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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.
*
*/
package com.actelion.research.chem;
import com.actelion.research.util.DoubleFormat;
import java.nio.charset.StandardCharsets;
/**
* Typically you should use IDCodeParser instead of this class. You may instantiate this class
* if you need to avoid a dependency to the CoordinateInventor and if you pass encoded coordinates
* together with any idcode for parsing.
* We needed to introduce this class to avoid a cyclic dependency between the IDCodeParser and
* the CoordinateInventor: If encoded atom coords are not given, then the IDcodeParser needs
* to invent then in order to assign proper up-/down-bonds. The CoordinateInventor needs the
* IDCodeParser to unpack its default template list.
*/
public class IDCodeParserWithoutCoordinateInvention {
private StereoMolecule mMol;
private byte[] mDecodingBytes;
private int mIDCodeBitsAvail,mIDCodeTempData,mIDCodeBufferIndex;
private boolean mNeglectSpaceDelimitedCoordinates;
protected boolean ensure2DCoordinates() {
return false;
}
/**
* IDCodeParsers allow passing idcode and coordinates as one String with a space
* as separator in between. If an idcode is followed by a space and more, and if
* the following shall not be interpreted as encoded coordinates, then call this
* method after instantiation.
*/
public void neglectSpaceDelimitedCoordinates() {
mNeglectSpaceDelimitedCoordinates = true;
}
/**
* Creates and returns a molecule from the idcode with its atom and bond arrays being
* just as large as needed to hold the molecule. Use this to conserve memory if no
* atoms or bonds are added to the molecule afterwards. This version of the method
* allows to pass idcode and atom coordinates in one String object.
* @param idcode null or idcode, which may contain coordinates separated by a space character
* @return
*/
public StereoMolecule getCompactMolecule(String idcode) {
return (idcode == null || idcode.isEmpty()) ? null : getCompactMolecule(idcode.getBytes(StandardCharsets.UTF_8));
}
/**
* Creates and returns a molecule from the idcode with its atom and bond arrays being
* just as large as needed to hold the molecule. Use this to conserve memory if no
* atoms or bonds are added to the molecule afterwards.
* @param idcode may be null
* @return
*/
public StereoMolecule getCompactMolecule(byte[] idcode) {
if (idcode == null || idcode.length == 0)
return null;
for (int i=2; i 8) // abits is the version number
abits = bbits;
int allAtoms = decodeBits(abits);
int allBonds = decodeBits(bbits);
StereoMolecule mol = new StereoMolecule(allAtoms, allBonds);
parse(mol, idcode, coordinates, idcodeStart, coordsStart);
return mol;
}
/**
* Parses the idcode and populates the given molecule to represent the passed idcode.
* This version of the method allows to pass idcode and atom coordinates in one String object.
* @param mol molecule object to be filled with the idcode content
* @param idcode null or idcode, which may contain coordinates separated by a space character
*/
public void parse(StereoMolecule mol, String idcode) {
if (idcode == null || idcode.isEmpty()) {
parse(mol, (byte[])null, (byte[])null);
return;
}
int index = idcode.indexOf(' ');
if (index > 0 && index < idcode.length()-1)
parse(mol, idcode.substring(0, index).getBytes(StandardCharsets.UTF_8), idcode.substring(index+1).getBytes(StandardCharsets.UTF_8));
else
parse(mol, idcode.getBytes(StandardCharsets.UTF_8), null);
}
/**
* Parses the idcode and populates the given molecule to represent the passed idcode.
* @param mol molecule object to be filled with the idcode content
* @param idcode null or valid idcode optionally concatenates with SPACE and encoded coordinates
*/
public void parse(StereoMolecule mol, byte[] idcode) {
parse(mol, idcode, null);
}
/**
* Parses the idcode and populates the given molecule to represent the passed idcode.
* @param mol molecule object to be filled with the idcode content
* @param idcode may be null
* @param coordinates may be null
*/
public void parse(StereoMolecule mol, String idcode, String coordinates) {
byte[] idcodeBytes = (idcode == null) ? null : idcode.getBytes(StandardCharsets.UTF_8);
byte[] coordinateBytes = (coordinates == null) ? null : coordinates.getBytes(StandardCharsets.UTF_8);
parse(mol, idcodeBytes, coordinateBytes);
}
/**
* Parses the idcode and populates the given molecule to represent the passed idcode.
* @param mol molecule object to be filled with the idcode content
* @param idcode may be null
* @param coordinates may be null
*/
public void parse(StereoMolecule mol, byte[] idcode, byte[] coordinates) {
if (idcode == null || idcode.length == 0) {
mol.clear();
return;
}
parse(mol, idcode, coordinates, 0, 0);
}
/**
* Parses the idcode and populates the given molecule to represent the passed idcode.
* @param mol molecule object to be filled with the idcode content
* @param idcode may be null
* @param idcodeStart offset in idcode array to first idcode byte
*/
public void parse(StereoMolecule mol, byte[] idcode, int idcodeStart) {
parse(mol, idcode, null, idcodeStart, -1);
}
/**
* Parses the idcode and populates the given molecule to represent the passed idcode.
* @param mol molecule object to be filled with the idcode content
* @param idcode may be null
* @param coordinates may be null
* @param idcodeStart offset in idcode array to first idcode byte
* @param coordsStart offset in coordinates array to first coords byte
*/
public void parse(StereoMolecule mol, byte[] idcode, byte[] coordinates, int idcodeStart, int coordsStart) {
mol.clear();
if (idcode==null || idcodeStart < 0 || idcodeStart >= idcode.length)
return;
mMol = mol;
int version = Canonizer.cIDCodeVersion2;
if (coordinates != null && (coordsStart < 0 || coordsStart >= coordinates.length))
coordinates = null;
decodeBitsStart(idcode, idcodeStart);
int abits = decodeBits(4);
int bbits = decodeBits(4);
if (abits > 8) { // abits is the version number
version = abits;
abits = bbits;
}
if (abits == 0) {
mMol.setFragment(decodeBits(1) == 1);
return;
}
int allAtoms = decodeBits(abits);
int allBonds = decodeBits(bbits);
int nitrogens = decodeBits(abits);
int oxygens = decodeBits(abits);
int otherAtoms = decodeBits(abits);
int chargedAtoms = decodeBits(abits);
for (int atom=0; atom= '\'');
double targetAVBL = 0.0;
double xOffset = 0.0;
double yOffset = 0.0;
double zOffset = 0.0;
boolean coordsAre3D = false;
boolean coordsAreAbsolute = false;
if (decodeOldCoordinates) { // old coordinate encoding
if ((coordinates.length > 2*allAtoms-2 && coordinates[2*allAtoms-2] == '\'')
|| (coordinates.length > 3*allAtoms-3 && coordinates[3*allAtoms-3] == '\'')) { // old faulty encoding
coordsAreAbsolute = true;
coordsAre3D = (coordinates.length == 3*allAtoms-3+9);
int index = coordsAre3D ? 3*allAtoms-3 : 2*allAtoms-2;
int avblInt = 86*((int)coordinates[index+1]-40)+(int)coordinates[index+2]-40;
targetAVBL = Math.pow(10.0, avblInt/2000.0-1.0);
index += 2;
int xInt = 86*((int)coordinates[index+1]-40)+(int)coordinates[index+2]-40;
xOffset = Math.pow(10.0, xInt/1500.0-1.0);
index += 2;
int yInt = 86*((int)coordinates[index+1]-40)+(int)coordinates[index+2]-40;
yOffset = Math.pow(10.0, yInt/1500.0-1.0);
if (coordsAre3D) {
index += 2;
int zInt = 86*((int)coordinates[index+1]-40)+(int)coordinates[index+2]-40;
zOffset = Math.pow(10.0, zInt/1500.0-1.0);
}
}
else {
coordsAre3D = (coordinates.length == 3*allAtoms-3);
}
}
// don't use 3D coordinates, if we need 2D
if (ensure2DCoordinates() && coordsAre3D) {
coordinates = null;
decodeOldCoordinates = false;
}
for (int i=1; i mIDCodeBufferIndex+1
&& (idcode[mIDCodeBufferIndex+1] == ' ' || idcode[mIDCodeBufferIndex+1] == '\t')) {
coordinates = idcode;
coordsStart = mIDCodeBufferIndex+2;
}
if (coordinates != null) {
try {
if (coordinates[coordsStart] == '!' || coordinates[coordsStart] == '#') { // new coordinate format
decodeBitsStart(coordinates, coordsStart + 1);
coordsAre3D = (decodeBits(1) == 1);
coordsAreAbsolute = (decodeBits(1) == 1);
int resolutionBits = 2 * decodeBits(4);
int binCount = (1 << resolutionBits);
double factor;
int from = 0;
int bond = 0;
for (int atom = 1; atom < allAtoms; atom++) {
if (bond < allBonds && mMol.getBondAtom(1, bond) == atom) {
from = mMol.getBondAtom(0, bond++);
factor = 1.0;
}
else {
from = 0;
factor = 8.0;
}
mMol.setAtomX(atom, mMol.getAtomX(from) + factor * (decodeBits(resolutionBits) - binCount / 2.0));
mMol.setAtomY(atom, mMol.getAtomY(from) + factor * (decodeBits(resolutionBits) - binCount / 2.0));
if (coordsAre3D)
mMol.setAtomZ(atom, mMol.getAtomZ(from) + factor * (decodeBits(resolutionBits) - binCount / 2.0));
}
if (coordinates[coordsStart] == '#') { // we have 3D-coordinates that include implicit hydrogen coordinates
int hydrogenCount = 0;
// we need to cache hCount, because otherwise getImplicitHydrogens() would create helper arrays with every call
int[] hCount = new int[allAtoms];
for (int atom = 0; atom < allAtoms; atom++)
hydrogenCount += (hCount[atom] = mMol.getImplicitHydrogens(atom));
for (int atom = 0; atom < allAtoms; atom++) {
for (int i = 0; i < hCount[atom]; i++) {
int hydrogen = mMol.addAtom(1);
mMol.addBond(atom, hydrogen, Molecule.cBondTypeSingle);
mMol.setAtomX(hydrogen, mMol.getAtomX(atom) + (decodeBits(resolutionBits) - binCount / 2.0));
mMol.setAtomY(hydrogen, mMol.getAtomY(atom) + (decodeBits(resolutionBits) - binCount / 2.0));
if (coordsAre3D)
mMol.setAtomZ(hydrogen, mMol.getAtomZ(atom) + (decodeBits(resolutionBits) - binCount / 2.0));
}
}
allAtoms += hydrogenCount;
allBonds += hydrogenCount;
}
double avblDefault = coordsAre3D ? 1.5 : Molecule.getDefaultAverageBondLength();
double avbl = mMol.getAverageBondLength(allAtoms, allBonds, avblDefault);
if (coordsAreAbsolute) {
targetAVBL = decodeAVBL(decodeBits(resolutionBits), binCount);
xOffset = targetAVBL * decodeShift(decodeBits(resolutionBits), binCount);
yOffset = targetAVBL * decodeShift(decodeBits(resolutionBits), binCount);
if (coordsAre3D)
zOffset = targetAVBL * decodeShift(decodeBits(resolutionBits), binCount);
factor = targetAVBL / avbl;
for (int atom = 0; atom < allAtoms; atom++) {
mMol.setAtomX(atom, xOffset + factor * mMol.getAtomX(atom));
mMol.setAtomY(atom, yOffset + factor * mMol.getAtomY(atom));
if (coordsAre3D)
mMol.setAtomZ(atom, zOffset + factor * mMol.getAtomZ(atom));
}
}
else { // with new format 2D and 3D coordinates are scaled to average bond lengths of 1.5 Angstrom
targetAVBL = 1.5;
factor = targetAVBL / avbl;
for (int atom = 0; atom < allAtoms; atom++) {
mMol.setAtomX(atom, factor * mMol.getAtomX(atom));
mMol.setAtomY(atom, factor * mMol.getAtomY(atom));
if (coordsAre3D)
mMol.setAtomZ(atom, factor * mMol.getAtomZ(atom));
}
}
}
else { // old coordinate format
if (coordsAre3D && !coordsAreAbsolute && targetAVBL == 0.0) // if no scaling factor is given, then scale to mean bond length = 1.5
targetAVBL = 1.5;
if (targetAVBL != 0.0 && mMol.getAllBonds() != 0) {
double avbl = 0.0;
for (int bond = 0; bond < mMol.getAllBonds(); bond++) {
double dx = mMol.getAtomX(mMol.getBondAtom(0, bond)) - mMol.getAtomX(mMol.getBondAtom(1, bond));
double dy = mMol.getAtomY(mMol.getBondAtom(0, bond)) - mMol.getAtomY(mMol.getBondAtom(1, bond));
double dz = coordsAre3D ? mMol.getAtomZ(mMol.getBondAtom(0, bond)) - mMol.getAtomZ(mMol.getBondAtom(1, bond)) : 0.0f;
avbl += Math.sqrt(dx * dx + dy * dy + dz * dz);
}
avbl /= mMol.getAllBonds();
double f = targetAVBL / avbl;
for (int atom = 0; atom < mMol.getAllAtoms(); atom++) {
mMol.setAtomX(atom, mMol.getAtomX(atom) * f + xOffset);
mMol.setAtomY(atom, mMol.getAtomY(atom) * f + yOffset);
if (coordsAre3D)
mMol.setAtomZ(atom, mMol.getAtomZ(atom) * f + zOffset);
}
}
}
}
catch (Exception e) {
e.printStackTrace();
System.err.println("Faulty id-coordinates:"+e+" "+new String(idcode, StandardCharsets.UTF_8)+" "+new String(coordinates, StandardCharsets.UTF_8));
coordinates = null;
coordsAre3D = false;
}
}
boolean coords2DAvailable = (coordinates != null && !coordsAre3D);
// If we have or create 2D-coordinates, then we need to set all double bonds to a cross bond, which
// - have distinguishable substituents on both ends, i.e. is a stereo double bond
// - are not in a small ring
// Here we don't know, whether a double bond without E/Z parity is a stereo bond with unknown
// configuration or not a stereo bond. Therefore, we need to set a flag, that causes the Canonizer
// during the next stereo recognition with atom coordinates to assign an unknown configuration rather
// than E or Z based on created or given coordinates.
// In a next step these double bonds are converted into cross bonds by
if (coords2DAvailable || ensure2DCoordinates()) {
mMol.ensureHelperArrays(Molecule.cHelperRings);
for (int bond=0; bond= coordsStart+3*allAtoms-3
&& coordinates[coordsStart+2*allAtoms-2] != '\'');
}
}
public boolean coordinatesAreAbsolute(String coordinates) {
return coordinates != null && coordinatesAreAbsolute(coordinates.getBytes(StandardCharsets.UTF_8));
}
public boolean coordinatesAreAbsolute(byte[] coordinates) {
return coordinatesAreAbsolute(coordinates, 0);
}
public boolean coordinatesAreAbsolute(byte[] coordinates, int coordStart) {
if (coordinates == null || coordinates.length <= coordStart)
return false;
if (coordinates[coordStart] >= '\'') { // old format uses ACSII 39 and higher
for (int i=coordStart; i 8) // abits is the version number
version = abits;
return version;
}
public int getAtomCount(String idcode) {
if (idcode == null || idcode.isEmpty())
return 0;
return getAtomCount(idcode.getBytes(StandardCharsets.UTF_8), 0);
}
public int getAtomCount(byte[] idcode, int offset) {
if (idcode == null || idcode.length <= offset)
return 0;
decodeBitsStart(idcode, offset);
int abits = decodeBits(4);
int bbits = decodeBits(4);
if (abits > 8) // abits is the version number
abits = bbits;
if (abits == 0)
return 0;
return decodeBits(abits);
}
/**
* Determines atom and bond counts of the given idcode
* @param idcode
* @param count null or int[2], which is filled and returned
* @return int[] with atom and bond count as first and second values
*/
public int[] getAtomAndBondCounts(String idcode, int[] count) {
if (idcode == null || idcode.isEmpty())
return null;
return getAtomAndBondCounts(idcode.getBytes(StandardCharsets.UTF_8), 0, count);
}
/**
* Determines atom and bond counts of the given idcode
* @param idcode
* @param offset
* @param count null or int[2], which is filled and returned
* @return int[] with atom and bond count as first and second values
*/
public int[] getAtomAndBondCounts(byte[] idcode, int offset, int[] count) {
if (idcode == null || idcode.length == 0)
return null;
decodeBitsStart(idcode, 0);
int abits = decodeBits(4);
int bbits = decodeBits(4);
if (abits > 8) // abits is the version number
abits = bbits;
if (count == null)
count = new int[2];
if (abits == 0) {
count[0] = 0;
count[1] = 0;
}
else {
count[0] = decodeBits(abits);
count[1] = decodeBits(bbits);
}
return count;
}
private void decodeBitsStart(byte[] bytes, int offset) {
mIDCodeBitsAvail = 6;
mIDCodeBufferIndex = offset;
mDecodingBytes = bytes;
mIDCodeTempData = (bytes[mIDCodeBufferIndex] & 0x3F) << 11;
}
private int decodeBits(int bits) {
int allBits = bits;
int data = 0;
while (bits != 0) {
if (mIDCodeBitsAvail == 0) {
mIDCodeTempData = (mDecodingBytes[++mIDCodeBufferIndex] & 0x3F) << 11;
mIDCodeBitsAvail = 6;
}
data |= ((0x00010000 & mIDCodeTempData) >> (16 - allBits + bits));
mIDCodeTempData <<= 1;
bits--;
mIDCodeBitsAvail--;
}
return data;
}
private double decodeAVBL(int value, int binCount) {
return Math.pow(10, Math.log10(200/0.1) * value / (binCount - 1) - 1);
}
private double decodeShift(int value, int binCount) {
int halfBinCount = binCount / 2;
boolean isNegative = (value >= halfBinCount);
if (isNegative)
value -= halfBinCount;
double steepness = binCount/32.0;
double doubleValue = steepness * value / (halfBinCount - value);
return isNegative ? -doubleValue : doubleValue;
}
public void printContent(byte[] idcode, byte[] coordinates) {
try {
int version = Canonizer.cIDCodeVersion2;
if (idcode == null || idcode.length == 0)
return;
if (coordinates != null && coordinates.length == 0)
coordinates = null;
System.out.println("idcode: " + new String(idcode, StandardCharsets.UTF_8));
if (coordinates != null)
System.out.println("coords: " + new String(coordinates, StandardCharsets.UTF_8));
decodeBitsStart(idcode, 0);
int abits = decodeBits(4);
int bbits = decodeBits(4);
if (abits > 8) { // abits is the version number
version = abits;
abits = bbits;
}
System.out.println("version:" + version);
int allAtoms = decodeBits(abits);
if (allAtoms == 0)
return;
int allBonds = decodeBits(bbits);
int nitrogens = decodeBits(abits);
int oxygens = decodeBits(abits);
int otherAtoms = decodeBits(abits);
int chargedAtoms = decodeBits(abits);
System.out.println("allAtoms:" + allAtoms + " allBonds:" + allBonds);
if (nitrogens != 0) {
System.out.print("nitrogens:");
for (int i = 0; i < nitrogens; i++)
System.out.print(" " + decodeBits(abits));
System.out.println();
}
if (oxygens != 0) {
System.out.print("oxygens:");
for (int i = 0; i < oxygens; i++)
System.out.print(" " + decodeBits(abits));
System.out.println();
}
if (otherAtoms != 0) {
System.out.print("otherAtoms:");
for (int i = 0; i < otherAtoms; i++)
System.out.print(" " + decodeBits(abits) + ":" + decodeBits(8));
System.out.println();
}
if (chargedAtoms != 0) {
System.out.print("chargedAtoms:");
for (int i = 0; i < chargedAtoms; i++)
System.out.print(" " + decodeBits(abits) + ":" + (decodeBits(4) - 8));
System.out.println();
}
int closureBonds = 1 + allBonds - allAtoms;
int dbits = decodeBits(4);
int base = 0;
int[][] bondAtom = new int[2][allBonds];
int bondCount = 0;
for (int i = 1; i < allAtoms; i++) {
int dif = decodeBits(dbits);
if (dif == 0) {
closureBonds++;
continue;
}
base += dif - 1;
bondAtom[0][bondCount] = base;
bondAtom[1][bondCount++] = i;
}
for (int i = 0; i < closureBonds; i++) {
bondAtom[0][bondCount] = decodeBits(abits);
bondAtom[1][bondCount++] = decodeBits(abits);
}
int[] bondOrder = new int[allBonds];
System.out.print("bonds:");
for (int bond = 0; bond < allBonds; bond++) {
System.out.print(" " + bondAtom[0][bond]);
bondOrder[bond] = decodeBits(2);
System.out.print(bondOrder[bond] == 0 ? "." : bondOrder[bond] == 1 ? "-" : bondOrder[bond] == 2 ? "=" : "#");
System.out.print("" + bondAtom[1][bond]);
}
System.out.println();
int THCount = decodeBits(abits);
if (THCount != 0) {
System.out.print("parities:");
for (int i = 0; i < THCount; i++) {
int atom = decodeBits(abits);
if (version == Canonizer.cIDCodeVersion2) {
int parity = decodeBits(2);
if (parity == 3) {
// this was the old discontinued Molecule.cAtomParityMix
// version2 idcodes had never more than one center with parityMix
System.out.print(" " + atom + ":1&0");
} else {
System.out.print(" " + atom + ":" + parity);
}
} else {
int parity = decodeBits(3);
switch (parity) {
case Canonizer.cParity1And:
System.out.print(" " + atom + ":1&" + decodeBits(3));
break;
case Canonizer.cParity2And:
System.out.print(" " + atom + ":2&" + decodeBits(3));
break;
case Canonizer.cParity1Or:
System.out.print(" " + atom + ":1|" + decodeBits(3));
break;
case Canonizer.cParity2Or:
System.out.print(" " + atom + ":2|" + decodeBits(3));
break;
default:
System.out.print(" " + atom + ":" + parity);
}
}
}
System.out.println();
}
if (version == Canonizer.cIDCodeVersion2)
if ((decodeBits(1) == 0)) // translate chiral flag
System.out.println("isRacemate");
int EZCount = decodeBits(bbits);
if (EZCount != 0) {
System.out.print("EZ:");
for (int i = 0; i < EZCount; i++) {
int bond = decodeBits(bbits);
if (bondOrder[bond] == 1) { // BINAP type of axial chirality
int parity = decodeBits(3);
switch (parity) {
case Canonizer.cParity1And:
System.out.print(" " + bond + ":1&" + decodeBits(3));
break;
case Canonizer.cParity2And:
System.out.print(" " + bond + ":2&" + decodeBits(3));
break;
case Canonizer.cParity1Or:
System.out.print(" " + bond + ":1|" + decodeBits(3));
break;
case Canonizer.cParity2Or:
System.out.print(" " + bond + ":2|" + decodeBits(3));
break;
default:
System.out.print(" " + bond + ":" + parity);
}
} else
System.out.print(" " + bond + ":" + decodeBits(2));
}
System.out.println();
}
if (decodeBits(1) == 1)
System.out.println("isFragment = true");
int offset = 0;
while (decodeBits(1) == 1) {
int dataType = offset + decodeBits(4);
int no;
switch (dataType) {
case 0: // datatype 'AtomQFNoMoreNeighbours'
no = decodeBits(abits);
System.out.print("noMoreNeighbours:");
for (int i = 0; i < no; i++)
System.out.print(" " + decodeBits(abits));
System.out.println();
break;
case 1: // datatype 'isotop'
no = decodeBits(abits);
System.out.print("mass:");
for (int i = 0; i < no; i++)
System.out.print(" " + decodeBits(abits) + ":" + decodeBits(8));
System.out.println();
break;
case 2: // datatype 'bond defined to be delocalized'
no = decodeBits(bbits);
System.out.print("delocalizedBonds (outdated, redundant and wrong):");
for (int i = 0; i < no; i++)
System.out.print(" " + decodeBits(bbits));
System.out.println();
break;
case 3: // datatype 'AtomQFMoreNeighbours'
no = decodeBits(abits);
System.out.print("moreNeighbours:");
for (int i = 0; i < no; i++)
System.out.print(" " + decodeBits(abits));
System.out.println();
break;
case 4: // datatype 'AtomQFRingState'
no = decodeBits(abits);
System.out.print("atomRingState:");
for (int i = 0; i < no; i++)
System.out.print(" " + decodeBits(abits) + ":" + decodeBits(Molecule.cAtomQFRingStateBits));
System.out.println();
break;
case 5: // datatype 'AtomQFAromState'
no = decodeBits(abits);
System.out.print("atomAromState:");
for (int i = 0; i < no; i++)
System.out.print(" " + decodeBits(abits) + ":" + decodeBits(Molecule.cAtomQFAromStateBits));
System.out.println();
break;
case 6: // datatype 'AtomQFAny'
no = decodeBits(abits);
System.out.print("atomAny:");
for (int i = 0; i < no; i++)
System.out.print(" " + decodeBits(abits));
System.out.println();
break;
case 7: // datatype 'AtomQFHydrogen'
no = decodeBits(abits);
System.out.print("atomHydrogen:");
for (int i = 0; i < no; i++)
System.out.print(" " + decodeBits(abits) + ":" + decodeBits(Molecule.cAtomQFHydrogenBits));
System.out.println();
break;
case 8: // datatype 'AtomList'
no = decodeBits(abits);
System.out.print("atomList:");
for (int i = 0; i < no; i++) {
int atom = decodeBits(abits);
int atoms = decodeBits(4);
System.out.print(" " + atom);
for (int j = 0; j < atoms; j++) {
System.out.print(j == 0 ? ":" : ",");
System.out.print("" + decodeBits(8));
}
}
System.out.println();
break;
case 9: // datatype 'BondQFRingState'
no = decodeBits(bbits);
System.out.print("bondRingState:");
for (int i = 0; i < no; i++)
System.out.print(" " + decodeBits(bbits) + ":" + decodeBits(Molecule.cBondQFRingStateBits));
System.out.println();
break;
case 10:// datatype 'BondQFBondTypes'
no = decodeBits(bbits);
System.out.print("bondTypes:");
for (int i = 0; i < no; i++)
System.out.print(" " + decodeBits(bbits) + ":" + decodeBits(Molecule.cBondQFBondTypesBits));
System.out.println();
break;
case 11: // datatype 'AtomQFMatchStereo'
no = decodeBits(abits);
System.out.print("atomMatchStereo:");
for (int i = 0; i < no; i++)
System.out.print(" " + decodeBits(abits));
System.out.println();
break;
case 12: // datatype 'bond defined to be a bridge from n1 to n2 atoms'
no = decodeBits(bbits);
for (int i = 0; i < no; i++) {
System.out.print("bridgeBond:" + decodeBits(bbits));
int min = decodeBits(Molecule.cBondQFBridgeMinBits);
int max = min + decodeBits(Molecule.cBondQFBridgeSpanBits);
System.out.println("(" + min + "-" + max + ")");
}
break;
case 13: // datatype 'AtomQFPiElectrons'
no = decodeBits(abits);
System.out.print("atomPiElectrons:");
for (int i = 0; i < no; i++)
System.out.print(" " + decodeBits(abits) + ":" + decodeBits(Molecule.cAtomQFPiElectronBits));
System.out.println();
break;
case 14: // datatype 'AtomQFNeighbours'
no = decodeBits(abits);
System.out.print("AtomQFNeighbours:");
for (int i = 0; i < no; i++)
System.out.print(" " + decodeBits(abits) + ":" + decodeBits(Molecule.cAtomQFNeighbourBits));
System.out.println();
break;
case 15: // datatype 'start second feature set'
case 31:
offset += 16;
System.out.println("");
break;
case 16: // datatype 'AtomQFSmallRingSize'
no = decodeBits(abits);
System.out.print("AtomQFSmallRingSize:");
for (int i = 0; i < no; i++)
System.out.print(" " + decodeBits(abits) + ":" + decodeBits(Molecule.cAtomQFSmallRingSizeBits));
System.out.println();
break;
case 17: // datatype 'AtomAbnormalValence'
no = decodeBits(abits);
System.out.print("AtomAbnormalValence:");
for (int i = 0; i < no; i++)
System.out.print(" " + decodeBits(abits) + ":" + decodeBits(4));
System.out.println();
break;
case 18: // datatype 'AtomCustomLabel'
no = decodeBits(abits);
System.out.print("AtomCustomLabel:");
int lbits = decodeBits(4);
for (int i = 0; i < no; i++) {
int atom = decodeBits(abits);
int count = decodeBits(lbits);
byte[] label = new byte[count];
for (int j = 0; j < count; j++)
label[j] = (byte) decodeBits(7);
System.out.print(" " + atom + ":" + new String(label, StandardCharsets.UTF_8));
}
System.out.println();
break;
case 19: // datatype 'AtomQFCharge'
no = decodeBits(abits);
System.out.print("AtomQFCharge:");
for (int i = 0; i < no; i++)
System.out.print(" " + decodeBits(abits) + ":" + decodeBits(Molecule.cAtomQFChargeBits));
System.out.println();
break;
case 20: // datatype 'BondQFRingSize'
no = decodeBits(bbits);
System.out.print("BondQFRingSize:");
for (int i = 0; i < no; i++)
System.out.print(" " + decodeBits(bbits) + ":" + decodeBits(Molecule.cBondQFRingSizeBits));
System.out.println();
break;
case 21: // datatype 'AtomRadicalState'
no = decodeBits(abits);
System.out.print("AtomRadicalState:");
for (int i = 0; i < no; i++)
System.out.print(" " + decodeBits(abits) + ":" + decodeBits(2));
System.out.println();
break;
case 22: // datatype 'flat nitrogen'
no = decodeBits(abits);
System.out.print("AtomQFFlatNitrogen:");
for (int i = 0; i < no; i++)
System.out.print(" " + decodeBits(abits));
System.out.println();
break;
case 23: // datatype 'cBondQFMatchStereo'
no = decodeBits(bbits);
System.out.print("cBondQFMatchStereo:");
for (int i = 0; i < no; i++)
System.out.print(" " + decodeBits(abits));
System.out.println();
break;
case 24: // datatype 'cBondQFAromatic'
no = decodeBits(bbits);
System.out.print("BondQFAromState:");
for (int i = 0; i < no; i++)
System.out.print(" " + decodeBits(bbits) + ":" + decodeBits(Molecule.cBondQFAromStateBits));
System.out.println();
break;
case 25: // datatype 'atom selection'
System.out.print("AtomSelection:");
for (int i = 0; i < allAtoms; i++)
if (decodeBits(1) == 1)
System.out.print(" " + i);
System.out.println();
break;
case 26: // datatype 'delocalized high order bond'
System.out.print("DelocalizedHigherOrderBonds:");
no = decodeBits(bbits);
for (int i = 0; i < no; i++)
System.out.print(" " + decodeBits(bbits));
break;
case 27: // datatype 'part of an exclude group'
no = decodeBits(abits);
System.out.print("AtomQFExcludeGroup:");
for (int i = 0; i < no; i++)
System.out.print(" " + decodeBits(abits));
System.out.println();
break;
case 28: // datatype 'coordinate bond'
no = decodeBits(bbits);
System.out.print("Coordinate Bonds:");
for (int i = 0; i < no; i++)
System.out.print(" " + decodeBits(bbits));
System.out.println();
break;
case 29:
no = decodeBits(abits);
System.out.print("ReactionParityHint:");
for (int i = 0; i < no; i++)
System.out.print(" " + decodeBits(abits) + ":" + decodeBits(Molecule.cAtomQFRxnParityBits));
System.out.println();
break;
case 30: // datatype 'AtomQFNewRingSize'
no = decodeBits(abits);
System.out.print("AtomQFNewRingSize:");
for (int i = 0; i < no; i++)
System.out.print(" " + decodeBits(abits) + ":" + decodeBits(Molecule.cAtomQFNewRingSizeBits));
System.out.println();
break;
case 32: // datatype 'AtomQFStereoStateBits'
no = decodeBits(abits);
System.out.print("AtomQFStereoState:");
for (int i = 0; i < no; i++)
System.out.print(" " + decodeBits(abits) + ":" + decodeBits(Molecule.cAtomQFStereoStateBits));
System.out.println();
break;
case 33: // datatype 'AtomQFENeighbours'
no = decodeBits(abits);
System.out.print("AtomQFENeighbours:");
for (int i = 0; i < no; i++)
System.out.print(" " + decodeBits(abits) + ":" + decodeBits(Molecule.cAtomQFENeighbourBits));
System.out.println();
break;
case 34: // datatype 'in hetero aromatic ring'
no = decodeBits(abits);
System.out.print("AtomQFHeteroAromatic:");
for (int i = 0; i < no; i++)
System.out.print(" " + decodeBits(abits));
System.out.println();
break;
case 35: // datatype 'cBondQFMatchFormalOrder'
no = decodeBits(bbits);
System.out.print("BondQFMatchFormalOrder:");
for (int i = 0; i < no; i++)
System.out.print(" " + decodeBits(abits));
System.out.println();
break;
case 36: // datatype 'cBondQFRareBondType'
no = decodeBits(bbits);
System.out.print("BondQFRareBondType:");
for (int i = 0; i < no; i++)
System.out.print(" " + decodeBits(bbits) + ":" + decodeBits(Molecule.cBondQFRareBondTypesBits));
System.out.println();
break;
case 37: // datatype 'rare bond type'
no = decodeBits(bbits);
System.out.print("Rare Bond Type:");
for (int i=0; i 0 && distance < lowDistance)
lowDistance = distance;
}
}
avbl = (lowDistance == Double.MAX_VALUE) ? defaultAVBL : lowDistance;
}
}
if (coordinates[0] == '#') { // we have 3D-coordinates that include implicit hydrogen coordinates
System.out.print("hydrogen coords (" + hydrogenCount + " expected): ");
int hydrogen = allAtoms;
for (int atom = 0; atom < allAtoms; atom++) {
if (hCount[atom] != 0)
System.out.print(atom);
for (int i = 0; i < hCount[atom]; i++) {
System.out.print(" (");
coords[0][hydrogen] = coords[0][atom] + (decodeBits(resolutionBits) - binCount / 2.0);
System.out.print((int) coords[0][hydrogen] + ",");
coords[1][hydrogen] = coords[1][atom] + (decodeBits(resolutionBits) - binCount / 2.0);
System.out.print((int) coords[1][hydrogen]);
if (coordsAre3D) {
coords[2][hydrogen] = coords[2][atom] + (decodeBits(resolutionBits) - binCount / 2.0);
System.out.print("," + (int) coords[2][hydrogen]);
}
System.out.print("), ");
hydrogen++;
}
}
System.out.println();
}
System.out.print(coordsAreAbsolute ? "absolute coords:" : "relative coords:");
if (hydrogenCount != 0)
System.out.println("Coordinates contain " + hydrogenCount + " hydrogen atoms!");
if (coordsAreAbsolute) {
double targetAVBL = decodeAVBL(decodeBits(resolutionBits), binCount);
double xOffset = targetAVBL * decodeShift(decodeBits(resolutionBits), binCount);
double yOffset = targetAVBL * decodeShift(decodeBits(resolutionBits), binCount);
double zOffset = 0;
if (coordsAre3D)
zOffset = targetAVBL * decodeShift(decodeBits(resolutionBits), binCount);
System.out.println("Abs-coord transformation: targetAVBL:" + targetAVBL + " xOffset:" + xOffset + " yOffset:" + yOffset + " zOffset:" + zOffset);
factor = targetAVBL / avbl;
for (int atom = 0; atom < allAtoms; atom++) {
coords[0][atom] = xOffset + factor * coords[0][atom];
coords[1][atom] = xOffset + factor * coords[1][atom];
if (coordsAre3D)
coords[2][atom] = xOffset + factor * coords[2][atom];
}
} else {
double targetAVBL = 1.5;
factor = targetAVBL / avbl;
for (int atom = 0; atom < allAtoms; atom++) {
System.out.print(atom + " (");
coords[0][atom] = coords[0][atom] * factor;
System.out.print(DoubleFormat.toString(coords[0][atom]) + ",");
coords[1][atom] = coords[1][atom] * factor;
System.out.print(DoubleFormat.toString(coords[1][atom]));
if (coordsAre3D) {
coords[2][atom] = coords[2][atom] * factor;
System.out.print("," + DoubleFormat.toString(coords[2][atom]));
}
System.out.print("), ");
if ((atom & 3) == 3 || atom == allAtoms - 1)
System.out.println();
}
}
}
}
System.out.println();
}
catch (Exception e) {
e.printStackTrace();
}
}
private double getDistance(double[][] coords, int atom1, int atom2, boolean coordsAre3D) {
double dx = coords[0][atom1] - coords[0][atom2];
double dy = coords[1][atom1] - coords[1][atom2];
double dz = coordsAre3D ? coords[2][atom1] - coords[2][atom2] : 0;
return Math.sqrt(dx*dx + dy*dy + dz*dz);
}
}