[Git][java-team/openchemlib][master] 4 commits: New upstream version 2021.1.1+dfsg
Andrius Merkys
gitlab at salsa.debian.org
Tue Jan 19 11:25:11 GMT 2021
Andrius Merkys pushed to branch master at Debian Java Maintainers / openchemlib
Commits:
3d4bbf95 by Andrius Merkys at 2021-01-19T03:37:17-05:00
New upstream version 2021.1.1+dfsg
- - - - -
d560b7b2 by Andrius Merkys at 2021-01-19T03:37:26-05:00
Update upstream source from tag 'upstream/2021.1.1+dfsg'
Update to upstream version '2021.1.1+dfsg'
with Debian dir 5dc01784eb206d0797abaaced8684d8cb2f34036
- - - - -
6d18c203 by Andrius Merkys at 2021-01-19T03:40:24-05:00
Updating copyright years.
- - - - -
6479ea7e by Andrius Merkys at 2021-01-19T03:41:14-05:00
Update changelog for 2021.1.1+dfsg-1 release
- - - - -
14 changed files:
- debian/changelog
- debian/copyright
- pom.xml
- src/main/java/com/actelion/research/calc/ArrayUtilsCalc.java
- src/main/java/com/actelion/research/calc/Matrix.java
- src/main/java/com/actelion/research/chem/descriptor/DescriptorHandlerHashedCFp.java
- − src/main/java/com/actelion/research/chem/descriptor/DescriptorHandlerHashedPharmSphere.java
- − src/main/java/com/actelion/research/chem/descriptor/DescriptorHandlerPharmPath.java
- src/main/java/com/actelion/research/chem/descriptor/FingerPrintGenerator.java
- − src/main/java/com/actelion/research/chem/descriptor/FingerPrintGeneratorPharmGraph.java
- src/main/java/com/actelion/research/chem/io/pdb/converter/BondsCalculator.java
- src/main/java/com/actelion/research/chem/io/pdb/parser/PDBFileParser.java
- src/main/java/com/actelion/research/chem/io/pdb/parser/Residue.java
- src/main/java/com/actelion/research/gui/JChemistryView.java
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,9 @@
+openchemlib (2021.1.1+dfsg-1) unstable; urgency=medium
+
+ * New upstream version 2021.1.1+dfsg
+
+ -- Andrius Merkys <merkys at debian.org> Tue, 19 Jan 2021 03:41:04 -0500
+
openchemlib (2021.1.0+dfsg-2) unstable; urgency=medium
* Not running autopkgtest on armhf and i386 due to missing libopenjfx-jni.
=====================================
debian/copyright
=====================================
@@ -9,7 +9,7 @@ Copyright: 1997-2021, Idorsia Pharmaceuticals Ltd, Hegenheimermattweg 91, CH-412
License: BSD-3-clause
Files: debian/*
-Copyright: 2021, Andrius Merkys <merkys at debian.org>
+Copyright: 2020-2021, Andrius Merkys <merkys at debian.org>
License: BSD-3-clause
Files: src/main/java/com/actelion/research/calc/statistics/median/MedianStatisticFunctions.java
=====================================
pom.xml
=====================================
@@ -8,7 +8,7 @@
Please follow the naming scheme YEAR.MONTH.RELEASE_NO_OF_MONTH
(eg. 2016.4.1 for second release in Apr 2016)
-->
- <version>2021.1.0</version>
+ <version>2021.1.1</version>
<name>OpenChemLib</name>
<description>Open Source Chemistry Library</description>
@@ -195,7 +195,7 @@
<connection>scm:git:git at github.com:Actelion/openchemlib.git</connection>
<developerConnection>scm:git:git at github.com:Actelion/openchemlib.git</developerConnection>
<url>https://github.com/Actelion/openchemlib</url>
- <tag>openchemlib-2021.1.0</tag>
+ <tag>openchemlib-2021.1.1</tag>
</scm>
<distributionManagement>
=====================================
src/main/java/com/actelion/research/calc/ArrayUtilsCalc.java
=====================================
@@ -178,33 +178,42 @@ public class ArrayUtilsCalc {
return var;
}
-
+ public static final double getVariance(int [] arr) {
+ double sum=0;
+ final double mean = getMean(arr);
+ for (int i = 0; i < arr.length; i++) {
+ sum += (arr[i]-mean)*(arr[i]-mean);
+ }
+ final double var = sum / (arr.length - 1);
+ return var;
+ }
+
public static final double getStandardDeviation(double [] arr) {
-
double sum=0;
-
double mean = getMean(arr);
-
for (int i = 0; i < arr.length; i++) {
sum += (arr[i]-mean)*(arr[i]-mean);
}
-
double sdv = Math.sqrt(sum / (arr.length - 1));
-
return sdv;
}
public static final double getMean(double [] arr) {
-
double sum = 0;
-
for (int i = 0; i < arr.length; i++) {
sum += arr[i];
}
-
return sum/arr.length;
}
-
+
+ public static final double getMean(int [] arr) {
+ double sum = 0;
+ for (int i = 0; i < arr.length; i++) {
+ sum += arr[i];
+ }
+ return sum/arr.length;
+ }
+
public static ModelMedianDouble getMedian(double [] arr) {
Arrays.sort(arr);
@@ -705,6 +714,7 @@ public class ArrayUtilsCalc {
return res;
}
+
public final static String [] toArray(List<String> list) {
String [] res = new String[list.size()];
for (int i = 0; i < list.size(); i++) {
@@ -750,6 +760,7 @@ public class ArrayUtilsCalc {
return res;
}
+
public final static List<Integer> toList(int [] a) {
if(a==null)
return null;
=====================================
src/main/java/com/actelion/research/calc/Matrix.java
=====================================
@@ -35,6 +35,7 @@ package com.actelion.research.calc;
import com.actelion.research.util.DoubleVec;
import com.actelion.research.util.convert.String2DoubleArray;
+import com.actelion.research.util.datamodel.IntegerDouble;
import com.actelion.research.util.datamodel.ScorePoint;
import java.awt.*;
@@ -538,12 +539,20 @@ public class Matrix {
public float [] getColAsFloat(int iCol) {
float [] arr = new float [rows()];
- for(int ii=0; ii < rows(); ii++){
- arr[ii] = (float)data[ii][iCol];
+ for(int i=0; i < rows(); i++){
+ arr[i] = (float)data[i][iCol];
}
return arr;
}
+ public int [] getColAsInt(int iCol) {
+ int [] arr = new int [rows()];
+ for(int i=0; i < rows(); i++){
+ arr[i] = (int)(data[i][iCol]+0.5);
+ }
+ return arr;
+ }
+
/**
*
* @param vecIndices
@@ -3031,6 +3040,35 @@ public class Matrix {
OUT_SEPARATOR_ROW = s;
}
+
+ public void shuffleRows() {
+ Random rnd = new Random();
+ int r = rows();
+ for(int i = r; i > 1; --i) {
+ swapRows(i, rnd.nextInt(i));
+ }
+ }
+
+ public void swapRows(int a, int b) {
+ double [] t = data[a];
+ data[a]=data[b];
+ data[b]=t;
+ }
+
+ public void sortRows(int col){
+ int r= rows();
+ List<IntegerDouble> li = new ArrayList<>(r);
+ for (int i = 0; i < r; i++) {
+ li.add(new IntegerDouble(i, get(i, col)));
+ }
+ Collections.sort(li, IntegerDouble.getComparatorDouble());
+ double [][] dataSorted = new double[r][];
+ for (int i = 0; i < r; i++) {
+ dataSorted[i]=data[li.get(i).getInt()];
+ }
+ data = dataSorted;
+ }
+
/**
* Get the standard scores, also known as z-scores.
* @return matrux with standardized values.
=====================================
src/main/java/com/actelion/research/chem/descriptor/DescriptorHandlerHashedCFp.java
=====================================
@@ -104,7 +104,7 @@ public class DescriptorHandlerHashedCFp extends AbstractDescriptorHandlerFP<Ster
int newMax = max;
for (int i=min; i<max; i++) {
int atom = atomList[i];
- for (int j=0; j<mol.getConnAtoms(atom); j++) {
+ for (int j=0; j<mol.getConnAtoms(atom) + mol.getMetalBondedConnAtoms(atom); j++) {
int connAtom = mol.getConnAtom(atom, j);
if (!atomMask[connAtom]) {
atomMask[connAtom] = true;
=====================================
src/main/java/com/actelion/research/chem/descriptor/DescriptorHandlerHashedPharmSphere.java deleted
=====================================
@@ -1,152 +0,0 @@
-/*
-* 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.
-*
-*/
-
-package com.actelion.research.chem.descriptor;
-
-import com.actelion.research.chem.Canonizer;
-import com.actelion.research.chem.Molecule;
-import com.actelion.research.chem.SSSearcherWithIndex;
-import com.actelion.research.chem.StereoMolecule;
-import com.actelion.research.util.BurtleHasher;
-import com.actelion.research.util.datamodel.IntVec;
-
-import java.util.Arrays;
-
-public class DescriptorHandlerHashedPharmSphere extends AbstractDescriptorHandlerFP<StereoMolecule> {
- private static final double CORRECTION_FACTOR = 0.6;
-
- private static DescriptorHandlerHashedPharmSphere sDefaultInstance;
-
- private static final int SPHERE_COUNT = 5;
- private static final int HASH_BITS = 10;
- private static final int HASH_INIT = 13;
- private static final int DESCRIPTOR_SIZE = (1 << HASH_BITS);
-
- public static DescriptorHandlerHashedPharmSphere getDefaultInstance() {
- synchronized(DescriptorHandlerHashedPharmSphere.class) {
- if (sDefaultInstance == null) {
- sDefaultInstance = new DescriptorHandlerHashedPharmSphere();
- }
- }
- return sDefaultInstance;
- }
-
- public DescriptorInfo getInfo() {
- return DescriptorConstants.DESCRIPTOR_HashedCFp;
- }
-
- public String getVersion() {
- return DescriptorConstants.DESCRIPTOR_HashedCFp.version;
- }
-
- /**
- * This descriptor requires proper up/down bonds, because it encodes stereo parities.
- * If a passed molecule is generated from idcode parsing, make sure that coordinates
- * and up/down/bonds are available, i.e. that the IDCodeParser was instantiated with
- * the respective option.
- */
- public int[] createDescriptor(StereoMolecule mol) {
- if (mol ==null)
- return null;
-
- mol.ensureHelperArrays(Molecule.cHelperRings);
- StereoMolecule fragment = new StereoMolecule(mol.getAllAtoms(), mol.getAllBonds());
-
- // byte[] descriptor = new byte[DESCRIPTOR_SIZE];
- int len = DESCRIPTOR_SIZE / Integer.SIZE;
- IntVec iv = new IntVec(len);
-
- int[] atomList = new int[mol.getAtoms()];
- boolean[] atomMask = new boolean[mol.getAtoms()];
- for (int rootAtom=0; rootAtom<mol.getAllAtoms(); rootAtom++) {
- if (rootAtom != 0)
- Arrays.fill(atomMask, false);
-
- int min = 0;
- int max = 0;
- for (int sphere=0; sphere<SPHERE_COUNT && max<mol.getAllAtoms(); sphere++) {
- if (max == 0) {
- atomList[0] = rootAtom;
- atomMask[rootAtom] = true;
- max = 1;
- }
- else {
- int newMax = max;
- for (int i=min; i<max; i++) {
- int atom = atomList[i];
- for (int j=0; j<mol.getAllConnAtoms(atom)+mol.getMetalBondedConnAtoms(atom); j++) {
- int connAtom = mol.getConnAtom(atom, j);
- if (!atomMask[connAtom]) {
- atomMask[connAtom] = true;
- atomList[newMax++] = connAtom;
- }
- }
- }
- min = max;
- max = newMax;
- }
-
- mol.copyMoleculeByAtoms(fragment, atomMask, true, null);
-
- // take fragment as it is
- String idcode = new Canonizer(fragment).getIDCode();
- int h = BurtleHasher.hashlittle(idcode, HASH_INIT);
- h = (h & BurtleHasher.hashmask(HASH_BITS));
- iv.setBit(h);
-
-//System.out.println("atom:"+rootAtom+"\tsphere:"+sphere+"\thash:"+h+"\t"+idcode);
- }
- }
-
- return iv.get();
- }
-
- public float getSimilarity(int[] o1, int[] o2) {
- return o1 == null
- || o2 == null
- || o1.length == 0
- || o2.length == 0 ? 0.0f
- : normalizeValue(SSSearcherWithIndex.getSimilarityTanimoto(o1, o2));
- }
-
- private float normalizeValue(double value) {
- return value <= 0.0f ? 0.0f
- : value >= 1.0f ? 1.0f
- : (float)(1.0-Math.pow(1-Math.pow(value, CORRECTION_FACTOR) ,1.0/CORRECTION_FACTOR));
- }
-
- public DescriptorHandler<int[], StereoMolecule> getThreadSafeCopy() {
- return this;
- }
-
-}
=====================================
src/main/java/com/actelion/research/chem/descriptor/DescriptorHandlerPharmPath.java deleted
=====================================
@@ -1,95 +0,0 @@
-/*
-* 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.
-*
-*/
-
-package com.actelion.research.chem.descriptor;
-
-import com.actelion.research.chem.StereoMolecule;
-
-public class DescriptorHandlerPharmPath extends AbstractDescriptorHandlerFP<StereoMolecule> implements DescriptorConstants {
- private static final double CORRECTION_FACTOR = 0.85;
-
- private static DescriptorHandlerPharmPath sDefaultInstance;
-
- public static DescriptorHandlerPharmPath getDefaultInstance() {
- synchronized (DescriptorHandlerPharmPath.class) {
- if (sDefaultInstance == null) {
- sDefaultInstance = new DescriptorHandlerPharmPath();
- }
- }
- return sDefaultInstance;
- }
-
- public DescriptorInfo getInfo() {
- return DESCRIPTOR_PFP512;
- }
-
- public String getVersion() {
- return DescriptorConstants.DESCRIPTOR_PFP512.version;
- }
-
- public int[] createDescriptor(StereoMolecule mol) {
- if (mol ==null)
- return null;
-
- java.util.BitSet bitset = new FingerPrintGeneratorPharmGraph().getFingerprint(mol);
-
- if (bitset == null)
- return FAILED_OBJECT;
-
- int[] fp = new int[16];
- int mask = 1;
- for (int i = 0; i < 32; i++) {
- for (int j = 0; j < 16; j++)
- if (bitset.get(16 * i + j))
- fp[j] += mask;
- mask <<= 1;
- }
-
- return fp;
- }
-
- public DescriptorHandler<int[], StereoMolecule> getThreadSafeCopy() {
- return this;
- }
-
- @Override
- public float getSimilarity(int[] o1, int[] o2) {
- return normalizeValue(super.getSimilarity(o1, o2));
- }
-
- private float normalizeValue(double value) {
- return value <= 0.0f ? 0.0f
- : value >= 1.0f ? 1.0f
- : (float)(1.0-Math.pow(1-Math.pow(value, CORRECTION_FACTOR) ,1.0/CORRECTION_FACTOR));
- }
-}
=====================================
src/main/java/com/actelion/research/chem/descriptor/FingerPrintGenerator.java
=====================================
@@ -151,7 +151,7 @@ public class FingerPrintGenerator
{
paths = new Hashtable();
debugCounter = 0;
- int atoms = mol.getAllAtoms();
+ int atoms = mol.getAtoms();
String s;
boolean[] flags = new boolean[atoms];
for (int atom = 0; atom < atoms; atom++) {
@@ -178,7 +178,7 @@ public class FingerPrintGenerator
*/
private void traverseDFS(StereoMolecule mol, int lastAtom, int rootAtom, String path, int depth, boolean flags[])
{
- int connAtoms = mol.getConnAtoms(rootAtom);
+ int connAtoms = mol.getConnAtoms(rootAtom) + mol.getMetalBondedConnAtoms(rootAtom);
int nextAtom = 0, bond = 0;
StringBuilder newPath = new StringBuilder();
@@ -206,6 +206,8 @@ public class FingerPrintGenerator
newPath.append("=");
} else if (mol.getBondOrder(bond) == 3) {
newPath.append("#");
+ } else if (mol.getBondOrder(bond) == 0) {
+ newPath.append(".");
} else
System.out.println(
"FingerPrintGenerator.depthFirstSearch() " +
=====================================
src/main/java/com/actelion/research/chem/descriptor/FingerPrintGeneratorPharmGraph.java deleted
=====================================
@@ -1,218 +0,0 @@
-/*
-* 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.
-*
-*/
-
-package com.actelion.research.chem.descriptor;
-
-import com.actelion.research.chem.IDCodeParser;
-import com.actelion.research.chem.Molecule;
-import com.actelion.research.chem.StereoMolecule;
-
-import java.io.BufferedReader;
-import java.io.InputStreamReader;
-import java.util.BitSet;
-import java.util.Enumeration;
-import java.util.Hashtable;
-
-
-/**
- * Generator of a path-based Fingerprint
- * Not thread safe!
- */
-public class FingerPrintGeneratorPharmGraph
-{
- private static final int MAX_BITS = 512;
- private static final int MAX_DEPTH = 6;
- private static final boolean DEBUG = false;
- private static int debugCounter = 0;
- private Hashtable paths;
-
-
- /**
- * Generates a fingerprint of the default size for the given ExtendedMolecule
- *
- * @param mol The ExtendedMolecule for which a Fingerprint is generated
- * @return The Fingerprint (A one-dimensional bit array)
- */
- public BitSet getFingerprint(StereoMolecule mol)
- {
- return getFingerprint(mol, MAX_BITS);
- }
-
-
- /**
- * Generates the fingerprint of a molecule
- *
- * @param mol The ExtendedMolecule for which a Fingerprint is generated
- * @param size The desired size of the fingerprint
- * @return The Fingerprint (A one-dimensional bit array)
- */
- public BitSet getFingerprint(StereoMolecule mol, int size)
- {
- String path = null;
- int index;
-
- mol.ensureHelperArrays(Molecule.cHelperRings);
- findAllPaths(mol);
- BitSet bs = new BitSet(size);
- for (Enumeration e = paths.elements(); e.hasMoreElements(); ) {
- path = (String) e.nextElement();
- index = new java.util.Random(path.hashCode()).nextInt(size);
- if (DEBUG)
- System.out.print(this.toString().substring(40) + " ");
-// System.out.println("Setting bit " + position + " for " + path);
- bs.set(index);
- }
- return bs;
- }
-
-
-
-
-
- /**
- * Find all paths up to MAX_DEPTH length.
- * The paths are acquired by a number of depth first searches, one for each atom.
- *
- * @param mol The Molecule which is to be searched.
- */
- private void findAllPaths(StereoMolecule mol)
- {
- paths = new Hashtable();
- debugCounter = 0;
- int atoms = mol.getAllAtoms();
- String s;
- boolean[] flags = new boolean[atoms];
- for (int atom = 0; atom < atoms; atom++) {
- s = mol.getAtomLabel(atom);
- for (int i = 0; i < atoms; i++)
- flags[i] = false;
- addPath(s);
- if (DEBUG)
- System.out.println("\t***Starting at atom " + atom + " with symbol " + mol.getAtomLabel(atom));
- traverseDFS(mol, -1, atom, s, 0, flags);
- }
- }
-
-
- /**
- * Performs a recursive depth first search
- *
- * @param mol The Molecule to be searched
- * @param lastAtom The Atom we came from
- * @param rootAtom The Atom to start the search at
- * @param path The Path that has been generated so far
- * @param depth The current depth in this recursive search
- * @param flags Helper flags
- */
-
- private void traverseDFS(StereoMolecule mol, int lastAtom, int rootAtom, String path, int depth, boolean flags[])
- {
- int connAtoms = mol.getConnAtoms(rootAtom)+mol.getMetalBondedConnAtoms(rootAtom);
- int nextAtom = 0, bond = 0;
- StringBuilder newPath = new StringBuilder();
-
- depth++;
- // Check all connected atoms
- for (int i = 0; i < connAtoms; i++) {
- // Flag starting point
- flags[rootAtom] = true;
- nextAtom = mol.getConnAtom(rootAtom, i);
- if (nextAtom == lastAtom) {
- continue;
- }
-
- // Not yet seen
- if (!flags[nextAtom]) {
- bond = mol.getConnBond(rootAtom, i);
- newPath.setLength(0);
- newPath.append(path);
- // Construct a string with Daylight kind of bond encoding
- if (mol.isDelocalizedBond(bond) || mol.isAromaticBond(bond)) {
- newPath.append(":");
- } else if (mol.getBondOrder(bond) == 1) {
- newPath.append("-");
- } else if (mol.getBondOrder(bond) == 2) {
- newPath.append("=");
- } else if (mol.getBondOrder(bond) == 3) {
- newPath.append("#");
- } else if (mol.getBondOrder(bond) == 0) {
- newPath.append(".");
- } else
- System.out.println(
- "FingerPrintGenerator.depthFirstSearch() " +
- "Error: Invalid Bond order! " + mol.getBondOrder(bond));
- newPath.append(mol.getAtomLabel(nextAtom));
-
- // Mark nextAtom as visited
- flags[nextAtom] = true;
- addPath(newPath.toString());
- if (depth == MAX_DEPTH) {
- // Unmark nextAtoms so we might visit it again during another run
- flags[nextAtom] = false;
- // System.out.println("Reached end of depth!!! " + newPath);
- }
- if (depth < MAX_DEPTH) {
- // System.out.println("Visiting " + rootAtom + " + " + nextAtom + " " + newPath);
- traverseDFS(mol, rootAtom, nextAtom, newPath.toString(), depth, flags);
- // Unmark nextAtoms so we might visit it again during another run
- flags[nextAtom] = false;
- }
- }
- }
- }
-
- private boolean addPath(String newPath)
- {
- String storePath = newPath;
- String reversePath = new StringBuilder(storePath).reverse().toString();
- boolean ok = false;
- // Find the "smaller" version
- if (reversePath.compareTo(newPath) < 0) {
- /* reversePath is smaller than newPath so we keep reversePath */
- storePath = reversePath;
- }
- if (DEBUG)
- System.out.println("Checking for existence of Path " + storePath);
- if (!paths.containsKey(storePath)) {
- paths.put(storePath, storePath);
- ok = true;
- if (DEBUG) {
- debugCounter++;
- System.out.println("Storing path no. " + debugCounter + ": " + storePath + ", Hash: " + storePath.hashCode());
- }
- }
- return ok;
- }
-
-
-}
=====================================
src/main/java/com/actelion/research/chem/io/pdb/converter/BondsCalculator.java
=====================================
The diff for this file was not included because it is too large.
=====================================
src/main/java/com/actelion/research/chem/io/pdb/parser/PDBFileParser.java
=====================================
@@ -519,7 +519,7 @@ public class PDBFileParser {
//
}
- indexLine--;
+ //indexLine--;
List<AtomRecord> hetAtomRecords = new ArrayList<AtomRecord>();
List<AtomRecord> protAtomRecords = new ArrayList<AtomRecord>();
modelParser.parse(liRaw, indexLine,protAtomRecords,hetAtomRecords);
=====================================
src/main/java/com/actelion/research/chem/io/pdb/parser/Residue.java
=====================================
@@ -89,13 +89,16 @@ public class Residue {
fragment.setAtomY(atom,record.getY());
fragment.setAtomZ(atom,record.getZ());
}
+
+ fragment.ensureHelperArrays(Molecule.cHelperCIP);
try {
- BondsCalculator.createBonds(fragment, true);
- BondsCalculator.calculateBondOrders(fragment);
+ BondsCalculator.createBonds(fragment, true,null);
+ BondsCalculator.calculateBondOrders(fragment,true);
} catch (Exception e) {
- System.err.println("Cannot process structure");
+ // TODO Auto-generated catch block
+ System.err.println();
}
- fragment.ensureHelperArrays(Molecule.cHelperCIP);
+
return fragment;
}
=====================================
src/main/java/com/actelion/research/gui/JChemistryView.java
=====================================
@@ -34,6 +34,8 @@
package com.actelion.research.gui;
import com.actelion.research.chem.*;
+import com.actelion.research.chem.io.CompoundFileHelper;
+import com.actelion.research.chem.io.RDFileParser;
import com.actelion.research.chem.io.RXNFileParser;
import com.actelion.research.chem.reaction.Reaction;
import com.actelion.research.gui.clipboard.ClipboardHandler;
@@ -373,11 +375,23 @@ public class JChemistryView extends JComponent
}
if (e.getActionCommand().equals(ITEM_OPEN_RXN) && mIsEditable) {
- File rxnFile = FileHelper.getFile(this, "Please select a reaction file", FileHelper.cFileTypeRXN);
+ File rxnFile = FileHelper.getFile(this, "Please select a reaction file",
+ FileHelper.cFileTypeRXN | CompoundFileHelper.cFileTypeRD);
if (rxnFile != null) {
try {
- Reaction reaction = new RXNFileParser().getReaction(rxnFile);
- pasteOrDropReaction(reaction);
+ Reaction reaction = null;
+
+ if (FileHelper.getFileType(rxnFile.getName()) == FileHelper.cFileTypeRXN) {
+ reaction = new RXNFileParser().getReaction(rxnFile);
+ }
+ else {
+ RDFileParser rdfParser = new RDFileParser(rxnFile);
+ if (rdfParser.isReactionNext())
+ reaction = rdfParser.getNextReaction();
+ }
+
+ if (reaction != null)
+ pasteOrDropReaction(reaction);
}
catch (Exception ex) {}
}
View it on GitLab: https://salsa.debian.org/java-team/openchemlib/-/compare/6f58c52f5edb935c5b289541aaf4be3d906693f5...6479ea7ed19dedf17fe8ee9bf03268d76dd07738
--
View it on GitLab: https://salsa.debian.org/java-team/openchemlib/-/compare/6f58c52f5edb935c5b289541aaf4be3d906693f5...6479ea7ed19dedf17fe8ee9bf03268d76dd07738
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