All files / src/parsers MMTF.ts

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import { base64ToArray } from "../utilities";
import { Matrix4 } from "../WebGL";
import { computeSecondaryStructure } from "./utils/computeSecondaryStructure";
import { processSymmetries } from "./utils/processSymmetries";
 
interface MMTFobj {
    decode(data:Uint8Array|ArrayBuffer): any;
}
declare var MMTF: MMTFobj;
 
var fromCharCode = function( charCodeArray ){
  return String.fromCharCode.apply( null, charCodeArray ).replace(/\0/g, '');
};
 
var convertSS = function(val) {
//convert mmtf code to 3dmol code
/*    
  0:  pi helix
  1:  bend
  2:  alpha helix
  3:  sheet extended
  4:  3-10 helix
  5:  bridge
  6:  turn
  7:  coil
 */
  if(val == 0 || val == 2 || val == 4) return 'h';
  if(val == 3) return 's';
  return 'c';
};
 
let mmtfHETATMtypes = new Set([
"D-SACCHARIDE",
"D-SACCHARIDE 1,4 AND 1,4 LINKING",
"D-SACCHARIDE 1,4 AND 1,6 LINKING",
"L-SACCHARIDE",
"L-SACCHARIDE 1,4 AND 1,4 LINKING",
"L-SACCHARIDE 1,4 AND 1,6 LINKING",
"NON-POLYMER",
"OTHER",
"PEPTIDE-LIKE",
"SACCHARIDE" ]);
 
/** @param bindata - binary UInt8Array buffer or a base64 encoded string
 *  @param ParserOptionsSpec
 *  @category Parsers
*/
export function MMTFparser(bindata, options) {
  
  var noH = !options.keepH; // suppress hydrogens by default
  var selAltLoc = options.altLoc ? options.altLoc : 'A'; //default alternate location to select if present
  var ignoreStruct = !!options.noSecondaryStructure; 
  var computeStruct = !options.noComputeSecondaryStructure;
  //extract symmetries - only take first assembly, apply to all models (ignoring changes for now)
  var noAssembly = !options.doAssembly; // don't assemble by default
  var assemblyIndex = options.assemblyIndex ? options.assemblyIndex : 0; 
  
  if(typeof(bindata) == "string") {
      //assume base64 encoded
      bindata = base64ToArray(bindata);
  }
  
  var mmtfData = MMTF.decode( bindata );       
  
  var atoms: any[][] & Record<string, any> = [[]];
  var modelData: any[] = atoms.modelData = [];
  
  // setup index counters
  var modelIndex = 0;
  var chainIndex = 0;
  var groupIndex = 0;
  var atomIndex = 0;
 
  // setup optional fields
  var secStructList = mmtfData.secStructList;
  var insCodeList = mmtfData.insCodeList;
  var sequenceIndexList = mmtfData.sequenceIndexList;
  var bFactorList = mmtfData.bFactorList;
  var altLocList = mmtfData.altLocList;
  var occupancyList = mmtfData.occupancyList;
  var bondAtomList = mmtfData.bondAtomList;
  var bondOrderList = mmtfData.bondOrderList;
  
  var numModels = mmtfData.numModels;
  Iif (numModels == 0) return atoms;
  if (!options.multimodel) numModels = 1; //first only
  // hoisted loop variables
  var i, j, k, kl, m, n;
  
 
  
  var symmetries: Matrix4[] = [];
  if(!noAssembly && mmtfData.bioAssemblyList && mmtfData.bioAssemblyList.length > 0) {
      var transforms = mmtfData.bioAssemblyList[assemblyIndex].transformList;
      for(i = 0, n = transforms.length; i < n; i++) {
          var matrix = new Matrix4(transforms[i].matrix);
          matrix.transpose();
          symmetries.push(matrix);
      }
  }
  var unitCell = null as Record<string, number> | null;
  //unit cell info
  if(mmtfData.unitCell) {
      var u = mmtfData.unitCell;
      unitCell = {'a' : u[0], 'b' : u[1], 'c' : u[2], 'alpha' : u[3], 'beta' : u[4], 'gamma' : u[5]};
  }
 
  let chainIsPolymer: boolean[] = [];
  mmtfData.entityList.forEach(entity => {
      entity.chainIndexList.forEach(ch => {
          chainIsPolymer[ch] = entity.type == "polymer";
      });
  });
  var bondAtomListStart = 0; //for current model
  //loop over models, 
  for (m = 0; m < numModels; m++ ) {
      var modelChainCount = mmtfData.chainsPerModel[m];
      var matoms = atoms[atoms.length-1];
      var serialToIndex: number[] = []; // map to matoms index, needed for noh
 
      modelData.push({symmetries:symmetries, cryst: unitCell});
      for( i = 0; i < modelChainCount; ++i ){
 
          var chainGroupCount = mmtfData.groupsPerChain[ chainIndex ];
          var chainId = fromCharCode(
              mmtfData.chainIdList.subarray( chainIndex * 4, chainIndex * 4 + 4 )
          );
          if(mmtfData.chainNameList) {
              chainId = fromCharCode(
                      mmtfData.chainNameList.subarray( chainIndex * 4, chainIndex * 4 + 4 )
              );
          }
 
          var startGroup = groupIndex;
          var prevSS = '';
          for( j = 0; j < chainGroupCount; ++j ){ //over residues (groups)
 
              var groupData = mmtfData.groupList[ mmtfData.groupTypeList[ groupIndex ] ];
              var groupAtomCount = groupData.atomNameList.length;
              var secStruct = 0;
              var secStructBegin = false;
              var secStructEnd = false;
              
              if( secStructList ){
                  secStruct = secStructList[ groupIndex ];
                  var sscode = convertSS(secStruct);
                  if(groupIndex  == 0 || sscode != prevSS) {
                      secStructBegin = true;
                  }
                  prevSS = sscode;
                  var nextgroup = groupIndex+1;
                  if(nextgroup >= secStructList.length || convertSS(secStructList[nextgroup] != sscode)) {
                      secStructEnd = true;
                  }
              }
              var insCode = null as string|null;
              if( mmtfData.insCodeList ){
                  insCode = String.fromCharCode( insCodeList[ groupIndex ] );
              }
              var sequenceIndex = null;
              if( sequenceIndexList ){
                  sequenceIndex = sequenceIndexList[ groupIndex ];
              }
 
              var groupId = mmtfData.groupIdList[ groupIndex ];
              var groupName = groupData.groupName;
              let groupType = groupData.chemCompType;
              var startAtom = atomIndex;
              //note the following is not identical to respecting HETATM records
              //this information isn't available in MMTF.  
              let isHETATM =  mmtfHETATMtypes.has(groupType) || !chainIsPolymer[chainIndex];
              
              for( k = 0; k < groupAtomCount; ++k ){
 
                  var element = groupData.elementList[ k ];
                  Iif(noH && element == 'H') {
                      atomIndex += 1;
                      continue;
                  }
                  
                  var bFactor = '';
                  if( bFactorList ){
                      bFactor = bFactorList[ atomIndex ];
                  }
                  var altLoc = '';
                  if( altLocList && altLocList[ atomIndex ]){ //not zero
                      altLoc = String.fromCharCode( altLocList[ atomIndex ] );
                  }
                  var occupancy = '';
                  if( occupancyList ){
                      occupancy = occupancyList[ atomIndex ];
                  }
 
                  if (altLoc != '' && altLoc != selAltLoc && selAltLoc != '*') {
                      atomIndex += 1;
                      continue; 
                  }
                  
                  var atomId = mmtfData.atomIdList[ atomIndex ];
                  var atomName = groupData.atomNameList[ k ];
                  var atomCharge = 0;
                  Iif(groupData.atomChargeList) atomCharge = groupData.atomChargeList[ k ];
                  var xCoord = mmtfData.xCoordList[ atomIndex ];
                  var yCoord = mmtfData.yCoordList[ atomIndex ];
                  var zCoord = mmtfData.zCoordList[ atomIndex ];
                      
                  serialToIndex[atomIndex] = matoms.length;
                  matoms.push({
                      'resn' : groupName,
                      'x' : xCoord,
                      'y' : yCoord,
                      'z' : zCoord,
                      'elem' : element,
                      'hetflag' : isHETATM,
                      'chain' : chainId,
                      'resi' : groupId,
                      'icode' : altLoc,
                      'rescode' : groupId + (altLoc != ' ' ? "^" + altLoc : ""), // combo
                      // resi
                      // and
                      // icode
                      'serial' : atomId,
                      'altLoc' : altLoc,
                      'index' : atomIndex,
                      'atom' : atomName,
                      'bonds' : [],
                      'ss' : convertSS(secStruct),
                      'ssbegin' : secStructBegin,
                      'ssend' : secStructEnd,
                      'bondOrder' : [],
                      'properties' : {charge: atomCharge, occupancy:occupancy},
                      'b' : bFactor,
                  });
 
                  atomIndex += 1;
              }
              
              // intra group bonds
              var groupBondAtomList = groupData.bondAtomList;
              for( k = 0, kl = groupData.bondOrderList.length; k < kl; ++k ){
                  var atomIndex1 = startAtom + groupBondAtomList[ k * 2 ];
                  var atomIndex2 = startAtom + groupBondAtomList[ k * 2 + 1 ];
                  var bondOrder = groupData.bondOrderList[ k ];
                  
                  //I assume bonds are only recorded once
                  var i1 = serialToIndex[atomIndex1];
                  var i2 = serialToIndex[atomIndex2];
                  var a1 = matoms[i1];
                  var a2 = matoms[i2];
                  if(a1 && a2) {
                      a1.bonds.push(i2);
                      a1.bondOrder.push(bondOrder);
                      a2.bonds.push(i1);
                      a2.bondOrder.push(bondOrder);         
                  }
              }
              
              groupIndex += 1;
          }
          
          //reset for bonds
          groupIndex = startGroup;
          for( j = 0; j < chainGroupCount; ++j ){ //over residues (groups)
              
              groupIndex += 1;
 
          }
 
          chainIndex += 1;
      }
 
      
      // inter group bonds
      if( bondAtomList ){
          for(let k = bondAtomListStart, kl = bondAtomList.length; k < kl; k += 2 ){
               let atomIndex1 = bondAtomList[ k ];
               let atomIndex2 = bondAtomList[ k + 1 ];
               let bondOrder = bondOrderList ? bondOrderList[ k / 2 ] : 1;
               
               Iif(atomIndex1 >= atomIndex) {
                   bondAtomListStart = k;
                   break; //on next model
               }
               //I assume bonds are only recorded once
               let i1 = serialToIndex[atomIndex1];
               let i2 = serialToIndex[atomIndex2];
               let a1 = matoms[i1];
               let a2 = matoms[i2];
               if(a1 && a2) {
                   a1.bonds.push(i2);
                   a1.bondOrder.push(bondOrder);
                   a2.bonds.push(i1);
                   a2.bondOrder.push(bondOrder);   
               }
          }
      }
      
      Iif (options.multimodel) {
          Iif (!options.onemol) atoms.push([]);
      }
 
      modelIndex += 1;
  } 
 
  if(!noAssembly) {
      for (let n = 0; n < atoms.length; n++) {        
          processSymmetries(modelData[n].symmetries, atoms[n], options,modelData[n].cryst);
      }
  }                
  
  if (computeStruct  && !ignoreStruct) {
      computeSecondaryStructure(atoms,options.hbondCutoff);
  }       
  
  return atoms;
};