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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.chem.coords.CoordinateInventor;
import com.actelion.research.chem.reaction.Reaction;
import com.actelion.research.util.ArrayUtils;
import java.util.TreeMap;
public class SmilesParser {
private static final int MAX_BRACKET_LEVELS = 64;
private static final int MAX_RE_CONNECTIONS = 64;
private static final int MAX_AROMATIC_RING_SIZE = 15;
private StereoMolecule mMol;
private boolean[] mIsAromaticBond;
private int mAromaticAtoms,mAromaticBonds;
public Reaction parseReaction(byte[] smiles) throws Exception {
int index1 = ArrayUtils.indexOf(smiles, (byte)'>');
int index2 = (index1 == -1) ? -1 : ArrayUtils.indexOf(smiles, (byte)'>', index1+1);
if (index2 == -1)
throw new Exception("Missing one or both separators ('>').");
if (ArrayUtils.indexOf(smiles, (byte)'>', index2+1) != -1)
throw new Exception("Found more than 2 separators ('>').");
StereoMolecule reactants = new StereoMolecule();
parse(reactants, smiles, 0, index1);
StereoMolecule products = new StereoMolecule();
parse(products, smiles, index2+1, smiles.length);
StereoMolecule catalysts = null;
if (index2 - index1 > 1) {
catalysts = new StereoMolecule();
parse(catalysts, smiles, index1+1, index2);
}
Reaction rxn = new Reaction();
rxn.addReactant(reactants);
rxn.addProduct(products);
if (catalysts != null)
rxn.addCatalyst(catalysts);
return rxn;
}
/**
* Parses the given smiles into the molecule, creates proper atom coordinates
* to reflect correct double bond geometries and translates tetrahedral and allene
* parities into up/down-bonds.
* @param mol
* @param smiles
* @throws Exception
*/
public void parse(StereoMolecule mol, String smiles) throws Exception {
parse(mol, smiles.getBytes(), true, true);
}
public void parse(StereoMolecule mol, byte[] smiles) throws Exception {
parse(mol, smiles, true, true);
}
public void parse(StereoMolecule mol, byte[] smiles, int position, int endIndex) throws Exception {
parse(mol, smiles, position, endIndex, true, true);
}
public void parse(StereoMolecule mol, byte[] smiles, boolean createCoordinates, boolean readStereoFeatures) throws Exception {
parse(mol, smiles, 0, smiles.length, createCoordinates, readStereoFeatures);
}
public void parse(StereoMolecule mol, byte[] smiles, int position, int endIndex, boolean createCoordinates, boolean readStereoFeatures) throws Exception {
mMol = mol;
mMol.clear();
mAromaticAtoms = 0;
TreeMap parityMap = null;
int[] baseAtom = new int[MAX_BRACKET_LEVELS];
baseAtom[0] = -1;
int[] ringClosureAtom = new int[MAX_RE_CONNECTIONS];
int[] ringClosurePosition = new int[MAX_RE_CONNECTIONS];
int[] ringClosureBondType = new int[MAX_RE_CONNECTIONS];
for (int i=0; i();
// using position as hydrogenPosition is close enough
parityMap.put(atom, new THParity(atom, fromAtom, explicitHydrogens, position, isClockwise));
}
}
continue;
}
if (theChar == '.') {
baseAtom[bracketLevel] = -1;
bondType = Molecule.cBondTypeDeleted;
continue;
}
if (theChar == '=') {
bondType = Molecule.cBondTypeDouble;
continue;
}
if (theChar == '#') {
bondType = Molecule.cBondTypeTriple;
continue;
}
if (Character.isDigit(theChar)) {
int number = theChar - '0';
if (squareBracketOpen) {
while (position < endIndex
&& Character.isDigit(smiles[position])) {
number = 10 * number + smiles[position] - '0';
position++;
}
atomMass = number;
}
else {
boolean hasBondType = (smiles[position-2] == '-'
|| smiles[position-2] == '/'
|| smiles[position-2] == '\\'
|| smiles[position-2] == '='
|| smiles[position-2] == '#'
|| smiles[position-2] == ':');
if (percentFound
&& position < endIndex
&& Character.isDigit(smiles[position])) {
number = 10 * number + smiles[position] - '0';
position++;
}
percentFound = false;
if (number >= MAX_RE_CONNECTIONS)
throw new Exception("SmilesParser: ringClosureAtom number out of range");
if (ringClosureAtom[number] == -1) {
ringClosureAtom[number] = baseAtom[bracketLevel];
ringClosurePosition[number] = position-1;
ringClosureBondType[number] = hasBondType ? bondType : -1;
}
else {
if (ringClosureAtom[number] == baseAtom[bracketLevel])
throw new Exception("SmilesParser: ring closure to same atom");
if (readStereoFeatures && parityMap != null) {
THParity parity = parityMap.get(ringClosureAtom[number]);
if (parity != null)
parity.addNeighbor(baseAtom[bracketLevel], ringClosurePosition[number], false);
parity = parityMap.get(baseAtom[bracketLevel]);
if (parity != null)
parity.addNeighbor(ringClosureAtom[number], position-1, false);
}
if (ringClosureBondType[number] != -1)
bondType = ringClosureBondType[number];
else if (bondType == Molecule.cBondTypeUp) // interpretation inverts, if we have the slash bond at the second closure digit rather than at the first
bondType = Molecule.cBondTypeDown;
else if (bondType == Molecule.cBondTypeDown)
bondType = Molecule.cBondTypeUp;
// ringClosureAtom is the parent atom, i.e. the baseAtom of the first occurrence of the closure digit
mMol.addBond(ringClosureAtom[number], baseAtom[bracketLevel], bondType);
ringClosureAtom[number] = -1; // for number re-usage
}
bondType = Molecule.cBondTypeSingle;
}
continue;
}
if (theChar == '+') {
if (!squareBracketOpen)
throw new Exception("SmilesParser: '+' found outside brackets");
int charge = 1;
while (smiles[position] == '+') {
charge++;
position++;
}
if (charge == 1 && Character.isDigit(smiles[position])) {
charge = smiles[position] - '0';
position++;
}
mMol.setAtomCharge(baseAtom[bracketLevel], charge);
continue;
}
if (theChar == '-') {
if (!squareBracketOpen)
continue; // single bond
int charge = -1;
while (smiles[position] == '-') {
charge--;
position++;
}
if (charge == -1 && Character.isDigit(smiles[position])) {
charge = '0' - smiles[position];
position++;
}
mMol.setAtomCharge(baseAtom[bracketLevel], charge);
continue;
}
if (theChar == '(') {
if (baseAtom[bracketLevel] == -1)
throw new Exception("Smiles with leading parenthesis are not supported");
baseAtom[bracketLevel+1] = baseAtom[bracketLevel];
bracketLevel++;
continue;
}
if (theChar == ')') {
bracketLevel--;
continue;
}
if (theChar == '[') {
if (squareBracketOpen)
throw new Exception("SmilesParser: nested square brackets found");
squareBracketOpen = true;
continue;
}
if (theChar == ']') {
if (!squareBracketOpen)
throw new Exception("SmilesParser: closing bracket without opening one");
squareBracketOpen = false;
continue;
}
if (theChar == '%') {
percentFound = true;
continue;
}
/* if (theChar == '.') {
if (bracketLevel != 0)
throw new Exception("SmilesParser: '.' found within brackets");
baseAtom[0] = -1;
// for (int i=0; i=4; qualifyingNo--) {
do {
qualifyingBondFound = false;
for (int bond=0; bond= 2)
if (!connectConjugatedRadicalPairs(isAromaticBond))
break;
if (mAromaticAtoms != 0)
throw new Exception("Assignment of aromatic double bonds failed");
if (mAromaticBonds != 0)
throw new Exception("Assignment of aromatic double bonds failed");
}
private boolean connectConjugatedRadicalPairs(boolean[] isAromaticBond) {
for (int atom=0; atom 3
&& mMol.getAtomPi(atom) > 0) {
for (int i=0; i 1)
&& mMol.isElectronegative(connAtom)) {
if (mMol.getBondType(connBond) == Molecule.cBondTypeTriple)
mMol.setBondType(connBond, Molecule.cBondTypeDouble);
else
mMol.setBondType(connBond, Molecule.cBondTypeSingle);
mMol.setAtomCharge(atom, mMol.getAtomCharge(atom) + 1);
mMol.setAtomCharge(connAtom, mMol.getAtomCharge(connAtom) - 1);
break;
}
}
}
}
}
private boolean assignKnownEZBondParities() {
mMol.ensureHelperArrays(Molecule.cHelperRings);
boolean paritiesFound = false;
int[] refAtom = new int[2];
int[] refBond = new int[2];
int[] otherAtom = new int[2];
for (int bond=0; bond mNeighborPosition[i]) {
minPosition = mNeighborPosition[i];
minIndex = i;
}
}
mFromAtom = mNeighborAtom[minIndex];
for (int i=minIndex+1; i 4 || totalNeighborCount < 3)
return Molecule.cAtomParityUnknown;
// We look from the hydrogen towards the central carbon if the fromAtom is a hydrogen or
// if there is no fromAtom but the central atom has an implicit hydrogen.
boolean fromAtomIsHydrogen = (mFromAtom == -1 && mImplicitHydrogen == 1)
|| (mFromAtom != -1 && mMol.isSimpleHydrogen(mFromAtom));
int hydrogenNeighborIndex = -1;
for (int i=0; i atom[i])
inversion = !inversion;
if (position[j] > position[i])
inversion = !inversion;
}
}
return inversion;
}
}
private static void testStereo() {
final String[][] data = { { "F/C=C/I", "F/C=C/I" },
{ "F/C=C\\I", "F/C=C\\I" },
{ "C(=C/I)/F", "F/C=C\\I" },
{ "[H]C(/F)=C/I", "F/C=C\\I" },
{ "C(=C\\1)/I.F1", "F/C=C/I" },
{ "C(=C1)/I.F/1", "F/C=C/I" },
{ "C(=C\\F)/1.I1", "F/C=C/I" },
{ "C(=C\\F)1.I\\1", "F/C=C/I" },
{ "C\\1=C/I.F1", "F/C=C/I" },
{ "C1=C/I.F/1", "F/C=C/I" },
{ "C(=C\\1)/2.F1.I2", "F/C=C/I" },
{ "C/2=C\\1.F1.I2", "F/C=C/I" },
{ "C/1=C/C=C/F.I1", "F/C=C/C=C\\I" },
{ "C1=C/C=C/F.I\\1", "F/C=C/C=C\\I" },
{ "C(/I)=C/C=C/1.F1", "F/C=C/C=C\\I" },
{ "C(/I)=C/C=C1.F\\1", "F/C=C/C=C\\I" },
{ "[C@](Cl)(F)(I)1.Br1", "F[C@](Cl)(Br)I" },
{ "Br[C@](Cl)(I)1.F1", "F[C@](Cl)(Br)I" },
{ "[C@H](F)(I)1.Br1", "F[C@H](Br)I" },
{ "Br[C@@H](F)1.I1", "F[C@H](Br)I" } };
StereoMolecule mol = new StereoMolecule();
for (String[] test:data) {
try {
new SmilesParser().parse(mol, test[0]);
String smiles = new IsomericSmilesCreator(mol).getSmiles();
System.out.print(test[0]+" "+smiles);
if (!test[1].equals(smiles))
System.out.println(" should be: "+test[1]);
else
System.out.println(" OK");
}
catch (Exception e) {
if (!test[2].equals("error"))
System.out.println("ERROR! "+test[1]+" smiles:"+test[0]+" exception:"+e.getMessage());
}
}
}
public static void main(String[] args) {
testStereo();
System.out.println("ID-code equivalence test:");
final String[][] data = { { "N[C@@]([H])(C)C(=O)O", "S-alanine", "gGX`BDdwMUM@@" },
{ "N[C@@H](C)C(=O)O", "S-alanine", "gGX`BDdwMUM@@" },
{ "N[C@H](C(=O)O)C", "S-alanine", "gGX`BDdwMUM@@" },
{ "[H][C@](N)(C)C(=O)O", "S-alanine", "gGX`BDdwMUM@@" },
{ "[C@H](N)(C)C(=O)O", "S-alanine", "gGX`BDdwMUM@@" },
{ "N[C@]([H])(C)C(=O)O", "R-alanine", "gGX`BDdwMUL`@" },
{ "N[C@H](C)C(=O)O", "R-alanine", "gGX`BDdwMUL`@" },
{ "N[C@@H](C(=O)O)C", "R-alanine", "gGX`BDdwMUL`@" },
{ "[H][C@@](N)(C)C(=O)O", "R-alanine", "gGX`BDdwMUL`@" },
{ "[C@@H](N)(C)C(=O)O", "R-alanine", "gGX`BDdwMUL`@" },
{ "C[C@H]1CCCCO1", "S-Methyl-pyran", "gOq@@eLm]UUH`@" },
{ "O1CCCC[C@@H]1C", "S-Methyl-pyran", "gOq@@eLm]UUH`@" },
{ "[C@H](F)(B)O", "S-Methyl-oxetan", "gCaDDICTBSURH@" },
{ "C1CO[C@H]1C", "S-Methyl-oxetan", "gKQ@@eLmUTb@" },
{ "C1CO[C@@H](C)1", "S-Methyl-oxetan", "gKQ@@eLmUTb@" },
{ "[C@H]1(C)CCO1", "S-Methyl-oxetan", "gKQ@@eLmUTb@" },
{ "[H][C@]1(C)CCO1", "S-Methyl-oxetan", "gKQ@@eLmUTb@" },
{ "[H][C@@]1(CCO1)C", "S-Methyl-oxetan", "gKQ@@eLmUTb@" },
{ "[C@@]1([H])(C)CCO1", "S-Methyl-oxetan", "gKQ@@eLmUTb@" },
{ "[C@]1(C)([H])CCO1", "S-Methyl-oxetan", "gKQ@@eLmUTb@" },
{ "C1[C@@H]2COC2=N1", "oxetan-azetin", "gGy@LDimDvfja`@" },
{ "CC(C)[C@@]12C[C@@H]1[C@@H](C)C(=O)C2", "alpha-thujone", "dmLH@@RYe~IfyjjjkDaIh@" },
{ "CN1CCC[C@H]1c2cccnc2", "Nicotine", "dcm@@@{IDeCEDUSh@UUECP@" },
{ "CC[C@H](O1)CC[C@@]12CCCO2", "2S,5R-Chalcogran", "dmLD@@qJZY|fFZjjjdbH`@" },
{ "CCCC", "butane", "gC`@Dij@@" },
{ "C1C.CC1", "butane", "gC`@Dij@@" },
{ "[CH3][CH2][CH2][CH3]", "butane", "gC`@Dij@@" },
{ "C-C-C-C", "butane", "gC`@Dij@@" },
{ "C12.C1.CC2", "butane", "gC`@Dij@@" },
{ "[Na+].[Cl-]", "NaCl", "eDARHm@zd@@" },
{ "[Na+]-[Cl-]", "NaCl", "error" },
{ "[Na+]1.[Cl-]1", "NaCl", "error" },
{ "c1ccccc1", "benzene", "gFp@DiTt@@@" },
{ "C1=C-C=C-C=C1", "benzene", "gFp@DiTt@@@" },
{ "C1:C:C:C:C:C:1", "benzene", "gFp@DiTt@@@" },
{ "c1ccncc1", "pyridine", "gFx@@eJf`@@@" },
{ "[nH]1cccc1", "pyrrole", "gKX@@eKcRp@" },
{ "N1C=C-C=C1", "pyrrole", "gKX@@eKcRp@" },
{ "[H]n1cccc1", "pyrrole", "gKX@@eKcRp@" },
{ "[H]n1cccc1", "pyrrole", "gKX@@eKcRp@" },
{ "c1cncc1", "pyrrole no [nH]", "error" },
{ "[13CH4]", "C13-methane", "fH@FJp@" },
{ "[35ClH]", "35-chlorane", "fHdP@qX`" },
{ "[35Cl-]", "35-chloride", "fHtPxAbq@" },
{ "[Na+].[O-]c1ccccc1", "Na-phenolate", "daxHaHCPBXyAYUn`@@@" },
{ "c1cc([O-].[Na+])ccc1", "Na-phenolate", "daxHaHCPBXyAYUn`@@@" },
{ "C[C@@](C)(O1)C[C@@H](O)[C@@]1(O2)[C@@H](C)[C@@H]3CC=C4[C@]3(C2)C(=O)C[C@H]5[C@H]4CC[C@@H](C6)[C@]5(C)Cc(n7)c6nc(C[C@@]89(C))c7C[C@@H]8CC[C@@H]%10[C@@H]9C[C@@H](O)[C@@]%11(C)C%10=C[C@H](O%12)[C@]%11(O)[C@H](C)[C@]%12(O%13)[C@H](O)C[C@@]%13(C)CO",
"Cephalostatin-1",
"gdKe@h@@K`H@XjKHuYlnoP\\bbdRbbVTLbTrJbRaQRRRbTJTRTrfrfTTOBPHtFODPhLNSMdIERYJmShLfs]aqy|uUMUUUUUUE@UUUUMUUUUUUTQUUTPR`nDdQQKB|RIFbiQeARuQt`rSSMNtGS\\ct@@" },
};
StereoMolecule mol = new StereoMolecule();
for (String[] test:data) {
try {
new SmilesParser().parse(mol, test[0]);
String idcode = new Canonizer(mol).getIDCode();
if (test[2].equals("error"))
System.out.println("Should create error! "+test[1]+" smiles:"+test[0]+" idcode:"+idcode);
else if (!test[2].equals(idcode))
System.out.println("ERROR! "+test[1]+" smiles:"+test[0]+" is:"+idcode+" must:"+test[2]);
}
catch (Exception e) {
if (!test[2].equals("error"))
System.out.println("ERROR! "+test[1]+" smiles:"+test[0]+" exception:"+e.getMessage());
}
}
}
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