainLetters = "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789";
// ChainAtoms[] chainAtomsList = new ChainAtoms [thisEntryCrystal.atomCat.ChainAtomList.Length];
int genNcsNum = 0;
foreach (NcsOperator ncsOp in thisEntryCrystal.ncsCat.NcsOperatorList)
{
if (ncsOp.code == "generate")
{
genNcsNum++;
}
}
if (genNcsNum == 0)
{
return;
}
else if (genNcsNum * thisEntryCrystal.atomCat.ChainAtomList.Length > chainLetters.Length)
/* else if (genNcsNum > chainLetters.Length) */
{
return;
}
List <ChainAtoms> asuChainList = new List <ChainAtoms>();
// RemoveOrigAsuChainNames (thisEntryCrystal.atomCat.ChainAtomList, ref chainLetters);
// int ncsChainCount = 1;
foreach (ChainAtoms chain in thisEntryCrystal.atomCat.ChainAtomList)
{
/* if (chain.PolymerType != "polypeptide")
* {
* continue;
* }*/
asuChainList.Add(chain);
// ncsChainCount = 1;
foreach (NcsOperator ncsOp in thisEntryCrystal.ncsCat.NcsOperatorList)
{
if (ncsOp.code == "given")
{
continue;
}
AtomInfo[] ncsAtoms = ApplyNcsMatrix(chain.CartnAtoms, ncsOp.ncsMatrix);
if (DoesChainExist(ncsAtoms, thisEntryCrystal.atomCat.ChainAtomList))
{
continue;
}
asuChanged = true;
ChainAtoms newChain = new ChainAtoms(chain);
newChain.CartnAtoms = ncsAtoms;
// newChain.AsymChain = chain.AsymChain + chainLetters[ncsChainCount].ToString ();
// newChain.AsymChain =GetAsymChainNameForNcsChain (ref ncsChainCount, chain.AsymChain, origAsymChains);
// name the new chain with original asymmetric chain + a number,
// this should distinguish the original asymmetri chains with these regenerated chains
// newChain.AsymChain = chain.AsymChain + ncsChainCount.ToString();
newChain.AsymChain = chain.AsymChain + ncsOp.ncsId.ToString();
// ncsChainCount ++;
asuChainList.Add(newChain);
}
}
thisEntryCrystal.atomCat.ChainAtomList = asuChainList.ToArray();
}
/// <summary>
/// add asymmetry chain
/// </summary>
/// <param name="chainAtoms"></param>
public void AddChainAtoms(ChainAtoms chainAtoms)
{
chainAtomsList.Add(chainAtoms);
}