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Open Source Chemistry Library
/*
* Copyright (c) 1997 - 2016
* Actelion Pharmaceuticals Ltd.
* Gewerbestrasse 16
* CH-4123 Allschwil, Switzerland
*
* All rights reserved.
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the above copyright notice, this
* list of conditions and the following disclaimer.
* 2. Redistributions in binary form must reproduce the above copyright notice,
* this list of conditions and the following disclaimer in the documentation
* and/or other materials provided with the distribution.
* 3. Neither the name of the the copyright holder nor the
* names of its contributors may be used to endorse or promote products
* derived from this software without specific prior written permission.
*
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
* ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
* WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
* DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
* ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
* (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
* LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
* ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
* (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
* SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*
* @author Modest v. Korff
*/
package com.actelion.research.chem.descriptor.flexophore;
import com.actelion.research.calc.ArrayUtilsCalc;
import com.actelion.research.chem.descriptor.flexophore.generator.ConstantsFlexophoreGenerator;
import com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator;
import com.actelion.research.util.StringFunctions;
import java.awt.*;
import java.io.Serializable;
import java.util.ArrayList;
import java.util.List;
public class MolDistHist extends DistHist implements Serializable, IMolDistHist {
private static final long serialVersionUID = 5042020;
public static final boolean VERBOSE = false;
private static final int SIZE_BUFFER = 16 * getNumBytesEntry();
// The pharmacophore nodes containing
// The first entry is the number of atom types in the node, followed by the atom types and the frequency.
// [nAtomsNode1, byte1_attype1, byte2_attype1, byte3_freq_attype1, nAtomsNode2, byte1_attype2, byte2_attype2, byte3_freq_attype2...]
private byte [] arrNode;
private int posNode;
private boolean finalized;
private byte modeFlexophore;
private int[][] nodeAtoms; // original atom index list for every node
public MolDistHist () {
initHistogramArray(0);
init();
}
public MolDistHist (int nNodes) {
initHistogramArray(nNodes);
init();
}
public MolDistHist (MolDistHist mdh) {
initHistogramArray(mdh.getNumPPNodes());
init();
mdh.copy(this);
}
public MolDistHist copy(){
MolDistHist copy = new MolDistHist();
copy(copy);
return copy;
}
private void init(){
modeFlexophore = ConstantsFlexophore.MODE_SOFT_PPPOINTS;
}
public boolean check(){
boolean bOK = true;
int nodes = getNumPPNodes();
for (int i = 0; i < nodes; i++) {
PPNode node = getNode(i);
int ats = node.getInteractionTypeCount();
for (int j = 0; j < ats; j++) {
int inttype = node.getInteractionType(j);
String s = InteractionAtomTypeCalculator.getString(inttype);
if(s.length()==0) {
bOK = false;
if(VERBOSE)
System.err.println("Node " + i + " atom " + j + " Interaction type " + inttype + ".");
}
}
}
return bOK;
}
/**
*
* @param copy: This object is written into copy.
*/
public void copy(MolDistHist copy){
super.copy(copy);
copy.arrNode = new byte [arrNode.length];
System.arraycopy(arrNode, 0, copy.arrNode, 0, arrNode.length);
copy.posNode = posNode;
copy.modeFlexophore = modeFlexophore;
copy.realize();
}
public boolean equals(Object o) {
boolean bEQ=true;
MolDistHist mdh=null;
try {
mdh = (MolDistHist)o;
} catch (RuntimeException e) {
return false;
}
if(getNumPPNodes() != mdh.getNumPPNodes())
return false;
for (int i = 0; i < getNumPPNodes(); i++) {
PPNode n1 = getNode(i);
PPNode n2 = mdh.getNode(i);
if(!n1.equals(n2)){
bEQ = false;
break;
}
}
for (int i = 0; i < getNumPPNodes(); i++) {
for (int j = i+1; j < getNumPPNodes(); j++) {
byte [] a1 = getDistHist(i,j);
byte [] a2 = mdh.getDistHist(i,j);
for (int k = 0; k < a2.length; k++) {
if(a1[k]!=a2[k]){
bEQ = false;
break;
}
}
}
}
return bEQ;
}
public byte getModeFlexophore() {
return modeFlexophore;
}
protected void initHistogramArray(int nNodes) {
super.initHistogramArray(nNodes);
arrNode = new byte[nNodes*(PPNode.getNumBytesEntry()+1)];
finalized = false;
}
/**
*
* @param node
*/
public void addNode(PPNode node) {
byte [] arr = node.get();
byte nInteractionTypeCount = (byte)node.getInteractionTypeCount();
int newLen = posNode + arr.length + 1;
if(arrNode.length < newLen){
int lenBuffer = SIZE_BUFFER;
while(arrNode.length + lenBuffer < newLen) {
lenBuffer *= 2;
}
resizeNodeArray(arrNode.length + lenBuffer);
}
arrNode[posNode++] = nInteractionTypeCount;
System.arraycopy(arr, 0, arrNode, posNode, arr.length);
posNode += arr.length;
finalized = false;
}
/**
* @return the arrNode
*/
protected byte[] getArrNode() {
return arrNode;
}
/**
* @param arrNode the arrNode to set
*/
protected void setArrNode(byte[] arrNode) {
this.arrNode = arrNode;
int pos=0;
while(arrNode[pos] > 0){
pos += arrNode[pos] * PPNode.NUM_BYTES_INTERACTION_TYPE + 1;
if(pos>=arrNode.length)
break;
}
}
/**
* Resizes the node array to the needed length.
*/
public void realize(){
int size = getNumPPNodes();
if(size==0){
throw new RuntimeException("No pharmacophore points in Flexophore.");
}
int pos = getPositionNode(size-1);
int len = pos + arrNode[pos] * PPNode.getNumBytesEntry() + 1;
resizeNodeArray(len);
if(getNumPPNodes()==0)
return;
finalized = true;
}
private void resizeNodeArray(int newsize){
byte [] arr = new byte [newsize];
System.arraycopy(arrNode, 0, arr, 0, Math.min(arrNode.length, newsize));
arrNode = arr;
finalized = false;
}
public int getConnAtom(int at, int index) {
if(index >= at)
index++;
return index;
}
/**
* @return the original atom indexes in node order, provided they have beed added when creating this MolDistHist
*/
public int[][] getNodeAtoms() {
return nodeAtoms;
}
/**
* Adds the original atom indexes in node order to this MolDistHist
* @param nodeAtoms
*/
public void setNodeAtoms(int[][] nodeAtoms) {
this.nodeAtoms = nodeAtoms;
}
@Override
public int hashCode() {
String s = toString();
s = s.replace(" ", "");
return s.hashCode();
}
public String toString(){
// Causes errors in debug mode
// if(!finalized)
// realize();
StringBuilder sb = new StringBuilder(toStringNodes());
sb.append(toStringHists());
return sb.toString();
}
public String toStringNodes(){
StringBuilder sb = new StringBuilder();
sb.append("[");
for (int i = 0; i < getNumPPNodes(); i++) {
sb.append(getNode(i).toString());
if(i0){
filled=true;
break;
}
}
return filled;
}
protected boolean isFinalized() {
return finalized;
}
/**
* The position of the size of the node. The node index starts with 0 and runs up to size-1 inclusive.
* @param index
* @return
*/
private int getPositionNode(int index){
int pos = 0;
for (int i = 0; i < index; i++) {
pos += arrNode[pos] * PPNode.getNumBytesEntry() + 1;
}
return pos;
}
/**
* !Slow method, it has to iterate through a loop to find the node in the array!
* @param index
* @return deep copy of the node.
*
*/
public PPNode getNode(int index){
PPNode node = new PPNode();
int pos = getPositionNode(index);
int len = arrNode[pos] * PPNode.getNumBytesEntry();
byte [] arr = new byte[len];
System.arraycopy(arrNode, pos+1, arr, 0, len);
node.set(arr, arrNode[pos]);
node.realize();
return node;
}
/**
*
* @param index
* @return number of pharmacophore points at the specified index
* slow method because it calls getPositionNode(index).
*/
public int getPPPoints(int index){
int pos = getPositionNode(index);
int nPPPoints = arrNode[pos];
return nPPPoints;
}
public int getSizeBytes(){
int s = super.getSizeBytes();
s += arrNode.length;
// bFinalized
s += (Integer.SIZE / 8)*(1);
return s;
}
/**
* Only for interface compliance needed.
*/
@Override
public int getNumMandatoryPharmacophorePoints() {
// TODO Auto-generated method stub
return 0;
}
@Override
public boolean isMandatoryPharmacophorePoint(int indexNode) {
return false;
}
@Override
public double getWeightPharmacophorePoint(int indexNode) {
return 1.0;
}
public static int getNumBytesEntry(){
return PPNode.getNumBytesEntry()+1;
}
/**
* reads a MolDistHist from the toString() method.
* @param strMolDistHist
* @return
*/
public static List readNodes(String strMolDistHist){
int start = strMolDistHist.indexOf('(');
boolean nodesProcessed = false;
List liPPNode = new ArrayList<>();
while(!nodesProcessed){
int end = StringFunctions.nextClosing(strMolDistHist, start, '(', ')');
if(end==-1){
throw new RuntimeException("Error for MolDistHist " + strMolDistHist);
}
String strNode = strMolDistHist.substring(start+1, end);
PPNode n = PPNode.read(strNode);
liPPNode.add(n);
start = strMolDistHist.indexOf('(', end);
if(start==-1){
nodesProcessed = true;
}
}
return liPPNode;
}
public static MolDistHist readNodes2MDH(String strMolDistHist){
List liPPNode = readNodes(strMolDistHist);
int size = liPPNode.size();
MolDistHist mdh = new MolDistHist(size);
for (PPNode ppNode : liPPNode) {
mdh.addNode(ppNode);
}
return mdh;
}
public static MolDistHist read(String strMolDistHist){
String pattern = "[0-9]+";
List liPPNode = readNodes( strMolDistHist);
int size = liPPNode.size();
MolDistHist mdh = new MolDistHist(size);
for (PPNode ppNode : liPPNode) {
mdh.addNode(ppNode);
}
boolean histsProcessed = false;
List liHist = new ArrayList();
int startHist = strMolDistHist.indexOf("][");
int nHistograms = ((size*size)-size)/2;
if(nHistograms==0){
histsProcessed=true;
}
while(!histsProcessed){
int endHist = StringFunctions.nextClosing(strMolDistHist, startHist, '[', ']');
String sub = strMolDistHist.substring(startHist, endHist);
List li = StringFunctions.match(sub, pattern);
if(li.size() != ConstantsFlexophoreGenerator.BINS_HISTOGRAM){
throw new RuntimeException("Error in histogram.");
}
byte [] arr = new byte [ConstantsFlexophoreGenerator.BINS_HISTOGRAM];
int cc=0;
for (Point p : li) {
String strCount = sub.substring(p.x, p.y);
arr[cc++] = (byte)(Integer.parseInt(strCount) & 0xFF);
}
liHist.add(arr);
startHist = strMolDistHist.indexOf('[', endHist);
if(liHist.size()==nHistograms){
histsProcessed=true;
}
}
int cc=0;
for (int i = 0; i < size; i++) {
for (int j = i+1; j < size; j++) {
mdh.setDistHist(i,j, liHist.get(cc++));
}
}
return mdh;
}
}