SLSMolecule+PDB.m

//
//  SLSMolecule.m
//  Molecules
//
//  The source code for Molecules is available under a BSD license.  See License.txt for details.
//
//  Created by Brad Larson on 6/26/2008.
//
//  This is the model class for the molecule object.  It parses a PDB file, generates a vertex buffer object, and renders that object to the screen

#import "SLSMolecule+PDB.h"
#import "NSData+Gzip.h"
#import "VCTitleCase.h"

static NSDictionary *pdbResidueLookupTable;

//const unsigned int PRECISION = 16; 
//inline GLfixed floatToFixed (GLfloat aValue)
//{ 
//	return (GLfixed) (aValue * 65536.0f); 
//}

//#define GL_UNSIGNED_INT                   0x1405

@implementation SLSMolecule (PDB)

#pragma mark -
#pragma mark Initialization and deallocation

- (void)createBondsForPDBResidue:(NSString *)residueType withAtomDictionary:(NSDictionary *)atomDictionary structureNumber:(NSInteger)structureNumber;
{
	if (pdbResidueLookupTable == nil)
	{
		// Set up the residue lookup table once for all molecules
		pdbResidueLookupTable = [[NSDictionary alloc] initWithObjectsAndKeys:
							  [NSNumber numberWithInteger:DEOXYADENINE], @"DA", 
							  [NSNumber numberWithInteger:DEOXYCYTOSINE], @"DC",
							  [NSNumber numberWithInteger:DEOXYGUANINE], @"DG",
							  [NSNumber numberWithInteger:DEOXYTHYMINE], @"DT",
							  [NSNumber numberWithInteger:ADENINE], @"A",
							  [NSNumber numberWithInteger:CYTOSINE], @"C",
							  [NSNumber numberWithInteger:GUANINE], @"G",
							  [NSNumber numberWithInteger:URACIL], @"U",
							  [NSNumber numberWithInteger:GLYCINE], @"GLY",
							  [NSNumber numberWithInteger:ALANINE], @"ALA",
							  [NSNumber numberWithInteger:VALINE], @"VAL",
							  [NSNumber numberWithInteger:LEUCINE], @"LEU",
							  [NSNumber numberWithInteger:ISOLEUCINE], @"ILE",
							  [NSNumber numberWithInteger:SERINE], @"SER",
							  [NSNumber numberWithInteger:CYSTEINE], @"CYS",
							  [NSNumber numberWithInteger:THREONINE], @"THR",
							  [NSNumber numberWithInteger:METHIONINE], @"MET",
							  [NSNumber numberWithInteger:PROLINE], @"PRO",
							  [NSNumber numberWithInteger:PHENYLALANINE], @"PHE",
							  [NSNumber numberWithInteger:TYROSINE], @"TYR",
							  [NSNumber numberWithInteger:TRYPTOPHAN], @"TRP",
							  [NSNumber numberWithInteger:HISTIDINE], @"HIS",
							  [NSNumber numberWithInteger:LYSINE], @"LYS",
							  [NSNumber numberWithInteger:ARGININE], @"ARG",
							  [NSNumber numberWithInteger:ASPARTICACID], @"ASP",
							  [NSNumber numberWithInteger:GLUTAMICACID], @"GLU",
							  [NSNumber numberWithInteger:ASPARAGINE], @"ASN",
							  [NSNumber numberWithInteger:GLUTAMINE], @"GLN",
							  nil];	
		
	}
	SLSResidueType residueIdentifier = [[pdbResidueLookupTable objectForKey:residueType] intValue];
	
	// Do the common atoms for classes of residues
	switch (residueIdentifier)
	{
		case ADENINE: // RNA nucleotides
		case CYTOSINE:
		case GUANINE:
		case URACIL:
		{
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"C2'"] endPoint:[atomDictionary objectForKey:@"O2'"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
		};
		case DEOXYADENINE: // DNA nucleotides
		case DEOXYCYTOSINE:
		case DEOXYGUANINE:
		case DEOXYTHYMINE:
		{
			// P -> O3' (Starts from 3' end, so no P in first nucleotide)
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"P"] endPoint:[atomDictionary objectForKey:@"OP1"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"P"] endPoint:[atomDictionary objectForKey:@"OP2"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"P"] endPoint:[atomDictionary objectForKey:@"O5'"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"O5'"] endPoint:[atomDictionary objectForKey:@"C5'"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"C5'"] endPoint:[atomDictionary objectForKey:@"C4'"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"C4'"] endPoint:[atomDictionary objectForKey:@"O4'"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"C4'"] endPoint:[atomDictionary objectForKey:@"C3'"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"C3'"] endPoint:[atomDictionary objectForKey:@"O3'"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"O4'"] endPoint:[atomDictionary objectForKey:@"C1'"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"C3'"] endPoint:[atomDictionary objectForKey:@"C2'"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"C2'"] endPoint:[atomDictionary objectForKey:@"C1'"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			
			// Link the nucleotides together
			if (self.previousTerminalAtomValue != nil)
				[self addBondToDatabaseWithStartPoint:self.previousTerminalAtomValue endPoint:[atomDictionary objectForKey:@"P"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			self.previousTerminalAtomValue = [atomDictionary objectForKey:@"O3'"];
		}; break;
		case GLYCINE: // Amino acids
		case ALANINE:
		case VALINE:
		case LEUCINE:
		case ISOLEUCINE:
		case SERINE:
		case CYSTEINE:
		case THREONINE:
		case METHIONINE:
		case PROLINE:
		case PHENYLALANINE:
		case TYROSINE:
		case TRYPTOPHAN:
		case HISTIDINE:
		case LYSINE:
		case ARGININE:
		case ASPARTICACID:
		case GLUTAMICACID:
		case ASPARAGINE:
		case GLUTAMINE:
		{
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"N"] endPoint:[atomDictionary objectForKey:@"CA"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"CA"] endPoint:[atomDictionary objectForKey:@"C"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"C"] endPoint:[atomDictionary objectForKey:@"O"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];

			// Peptide bond
			if (self.previousTerminalAtomValue != nil)
				[self addBondToDatabaseWithStartPoint:self.previousTerminalAtomValue endPoint:[atomDictionary objectForKey:@"N"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			self.previousTerminalAtomValue = [atomDictionary objectForKey:@"C"];
			
		}; break;
	}

	// Now do the residue-specific atoms
	switch (residueIdentifier)
	{
		case ADENINE:
		case DEOXYADENINE:
		{
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"C1'"] endPoint:[atomDictionary objectForKey:@"N9"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"N9"] endPoint:[atomDictionary objectForKey:@"C4"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"C4"] endPoint:[atomDictionary objectForKey:@"N3"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"N3"] endPoint:[atomDictionary objectForKey:@"C2"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"C2"] endPoint:[atomDictionary objectForKey:@"N1"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"N1"] endPoint:[atomDictionary objectForKey:@"C6"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"C6"] endPoint:[atomDictionary objectForKey:@"N6"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"C6"] endPoint:[atomDictionary objectForKey:@"C5"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"C5"] endPoint:[atomDictionary objectForKey:@"C4"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"C5"] endPoint:[atomDictionary objectForKey:@"N7"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"N7"] endPoint:[atomDictionary objectForKey:@"C8"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"C8"] endPoint:[atomDictionary objectForKey:@"N9"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
		}; break;
		case CYTOSINE:
		case DEOXYCYTOSINE:
		{
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"C1'"] endPoint:[atomDictionary objectForKey:@"N1"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"N1"] endPoint:[atomDictionary objectForKey:@"C2"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"C2"] endPoint:[atomDictionary objectForKey:@"O2"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"C2"] endPoint:[atomDictionary objectForKey:@"N3"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"N3"] endPoint:[atomDictionary objectForKey:@"C4"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"C4"] endPoint:[atomDictionary objectForKey:@"N4"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"C4"] endPoint:[atomDictionary objectForKey:@"C5"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"C5"] endPoint:[atomDictionary objectForKey:@"C6"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"C6"] endPoint:[atomDictionary objectForKey:@"N1"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
		}; break;
		case GUANINE:
		case DEOXYGUANINE:
		{
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"C1'"] endPoint:[atomDictionary objectForKey:@"N9"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"N9"] endPoint:[atomDictionary objectForKey:@"C4"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"C4"] endPoint:[atomDictionary objectForKey:@"N3"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"N3"] endPoint:[atomDictionary objectForKey:@"C2"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"C2"] endPoint:[atomDictionary objectForKey:@"N2"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"C2"] endPoint:[atomDictionary objectForKey:@"N1"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"N1"] endPoint:[atomDictionary objectForKey:@"C6"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"C6"] endPoint:[atomDictionary objectForKey:@"O6"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"C6"] endPoint:[atomDictionary objectForKey:@"C5"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"C5"] endPoint:[atomDictionary objectForKey:@"C4"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"C5"] endPoint:[atomDictionary objectForKey:@"N7"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"N7"] endPoint:[atomDictionary objectForKey:@"C8"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"C8"] endPoint:[atomDictionary objectForKey:@"N9"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
		}; break;
		case DEOXYTHYMINE:
		{
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"C5"] endPoint:[atomDictionary objectForKey:@"C7"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
		};
		case URACIL:
		{
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"C1'"] endPoint:[atomDictionary objectForKey:@"N1"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"N1"] endPoint:[atomDictionary objectForKey:@"C2"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"C2"] endPoint:[atomDictionary objectForKey:@"O2"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"C2"] endPoint:[atomDictionary objectForKey:@"N3"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"N3"] endPoint:[atomDictionary objectForKey:@"C4"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"C4"] endPoint:[atomDictionary objectForKey:@"O4"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"C4"] endPoint:[atomDictionary objectForKey:@"C5"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"C5"] endPoint:[atomDictionary objectForKey:@"C6"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"C5"] endPoint:[atomDictionary objectForKey:@"N1"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
		}; break;
		case ALANINE:
		{
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"CA"] endPoint:[atomDictionary objectForKey:@"CB"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
		}; break;
		case VALINE:
		{
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"CA"] endPoint:[atomDictionary objectForKey:@"CB"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"CB"] endPoint:[atomDictionary objectForKey:@"CG1"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"CB"] endPoint:[atomDictionary objectForKey:@"CG2"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
		}; break;
		case LEUCINE:
		{
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"CA"] endPoint:[atomDictionary objectForKey:@"CB"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"CB"] endPoint:[atomDictionary objectForKey:@"CG"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"CG"] endPoint:[atomDictionary objectForKey:@"CD1"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"CG"] endPoint:[atomDictionary objectForKey:@"CD2"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
		}; break;
		case ISOLEUCINE:
		{
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"CA"] endPoint:[atomDictionary objectForKey:@"CB"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"CB"] endPoint:[atomDictionary objectForKey:@"CG1"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"CB"] endPoint:[atomDictionary objectForKey:@"CG2"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"CG1"] endPoint:[atomDictionary objectForKey:@"CD1"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
		}; break;
		case SERINE:
		{
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"CA"] endPoint:[atomDictionary objectForKey:@"CB"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"CB"] endPoint:[atomDictionary objectForKey:@"OB"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
		}; break;
		case CYSTEINE:
		{
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"CA"] endPoint:[atomDictionary objectForKey:@"CB"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"CB"] endPoint:[atomDictionary objectForKey:@"SG"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
		}; break;
		case THREONINE:
		{
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"CA"] endPoint:[atomDictionary objectForKey:@"CB"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"CB"] endPoint:[atomDictionary objectForKey:@"OG1"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"CB"] endPoint:[atomDictionary objectForKey:@"CG2"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
		}; break;
		case METHIONINE:
		{
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"CA"] endPoint:[atomDictionary objectForKey:@"CB"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"CB"] endPoint:[atomDictionary objectForKey:@"CG"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"CG"] endPoint:[atomDictionary objectForKey:@"SD"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"SD"] endPoint:[atomDictionary objectForKey:@"CE"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
		}; break;
		case PROLINE:
		{
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"CA"] endPoint:[atomDictionary objectForKey:@"CB"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"CB"] endPoint:[atomDictionary objectForKey:@"CG"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"CG"] endPoint:[atomDictionary objectForKey:@"CD"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"CD"] endPoint:[atomDictionary objectForKey:@"N"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
		}; break;
		case PHENYLALANINE:
		{
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"CA"] endPoint:[atomDictionary objectForKey:@"CB"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"CB"] endPoint:[atomDictionary objectForKey:@"CG"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"CG"] endPoint:[atomDictionary objectForKey:@"CD1"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"CG"] endPoint:[atomDictionary objectForKey:@"CD2"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"CD1"] endPoint:[atomDictionary objectForKey:@"CE1"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"CD2"] endPoint:[atomDictionary objectForKey:@"CE2"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"CE1"] endPoint:[atomDictionary objectForKey:@"CZ"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"CE2"] endPoint:[atomDictionary objectForKey:@"CZ"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
		}; break;
		case TYROSINE:
		{
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"CA"] endPoint:[atomDictionary objectForKey:@"CB"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"CB"] endPoint:[atomDictionary objectForKey:@"CG"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"CG"] endPoint:[atomDictionary objectForKey:@"CD1"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"CG"] endPoint:[atomDictionary objectForKey:@"CD2"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"CD1"] endPoint:[atomDictionary objectForKey:@"CE1"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"CD2"] endPoint:[atomDictionary objectForKey:@"CE2"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"CE1"] endPoint:[atomDictionary objectForKey:@"CZ"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"CE2"] endPoint:[atomDictionary objectForKey:@"CZ"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"CZ"] endPoint:[atomDictionary objectForKey:@"OH"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
		}; break;
		case TRYPTOPHAN:
		{
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"CA"] endPoint:[atomDictionary objectForKey:@"CB"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"CB"] endPoint:[atomDictionary objectForKey:@"CG"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"CG"] endPoint:[atomDictionary objectForKey:@"CD1"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"CG"] endPoint:[atomDictionary objectForKey:@"CD2"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"CD1"] endPoint:[atomDictionary objectForKey:@"NE1"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"NE1"] endPoint:[atomDictionary objectForKey:@"CE2"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"CD2"] endPoint:[atomDictionary objectForKey:@"NE1"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"NE1"] endPoint:[atomDictionary objectForKey:@"CZ2"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"CZ2"] endPoint:[atomDictionary objectForKey:@"CH2"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"CH2"] endPoint:[atomDictionary objectForKey:@"CZ3"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"CZ3"] endPoint:[atomDictionary objectForKey:@"CE3"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"CE3"] endPoint:[atomDictionary objectForKey:@"CD2"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
		}; break;
		case HISTIDINE:
		{
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"CA"] endPoint:[atomDictionary objectForKey:@"CB"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"CB"] endPoint:[atomDictionary objectForKey:@"CG"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"CG"] endPoint:[atomDictionary objectForKey:@"ND1"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"CG"] endPoint:[atomDictionary objectForKey:@"CD2"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"ND1"] endPoint:[atomDictionary objectForKey:@"CE1"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"CD2"] endPoint:[atomDictionary objectForKey:@"NE2"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"CE1"] endPoint:[atomDictionary objectForKey:@"NE2"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
		}; break;
		case LYSINE:
		{
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"CA"] endPoint:[atomDictionary objectForKey:@"CB"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"CB"] endPoint:[atomDictionary objectForKey:@"CG"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"CG"] endPoint:[atomDictionary objectForKey:@"CD"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"CD"] endPoint:[atomDictionary objectForKey:@"CE"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"CE"] endPoint:[atomDictionary objectForKey:@"NZ"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
		}; break;
		case ARGININE:
		{
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"CA"] endPoint:[atomDictionary objectForKey:@"CB"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"CB"] endPoint:[atomDictionary objectForKey:@"CG"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"CG"] endPoint:[atomDictionary objectForKey:@"CD"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"CD"] endPoint:[atomDictionary objectForKey:@"NE"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"NE"] endPoint:[atomDictionary objectForKey:@"CZ"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"CZ"] endPoint:[atomDictionary objectForKey:@"NH1"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"CZ"] endPoint:[atomDictionary objectForKey:@"NH2"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
		}; break;
		case ASPARTICACID:
		{
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"CA"] endPoint:[atomDictionary objectForKey:@"CB"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"CB"] endPoint:[atomDictionary objectForKey:@"CG"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"CG"] endPoint:[atomDictionary objectForKey:@"OD1"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"CG"] endPoint:[atomDictionary objectForKey:@"OD2"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
		}; break;
		case GLUTAMICACID:
		{
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"CA"] endPoint:[atomDictionary objectForKey:@"CB"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"CB"] endPoint:[atomDictionary objectForKey:@"CG"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"CG"] endPoint:[atomDictionary objectForKey:@"CD"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"CD"] endPoint:[atomDictionary objectForKey:@"OE1"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"CD"] endPoint:[atomDictionary objectForKey:@"OE2"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
		}; break;
		case ASPARAGINE:
		{
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"CA"] endPoint:[atomDictionary objectForKey:@"CB"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"CB"] endPoint:[atomDictionary objectForKey:@"CG"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"CG"] endPoint:[atomDictionary objectForKey:@"OD1"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"CG"] endPoint:[atomDictionary objectForKey:@"ND2"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
		}; break;
		case GLUTAMINE:
		{
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"CA"] endPoint:[atomDictionary objectForKey:@"CB"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"CB"] endPoint:[atomDictionary objectForKey:@"CG"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"CG"] endPoint:[atomDictionary objectForKey:@"CD"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"CD"] endPoint:[atomDictionary objectForKey:@"OE1"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
			[self addBondToDatabaseWithStartPoint:[atomDictionary objectForKey:@"CD"] endPoint:[atomDictionary objectForKey:@"NE2"] bondType:SINGLEBOND structureNumber:structureNumber residueKey:residueIdentifier];
		}; break;			
	}
}

- (BOOL)readFromPDBFileToDatabase:(NSError **)error;
{
	// TODO: Add structure number
	unsigned int currentStructureNumber = 1;
	
	NSMutableDictionary *atomCoordinates = [[NSMutableDictionary alloc] init];
	NSMutableDictionary *residueAtoms = nil;
	NSString *currentResidueType = nil;
	int currentResidueNumber = -1;
		
	stillCountingAtomsInFirstStructure = YES;
	numberOfAtoms = 0;
	float tallyForCenterOfMassInX = 0.0f, tallyForCenterOfMassInY = 0.0f, tallyForCenterOfMassInZ = 0.0f;
	minimumXPosition = 1000.0f;
	maximumXPosition = 0.0f;
	minimumYPosition = 1000.0f;
	maximumYPosition = 0.0f;
	minimumZPosition = 1000.0f;
	maximumZPosition = 0.0f;

	// Find the file, Gunzip it
	// TODO: Better error handling on file missing, etc.
	NSArray *paths = NSSearchPathForDirectoriesInDomains(NSDocumentDirectory, NSUserDomainMask, YES);
	NSString *documentsDirectory = [paths objectAtIndex:0];
	
	NSData *pdbData;
	
	if ([[filename pathExtension] isEqualToString:@"pdb"]) // Uncompressed PDB file
	{
		pdbData = [[NSData alloc] initWithContentsOfFile:[documentsDirectory stringByAppendingPathComponent:filename]];
	}
	else // Deal with Gzipped files
	{
		NSData *gzippedPDBFile = [[NSData alloc] initWithContentsOfFile:[documentsDirectory stringByAppendingPathComponent:filename]];
		pdbData = [[NSData alloc] initWithGzippedData:gzippedPDBFile];
		[gzippedPDBFile release];
	}

	if (pdbData == nil)
	{
		[atomCoordinates release];
		return NO;
	}
	
	// Wrap all SQLite write operations in a BEGIN, COMMIT block to make writing one operation
	[SLSMolecule beginTransactionWithDatabase:database];
	
	// Load the file into a string for processing
	NSString *pdbFileContents = [[NSString alloc] initWithData:pdbData encoding:NSASCIIStringEncoding];
	[pdbData release];
	NSUInteger length = [pdbFileContents length];
	NSUInteger lineStart = 0, lineEnd = 0, contentsEnd = 0;
	NSRange currentRange;
	
	while (lineEnd < length) 
	{
		NSAutoreleasePool *pool = [[NSAutoreleasePool alloc] init];
		[pdbFileContents getParagraphStart:&lineStart end:&lineEnd contentsEnd:&contentsEnd forRange:NSMakeRange(lineEnd, 0)];
		currentRange = NSMakeRange(lineStart, contentsEnd - lineStart);
		NSString *currentLine = [pdbFileContents substringWithRange:currentRange];
		
		if ([currentLine length] >= 6) // Make sure that we at least have a line identifier present, move on the the next line otherwise
		{
			NSString *lineIdentifier = [[currentLine substringWithRange:NSMakeRange(0, 6)] stringByTrimmingCharactersInSet:[NSCharacterSet whitespaceCharacterSet]];
			if (([lineIdentifier isEqualToString:@"ATOM"]) || ([lineIdentifier isEqualToString:@"HETATM"]))
			{
				// Process the bonds in the previous residue if starting a new residue
				if (![lineIdentifier isEqualToString:@"HETATM"])
				{
					int residueNumber = [[currentLine substringWithRange:NSMakeRange(22, 5)] intValue];
					if (residueNumber != currentResidueNumber)
					{
						if (residueAtoms != nil)
						{
							[self createBondsForPDBResidue:currentResidueType withAtomDictionary:residueAtoms structureNumber:currentStructureNumber];
							[residueAtoms release];
							residueAtoms = nil;
							[currentResidueType release];
							currentResidueType = nil;
						}
						residueAtoms = [[NSMutableDictionary alloc] init];
						currentResidueNumber = residueNumber;
						currentResidueType = [[[currentLine substringWithRange:NSMakeRange(17, 3)] stringByTrimmingCharactersInSet:[NSCharacterSet whitespaceCharacterSet]] retain];
					}
				}
				else // Bond (-0.231000,89.028999,38.627998)
				{
					if (residueAtoms != nil)
					{
						[self createBondsForPDBResidue:currentResidueType withAtomDictionary:residueAtoms structureNumber:currentStructureNumber];
						[residueAtoms release];
						residueAtoms = nil;
						[currentResidueType release];
						currentResidueType = nil;
					}
					
					self.previousTerminalAtomValue = nil;
				}			
				
				SLS3DPoint atomCoordinate;
				
				atomCoordinate.x = [[currentLine substringWithRange:NSMakeRange(30, 8)] floatValue];
				atomCoordinate.y = [[currentLine substringWithRange:NSMakeRange(38, 8)] floatValue];
				atomCoordinate.z = [[currentLine substringWithRange:NSMakeRange(46, 8)] floatValue];
				if (stillCountingAtomsInFirstStructure)
				{
					tallyForCenterOfMassInX += atomCoordinate.x;
					if (minimumXPosition > atomCoordinate.x)
						minimumXPosition = atomCoordinate.x;
					if (maximumXPosition < atomCoordinate.x)
						maximumXPosition = atomCoordinate.x;
					
					tallyForCenterOfMassInY += atomCoordinate.y;
					if (minimumYPosition > atomCoordinate.y)
						minimumYPosition = atomCoordinate.y;
					if (maximumYPosition < atomCoordinate.y)
						maximumYPosition = atomCoordinate.y;
					
					tallyForCenterOfMassInZ += atomCoordinate.z;
					if (minimumZPosition > atomCoordinate.z)
						minimumZPosition = atomCoordinate.z;
					if (maximumZPosition < atomCoordinate.z)
						maximumZPosition = atomCoordinate.z;
				}
				
				unsigned int atomSerialNumber = [[currentLine substringWithRange:NSMakeRange(6, 5)] intValue];
				[atomCoordinates setObject:[NSValue valueWithBytes:&atomCoordinate objCType:@encode(SLS3DPoint)] forKey:[NSNumber numberWithInt:atomSerialNumber]];
				if (![lineIdentifier isEqualToString:@"HETATM"])
				{
					NSString *atomResidueIdentifier = [[currentLine substringWithRange:NSMakeRange(12, 4)] stringByTrimmingCharactersInSet:[NSCharacterSet whitespaceCharacterSet]];
					[residueAtoms setObject:[NSValue valueWithBytes:&atomCoordinate objCType:@encode(SLS3DPoint)] forKey:atomResidueIdentifier];
				}
				
				NSString *atomElement;
				if ([currentLine length] < 78)
				{
					atomElement = [currentLine substringWithRange:NSMakeRange(12, 2)];
				}
				else
				{
					atomElement = [currentLine substringWithRange:NSMakeRange(76, 2)];
				}
				SLSAtomType processedAtomType;
				if ([atomElement isEqualToString:@" C"])
					processedAtomType = CARBON;
				else if ([atomElement isEqualToString:@" H"])
					processedAtomType = HYDROGEN;
				else if ([atomElement isEqualToString:@" O"])
					processedAtomType = OXYGEN;
				else if ([atomElement isEqualToString:@" N"])
					processedAtomType = NITROGEN;
				else if ([atomElement isEqualToString:@" S"])
					processedAtomType = SULFUR;
				else if ([atomElement isEqualToString:@" P"])
					processedAtomType = PHOSPHOROUS;
				else if ([atomElement isEqualToString:@"FE"])
					processedAtomType = IRON;
				else if ([atomElement isEqualToString:@"SI"])
					processedAtomType = SILICON;
				else 
					processedAtomType = UNKNOWN;
				
				if ([lineIdentifier isEqualToString:@"HETATM"])
				{
					NSString *atomResidueIdentifier = [[currentLine substringWithRange:NSMakeRange(16, 4)] stringByTrimmingCharactersInSet:[NSCharacterSet whitespaceCharacterSet]];
					if ([atomResidueIdentifier isEqualToString:@"HOH"])
						[self addAtomToDatabase:processedAtomType atPoint:atomCoordinate structureNumber:currentStructureNumber residueKey:WATER];
					else
						[self addAtomToDatabase:processedAtomType atPoint:atomCoordinate structureNumber:currentStructureNumber residueKey:UNKNOWNRESIDUE];
				}
				else
					[self addAtomToDatabase:processedAtomType atPoint:atomCoordinate structureNumber:currentStructureNumber residueKey:SERINE];
			}
			else if ([lineIdentifier isEqualToString:@"TER"])
			{
				// Catch the last residue of the chain
				if (residueAtoms != nil)
				{
					[self createBondsForPDBResidue:currentResidueType withAtomDictionary:residueAtoms structureNumber:currentStructureNumber];
					[residueAtoms release];
					residueAtoms = nil;
					[currentResidueType release];
					currentResidueType = nil;
				}
				
				self.previousTerminalAtomValue = nil;
			}
			else if ([lineIdentifier isEqualToString:@"CONECT"])
			{
				NSValue *startValue = nil;
				int indexForFirstAtom = [[currentLine substringWithRange:NSMakeRange(6, 5)] intValue];
				if ( (indexForFirstAtom <= [atomCoordinates count]) && (indexForFirstAtom > 0) )
					startValue = [atomCoordinates objectForKey:[NSNumber numberWithInt:indexForFirstAtom]];
				if (indexForFirstAtom > 0)
				{
					int indexForNextAtom;
					if ([currentLine length] > 15)
					{
						indexForNextAtom = [[currentLine substringWithRange:NSMakeRange(11, 5)] intValue];
						if ( (indexForNextAtom > 0) && (indexForNextAtom <= [atomCoordinates count]) )
						{
							[self addBondToDatabaseWithStartPoint:startValue endPoint:[atomCoordinates objectForKey:[NSNumber numberWithInt:indexForNextAtom]] bondType:SINGLEBOND structureNumber:currentStructureNumber residueKey:UNKNOWNRESIDUE];
						}
					}
					
					if ([currentLine length] > 20)
					{
						indexForNextAtom = [[currentLine substringWithRange:NSMakeRange(16, 5)] intValue];
						if ( (indexForNextAtom > 0) && (indexForNextAtom <= [atomCoordinates count]) )
						{
							[self addBondToDatabaseWithStartPoint:startValue endPoint:[atomCoordinates objectForKey:[NSNumber numberWithInt:indexForNextAtom]] bondType:SINGLEBOND structureNumber:currentStructureNumber residueKey:UNKNOWNRESIDUE];
						}
					}
					
					if ([currentLine length] > 25)
					{
						indexForNextAtom = [[currentLine substringWithRange:NSMakeRange(21, 5)] intValue];
						if ( (indexForNextAtom > 0) && (indexForNextAtom <= [atomCoordinates count]) )
						{
							[self addBondToDatabaseWithStartPoint:startValue endPoint:[atomCoordinates objectForKey:[NSNumber numberWithInt:indexForNextAtom]] bondType:SINGLEBOND structureNumber:currentStructureNumber residueKey:UNKNOWNRESIDUE];
						}
					}
				}
			}
			else if ([lineIdentifier isEqualToString:@"MODEL"])
			{
				currentStructureNumber = [[currentLine substringWithRange:NSMakeRange(12, 4)] intValue];
				if (currentStructureNumber > numberOfStructures)
					numberOfStructures = currentStructureNumber;
			}
			else if ([lineIdentifier isEqualToString:@"ENDMDL"])
			{
				stillCountingAtomsInFirstStructure = NO;
			}
			else if ([lineIdentifier isEqualToString:@"TITLE"])
			{
				if (title == nil)
					title = [[[currentLine substringFromIndex:10] stringByTrimmingCharactersInSet:[NSCharacterSet whitespaceCharacterSet]] retain];
				else
					title = [[[title autorelease] stringByAppendingFormat:@" %@", [[currentLine substringFromIndex:10] stringByTrimmingCharactersInSet:[NSCharacterSet whitespaceCharacterSet]]] retain];
			}
			else if ([lineIdentifier isEqualToString:@"COMPND"])
			{
				NSString *compoundIdentifier = [[currentLine substringWithRange:NSMakeRange(10, 10)] stringByTrimmingCharactersInSet:[NSCharacterSet whitespaceCharacterSet]];
				if ([compoundIdentifier isEqualToString:@"MOLECULE:"])
				{
					if (compound == nil)
						compound = [[[currentLine substringFromIndex:20] stringByTrimmingCharactersInSet:[NSCharacterSet whitespaceCharacterSet]] retain];
				}
			}
			else if ([lineIdentifier isEqualToString:@"SOURCE"])
			{
				if (source == nil)
					source = [[[currentLine substringFromIndex:10] stringByTrimmingCharactersInSet:[NSCharacterSet whitespaceCharacterSet]] retain];
				else
					source = [[[source autorelease] stringByAppendingFormat:@" %@", [[currentLine substringFromIndex:10] stringByTrimmingCharactersInSet:[NSCharacterSet whitespaceCharacterSet]]] retain];
			}
			else if ([lineIdentifier isEqualToString:@"AUTHOR"])
			{
				if (author == nil)
					author = [[[currentLine substringFromIndex:10] stringByTrimmingCharactersInSet:[NSCharacterSet whitespaceCharacterSet]] retain];
				else
					author = [[[author autorelease] stringByAppendingFormat:@" %@", [[currentLine substringFromIndex:10] stringByTrimmingCharactersInSet:[NSCharacterSet whitespaceCharacterSet]]] retain];
			}
			else if ([lineIdentifier isEqualToString:@"JRNL"])
			{
				NSString *journalIdentifier = [[currentLine substringWithRange:NSMakeRange(12, 4)] stringByTrimmingCharactersInSet:[NSCharacterSet whitespaceCharacterSet]];
				if ([journalIdentifier isEqualToString:@"AUTH"])
				{
					if (journalAuthor == nil)
						journalAuthor = [[[currentLine substringFromIndex:18] stringByTrimmingCharactersInSet:[NSCharacterSet whitespaceCharacterSet]] retain];
					else
						journalAuthor = [[[journalAuthor autorelease] stringByAppendingFormat:@" %@", [[currentLine substringFromIndex:18] stringByTrimmingCharactersInSet:[NSCharacterSet whitespaceCharacterSet]]] retain];
				}
				else if ([journalIdentifier isEqualToString:@"TITL"])
				{
					if (journalTitle == nil)
						journalTitle = [[[currentLine substringFromIndex:18] stringByTrimmingCharactersInSet:[NSCharacterSet whitespaceCharacterSet]] retain];
					else
						journalTitle = [[[journalTitle autorelease] stringByAppendingFormat:@" %@", [[currentLine substringFromIndex:18] stringByTrimmingCharactersInSet:[NSCharacterSet whitespaceCharacterSet]]] retain];
				}
				else if ( ([journalIdentifier isEqualToString:@"REF"]) || ([journalIdentifier isEqualToString:@"REFN"]) )
				{
					if (journalReference == nil)
						journalReference = [[[currentLine substringFromIndex:18] stringByTrimmingCharactersInSet:[NSCharacterSet whitespaceCharacterSet]] retain];
					else
						journalReference = [[[journalReference autorelease] stringByAppendingFormat:@" %@", [[currentLine substringFromIndex:18] stringByTrimmingCharactersInSet:[NSCharacterSet whitespaceCharacterSet]]] retain];
				}
			}		
			else if ([lineIdentifier isEqualToString:@"SEQRES"])
			{
				if (sequence == nil)
					sequence = [[[currentLine substringFromIndex:14] stringByTrimmingCharactersInSet:[NSCharacterSet whitespaceCharacterSet]] retain];
				else
					sequence = [[[sequence autorelease] stringByAppendingFormat:@"\n%@", [[currentLine substringFromIndex:14] stringByTrimmingCharactersInSet:[NSCharacterSet whitespaceCharacterSet]]] retain];
			}
			
			// 	NSString *pdbCode, *title, *keywords, *journalReference, *sequence, *compound;			
		}
		
		[pool release];
	}
	[residueAtoms release];
	residueAtoms = nil;
	[currentResidueType release];
	currentResidueType = nil;
	[pdbFileContents release];
	
	if (numberOfAtoms > 0)
	{		
		centerOfMassInX = tallyForCenterOfMassInX / (float)numberOfAtoms;
		centerOfMassInY = tallyForCenterOfMassInY / (float)numberOfAtoms;
		centerOfMassInZ = tallyForCenterOfMassInZ / (float)numberOfAtoms;
		scaleAdjustmentForX = 1.5 / (maximumXPosition - minimumXPosition);
		scaleAdjustmentForY = 1.5 / (maximumYPosition - minimumYPosition);
		scaleAdjustmentForZ = (1.5 * 1.25) / (maximumZPosition - minimumZPosition);
		if (scaleAdjustmentForY < scaleAdjustmentForX)
			scaleAdjustmentForX = scaleAdjustmentForY;
		if (scaleAdjustmentForZ < scaleAdjustmentForX)
			scaleAdjustmentForX = scaleAdjustmentForZ;
	}
	
	// Convert the strings to title case and strip off the ;s at the end of lines
	NSCharacterSet *semicolonSet = [NSCharacterSet characterSetWithCharactersInString:@";"];

	if (title != nil)
	{
		title = [[title autorelease] lowercaseString];
		title = [title titlecaseString];
		title = [title stringByTrimmingCharactersInSet:semicolonSet];
		[title retain];
	}
	else
	{
		title = [filename copy];
	}

	if (compound != nil)
	{
		compound = [[compound autorelease] lowercaseString];
		compound = [compound titlecaseString];
		compound = [compound stringByTrimmingCharactersInSet:semicolonSet];
		[compound retain];
	}
	else
	{
		compound = [filename copy];
	}

	[self writeMoleculeDataToDatabase];

	if (source != nil)
	{
		source = [[source autorelease] lowercaseString];
		source = [source titlecaseString];
		source = [source stringByTrimmingCharactersInSet:semicolonSet];
		[source retain];
		[self addMetadataToDatabase:source type:MOLECULESOURCE];
	}

	if (author != nil)
	{
		author = [[author autorelease] capitalizedString];
		author = [author stringByTrimmingCharactersInSet:semicolonSet];
		[author retain];
		[self addMetadataToDatabase:author type:MOLECULEAUTHOR];
	}

 	if (journalAuthor != nil)
	{
		journalAuthor = [[journalAuthor autorelease] capitalizedString];
		journalAuthor = [journalAuthor stringByTrimmingCharactersInSet:semicolonSet];
		[journalAuthor retain];
		[self addMetadataToDatabase:journalAuthor type:JOURNALAUTHOR];
	}
	
	if (journalTitle != nil)
	{
		journalTitle = [[journalTitle autorelease] lowercaseString];
		journalTitle = [journalTitle titlecaseString];
		journalTitle = [journalTitle stringByTrimmingCharactersInSet:semicolonSet];
		[journalTitle retain];
		[self addMetadataToDatabase:journalTitle type:JOURNALTITLE];
	}

	if (journalReference != nil)
	{
		journalReference = [[journalReference autorelease] capitalizedString];
		journalReference = [journalReference stringByTrimmingCharactersInSet:semicolonSet];
		[journalReference retain];
		[self addMetadataToDatabase:journalReference type:JOURNALREFERENCE];
	}

	if (sequence != nil)
		[self addMetadataToDatabase:sequence type:MOLECULESEQUENCE];
			
	[atomCoordinates release];
	
	// End the SQLite BEGIN, COMMIT block and write it out to disk
	[SLSMolecule endTransactionWithDatabase:database];

	return YES;
}

@end