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Added a new reduced encoder to produce the reduced format of the data.
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mmtf-encoder/src/main/java/org/rcsb/mmtf/encoder/ReducedEncoder.java
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| package org.rcsb.mmtf.encoder; | ||
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| import java.util.ArrayList; | ||
| import java.util.List; | ||
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| import org.rcsb.mmtf.api.StructureDataInterface; | ||
| import org.rcsb.mmtf.dataholders.MmtfStructure; | ||
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| /** | ||
| * Convert a full format of the file to a reduced format. | ||
| * @author Anthony Bradley | ||
| * | ||
| */ | ||
| public class ReducedEncoder { | ||
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| private static MmtfStructure mmtfStructure; | ||
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| private static final String CALPHA_NAME = "CA"; | ||
| private static final String CARBON_ELEMENT = "C"; | ||
| private static final String PHOSPHATE_NAME = "P"; | ||
| private static final String PHOSPHATE_ELEMENT = "P"; | ||
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| /** | ||
| * Constructor to implement the reduced encoder of the {@link StructureDataInterface}. | ||
| * @param structureDataInterface the input {@link StructureDataInterface} | ||
| */ | ||
| public ReducedEncoder(StructureDataInterface structureDataInterface) { | ||
| // First convert to a reduced data type | ||
| structureDataInterface = ReducedEncoder.getReduced(structureDataInterface); | ||
| // Now just apply the default encoder on top of it | ||
| DefaultEncoder defaultEncoder = new DefaultEncoder(structureDataInterface); | ||
| setMmtfStructure(defaultEncoder.getMmtfEncodedStructure()); | ||
| } | ||
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| /** | ||
| * Get the reduced form of the input {@link StructureDataInterface}. | ||
| * @param structureDataInterface the input {@link StructureDataInterface} | ||
| * @return the reduced form of the {@link StructureDataInterface} as another {@link StructureDataInterface} | ||
| */ | ||
| public static StructureDataInterface getReduced(StructureDataInterface structureDataInterface) { | ||
| // The transmission of the data goes through this | ||
| AdapterToStructureData adapterToStructureData = new AdapterToStructureData(); | ||
| adapterToStructureData.initStructure(structureDataInterface.getNumBonds(), structureDataInterface.getNumAtoms(), structureDataInterface.getNumGroups(), | ||
| structureDataInterface.getNumChains(), structureDataInterface.getNumModels(), structureDataInterface.getStructureId()); | ||
| // Add the header and crystallographic information | ||
| adapterToStructureData.setXtalInfo(structureDataInterface.getSpaceGroup(), structureDataInterface.getUnitCell()); | ||
| adapterToStructureData.setHeaderInfo(structureDataInterface.getRfree(), structureDataInterface.getRfree(),structureDataInterface.getResolution(), | ||
| structureDataInterface.getTitle(), structureDataInterface.getDepositionDate(), structureDataInterface.getReleaseDate(), structureDataInterface.getExperimentalMethods()); | ||
| // Transfer the bioassembly info | ||
| for(int i=0; i<structureDataInterface.getNumBioassemblies(); i++) { | ||
| for(int j =0; j<structureDataInterface.getNumTransInBioassembly(i); j++){ | ||
| adapterToStructureData.setBioAssemblyTrans(i, | ||
| structureDataInterface.getChainIndexListForTransform(i, j), | ||
| structureDataInterface.getMatrixForTransform(i, j)); | ||
| } | ||
| } | ||
| // Transfer the entity info | ||
| for(int i=0; i<structureDataInterface.getNumEntities(); i++){ | ||
| adapterToStructureData.setEntityInfo(structureDataInterface.getEntityChainIndexList(i), structureDataInterface.getEntitySequence(i), | ||
| structureDataInterface.getEntityDescription(i), structureDataInterface.getEntityType(i)); | ||
| } | ||
| // Loop through the Structure data interface this with the appropriate data | ||
| int atomCounter=-1; | ||
| int groupCounter=-1; | ||
| int chainCounter=-1; | ||
| for (int i=0; i<structureDataInterface.getNumModels(); i++){ | ||
| int numChains = structureDataInterface.getChainsPerModel()[i]; | ||
| adapterToStructureData.setModelInfo(i, numChains); | ||
| for(int j=0; j<numChains; j++){ | ||
| chainCounter++; | ||
| String chainType = getTypeFromChainId(structureDataInterface, chainCounter); | ||
| int numGroups=0; | ||
| for(int k=0; k<structureDataInterface.getGroupsPerChain()[chainCounter]; k++){ | ||
| groupCounter++; | ||
| int groupType = structureDataInterface.getGroupTypeIndices()[groupCounter]; | ||
| List<Integer> indicesToAdd = getIndicesToAdd(structureDataInterface, groupType, chainType); | ||
| // If there's an atom to add in this group - add it | ||
| if(indicesToAdd.size()>0){ | ||
| adapterToStructureData.setGroupInfo(structureDataInterface.getGroupName(groupType), structureDataInterface.getGroupIds()[groupCounter], | ||
| structureDataInterface.getInsCodes()[groupCounter], structureDataInterface.getGroupChemCompType(groupType), structureDataInterface.getGroupAtomCharges(groupType).length, | ||
| structureDataInterface.getGroupBondOrders(groupType).length, structureDataInterface.getGroupSingleLetterCode(groupType), structureDataInterface.getGroupSequenceIndices()[groupCounter], | ||
| structureDataInterface.getSecStructList()[groupCounter]); | ||
| numGroups++; | ||
| } | ||
| for(int l=0; l<structureDataInterface.getNumAtomsInGroup(groupType);l++){ | ||
| atomCounter++; | ||
| if(indicesToAdd.contains(l)){ | ||
| adapterToStructureData.setAtomInfo(structureDataInterface.getGroupAtomNames(groupType)[l], structureDataInterface.getAtomIds()[atomCounter], structureDataInterface.getAltLocIds()[atomCounter], | ||
| structureDataInterface.getxCoords()[atomCounter], structureDataInterface.getyCoords()[atomCounter], structureDataInterface.getzCoords()[atomCounter], | ||
| structureDataInterface.getOccupancies()[atomCounter], structureDataInterface.getbFactors()[atomCounter], structureDataInterface.getGroupElementNames(groupType)[l], structureDataInterface.getGroupAtomCharges(groupType)[l]); | ||
| } | ||
| } | ||
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| // Add the bonds if we've copied all the elements | ||
| if(indicesToAdd.size()>1 && indicesToAdd.size()==structureDataInterface.getGroupBondOrders(groupType).length){ | ||
| for(int l=0; l<structureDataInterface.getGroupBondOrders(groupType).length; l++){ | ||
| int bondOrder = structureDataInterface.getGroupBondOrders(groupType)[l]; | ||
| int bondIndOne = structureDataInterface.getGroupBondIndices(groupType)[l*2]; | ||
| int bondIndTwo = structureDataInterface.getGroupBondIndices(groupType)[l*2+1]; | ||
| adapterToStructureData.setInterGroupBond(bondIndOne, bondIndTwo, bondOrder); | ||
| } | ||
| } | ||
| } | ||
| adapterToStructureData.setChainInfo(structureDataInterface.getChainIds()[i], | ||
| structureDataInterface.getChainNames()[i], numGroups); | ||
| } | ||
| } | ||
| adapterToStructureData.finalizeStructure(); | ||
| // Return the AdapterToStructureData | ||
| return adapterToStructureData; | ||
| } | ||
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| /** | ||
| * Get the indices of atoms to add in this group. This is C-alpha, phosphate (DNA) and ligand atoms | ||
| * @param structureDataInterface the input {@link StructureDataInterface} | ||
| * @param groupType the index of this group in the groupList | ||
| * @param chainType the type of the chain (polymer, non-polymer, water). | ||
| * @return the list of indices (within the group) of atoms to consider | ||
| */ | ||
| private static List<Integer> getIndicesToAdd(StructureDataInterface structureDataInterface, int groupType, | ||
| String chainType) { | ||
| // The list to return | ||
| List<Integer> outList = new ArrayList<>(); | ||
| // Get chain type | ||
| if(chainType.equals("polymer")){ | ||
| for(int i=0; i<structureDataInterface.getNumAtomsInGroup(groupType); i++){ | ||
| String atomName = structureDataInterface.getGroupAtomNames(groupType)[i]; | ||
| String elementName = structureDataInterface.getGroupElementNames(groupType)[i]; | ||
| // Check if it's a Protein C-alpha | ||
| if(atomName.equals(CALPHA_NAME) && elementName.equals(CARBON_ELEMENT)){ | ||
| outList.add(i); | ||
| } | ||
| // Check if it's a DNA phosphate | ||
| if(atomName.equals(PHOSPHATE_NAME) && elementName.equals(PHOSPHATE_ELEMENT)){ | ||
| outList.add(i); | ||
| } | ||
| } | ||
| } | ||
| // Check if it's a non-polymer | ||
| else if (chainType.equals("non-polymer")){ | ||
| for(int i=0; i<structureDataInterface.getNumAtomsInGroup(groupType); i++){ | ||
| outList.add(i); | ||
| } | ||
| } | ||
| else if(chainType.equals("water")){ | ||
| // We skip water | ||
| } | ||
| else{ | ||
| System.err.println("Unrecoginised entity type: "+chainType); | ||
| } | ||
| return outList; | ||
| } | ||
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| /** | ||
| * Get the type of a given chain index. | ||
| * @param structureDataInterface the input {@link StructureDataInterface} | ||
| * @param chainInd the index of the relevant chain | ||
| * @return the {@link String} describing the chain | ||
| */ | ||
| public static String getTypeFromChainId(StructureDataInterface structureDataInterface, int chainInd) { | ||
| for(int i=0; i<structureDataInterface.getNumEntities(); i++){ | ||
| for(int chainIndex : structureDataInterface.getEntityChainIndexList(i)){ | ||
| if(chainInd==chainIndex){ | ||
| return structureDataInterface.getEntityType(i); | ||
| } | ||
| } | ||
| } | ||
| System.err.println("ERROR FINDING ENTITY FOR CHAIN: "+chainInd); | ||
| return "NULL"; | ||
| } | ||
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| /** | ||
| * @return the mmtfStructure | ||
| */ | ||
| public static MmtfStructure getMmtfStructure() { | ||
| return mmtfStructure; | ||
| } | ||
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| /** | ||
| * @param mmtfStructure the mmtfStructure to set | ||
| */ | ||
| public static void setMmtfStructure(MmtfStructure mmtfStructure) { | ||
| ReducedEncoder.mmtfStructure = mmtfStructure; | ||
| } | ||
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| } |