com.actelion.research.chem.descriptor.flexophore.MolDistHist Maven / Gradle / Ivy
Go to download
Show more of this group Show more artifacts with this name
Show all versions of openchemlib Show documentation
Show all versions of openchemlib Show documentation
Open Source Chemistry Library
/*
* Copyright (c) 2020.
* Idorsia Pharmaceuticals Ltd., Hegenheimermattweg 91, CH-4123 Allschwil, Switzerland
*
* This file is part of DataWarrior.
*
* DataWarrior 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 3 of
* the License, or (at your option) any later version.
*
* DataWarrior is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY;
* without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
* See the GNU General Public License for more details.
* You should have received a copy of the GNU General Public License along with DataWarrior.
* If not, see http://www.gnu.org/licenses/.
*
* @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;
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;
}
@Override
public int hashCode() {
String s = toString();
s = s.replace(" ", "");
return s.hashCode();
}
public String toString(){
// Causes errors in debug mode
// if(!finalized)
// realize();
StringBuffer b = new StringBuffer();
b.append("[");
for (int i = 0; i < getNumPPNodes(); i++) {
b.append(getNode(i).toString());
if(i liPPNode = new ArrayList();
while(!nodesProcessed){
int end = StringFunctions.nextClosing(strMolDistHist, start, '(', ')');
String sub = strMolDistHist.substring(start+1, end);
List li = StringFunctions.match(sub, pattern);
PPNode n = new PPNode();
for (Point p : li) {
String strInteractionType = sub.substring(p.x, p.y);
n.add(Integer.parseInt(strInteractionType));
}
n.realize();
liPPNode.add(n);
start = strMolDistHist.indexOf('(', end);
if(start==-1){
nodesProcessed = true;
}
}
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;
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;
}
}
© 2015 - 2025 Weber Informatics LLC | Privacy Policy