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   Project: UL

   Copyright (C) 2005 Michael Johnston & Jordi Villa-Freixa

   Author: Michael Johnston

   Created: 2005-06-06 12:17:25 +0200 by michael johnston

   This application is free software; you can redistribute it and/or
   modify it under the terms of the GNU General Public
   License as published by the Free Software Foundation; either
   version 2 of the License, or (at your option) any later version.

   This application is distributed in the hope that it will be useful,
   but WITHOUT ANY WARRANTY; without even the implied warranty of
   Library General Public License for more details.

   You should have received a copy of the GNU General Public
   License along with this library; if not, write to the Free
   Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111 USA.

#include "ULTopologyFrameBuilder.h"
#include "XMLLib/XMLLib.h"

It would be better if this was more general. 
i.e. read in the required topology type and then
have a standard way to generate the tables ...

@implementation ULTopologyFrameBuilder

- (NSArray*) _getMoleculeNodesForSequence: (NSArray*) sequence
      NSEnumerator* seqEnum;
      id mol, class, node;
      NSMutableArray* moleculeNodes, *missingMolecules;

      moleculeNodes = [NSMutableArray array];
      missingMolecules = [NSMutableArray array];
      class =[[[[[[topologyLibrary children] objectAtIndex:0] children] objectAtIndex:1] children] objectAtIndex:0];
      seqEnum = [sequence objectEnumerator];

      while(mol = [seqEnum nextObject])
            node = [class findMoleculeNodeWithName: mol];
            if(node == nil)
                  NSWarnLog(@"Couldnt find residue - %@ - in library!", mol);
                  //this is redundant - cant remember what is was for ...
                  [moleculeNodes addObject: @"Missing"];
                  if(![missingMolecules containsObject: mol])
                        [missingMolecules addObject: mol];
                  [moleculeNodes addObject: node];

      if([missingMolecules count] != 0)
            [NSException raise: @"ULBuildException"
                  @"The following residues were not in the library\n%@\n", missingMolecules]; 
      return moleculeNodes;

00071 - (id) initWithTopologyLibrary: (NSString*) topLib
      NSString* topPath;

      //FIXME: We load enzymix directly at the moment becuase its the only force field    

      topPath = [[[NSBundle mainBundle] resourcePath]       
                  stringByAppendingPathComponent: @"EnzymixTopology.ffml"];

      NSDebugLLog(@"ULTopologyFrameBuilder", @"Creating document tree for amino98");
      topologyLibrary = [[ULMolecularLibraryTree alloc] documentTreeForXMLFile: topPath];
      NSDebugLLog(@"ULTopologyFrameBuilder", @"Complete.");
      return self;

00087 - (id) buildTopologyForSystem: (NSArray*) sequences 
            withOptions: (NSDictionary*) options
            error: (NSError**) buildError
            userInfo: (NSString**) buildInfo
      int no_atoms, monomerCount, arrayIndexOffset;
      id nodeArray, atomHolder, node, sequence;
      NSMutableArray* pdbNameList, *libraryNameList, *residueList, *residueIndexes;
      NSMutableArray *atomsPerResidue, *bondedAtoms;
      NSMutableArray* connectArray, *partialCharges;
      NSMutableDictionary* topologyFrame;
      NSEnumerator *nodeEnum, *sequenceEnum;
      NSRange residueRange;

      sequenceEnum = [sequences objectEnumerator];
      pdbNameList = [NSMutableArray array];
      libraryNameList = [NSMutableArray array];
      residueList = [NSMutableArray array];     
      residueIndexes = [NSMutableArray array]; 
      atomsPerResidue = [NSMutableArray array]; 
      partialCharges = [NSMutableArray array]; 
      connectArray = [NSMutableArray array]; //for the interresidue connections
      bondedAtoms = [NSMutableArray array];

      [buildString release];
      buildString = [[NSMutableString stringWithCapacity: 1] retain];
      *buildInfo = buildString;

      NSDebugLLog(@"ULTopologyFrameBuilder", @"\nTopology Frame\n Chains %@", sequences);

      [buildString appendString: @"\nBuilding topology frame using EnzymixTopology.ffml\n"];

      no_atoms = 0;
      arrayIndexOffset = 1;
      while(sequence = [sequenceEnum nextObject])
            //have to add a handler here when the library is missing elements
            NSDebugLLog(@"ULTopologyFrameBuilder", @"Getting nodeArray");
            nodeArray = [self _getMoleculeNodesForSequence: sequence];
            [buildString appendString: @"Found all residues.\n"];
            NSDebugLLog(@"ULTopologyFrameBuilder", @"Complete");
            nodeEnum = [nodeArray objectEnumerator];
            //array index offset is 1 if the atom indices in the molecular library
            //being used start at 1 and zero if they start at zero. We want them
            //to start at 0 since these means that the indexes will correspond to 
            //the entries in atomList. Assuming for now that they start at 1 (typical fortran)
            monomerCount =  0;

            while(node = [nodeEnum nextObject]) 
                  [residueList addObject: [node moleculeName]];

                  atomHolder = [node atomNamesFromExternalSource: @"PDB"];
                  [pdbNameList addObjectsFromArray: atomHolder];

                  residueRange.location = [libraryNameList count];
                  atomHolder = [node atomNames];
                  [libraryNameList addObjectsFromArray: atomHolder];
                  residueRange.length = [libraryNameList count] - residueRange.location;
                  [residueIndexes addObject: [NSIndexSet indexSetWithIndexesInRange: residueRange]];

                  [partialCharges addObjectsFromArray: [node partialCharges]];
                  [atomsPerResidue addObject: [NSNumber numberWithInt: [atomHolder count]]];
                  [bondedAtoms addObjectsFromArray: 
                        [node bondedAtomsListWithOffset: no_atoms - arrayIndexOffset]];

                  //handle the connections between monomer units

                  if([node isMonomer])
                        if(monomerCount == 0)
                              [connectArray insertObject: 
                                    [NSNumber numberWithInt: 
                                    [node connectionForDirection: @"Out"] + no_atoms - arrayIndexOffset] 
                                    atIndex: 0];
                              [connectArray insertObject:
                                    [NSNumber numberWithInt: 
                                    [node connectionForDirection: @"In"] + no_atoms - arrayIndexOffset]
                                    atIndex: 1];
                              //we have an inter residue bond - add the atom indexes to the appropriate
                              //bonded atoms list     

                              [[bondedAtoms objectAtIndex: 
                                          [[connectArray objectAtIndex: 0] intValue]]
                                          addObject: [connectArray objectAtIndex: 1]];
                              [[bondedAtoms objectAtIndex: 
                                          [[connectArray objectAtIndex: 1] intValue]]
                                          addObject: [connectArray objectAtIndex: 0]];
                              [connectArray removeAllObjects];
                              [connectArray insertObject: 
                                    [NSNumber numberWithInt: 
                                    [node connectionForDirection: @"Out"] + no_atoms - arrayIndexOffset]
                                    atIndex: 0];
                        monomerCount = 0;
                        [connectArray removeAllObjects];

                  no_atoms += [atomHolder count];

      NSDebugLLog(@"ULTopologyFrameBuilder", @"Residue names %@", residueList);
      NSDebugLLog(@"ULTopologyFrameBuilder", @"There are %d atoms", [libraryNameList count]);
      [buildString appendFormat: @"There are %d atoms in the topology frame\n", 
                              [libraryNameList count]];
      [buildString appendFormat: @"\nCompleted topology frame build\n"];

      topologyFrame =  [NSMutableDictionary dictionaryWithCapacity:1];
      [topologyFrame setObject: pdbNameList forKey:@"AtomNames"];
      [topologyFrame setObject: libraryNameList forKey:@"LibraryNames"];
      [topologyFrame setObject: atomsPerResidue forKey:@"AtomsPerResidue"];
      [topologyFrame setObject: partialCharges forKey:@"PartialCharges"];
      [topologyFrame setObject: bondedAtoms forKey:@"BondedAtoms"];
      [topologyFrame setObject: residueIndexes forKey:@"ResidueIndexes"];
      [topologyFrame setObject: residueList forKey:@"ResidueList"];

      return topologyFrame;


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