/// <summary>
///
/// </summary>
public static void InitializeGroupTable()
{
DbCreator dbCreator = new DbCreator();
string createTableString = "";
string createIndexString = "";
string tableName = ProtCidSettings.dataType + "HomoSeqInfo";
createTableString = "CREATE TABLE " + tableName + " ( " +
"GroupSeqID INTEGER NOT NULL, " +
"PdbID CHAR(4) NOT NULL, " +
"SpaceGroup VARCHAR(30) NOT NULL, " +
"ASU VARCHAR(50) NOT NULL, " +
"Method VARCHAR(100) NOT NULL, " +
"Resolution FLOAT NOT NULL, " +
"InPfam CHAR NOT NULL);";
dbCreator.CreateTableFromString(ProtCidSettings.protcidDbConnection, createTableString, tableName);
createIndexString = string.Format("CREATE INDEX {0}_idx1 ON {0} (GroupSeqID);", tableName);
dbCreator.CreateIndex(ProtCidSettings.protcidDbConnection, createIndexString, tableName);
createIndexString = string.Format("CREATE INDEX {0}_idx2 ON {0} (PdbID);", tableName);
dbCreator.CreateIndex(ProtCidSettings.protcidDbConnection, createIndexString, tableName);
tableName = ProtCidSettings.dataType + "Groups";
createTableString = "CREATE TABLE " + tableName + " ( " +
"GroupSeqID INTEGER NOT NULL, " +
"EntryPfamArch BLOB Sub_Type TEXT NOT NULL);";
dbCreator.CreateTableFromString(ProtCidSettings.protcidDbConnection, createTableString, tableName);
createIndexString = string.Format("CREATE INDEX {0}_idx1 ON {0} (GroupSeqID);", tableName);
dbCreator.CreateIndex(ProtCidSettings.protcidDbConnection, createIndexString, tableName);
}
/// <summary>
///
/// </summary>
private void InitializeResiduesContactsTables()
{
DbCreator dbCreator = new DbCreator();
string tableName = "SgInterfaceResidues";
string createTableString = "CREATE TABLE " + tableName + " ( " +
"PDBID CHAR(4) NOT NULL, " +
"INTERFACEID INTEGER NOT NULL, " +
"RESIDUE1 CHAR(3) NOT NULL, " +
"SEQID1 CHAR(5) NOT NULL, " +
"RESIDUE2 CHAR(3) NOT NULL, " +
"SEQID2 CHAR(5) NOT NULL, " +
"DISTANCE FLOAT NOT NULL);";
dbCreator.CreateTableFromString(ProtCidSettings.protcidDbConnection, createTableString, tableName);
string createIdxString = string.Format("CREATE INDEX {0}_Idx1 ON {0} (PdbID, InterfaceID);", tableName);
dbCreator.CreateIndex(ProtCidSettings.protcidDbConnection, createIdxString, tableName);
tableName = "SgInterfaceContacts";
createTableString = "CREATE TABLE " + tableName + " ( " +
"PDBID CHAR(4) NOT NULL, " +
"INTERFACEID INTEGER NOT NULL, " +
"RESIDUE1 CHAR(3) NOT NULL, " +
"SEQID1 CHAR(5) NOT NULL, " +
"RESIDUE2 CHAR(3) NOT NULL, " +
"SEQID2 CHAR(5) NOT NULL, " +
"DISTANCE FLOAT NOT NULL);";
dbCreator.CreateTableFromString(ProtCidSettings.protcidDbConnection, createTableString, tableName);
createIdxString = string.Format("CREATE INDEX {0}_Idx1 ON {0} (PdbID, InterfaceID);", tableName);
dbCreator.CreateIndex(ProtCidSettings.protcidDbConnection, createIdxString, tableName);
}
/// <summary>
///
/// </summary>
private void InitializeDbTables()
{
DbCreator dbCreate = new DbCreator();
if (dbCreate.IsTableExist(ProtCidSettings.protcidDbConnection, crystBuInterfaceCompTables[(int)BuType.PDB].TableName))
{
return;
}
string createTableString = string.Format("Create Table {0} ( " +
"PdbID CHAR(4) NOT NULL, InterfaceId INTEGER NOT NULL, " +
"BuID VARCHAR(8), BuInterfaceID INTEGER, QScore FLOAT);",
crystBuInterfaceCompTables[(int)BuType.PDB].TableName);
dbCreate.CreateTableFromString(ProtCidSettings.protcidDbConnection, createTableString, crystBuInterfaceCompTables[(int)BuType.PDB].TableName);
string indexString = string.Format("Create INDEX {0}_Idx1 " +
" ON {0} (PdbID, InterfaceID);", crystBuInterfaceCompTables[(int)BuType.PDB].TableName);
dbCreate.CreateIndex(ProtCidSettings.protcidDbConnection, indexString, crystBuInterfaceCompTables[(int)BuType.PDB].TableName);
createTableString = string.Format("Create Table {0} ( " +
"PdbID CHAR(4) NOT NULL, InterfaceId INTEGER NOT NULL, " +
"BuID VARCHAR(8), BuInterfaceID INTEGER, QScore FLOAT);",
crystBuInterfaceCompTables[(int)BuType.PISA].TableName);
dbCreate.CreateTableFromString(ProtCidSettings.protcidDbConnection, createTableString, crystBuInterfaceCompTables[(int)BuType.PISA].TableName);
indexString = string.Format("Create INDEX {0}_Idx1 " +
" ON {0} (PdbID, InterfaceID);", crystBuInterfaceCompTables[(int)BuType.PISA].TableName);
dbCreate.CreateIndex(ProtCidSettings.protcidDbConnection, indexString, crystBuInterfaceCompTables[(int)BuType.PISA].TableName);
}
/// <summary>
///
/// </summary>
public static void InitializeDomainDbTables()
{
DbCreator dbCreator = new DbCreator();
string tableName = "";
string createTableString = "";
string createIndexString = "";
#region domain interfaces data
foreach (string buType in BuCompBuilder.buTypes)
{
if (buType == "asu")
{
tableName = buType + "PfamDomainInterfaces";
}
else
{
tableName = buType + "PfamBuDomainInterfaces";
}
createTableString = "CREATE TABLE " + tableName + " ( " +
"RelSeqID INTEGER NOT NULL, " +
"PdbID CHAR(4) NOT NULL, " +
"BUID VARCHAR(8) NOT NULL, " +
"InterfaceID INTEGER NOT NULL, " +
"DomainInterfaceID INTEGER NOT NULL, " +
"DomainID1 INTEGER NOT NULL, " +
"DomainID2 INTEGER NOT NULL, " +
"IsReversed CHAR(1) NOT NULL );";
dbCreator.CreateTableFromString(ProtCidSettings.buCompConnection, createTableString, tableName);
createIndexString = string.Format("CREATE INDEX {0}_Idx1 ON {0} (PdbID, BuID);", tableName);
dbCreator.CreateIndex(ProtCidSettings.buCompConnection, createIndexString, tableName);
if (buType == "asu")
{
tableName = "AsuIntraDomainInterfaces";
createTableString = "CREATE TABLE AsuIntraDomainInterfaces ( " +
"RelSeqID INTEGER NOT NULL, " +
"PdbID CHAR(4) NOT NULL, " +
"AsymChain CHAR(3) NOT NULL, " +
"DomainInterfaceID INTEGER NOT NULL, " +
"DomainID1 INTEGER NOT NULL, " +
"DomainID2 INTEGER NOT NULL, " +
"IsReversed CHAR(1) NOT NULL);";
dbCreator.CreateTableFromString(ProtCidSettings.buCompConnection, createTableString, tableName);
createIndexString = string.Format("CREATE INDEX AsuIntraDInterfaces_Idx1 ON {0} (PdbID, AsymChain);", tableName);
dbCreator.CreateIndex(ProtCidSettings.buCompConnection, createIndexString, tableName);
}
}
tableName = "PfamRelations";
createTableString = "CREATE TABLE " + tableName + " ( " +
"RelSeqID INTEGER NOT NULL, " +
"FamilyCode1 VARCHAR(15) NOT NULL, " +
"FamilyCode2 VARCHAR(15) NOT NULL );";
dbCreator.CreateTableFromString(ProtCidSettings.buCompConnection, createTableString, tableName);
createIndexString = string.Format("CREATE INDEX {0}_Idx1 ON {0} (RelSeqID);", tableName);
dbCreator.CreateIndex(ProtCidSettings.buCompConnection, createIndexString, tableName);
#endregion
}
/// <summary>
///
/// </summary>
/// <returns></returns>
private DataTable CreateTables(bool isUpdate)
{
DataTable pepInterfaceClusterStatTable = new DataTable("PfamPepClusterSumInfo");
string[] sumColumns = { "PfamID", "ClusterID", "NumEntries", "NumPepPfams", "NumUnpSeqs", "NumCFs",
"NumPepUnpSeqs", "NumPepSeqs", "SurfaceArea", "MinSeqIdentity", "ClusterInterface" };
foreach (string col in sumColumns)
{
pepInterfaceClusterStatTable.Columns.Add(new DataColumn(col));
}
if (!isUpdate)
{
DbCreator dbCreate = new DbCreator();
string createTableString = "Create Table " + pepInterfaceClusterStatTable.TableName + " ( " +
" PfamID VARCHAR(40) NOT NULL, " +
" ClusterID Integer Not NULL, " +
" NumEntries Integer NOT NULL, " +
" NumCFs Integer NOT NULL," +
" NumPepPfams Integer NOT NULL, " +
" NumUnpSeqs Integer NOT NULL, " +
" NumPepUnpSeqs Integer Not NULL, " +
" NumPepSeqs Integer Not NULL, " +
" SurfaceArea FLOAT, " +
" MinSeqIdentity FLOAT, " +
" ClusterInterface CHAR(10));";
dbCreate.CreateTableFromString(ProtCidSettings.protcidDbConnection, createTableString, pepInterfaceClusterStatTable.TableName);
}
return(pepInterfaceClusterStatTable);
}
/// <summary>
///
/// </summary>
/// <param name="isUpdate"></param>
/// <returns></returns>
private DataTable CreateTable(bool isUpdate)
{
string tableName = "PfamClansInPDB";
string[] clanColumns = { "ClanAcc", "NumPfams", "NumPfamsPdb", "NumPfamsPeptide", "NumPfamsDnaRna", "NumEntries", "NumUniprots" };
DataTable pfamClansPdbTable = new DataTable(tableName);
foreach (string col in clanColumns)
{
pfamClansPdbTable.Columns.Add(new DataColumn(col));
}
if (!isUpdate)
{
string createTableString = "Create Table " + tableName + " ( " +
" ClanAcc VARCHAR(10) NOT NULL, " +
" NumPfams Integer NOT NULL, " +
" NumPfamsPdb Integer NOT NULL, " +
" NumPfamsPeptide Integer NOT NULL, " +
" NumPfamsDnaRna Integer NOT NULL, " +
" NumEntries Integer NOT NULL, " +
" NumUniProts Integer NOT NULL " +
");";
DbCreator dbCreator = new DbCreator();
dbCreator.CreateTableFromString(ProtCidSettings.pdbfamDbConnection, createTableString, "PfamClansInPDB");
}
return(pfamClansPdbTable);
}
/// <summary>
///
/// </summary>
/// <param name="isUpdate"></param>
private void CreateTables(bool isUpdate)
{
pfamLigandClusterTable = new DataTable(tableName);
string[] clusterCols = { "PfamID", "ClusterID", "PdbID", "ChainDomainID", "LigandChain", "LigandFileChain" };
foreach (string col in clusterCols)
{
pfamLigandClusterTable.Columns.Add(new DataColumn(col));
}
if (!isUpdate)
{
DbCreator dbCreate = new DbCreator();
string createTableString = "Create Table " + tableName + " ( " +
"PfamID varchar(40) NOT NULL, " +
"ClusterID Integer NOT NULL, " +
"PdbID char(4) Not Null, " +
"ChainDomainID Integer Not Null, " +
"LigandChain char(3) Not Null, " +
"LigandFileChain char(3) Not Null);";
dbCreate.CreateTableFromString(ProtCidSettings.protcidDbConnection, createTableString, tableName);
string createIndexString = "Create Index " + tableName + "_cluster ON " + tableName + "(PfamID, ClusterID);";
dbCreate.CreateIndex(ProtCidSettings.protcidDbConnection, createIndexString, tableName);
createIndexString = "Create Index " + tableName + "_pdb ON " + tableName + "(PdbID, ChainDomainID);";
dbCreate.CreateIndex(ProtCidSettings.protcidDbConnection, createIndexString, tableName);
}
}
/// <summary>
///
/// </summary>
/// <param name="isUpdate"></param>
private void InitializeTables(bool isUpdate)
{
string tableName = "PdbPfamDomainFileInfo";
string[] tableCols = { "PdbID", "DomainID", "EntityID", "AsymChain", "SeqStart", "SeqEnd", "FileStart", "FileEnd" };
domainFileInfoTable = new DataTable(tableName);
foreach (string col in tableCols)
{
domainFileInfoTable.Columns.Add(new DataColumn(col));
}
if (!isUpdate)
{
DbCreator dbCreate = new DbCreator();
string createTableString = "CREATE TABLE " + tableName + " ( " +
"PdbID CHAR(4) NOT NULL, " +
"DomainID BIGINT NOT NULL, " +
"EntityID INTEGER NOT NULL, " +
"AsymChain CHAR(3) NOT NULL, " +
"SeqStart INTEGER NOT NULL, " +
"SeqEnd INTEGER NOT NULL, " +
"FileStart INTEGER NOT NULL, " +
"FileEnd INTEGER NOT NULL );";
dbCreate.CreateTableFromString(createTableString, tableName);
string createIndexString = "CREATE INDEX " + tableName + "_idx1 ON " + tableName + "(PdbID);";
dbCreate.CreateIndex(createIndexString, tableName);
createIndexString = "CREATE INDEX " + tableName + "_idx2 ON " + tableName + "(DomainID);";
dbCreate.CreateIndex(createIndexString, tableName);
}
}
/// <summary>
///
/// </summary>
/// <param name="isUpdate"></param>
private void CreateTables(bool isUpdate)
{
InitializeComHmmTable();
if (! isUpdate)
{
DbCreator dbCreate = new DbCreator ();
string dbCreateTableString = "Create Table " + tableName + " ( " +
"PfamID Varchar(40) Not Null, " +
"PdbID1 char(4) Not Null, " +
"ChainDomainID1 Integer Not Null, " +
"LigandChain1 char(3) Not Null, " +
"PdbID2 char(4) Not Null, " +
"ChainDomainID2 Integer Not Null, " +
"LigandChain2 char(3) Not Null, " +
"NumOfHmmSites1 Integer Not Null, " +
"NumOfHmmSites2 Integer Not Null, " +
"NumOfComHmmSites Integer Not Null, " +
"Jscore FLOAT Not Null);";
dbCreate.CreateTableFromString(ProtCidSettings.protcidDbConnection, dbCreateTableString, tableName);
string indexString = "Create Index PfamLigandComHmm_pfam on " + tableName + " (PfamID)";
dbCreate.CreateIndex(ProtCidSettings.protcidDbConnection, indexString, tableName);
indexString = "Create Index PfamLigandComHmm_pdb on " + tableName + "(PdbID1, PdbID2)";
dbCreate.CreateIndex(ProtCidSettings.protcidDbConnection, indexString, tableName);
indexString = "Create Index PfamLigandComHmm_pdb1 on " + tableName + "(PdbID1, ChainDomainID1)";
dbCreate.CreateIndex(ProtCidSettings.protcidDbConnection, indexString, tableName);
indexString = "Create Index PfamLigandComHmm_pdb2 on " + tableName + "(PdbID2, ChainDomainID2)";
dbCreate.CreateIndex(ProtCidSettings.protcidDbConnection, indexString, tableName);
}
}
private void InitializeDbTable()
{
DbCreator dbCreat = new DbCreator();
string createTableString = string.Format("CREATE TABLE {0} ( " +
" GroupSeqID INTEGER NOT NULL, " +
" CfGroupID INTEGER NOT NULL, " +
" PdbID CHAR(4) NOT NULL, " +
" SpaceGroup VARCHAR(30) NOT NULL, " +
" ASU VARCHAR(255) NOT NULL);",
GroupDbTableNames.dbTableNames[GroupDbTableNames.NonredundantCfGroups]);
dbCreat.CreateTableFromString(ProtCidSettings.protcidDbConnection, createTableString,
GroupDbTableNames.dbTableNames[GroupDbTableNames.NonredundantCfGroups]);
string indexString = string.Format("Create Index {0}_pdb on {0} (PdbID);",
GroupDbTableNames.dbTableNames[GroupDbTableNames.NonredundantCfGroups]);
dbCreat.CreateIndex(ProtCidSettings.protcidDbConnection, indexString,
GroupDbTableNames.dbTableNames[GroupDbTableNames.NonredundantCfGroups]);
indexString = string.Format("Create Index {0}_groupcf on {0} (GroupSeqID, CfGroupID);",
GroupDbTableNames.dbTableNames[GroupDbTableNames.NonredundantCfGroups]);
dbCreat.CreateIndex(ProtCidSettings.protcidDbConnection, indexString,
GroupDbTableNames.dbTableNames[GroupDbTableNames.NonredundantCfGroups]);
}
/// <summary>
///
/// </summary>
/// <param name="isUpdate"></param>
/// <returns></returns>
private DataTable CreatePfamDnaRnaInteractTable(bool isUpdate)
{
string[] pfamDnaRnaCols = { "PdbID", "BuID", "ChainDomainID", "PfamID", "DnaRnaChain", "DnaRnaSymmetryString",
"AsymChain", "SymmetryString", "DnaRnaSeqID", "SeqID", "HmmSeqID" };
DataTable pfamDnaRnaTable = new DataTable("pfamDnaRnas");
foreach (string col in pfamDnaRnaCols)
{
pfamDnaRnaTable.Columns.Add(new DataColumn(col));
}
if (!isUpdate)
{
DbCreator dbCreate = new DbCreator();
string createTableString = "Create Table " + pfamDnaRnaTable.TableName + " ( " +
" PdbID CHAR(4) NOT NULL, " +
" BuID VARCHAR(8) NOT NULL, " +
" PfamID VARCHAR(40) NOT NULL, " +
" ChainDomainID INTEGER NOT NULL, " +
" DnaRnaChain CHAR(3) NOT NULL, " +
" DnaRnaSymmetryString VARCHAR(15), " +
" DnaRnaSeqID INTEGER NOT NULL, " +
" AsymChain CHAR(3) NOT NULL, " +
" SymmetryString VARCHAR(15), " +
" SeqID INTEGER NOT NULL, " +
" HmmSeqID INTEGER NOT NULL);";
dbCreate.CreateTableFromString(ProtCidSettings.protcidDbConnection, createTableString, pfamDnaRnaTable.TableName);
string createIndexString = "CREATE INDEX " + pfamDnaRnaTable.TableName + "_idx1 ON " + pfamDnaRnaTable.TableName + "(PdbID, ChainDomainID);";
dbCreate.CreateIndex(ProtCidSettings.protcidDbConnection, createIndexString, pfamDnaRnaTable.TableName);
}
return(pfamDnaRnaTable);
}
/// <summary>
///
/// </summary>
private DataTable InitializeTable(bool isUpdate)
{
string[] pfamLigandColumns = { "PdbID", "AsymID", "ChainAsymID", "SeqID", "ChainSeqID", "Distance",
"Atom", "ChainAtom", "Residue", "ChainResidue" };
DataTable pfamLigandTable = new DataTable("ChainLigands");
foreach (string ligandCol in pfamLigandColumns)
{
pfamLigandTable.Columns.Add(new DataColumn(ligandCol));
}
if (!isUpdate)
{
DbCreator dbCreate = new DbCreator();
string createTableString = "Create Table " + pfamLigandTable.TableName + " (" +
" PdbID CHAR(4) NOT NULL, " +
" AsymID CHAR(3) NOT NULL, " +
// " Ligand CHAR(5) NOT NULL, " +
" ChainAsymID CHAR(3), " +
" SeqID INTEGER NOT NULL, " +
" ChainSeqID INTEGER NOT NULL, " +
" ATOM CHAR(4) NOT NULL, " +
" ChainATom CHAR(4), " +
" Residue CHAR(3), " +
" ChainResidue CHAR(3), " +
" Distance FLOAT" +
" );";
dbCreate.CreateTableFromString(ProtCidSettings.buCompConnection, createTableString, pfamLigandTable.TableName);
string createIndexString = "CREATE INDEX " + pfamLigandTable.TableName + "_idx1 ON " + pfamLigandTable.TableName + "(PdbID, AsymID)";
dbCreate.CreateIndex(ProtCidSettings.buCompConnection, createIndexString, pfamLigandTable.TableName);
}
return(pfamLigandTable);
}
private void InitializeDbTables()
{
DbCreator dbCreate = new DbCreator();
string createTableString = string.Format("CREATE Table {0} ( " +
" GroupSeqID INTEGER NOT NULL, " +
" SpaceGroup1 VARCHAR(30) NOT NULL, ASU1 VARCHAR(255) NOT NULL, PDBID1 CHAR(4) NOT NULL, " +
" NumOfInterfaces1 INTEGER NOT NULL, " +
" NumOfSgInterfaces1 INTEGER NOT NULL, NumOfSimInterfaces1 INTEGER NOT NULL, " +
" SpaceGroup2 VARCHAR(30) NOT NULL, ASU2 VARCHAR(255) NOT NULL, PDBID2 CHAR(4) NOT NULL, " +
" NumOfInterfaces2 INTEGER NOT NULL, " +
" NumOfSgInterfaces2 INTEGER NOT NULL, NumOfSimInterfaces2 INTEGER NOT NULL, " +
" MaxQ FLOAT NOT NULL, MinQ FLOAT NOT NULL, " +
" LeftMaxQ FLOAT NOT NULL, LeftMinQ FLOAT NOT NULL, Identity FLOAT NOT NULL, " +
" LeftMaxAsa1 FLOAT NOT NULL, LeftMaxAsa2 FLOAT NOT NULL);",
GroupDbTableNames.dbTableNames[GroupDbTableNames.ReduntCrystForms]);
dbCreate.CreateTableFromString(ProtCidSettings.protcidDbConnection, createTableString,
GroupDbTableNames.dbTableNames[GroupDbTableNames.ReduntCrystForms]);
string indexString = string.Format("CREATE INDEX {0}_Idx1 ON {0} (PdbID1);",
GroupDbTableNames.dbTableNames[GroupDbTableNames.ReduntCrystForms]);
dbCreate.CreateIndex(ProtCidSettings.protcidDbConnection, indexString,
GroupDbTableNames.dbTableNames[GroupDbTableNames.ReduntCrystForms]);
indexString = string.Format("CREATE INDEX {0}_Idx2 ON {0} (PdbID2);",
GroupDbTableNames.dbTableNames[GroupDbTableNames.ReduntCrystForms]);
dbCreate.CreateIndex(ProtCidSettings.protcidDbConnection, indexString,
GroupDbTableNames.dbTableNames[GroupDbTableNames.ReduntCrystForms]);
}
/// <summary>
///
/// </summary>
/// <param name="dataType"></param>
private void CreateDbRefTablesInDb(string dataType)
{
string createTableString = "";
string createIndexString = "";
DbCreator dbCreator = new DbCreator();
if (dataType == "sws")
{
createTableString = "CREATE TABLE " + dbRefTable.TableName + " ( " +
" PdbID CHAR(4) NOT NULL, " +
" RefID INTEGER NOT NULL, " +
" EntityID INTEGER NOT NULL, " +
// " AuthorChain CHAR(3) NOT NULL, " +
" DbAccession VARCHAR(15) NOT NULL, " +
" PRIMARY KEY (PdbID, RefID));";
}
else
{
createTableString = "CREATE TABLE " + dbRefTable.TableName + " ( " +
" PdbID CHAR(4) NOT NULL, " +
" RefID INTEGER NOT NULL, " +
" EntityID INTEGER NOT NULL, " +
// " AuthorChain CHAR(3) NOT NULL, " +
" DbAccession VARCHAR(15) NOT NULL, " +
" Isoform INTEGER NOT NULL, " +
" PRIMARY KEY (PdbID, RefID));";
}
dbCreator.CreateTableFromString(createTableString, dbRefTable.TableName);
createIndexString = "CREATE INDEX " + dbRefTable.TableName + "_idx1 ON " + dbRefTable.TableName + "(PdbID, EntityID);";
dbCreator.CreateIndex(createIndexString, dbRefTable.TableName);
createTableString = "CREATE TABLE" + dbRefSeqTable.TableName + " ( " +
" AlignID INTEGER NOT NULL, " +
" PdbID CHAR(4) NOT NULL, " +
" RefID INTEGER NOT NULL, " +
" AuthorChain CHAR(3) NOT NULL, " +
" DbAlignBeg INTEGER NOT NULL, " +
" DbAlignEnd INTEGER NOT NULL, " +
" AuthorAlignBeg INTEGER NOT NULL, " +
" AuthorAlignEnd INTEGER NOT NULL, " +
" SeqAlignBeg INTEGER NOT NULL, " +
" SeqAlignEnd INTEGER NOT NULL, " +
" PRIMARY KEY (PdbID, AlignID));";
dbCreator.CreateTableFromString(createTableString, dbRefSeqTable.TableName);
createIndexString = "CREATE INDEX " + dbRefSeqTable.TableName + "_idx1 ON " + dbRefSeqTable.TableName + "(PdbID, RefID);";
dbCreator.CreateIndex(createIndexString, dbRefSeqTable.TableName);
}
/// <summary>
///
/// </summary>
/// <param name="isUpdate"></param>
/// <returns></returns>
public DataTable CreateHHAlignmentTable(bool isUpdate, string tableName)
{
string[] hhrAlignColumns = { "HitNo", "Query", "Hit", "QueryLength", "HitLength", "AlignLength",
"Identity", "Evalue", "PValue", "Score", "Similarity", "Prob",
"Sum_Probs", "QueryStart", "QueryEnd", "HitStart", "HitEnd",
"QueryAlignment", "HitAlignment" /*, "QueryConsensus", "HitConsensus",
* "QueryDssp", "HitDssp", "Confidence", "Match"*/};
DataTable pfamHHalignTable = new DataTable(tableName);
foreach (string hhCol in hhrAlignColumns)
{
pfamHHalignTable.Columns.Add(new DataColumn(hhCol));
}
if (!isUpdate)
{
DbCreator dbCreate = new DbCreator();
string createIndexString = "";
string createTableString = "CREATE TABLE " + tableName + " ( " +
"HitNO INTEGER NOT NULL, " +
"Query VARCHAR(32) NOT NULL," +
"Hit VARCHAR(32) NOT NULL, " +
"QueryLength INTEGER, " +
"HitLength INTEGER, " +
"AlignLength INTEGER, " +
"Identity FLOAT, " +
"EValue DOUBLE PRECISION, " +
"PValue DOUBLE PRECISION, " +
"Score DOUBLE PRECISION, " +
"Similarity FLOAT, " +
"Prob FLOAT, " +
"Sum_Probs FLOAT, " +
"QueryStart INTEGER, " + // for the input sequence
"QueryEnd INTEGER, " +
"HitStart INTEGER, " +
"HitEnd INTEGER, " +
"QueryAlignment BLOB Sub_Type 1, " +
"HitAlignment BLOB Sub_Type 1);";
/* "QueryConsensus BLOB Sub_Type 1, " +
* "HitConsensus BLOB Sub_Type 1, " +
* "QueryDssp BLOB Sub_Type 1, " +
* "HitDssp BLOB Sub_Type 1, " +
* "Confidence BLOB Sub_Type 1, " +
* "Match BLOB Sub_Type 1);"; */
dbCreate.CreateTableFromString(ProtCidSettings.alignmentDbConnection, createTableString, tableName);
createIndexString = "CREATE Index " + tableName + "_query ON " + tableName + "(Query)";
dbCreate.CreateIndex(ProtCidSettings.alignmentDbConnection, createIndexString, tableName);
createIndexString = "CREATE Index " + tableName + "_hit ON " + tableName + "(Hit)";
}
return(pfamHHalignTable);
}
/// <summary>
///
/// </summary>
private void CreatProtBudBuTableInDb()
{
string[] buColumns = buQuery.BuTableColumns;
string createTableString = "Create Table " + buTableName + "( ";
string lowerCaseBuCol = "";
foreach (string buCol in buColumns)
{
lowerCaseBuCol = buCol.ToLower();
if (lowerCaseBuCol == "pdbid")
{
createTableString += "PdbID CHAR(4) NOT NULL, ";
}
else if (lowerCaseBuCol.IndexOf("buid") > -1)
{
createTableString += (buCol + " VARCHAR(10), ");
}
else if (lowerCaseBuCol.IndexOf("_entity") > -1 ||
lowerCaseBuCol.IndexOf("_asymid") > -1 ||
lowerCaseBuCol.IndexOf("_auth") > -1 ||
lowerCaseBuCol.IndexOf("_abc") > -1)
{
createTableString += (buCol + " BLOB SUB_TYPE TEXT NOT NULL, ");
}
else if (lowerCaseBuCol == "samebus")
{
createTableString += (buCol + " CHAR(9), ");
}
else if (lowerCaseBuCol == "dna" || lowerCaseBuCol == "rna" || lowerCaseBuCol == "ligands")
{
createTableString += (buCol + " CHAR(3), ");
}
else if (lowerCaseBuCol == "resolution")
{
createTableString += (buCol + " VARCHAR(32), ");
}
else if (lowerCaseBuCol == "names")
{
createTableString += (buCol + " BLOB SUB_TYPE TEXT NOT NULL, ");
}
}
createTableString = createTableString.TrimEnd(", ".ToCharArray());
createTableString += ");";
DbCreator dbCreat = new DbCreator();
dbCreat.CreateTableFromString(ProtCidSettings.pdbfamDbConnection, createTableString, buTableName);
string createIndexString = "Create Index " + buTableName + "_idx1 ON " + buTableName +
" ( PdbID, PdbBuID, PisaBuID);";
dbCreat.CreateIndex(ProtCidSettings.pdbfamDbConnection, createIndexString, buTableName);
}
/// <summary>
/// initialize tables in database
/// </summary>
public static void InitializeDbTables()
{
DbCreator dbCreator = new DbCreator();
string createTableString = "";
string createIndexString = "";
string buCompTableName = "PdbPisaBuComp";
string buInterfaceCompTableName = "PdbPisaBuInterfaceComp";
// for BU Comparison
createTableString = "CREATE TABLE " + buCompTableName + " ( " +
"PdbID CHAR(4) NOT NULL, " +
"BuID1 VARCHAR(8) NOT NULL, " +
"BuID2 VARCHAR(8) NOT NULL, " +
"InterfaceNum1 INTEGER NOT NULL, " +
"InterfaceNum2 INTEGER NOT NULL, " +
"IsSame CHAR(1) NOT NULL);";
dbCreator.CreateTableFromString(ProtCidSettings.buCompConnection, createTableString, buCompTableName);
createIndexString = string.Format("CREATE INDEX {0}_idx1 ON {0} (PdbID, BuID1, BuID2);", buCompTableName);
dbCreator.CreateIndex(ProtCidSettings.buCompConnection, createIndexString, buCompTableName);
// for BU Interface comparison
createTableString = "CREATE TABLE " + buInterfaceCompTableName + " ( " +
"PdbID CHAR(4) NOT NULL, " +
"BuID1 VARCHAR(8) NOT NULL, " +
"BuID2 VARCHAR(8) NOT NULL, " +
"InterfaceID1 INTEGER NOT NULL, " +
"InterfaceID2 INTEGER NOT NULL, " +
"QScore FLOAT NOT NULL);";
dbCreator.CreateTableFromString(ProtCidSettings.buCompConnection, createTableString, buInterfaceCompTableName);
createIndexString = string.Format("CREATE INDEX {0}_idx1 ON {0} (PdbID, BuID1, BuID2);", buInterfaceCompTableName);
dbCreator.CreateIndex(ProtCidSettings.buCompConnection, createIndexString, buInterfaceCompTableName);
}
private void InitializeDbTable()
{
DbCreator dbCreator = new DbCreator();
if (!dbCreator.IsTableExist(ProtCidSettings.buCompConnection, buGroupTable.TableName))
{
string createTableString = "Create Table " + buGroupTable.TableName + " ( " +
" GroupSeqID INTEGER NOT NULL, " +
" PdbID CHAR(4) NOT NULL, " +
" BuID VARCHAR(8) NOT NULL, " +
" EntityFormat VARCHAR(255) NOT NULL, " +
" AsymFormat VARCHAR(255) NOT NULL, " +
" AbcFormat VARCHAR(255) NOT NULL );";
dbCreator.CreateTableFromString(ProtCidSettings.buCompConnection, createTableString, buGroupTable.TableName);
string createIndexString = "Create INDEX " + buGroupTable.TableName + "_Idx1 ON " +
buGroupTable.TableName + "(PdbID, BuID);";
dbCreator.CreateIndex(ProtCidSettings.buCompConnection, createIndexString, buGroupTable.TableName);
createIndexString = "Create INDEX " + buGroupTable.TableName + "_idx2 ON " +
buGroupTable.TableName + "(GroupSeqID);";
dbCreator.CreateIndex(ProtCidSettings.buCompConnection, createIndexString, buGroupTable.TableName);
}
if (!dbCreator.IsTableExist(ProtCidSettings.buCompConnection, groupTable.TableName))
{
string createTableString = "Create Table " + groupTable.TableName + " ( " +
" GroupSeqID INTEGER NOT NULL, " +
" FamilyString BLOB Sub_Type Text NOT NULL);";
dbCreator.CreateTableFromString(ProtCidSettings.buCompConnection, createTableString, groupTable.TableName);
/* string createIndexString = "Create INDEX " + groupTable.TableName + "_idx1 ON " +
* groupTable.TableName + "(GroupSeqID);";
* dbCreator.CreateTable(ProtCidSettings.buCompConnection, createIndexString, groupTable.TableName);*/
}
}
/// <summary>
///
/// </summary>
/// <param name="isUpdate"></param>
private void CreateDbTable(bool isUpdate)
{
if (!isUpdate)
{
DbCreator dbCreate = new DbCreator();
string createTableString = "Create Table " + tableName + " ( " +
"PfamID varchar(40) NOT NULL, " +
"ClusterID Integer NOT NULL, " +
"PdbID char(4) Not Null, " +
"ChainDomainID Integer Not Null, " +
"LigandChain char(3) Not Null);";
dbCreate.CreateTableFromString(ProtCidSettings.protcidDbConnection, createTableString, tableName);
string createIndexString = "Create Index " + tableName + "_cluster ON " + tableName + "(PfamID, ClusterID);";
dbCreate.CreateIndex(ProtCidSettings.protcidDbConnection, createIndexString, tableName);
createIndexString = "Create Index " + tableName + "_pdb ON " + tableName + "(PdbID, ChainDomainID);";
dbCreate.CreateIndex(ProtCidSettings.protcidDbConnection, createIndexString, tableName);
}
}
/// <summary>
///
/// </summary>
private void InitializeDbTable()
{
DbCreator dbCreator = new DbCreator();
if (!dbCreator.IsTableExist(ProtCidSettings.buCompConnection, domainInterfaceCompTable.TableName))
{
string createTableString = "CREATE TABLE " + domainInterfaceCompTable.TableName + " ( " +
"RelSeqID INTEGER NOT NULL, " +
"PdbID1 VARCHAR(4) NOT NULL, " +
"PdbID2 VARCHAR(4) NOT NULL, " +
"BuID1 VARCHAR(8) NOT NULL, " +
"BuID2 VARCHAR(8) NOT NULL, " +
"DomainInterfaceID1 INTEGER NOT NULL, " +
"DomainInterfaceID2 INTEGER NOT NULL, " +
"Qscore FLOAT NOT NULL);";
dbCreator.CreateTableFromString(ProtCidSettings.buCompConnection, createTableString, domainInterfaceCompTable.TableName);
}
}
public void InitializeStatInfoTable(string type)
{
string[] statInfoCols = { "Category", "Single", "Pair", "Total" };
dbStatInfoTable = new DataTable(type + "StatInfo");
foreach (string statInfoCol in statInfoCols)
{
dbStatInfoTable.Columns.Add(new DataColumn(statInfoCol));
}
DbCreator dbCreate = new DbCreator();
string createTableString = "Create Table " + type + "StatInfo ( " +
" Category VARCHAR(30) NOT NULL, " +
" Single Integer NOT NULL, " +
" Pair Integer NOT NULL, " +
" Total Integer NOT NULL );";
dbCreate.CreateTableFromString(ProtCidSettings.protcidDbConnection, createTableString, type + "StatInfo");
}
private void InitializeFamilyTablesInDb()
{
DbCreator dbCreator = new DbCreator();
string tableName = ProtCidSettings.dataType + "SgInterfaces";
string createTableString = string.Format("CREATE TABLE {0} (" +
" GroupSeqID INTEGER NOT NULL, " +
" SpaceGroup VARCHAR(30) NOT NULL, " +
" ASU BLOB Sub_Type TEXT NOT NULL, " +
" PDBID CHAR(4) NOT NULL, " +
" InterfaceID INTEGER NOT NULL, " +
" NumOfSG INTEGER NOT NULL, " +
" NumOfSG_Identity INTEGER NOT NULL, " +
" SurfaceArea FLOAT );", tableName);
dbCreator.CreateTableFromString(ProtCidSettings.protcidDbConnection, createTableString, tableName);
string createIdxString = string.Format("CREATE INDEX {0}_Idx1 " +
" ON {0} (GroupSeqID, PdbID, InterfaceID);", tableName);
dbCreator.CreateIndex(ProtCidSettings.protcidDbConnection, createIdxString, tableName);
}
/// <summary>
///
/// </summary>
private void InitializeDbTable()
{
string createTableString = string.Format("CREATE Table {0} (" +
" ClanSeqID INTEGER NOT NULL, " +
" ClusterID INTEGER NOT NULL, " +
// " RelSeqID INTEGER NOT NULL, " +
" GroupSeqID INTEGER NOT NULL, " +
" CFGroupID INTEGER NOT NULL, " +
" SpaceGroup VARCHAR(30) NOT NULL, " +
" ASU VARCHAR(50) NOT NULL, " +
" PDBID CHAR(4) NOT NULL, " +
" DomainInterfaceID INTEGER NOT NULL);",
tableName);
DbCreator dbCreate = new DbCreator();
dbCreate.CreateTableFromString(ProtCidSettings.protcidDbConnection, createTableString, tableName, true);
string indexString = string.Format("Create INDEX {0}_Idx1 ON {0} (ClanSeqID, PdbID, DomainInterfaceID);",
tableName);
dbCreate.CreateIndex(ProtCidSettings.protcidDbConnection, indexString, tableName);
}
/// <summary>
///
/// </summary>
/// <param name="dataType"></param>
private void CreateDbTable(string dataType)
{
DbCreator dbCreate = new DbCreator();
string createTableString = "";
createTableString = "CREATE TABLE " + pdbUnpDbTable.TableName + " ( " +
" PdbID CHAR(4) NOT NULL, ";
if (dataType == "ssmap")
{
createTableString += "Isoform INTEGER NOT NULL, ";
}
createTableString += (" AuthorChain CHAR(3) NOT NULL, " +
" EntityID INTEGER NOT NULL, " +
" DbAccession CHAR(6) NOT NULL, " +
" PdbSequence BLOB Sub_Type Text NOT NULL, " +
" UnpSequence BLOB Sub_Type Text NOT NULL, " +
" AuthorSeqNumbers BLOB Sub_Type Text NOT NULL, " +
" UnpSeqNumbers BLOB Sub_Type Text NOT NULL, " +
" SeqNumbers BLOB Sub_Type Text NOT NULL );");
dbCreate.CreateTableFromString(createTableString, pdbUnpDbTable.TableName);
string createIndexString = "CREATE INDEX " + pdbUnpDbTable.TableName + "_idx1 ON " + pdbUnpDbTable.TableName + "(PdbID, AuthorChain);";
dbCreate.CreateIndex(createIndexString, pdbUnpDbTable.TableName);
}
/// <summary>
///
/// </summary>
public static void InitializeDbTables()
{
DbCreator dbCreator = new DbCreator();
string tableName = "";
string createTableString = "";
string createIndexString = "";
foreach (string buType in BuCompBuilder.buTypes)
{
if (buType == "asu")
{
tableName = buType + "Interfaces";
}
else
{
tableName = buType + "BuInterfaces";
}
createTableString = "Create Table " + tableName + "( " +
"PdbID CHAR(4) NOT NULL, " +
"BuID VARCHAR(8) NOT NULL, " +
"InterfaceID INTEGER NOT NULL, " +
"AsymChain1 CHAR(3) NOT NULL, " +
"AsymChain2 CHAR(3) NOT NULL, " +
"AuthChain1 CHAR(3) NOT NULL, " +
"AuthChain2 CHAR(3) NOT NULL, " +
"EntityID1 INTEGER NOT NULL, " +
"EntityID2 INTEGER NOT NULL, " +
"SurfaceArea FLOAT NOT NULL, " +
"NumOfCopy INTEGER NOT NULL, " +
"PRIMARY KEY (PdbID, BuID, InterfaceID))";
dbCreator.CreateTableFromString(ProtCidSettings.buCompConnection, createTableString, tableName);
if (buType == "asu")
{
tableName = buType + "SameInterfaces";
}
else
{
tableName = buType + "BuSameInterfaces";
}
createTableString = "CREATE TABLE " + tableName + "( " +
"PdbID CHAR(4) NOT NULL, " +
"BuID VARCHAR(8) NOT NULL, " +
"InterfaceID INTEGER NOT NULL, " +
"SameInterfaceID INTEGER NOT NULL, " +
"Chain1 CHAR(3) NOT NULL, " +
"SymmetryString1 VARCHAR(50) NOT NULL, " +
"Chain2 CHAR(3) NOT NULL, " +
"SymmetryString2 VARCHAR(50) NOT NULL, " +
"QScore FLOAT NOT NULL);";
dbCreator.CreateTableFromString(ProtCidSettings.buCompConnection, createTableString, tableName);
createIndexString = string.Format("CREATE INDEX {0}_idx1 ON {0} (PdbID, BuID, InterfaceID);", tableName);
dbCreator.CreateIndex(ProtCidSettings.buCompConnection, createIndexString, tableName);
if (buType != "asu")
{
tableName = buType + "EntryBuInterfaceComp";
createTableString = "CREATE TABLE " + tableName + " ( " +
"PdbID CHAR(4) NOT NULL, " +
"BuID1 VARCHAR(8) NOT NULL, " +
"InterfaceID1 INTEGER NOT NULL, " +
"BuID2 VARCHAR(8) NOT NULL, " +
"InterfaceID2 INTEGER NOT NULL, " +
"QScore FLOAT NOT NULL);";
dbCreator.CreateTableFromString(ProtCidSettings.buCompConnection, createTableString, tableName);
createIndexString = string.Format("CREATE INDEX {0}BuInterfaceComp_idx1 " +
" ON {0}EntryBuInterfaceComp (PdbID, BuID1, BuID2);", buType);
dbCreator.CreateIndex(ProtCidSettings.buCompConnection, createIndexString, tableName);
tableName = buType + "EntryBuComp";
createTableString = "CREATE TABLE " + tableName + " ( " +
"PdbID CHAR(4) NOT NULL, " +
"BUID1 VARCHAR(8) NOT NULL, " +
"BUID2 VARCHAR(8) NOT NULL, " +
"EntityFormat1 VARCHAR(150) NOT NULL, " +
"EntityFormat2 VARCHAR(150) NOT NULL, " +
"NumOfInterfaces1 INTEGER NOT NULL, " +
"NumOfInterfaces2 INTEGER NOT NULL, " +
"SameBUs CHAR(1) NOT NULL);";
dbCreator.CreateTableFromString(ProtCidSettings.buCompConnection, createTableString, tableName);
createIndexString = string.Format("CREATE INDEX {0}BuComp_Idx1 " +
" ON {0}EntryBuComp (PdbID, BuID1, BuID2);", buType);
dbCreator.CreateIndex(ProtCidSettings.buCompConnection, createIndexString, tableName);
}
}
}
public static void InitializeDbTables()
{
string createTableString = "";
string createIndexString = "";
string tableName = "";
DbCreator dbCreator = new DbCreator();
tableName = "CRYSTENTRYINTERFACES";
createTableString = "CREATE TABLE CRYSTENTRYINTERFACES ( " +
"PDBID CHAR(4) NOT NULL," +
"INTERFACEID INTEGER NOT NULL," +
"ASYMCHAIN1 CHAR(4) NOT NULL," +
"AUTHCHAIN1 CHAR(3) NOT NULL," +
"ENTITYID1 INTEGER NOT NULL," +
"SYMMETRYSTRING1 VARCHAR(15) NOT NULL," +
"FULLSYMMETRYSTRING1 VARCHAR(30) NOT NULL," +
"ASYMCHAIN2 CHAR(4) NOT NULL," +
"AUTHCHAIN2 CHAR(3) NOT NULL," +
"ENTITYID2 INTEGER NOT NULL," +
"SYMMETRYSTRING2 VARCHAR(15) NOT NULL," +
"FULLSYMMETRYSTRING2 VARCHAR(30) NOT NULL," +
"SURFACEAREA FLOAT DEFAULT -1 NOT NULL" +
"SymmetryIndex FLOAT DEFAULT 0);"; // added on August 16, 2018 whether the interface with same pfam architecture is in symmetry
dbCreator.CreateTableFromString(ProtCidSettings.protcidDbConnection, createTableString, tableName);
createIndexString = "CREATE INDEX CRYSTENTRYINTERFACES_IDX1 ON CRYSTENTRYINTERFACES (PDBID, INTERFACEID);";
dbCreator.CreateIndex(ProtCidSettings.protcidDbConnection, createIndexString, tableName);
tableName = "DIFENTRYINTERFACECOMP";
createTableString = "CREATE TABLE DIFENTRYINTERFACECOMP (" +
"PDBID1 CHAR(4) NOT NULL," +
"INTERFACEID1 INTEGER NOT NULL," +
"PDBID2 CHAR(4) NOT NULL," +
"INTERFACEID2 INTEGER NOT NULL," +
"QSCORE FLOAT NOT NULL," +
"IDENTITY FLOAT NOT NULL, " +
"ISREVERSED INTEGER NOT NULL );";
dbCreator.CreateTableFromString(ProtCidSettings.protcidDbConnection, createTableString, tableName);
createIndexString = "CREATE INDEX DIFENTRYINTERFACECOMP_IDX1 ON DIFENTRYINTERFACECOMP (PDBID1, INTERFACEID1);";
dbCreator.CreateIndex(ProtCidSettings.protcidDbConnection, createIndexString, tableName);
createIndexString = "CREATE INDEX DIFENTRYINTERFACECOMP_IDX2 ON DIFENTRYINTERFACECOMP (PDBID2, INTERFACEID2);";
dbCreator.CreateIndex(ProtCidSettings.protcidDbConnection, createIndexString, tableName);
tableName = "ENTRYINTERFACECOMP";
createTableString = "CREATE TABLE ENTRYINTERFACECOMP (" +
"PDBID CHAR(4) NOT NULL," +
"INTERFACEID1 INTEGER NOT NULL," +
"INTERFACEID2 INTEGER NOT NULL," +
"QSCORE FLOAT NOT NULL," +
"ISREVERSED INTEGER NOT NULL);";
dbCreator.CreateTableFromString(ProtCidSettings.protcidDbConnection, createTableString, tableName);
createIndexString = "CREATE INDEX ENTRYINTERFACECOMP_IDX1 ON ENTRYINTERFACECOMP (PDBID);";
dbCreator.CreateIndex(ProtCidSettings.protcidDbConnection, createIndexString, tableName);
/*
* Not maintain since Pfam30 since November 2016, due to the size of tables
* */
/*
* tableName = "SGINTERFACECONTACTS";
* createTableString = "CREATE TABLE SGINTERFACECONTACTS (" +
* "PDBID CHAR(4) NOT NULL," +
* "INTERFACEID INTEGER NOT NULL," +
* "RESIDUE1 CHAR(3) NOT NULL," +
* "SEQID1 CHAR(5) NOT NULL," +
* "RESIDUE2 CHAR(3) NOT NULL," +
* "SEQID2 CHAR(5) NOT NULL," +
* "DISTANCE FLOAT NOT NULL);";
* dbCreator.CreateTableFromString(ProtCidSettings.protcidDbConnection, createTableString, tableName);
* createIndexString = "CREATE INDEX SGINTERFACECONTACTS_IDX1 ON SGINTERFACECONTACTS (PDBID, INTERFACEID);";
* dbCreator.CreateIndex(ProtCidSettings.protcidDbConnection, createIndexString, tableName);
*
* tableName = "SGINTERFACERESIDUES";
* createTableString = "CREATE TABLE SGINTERFACERESIDUES (" +
* "PDBID CHAR(4) NOT NULL," +
* "INTERFACEID INTEGER NOT NULL," +
* "RESIDUE1 CHAR(3) NOT NULL," +
* "SEQID1 CHAR(5) NOT NULL," +
* "RESIDUE2 CHAR(3) NOT NULL," +
* "SEQID2 CHAR(5) NOT NULL," +
* "DISTANCE FLOAT NOT NULL);";
* dbCreator.CreateTableFromString(ProtCidSettings.protcidDbConnection, createTableString, tableName);
* createIndexString = "CREATE INDEX SGINTERFACERESIDUES_IDX1 ON SGINTERFACERESIDUES (PDBID, INTERFACEID);";
* dbCreator.CreateIndex(ProtCidSettings.protcidDbConnection, createIndexString, tableName);*/
}
/// <summary>
/// create table structures in the database
/// </summary>
public static void InitializeDbTables(DbConnect alignmentDbConnect)
{
if (!alignmentDbConnect.IsConnected())
{
alignmentDbConnect.ConnectToDatabase();
}
DbCreator dbCreator = new DbCreator();
/* string createTableString = "CREATE TABLE PsiBlastAlignments ( " +
* "QueryEntry CHAR(4) NOT NULL," +
* "QueryChain CHAR(3) NOT NULL," +
* "QueryAsymChain CHAR(3)," +
* "HitEntry CHAR(4) NOT NULL," +
* "HitChain CHAR(3) NOT NULL," +
* "HitAsymChain CHAR(3)," +
* "QueryLength INTEGER NOT NULL," +
* "HitLength INTEGER NOT NULL," +
* "Identity FLOAT NOT NULL," +
* "AlignmentLength INTEGER NOT NULL," +
* "E_value DOUBLE PRECISION NOT NULL," +
* "QueryStart INTEGER NOT NULL," +
* "QueryEnd INTEGER NOT NULL," +
* "HitStart INTEGER NOT NULL," +
* "HitEnd INTEGER NOT NULL," +
* "QuerySequence BLOB SUB_TYPE TEXT NOT NULL," +
* "HitSequence BLOB SUB_TYPE TEXT NOT NULL);";
* dbCreator.CreateTableFromString(alignmentDbConnect, createTableString, "PsiBlastAlignments");
* string createIdxString = "CREATE INDEX PsiblastAlign_queryindex ON PsiBlastAlignments(QueryEntry, QueryChain);";
* dbCreator.CreateIndex(alignmentDbConnect, createIdxString, "PsiBlastAlignments");
* createIdxString = "CREATE INDEX PsiblastAlign_Hitindex ON PsiBlastAlignments(HitEntry, HitChain);";
* dbCreator.CreateIndex(alignmentDbConnect, createIdxString, "PsiBlastAlignments");
*
* createTableString = "CREATE TABLE CeAlignments ( " +
* "QueryEntry CHAR(4) NOT NULL," +
* "QueryChain CHAR(3) NOT NULL," +
* "QueryAsymChain CHAR(3)," +
* "HitEntry CHAR(4) NOT NULL," +
* "HitChain CHAR(3) NOT NULL," +
* "HitAsymChain CHAR(3)," +
* "QueryLength INTEGER NOT NULL," +
* "HitLength INTEGER NOT NULL," +
* "Identity FLOAT NOT NULL," +
* "AlignmentLength INTEGER NOT NULL," +
* "E_value DOUBLE PRECISION NOT NULL," +
* "QueryStart INTEGER NOT NULL," +
* "QueryEnd INTEGER NOT NULL," +
* "HitStart INTEGER NOT NULL," +
* "HitEnd INTEGER NOT NULL," +
* "QuerySequence BLOB SUB_TYPE TEXT NOT NULL," +
* "HitSequence BLOB SUB_TYPE TEXT NOT NULL);";
* dbCreator.CreateTableFromString(alignmentDbConnect, createTableString, "CeAlignments");
* createIdxString = "CREATE INDEX CeAlign_queryindex ON CeAlignments(QueryEntry, QueryChain);";
* dbCreator.CreateIndex(alignmentDbConnect, createIdxString, "CeAlignments");
* createIdxString = "CREATE INDEX CeAlign_Hitindex ON CeAlignments(HitEntry, HitChain);";
* dbCreator.CreateIndex(alignmentDbConnect, createIdxString, "CeAlignments");
*/
string createTableString = "CREATE TABLE RedundantPdbChains ( " +
"PdbID1 CHAR(4) NOT NULL," +
"ChainID1 CHAR(3) NOT NULL," +
"AsymChainID1 CHAR(3)," +
"EntityID1 INTEGER, " +
"PdbID2 CHAR(4) NOT NULL," +
"ChainID2 CHAR(3) NOT NULL, " +
"AsymChainID2 CHAR(3), " +
"EntityID2 INTEGER);";
dbCreator.CreateTableFromString(alignmentDbConnect, createTableString, "RedundantPdbChains");
string createIdxString = "CREATE INDEX RedundantPdbChains_indexPdbid1 ON RedundantPdbChains(PdbID1);";
dbCreator.CreateIndex(alignmentDbConnect, createIdxString, "RedundantPdbChains");
createIdxString = "CREATE INDEX RedundantPdbChains_indexPdbid2 ON RedundantPdbChains(PdbID2);";
dbCreator.CreateIndex(alignmentDbConnect, createIdxString, "RedundantPdbChains");
}
/// <summary>
///
/// </summary>
public static void InitializeAllGroupDbTables()
{
DbCreator dbCreator = new DbCreator();
string createTableString = "";
string createIndexString = "";
string tableName = ProtCidSettings.dataType + "HomoSeqInfo";
createTableString = "CREATE TABLE " + tableName + " ( " +
"GroupSeqID INTEGER NOT NULL, " +
"PdbID CHAR(4) NOT NULL, " +
"SpaceGroup VARCHAR(30) NOT NULL, " +
"ASU BLOB Sub_Type TEXT NOT NULL, " +
"Method VARCHAR(100) NOT NULL, " +
"Resolution FLOAT NOT NULL, " +
"InPfam CHAR NOT NULL);";
dbCreator.CreateTableFromString(ProtCidSettings.protcidDbConnection, createTableString, tableName);
createIndexString = string.Format("CREATE INDEX {0}_idx1 ON {0} (GroupSeqID);", tableName);
dbCreator.CreateIndex(ProtCidSettings.protcidDbConnection, createIndexString, tableName);
createIndexString = string.Format("CREATE INDEX {0}_idx2 ON {0} (PdbID);", tableName);
dbCreator.CreateIndex(ProtCidSettings.protcidDbConnection, createIndexString, tableName);
tableName = ProtCidSettings.dataType + "HomoRepEntryAlign";
createTableString = "CREATE TABLE " + tableName + " ( " +
"GroupSeqID INTEGER NOT NULL," +
"PdbID1 CHAR(4) NOT NULL," +
"EntityID1 INTEGER NOT NULL," +
"PdbID2 CHAR(4) NOT NULL," +
"EntityID2 INTEGER NOT NULL," +
"Identity FLOAT NOT NULL," +
"QueryStart INTEGER NOT NULL," +
"QueryEnd INTEGER NOT NULL," +
"HitStart INTEGER NOT NULL," +
"HitEnd INTEGER NOT NULL," +
"QuerySequence BLOB Sub_Type TEXT NOT NULL," +
"HitSequence BLOB Sub_Type TEXT NOT NULL);";
dbCreator.CreateTableFromString(ProtCidSettings.protcidDbConnection, createTableString, tableName);
createIndexString = string.Format("CREATE INDEX {0}_idx1 ON {0} (PdbID1);", tableName);
dbCreator.CreateIndex(ProtCidSettings.protcidDbConnection, createIndexString, tableName);
createIndexString = string.Format("CREATE INDEX {0}_idx2 ON {0} (PdbID2);", tableName);
dbCreator.CreateIndex(ProtCidSettings.protcidDbConnection, createIndexString, tableName);
tableName = ProtCidSettings.dataType + "HomoGroupEntryAlign";
createTableString = "CREATE TABLE " + tableName + " ( " +
"GroupSeqID INTEGER NOT NULL," +
"PdbID1 CHAR(4) NOT NULL," +
"EntityID1 INTEGER NOT NULL," +
"PdbID2 CHAR(4) NOT NULL," +
"EntityID2 INTEGER NOT NULL," +
"Identity FLOAT NOT NULL," +
"QueryStart INTEGER NOT NULL," +
"QueryEnd INTEGER NOT NULL," +
"HitStart INTEGER NOT NULL," +
"HitEnd INTEGER NOT NULL," +
"QuerySequence BLOB Sub_Type TEXT NOT NULL," +
"HitSequence BLOB Sub_Type TEXT NOT NULL);";
dbCreator.CreateTableFromString(ProtCidSettings.protcidDbConnection, createTableString, tableName);
string indexName = ProtCidSettings.dataType + "GroupEntryAlign";
createIndexString = string.Format("CREATE INDEX {0}_idx1 ON {1} (PdbID1);", indexName, tableName);
dbCreator.CreateIndex(ProtCidSettings.protcidDbConnection, createIndexString, tableName);
createIndexString = string.Format("CREATE INDEX {0}_idx2 ON {1} (PdbID2);", indexName, tableName);
dbCreator.CreateIndex(ProtCidSettings.protcidDbConnection, createIndexString, tableName);
tableName = ProtCidSettings.dataType + "Groups";
createTableString = "CREATE TABLE " + tableName + " ( " +
"GroupSeqID INTEGER NOT NULL, " +
"EntryPfamArch BLOB Sub_Type TEXT NOT NULL);";
dbCreator.CreateTableFromString(ProtCidSettings.protcidDbConnection, createTableString, tableName);
createIndexString = string.Format("CREATE INDEX {0}_idx1 ON {0} (GroupSeqID);", tableName);
dbCreator.CreateIndex(ProtCidSettings.protcidDbConnection, createIndexString, tableName);
}
/// <summary>
///
/// </summary>
private void InitializeBamDbTables()
{
DbCreator dbCreator = new DbCreator();
string createTableString = "";
string createIndexString = "";
string tableName = "pdb_entry";
createTableString = "Create Table " + tableName + " ( " +
"PDB_ID CHAR(4) Not Null, " +
"TITLE BLOB sub_type TEXT Not Null, " +
"DESCRIPTION BLOB sub_type TEXT Not Null, " +
"EXPDTA VARCHAR(250) Not Null, " +
"KEYWORDS VARCHAR(250) Not Null, " +
"KEYWORDS_TEXT BLOB sub_type TEXT Not Null, " +
"PDB_ORI_DATE Date Not Null, " +
"RESOLUTION FLOAT);";
dbCreator.CreateTableFromString(bamDbConnect, createTableString, tableName);
createIndexString = "Create Index " + tableName + "_pdb ON " + tableName + "(PDB_ID);";
dbCreator.CreateIndex(bamDbConnect, createIndexString, tableName);
tableName = "pdb_dbref";
createTableString = "Create Table " + tableName + " ( " +
"PDB_ID CHAR(4) Not Null, " +
"REF_ID INTEGER Not Null, " +
"ENTITY_ID INTEGER Not Null, " +
"DB_NAME VARCHAR(10) Not Null, " +
"DB_CODE VARCHAR(32) Not Null, " +
"DB_ACCESSION VARCHAR(32) Not Null);";
dbCreator.CreateTableFromString(bamDbConnect, createTableString, tableName);
createIndexString = "Create Index " + tableName + "_pdb ON " + tableName + "(PDB_ID, Entity_ID);";
dbCreator.CreateIndex(bamDbConnect, createIndexString, tableName);
tableName = "pdb_seq";
createTableString = "Create Table " + tableName + " ( " +
"PDB_ID CHAR(4) Not Null, " +
"ENTITY_ID INTEGER Not Null, " +
"TYPE VARCHAR(64) Not Null, " +
"NSTD_MONOMER CHAR(1) Not Null, " +
"SEQ_CODE BLOB sub_type TEXT Not Null, " +
"SEQ_CODE_CANONICAL BLOB sub_type TEXT Not Null);";
dbCreator.CreateTableFromString(bamDbConnect, createTableString, tableName);
createIndexString = "Create Index " + tableName + "_pdb ON " + tableName + "(PDB_ID, Entity_ID);";
dbCreator.CreateIndex(bamDbConnect, createIndexString, tableName);
tableName = "pdb_asym_auth";
createTableString = "Create Table " + tableName + " ( " +
"PDB_ID CHAR(4) Not Null, " +
"ENTITY_ID INTEGER Not Null, " +
"ASYM_ID VARCHAR(3) Not Null, " +
"AUTH_ASYM_ID VARCHAR(4) Not Null);";
dbCreator.CreateTableFromString(bamDbConnect, createTableString, tableName);
createIndexString = "Create Index " + tableName + "_pdb ON " + tableName + "(PDB_ID);";
dbCreator.CreateIndex(bamDbConnect, createIndexString, tableName);
tableName = "pdb_pfam";
createTableString = "Create Table " + tableName + " ( " +
"PDB_ID CHAR(4) Not Null, " +
"ENTITY_ID INTEGER Not Null, " +
"MODEL VARCHAR(50) Not Null, " +
"PFAM_accession VARCHAR(10) Not Null, " +
"Description VARCHAR(1200) Not Null, " +
"SEQ_F INTEGER Not Null, " +
"SEQ_T INTEGER Not Null, " +
"HMM_F INTEGER Not Null, " +
"HMM_T INTEGER Not Null, " +
"SCORE FLOAT, " +
"E_VALUE FLOAT);";
dbCreator.CreateTableFromString(bamDbConnect, createTableString, tableName);
createIndexString = "Create Index " + tableName + "_pdb ON " + tableName + "(PDB_ID, Entity_ID);";
dbCreator.CreateIndex(bamDbConnect, createIndexString, tableName);
tableName = "pdb_protbud";
createTableString = "Create Table " + tableName + " ( " +
"PDB_ID CHAR(4) Not Null, " +
"NAME BLOB sub_type TEXT, " +
"PDBBUID VARCHAR(10) Not Null, " +
"PISABUID VARCHAR(10) Not Null, " +
"ASU_ENTITY BLOB sub_type TEXT Not Null, " +
"ASU_ASYMID BLOB sub_type TEXT Not Null, " +
"ASU_AUTH BLOB sub_type TEXT Not Null, " +
"ASU_ABC BLOB sub_type TEXT Not Null, " +
"PDBBU_ENTITY BLOB sub_type TEXT Not Null, " +
"PDBBU_ASYMID BLOB sub_type TEXT Not Null, " +
"PDBBU_AUTH BLOB sub_type TEXT Not Null, " +
"PDBBU_ABC BLOB sub_type TEXT Not Null, " +
"PISABU_ENTITY BLOB sub_type TEXT Not Null, " +
"PISABU_ASYMID BLOB sub_type TEXT Not Null, " +
"PISABU_AUTH BLOB sub_type TEXT Not Null, " +
"PISABU_ABC BLOB sub_type TEXT Not Null, " +
"SAMEBUS CHAR(9), " +
"DNA CHAR(3), " +
"RNA CHAR(3), " +
"LIGANDS CHAR(3), " +
"RESOLUTION VARCHAR(32));";
dbCreator.CreateTableFromString(bamDbConnect, createTableString, tableName);
createIndexString = "Create Index " + tableName + "_pdb ON " + tableName + "(PDB_ID);";
dbCreator.CreateIndex(bamDbConnect, createIndexString, tableName);
}
/// <summary>
///
/// </summary>
/// <param name="dbConnect"></param>
/// <param name="dbTableName"></param>
public static void InitializeDbTable(DbConnect dbConnect, string dbTableName)
{
string createTableString = "";
string createIndexString = "";
DbCreator dbCreator = new DbCreator();
string pfamAlignType = "";
if (dbTableName.ToLower().IndexOf("pfam") > -1)
{
if (dbTableName.ToLower().IndexOf("pfamweak") > -1)
{
pfamAlignType = "PfamDomainWeak";
if (dbTableName.ToLower().IndexOf("rigid") > -1)
{
pfamAlignType = "PfamDomainWeakRigid";
}
}
else
{
pfamAlignType = "PfamDomain";
if (dbTableName.ToLower().IndexOf("rigid") > -1)
{
pfamAlignType = "PfamDomainRigid";
}
}
createTableString = string.Format("CREATE TABLE {0} ( " +
" QueryEntry CHAR(4) NOT NULL, QueryEntity INTEGER NOT NULL, " +
" QueryDomainID BIGINT NOT NULL, " +
" QueryDomainStart INTEGER NOT NULL, QueryLength INTEGER NOT NULL, " +
" HitEntry CHAR(4) NOT NULL, HitEntity INTEGER NOT NULL, " +
" HitDOmainID BIGINT NOT NULL, " +
" HitDomainStart INTEGER NOT NULL, HitLength INTEGER NOT NULL, " +
" Align_Len INTEGER NOT NULL, Score FLOAT NOT NULL, Gaps INTEGER NOT NULL, " +
" E_Value DOUBLE PRECISION NOT NULL, Identity FLOAT NOT NULL, Similarity FLOAT NOT NULL, " +
" AlignmentLength INTEGER NOT NULL, " +
" QuerySequence BLOB Sub_Type TEXT NOT NULL, HitSequence BLOB Sub_Type TEXT NOT NULL, ",
dbTableName);
if (dbTableName.ToLower().IndexOf("weak") < 0)
{
createTableString = createTableString +
" QuerySeqNumbers BLOB Sub_Type TEXT NOT NULL, HitSeqNumbers BLOB Sub_Type TEXT NOT NULL, ";
}
createTableString = createTableString +
" QueryStart INTEGER NOT NULL, QueryEnd INTEGER NOT NULL, " +
" HitStart INTEGER NOT NULL, HitEnd INTEGER NOT NULL);";
dbCreator.CreateTableFromString(dbConnect, createTableString, dbTableName);
createIndexString = string.Format("CREATE INDEX {0}_Idx1 ON {1} (QueryEntry, QueryEntity);", pfamAlignType, dbTableName);
dbCreator.CreateIndex(dbConnect, createIndexString, dbTableName);
createIndexString = string.Format("CREATE INDEX {0}_Idx2 ON {1} (HitEntry, HitEntity);", pfamAlignType, dbTableName);
dbCreator.CreateIndex(dbConnect, createIndexString, dbTableName);
createIndexString = string.Format("CREATE INDEX {0}_Idx3 ON {1} (QueryEntry, QueryDomainID);", pfamAlignType, dbTableName);
dbCreator.CreateIndex(dbConnect, createIndexString, dbTableName);
createIndexString = string.Format("CREATE INDEX {0}_Idx4 ON {1} (HitEntry, HitDomainID);", pfamAlignType, dbTableName);
dbCreator.CreateIndex(dbConnect, createIndexString, dbTableName);
}
else
{
createTableString = string.Format("CREATE TABLE {0} ( " +
" QueryEntry CHAR(4) NOT NULL, QueryChain CHAR(3) NOT NULL, QueryLength INTEGER NOT NULL, " +
" HitEntry CHAR(4) NOT NULL, HitChain CHAR(3) NOT NULL, HitLength INTEGER NOT NULL, " +
" Align_Len INTEGER NOT NULL, Score FLOAT NOT NULL, Gaps INTEGER NOT NULL, " +
" E_Value DOUBLE PRECISION NOT NULL, Identity FLOAT NOT NULL, Similarity FLOAT NOT NULL, " +
" AlignmentLength INTEGER NOT NULL, " +
" QuerySequence BLOB Sub_Type TEXT NOT NULL, HitSequence BLOB Sub_Type TEXT NOT NULL, " +
" QueryStart INTEGER NOT NULL, QueryEnd INTEGER NOT NULL, " +
" HitStart INTEGER NOT NULL, HitEnd INTEGER NOT NULL, " +
" QueryAsymChain CHAR(3), HitAsymChain CHAR(3));",
dbTableName);
dbCreator.CreateTableFromString(dbConnect, createTableString, dbTableName);
createIndexString = string.Format("CREATE INDEX FatcatAlign_Idx1 ON {0} (QueryEntry, QueryChain);", dbTableName);
dbCreator.CreateIndex(dbConnect, createIndexString, dbTableName);
createIndexString = string.Format("CREATE INDEX FatcatAlign_Idx2 ON {0} (HitEntry, HitChain);", dbTableName);
dbCreator.CreateIndex(dbConnect, createIndexString, dbTableName);
}
}