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andreasprlicandreasprlic
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Merge pull request biojava#381 from abradle/master
Added functionality to write groups to MDL molblocks (as strings)
2 parents 5edfed4 + 7e69a98 commit bae2067

3 files changed

Lines changed: 156 additions & 1 deletion

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‎biojava-structure/src/main/java/org/biojava/nbio/structure/Group.java‎

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@@ -330,4 +330,9 @@ public interface Group {
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*/
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public void trimToSize();
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/**
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* Function to get the Group as an MDL molblock
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* @return the string of the MDL molblock
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*/
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public String toSDF();
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}

‎biojava-structure/src/main/java/org/biojava/nbio/structure/HetatomImpl.java‎

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@@ -23,6 +23,7 @@
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*/
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package org.biojava.nbio.structure;
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import org.biojava.nbio.structure.io.GroupToSDF;
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import org.biojava.nbio.structure.io.mmcif.ChemCompGroupFactory;
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import org.biojava.nbio.structure.io.mmcif.model.ChemComp;
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import org.slf4j.Logger;
@@ -525,6 +526,17 @@ public void trimToSize(){
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}
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}
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}
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@Override
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public String toSDF() {
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// Function to return the SDF of a given strucutre
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GroupToSDF gts = new GroupToSDF();
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return gts.getText(this);
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}
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}

‎biojava-structure/src/main/java/org/biojava/nbio/structure/io/GroupToSDF.java‎

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package org.biojava.nbio.structure.io;
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import java.text.DecimalFormat;
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import java.util.ArrayList;
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import java.util.List;
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import org.biojava.nbio.structure.Atom;
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import org.biojava.nbio.structure.Bond;
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import org.biojava.nbio.structure.Group;
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public class GroupToSDF {
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public String getText(Group thisGroup) {
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// Fuction to convert a Group to a strign of the MDL molnlock
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StringBuilder sb = new StringBuilder();
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sb.append(getHeader(thisGroup));
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sb.append(getCtab(thisGroup));
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return sb.toString();
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}
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private String getCtab(Group thisGroup){
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DecimalFormat df = new DecimalFormat("0.0000");
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// The thre string builders for the three parts of the MDL block
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StringBuilder header = new StringBuilder();
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StringBuilder atomList = new StringBuilder();
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StringBuilder bondOrders = new StringBuilder();
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int numBonds = 0;
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List<Atom> atoms = thisGroup.getAtoms();
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for(Atom a: thisGroup.getAtoms()){
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/// ALL SHOULD BE TO FOUR DECIMAL PLACES WITH A CERTAIN NUMBER OF SPACES BEFOREa
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String spaceX = getSpace(10, df.format(a.getX()));
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String spaceY = getSpace(10, df.format(a.getY()));
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String spaceZ = getSpace(10, df.format(a.getZ()));
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String spaceEle = getSpace(4, a.getElement().toString());
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atomList.append(spaceX+df.format(a.getX())+spaceY+df.format(a.getY())+spaceZ+df.format(a.getZ())+" "+a.getElement().toString()+spaceEle+"0 0 0 0 0 0 0 0 0 0 0 0\n");
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for(Bond b: a.getBonds()){
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Atom otherAtom = b.getOther(a);
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if(atoms.indexOf(otherAtom)>=atoms.indexOf(a)){
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continue;
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}
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if(atoms.indexOf(otherAtom)<0){
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continue;
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}
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if(atoms.indexOf(a)<0){
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continue;
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}
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numBonds++;
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// Deal with the index infromation
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String indexOther = Integer.toString(atoms.indexOf(otherAtom)+1);
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String index = Integer.toString(atoms.indexOf(a)+1);
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String order = Integer.toString(b.getBondOrder());
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String spaceIndOne = getSpace(3, index);
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String spaceIndTwo = getSpace(3, indexOther);
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String spaceOrder = getSpace(3, order);
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bondOrders.append(spaceIndOne+index+spaceIndTwo+indexOther+spaceOrder+order+" 0\n");
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}
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}
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StringBuilder outString = new StringBuilder();
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// Add the first line now
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String spaceNumAtoms = getSpace(3, Integer.toString(thisGroup.getAtoms().size()));
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String spaceNumBonds = getSpace(3, Integer.toString(numBonds));
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header.append("\n");
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header.append(spaceNumAtoms+thisGroup.getAtoms().size()+spaceNumBonds+numBonds+" 0 0 0 0 0 0 0 0999 V2000\n");
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// Now add the header, atom, bond and charge information togeyher
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outString.append(header.toString());
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outString.append(atomList.toString());
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outString.append(bondOrders.toString());
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outString.append(getCharges(thisGroup));
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// Add the final line and the $$$$ delimiter
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outString.append("M END\n$$$$");
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// Get the string and return it
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return outString.toString();
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}
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private Object getCharges(Group thisGroup) {
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// Get the array of charges
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List<Number> chargeList = getAtomCharges(thisGroup);
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// Build the string
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StringBuilder outS = new StringBuilder();
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int chargeCount=0;
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// Loop through the charges -> maximum 8 charges per line
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for(int i =0; i<chargeList.size();i++){
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short charge = (Short) chargeList.get(i);
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if(charge!=0){
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if(chargeCount==0){
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outS.append("M CHG N");
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}
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outS.append(getSpace(4, Integer.toString(i))+(i+1));
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outS.append(getSpace(4, Short.toString(charge))+charge);
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chargeCount++;
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}
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//
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if(chargeCount==8){
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outS.append("\n");
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outS.replace(0, 10, "M CHG "+chargeCount);
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chargeCount=0;
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}
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}
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if(chargeCount==0){
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return "";
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}
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// Now add the charge count
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outS.replace(0, 10, "M CHG "+chargeCount);
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outS.append("\n");
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// Now return the string
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return outS.toString();
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}
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private static List<Number> getAtomCharges(Group group) {
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// The list to store the answer
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List<Number> outArr = new ArrayList<Number>();
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// Get the atom charge Information
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for(Atom a: group.getAtoms()){
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outArr.add(a.getCharge());
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}
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return outArr;
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}
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private String getSpace(int inputNum, String format) {
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// Function to get the spaces between numbers
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StringBuilder sb = new StringBuilder();
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for(int i=0; i<(inputNum-format.length());i++){
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sb.append(" ");
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}
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return sb.toString();
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}
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private String getHeader(Group thisGroup) {
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// Make the header info for the start of the block
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StringBuilder sb = new StringBuilder();
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sb.append(thisGroup.getPDBName()+"\n");
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sb.append("Made by BioJava");
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sb.append("\n");
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return sb.toString();
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}
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}

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