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[Jmol-commits] SF.net SVN: jmol:[13019] trunk/Jmol
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From: <ha...@us...> - 2010-05-05 15:36:25
|
Revision: 13019
http://jmol.svn.sourceforge.net/jmol/?rev=13019&view=rev
Author: hansonr
Date: 2010-05-05 15:36:14 +0000 (Wed, 05 May 2010)
Log Message:
-----------
version=12.0.RC10_dev
# new feature: smiles/smarts/substructure with tetrahedral chirality
# select smarts("C[C@@]([C]=O)([CH])[CH2]")
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/script/ScriptMathProcessor.java
trunk/Jmol/src/org/jmol/smiles/SmilesAtom.java
trunk/Jmol/src/org/jmol/smiles/SmilesMatcher.java
trunk/Jmol/src/org/jmol/smiles/SmilesParser.java
trunk/Jmol/src/org/jmol/smiles/SmilesSearch.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/test/org/jmol/smiles/TestSmilesParser.java
Removed Paths:
-------------
trunk/Jmol/src/org/jmol/smiles/SmartsParser.java
Modified: trunk/Jmol/src/org/jmol/script/ScriptMathProcessor.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptMathProcessor.java 2010-05-05 06:34:14 UTC (rev 13018)
+++ trunk/Jmol/src/org/jmol/script/ScriptMathProcessor.java 2010-05-05 15:36:14 UTC (rev 13019)
@@ -2056,6 +2056,7 @@
matches[j] = Escape.escape(b[j]);
return matches;
} catch (Exception e) {
+ //e.printStackTrace();
eval.evalError(e.getMessage(), null);
return null; // unattainable
}
Deleted: trunk/Jmol/src/org/jmol/smiles/SmartsParser.java
===================================================================
--- trunk/Jmol/src/org/jmol/smiles/SmartsParser.java 2010-05-05 06:34:14 UTC (rev 13018)
+++ trunk/Jmol/src/org/jmol/smiles/SmartsParser.java 2010-05-05 15:36:14 UTC (rev 13019)
@@ -1,66 +0,0 @@
-/* $RCSfile$
- * $Author: hansonr $
- * $Date: 2010-05-04 07:53:26 -0500 (Tue, 04 May 2010) $
- * $Revision: 13011 $
- *
- * Copyright (C) 2005 The Jmol Development Team
- *
- * Contact: jmo...@li...
- *
- * This library is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public
- * License as published by the Free Software Foundation; either
- * version 2.1 of the License, or (at your option) any later version.
- *
- * This library 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
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this library; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
- */
-
-package org.jmol.smiles;
-
-/**
- * Parses a SMARTS String to create a <code>SmilesMolecule</code>.
- * The SMILES specification has been found at the
- * <a href="http://www.daylight.com/smiles/">SMILES Home Page</a>.
- * An other explanation can be found in the
- * <a href="http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html">Daylight Smarts Theory Manual</a>. <br>
- *
- * Currently this parser supports only parts of the SMARTS specification. <br>
- *
- * An example on how to use it:
- * <pre><code>
- * try {
- * SmartsParser sp = new SmartsParser();
- * SmilesMolecule sm = sp.parseSmarts("CC(C)C(=O)O");
- * // Use the resulting molecule
- * } catch (InvalidSmilesException e) {
- * // Exception management
- * }
- * </code></pre>
- *
- * @see <a href="http://www.daylight.com/smiles/">SMILES Home Page</a>
- */
-public class SmartsParser extends SmilesParser {
-
- public static SmilesSearch getMolecule(String smarts) throws InvalidSmilesException {
- return (new SmartsParser()).parse(smarts);
- }
-
- /**
- * Parses a SMARTS String
- *
- * @param smarts SMILES String
- * @return Molecule corresponding to <code>smiles</code>
- * @throws InvalidSmilesException
- */
- SmilesSearch parse(String smarts) throws InvalidSmilesException {
- isSmarts = true;
- return super.parse(smarts);
- }
-}
Modified: trunk/Jmol/src/org/jmol/smiles/SmilesAtom.java
===================================================================
--- trunk/Jmol/src/org/jmol/smiles/SmilesAtom.java 2010-05-05 06:34:14 UTC (rev 13018)
+++ trunk/Jmol/src/org/jmol/smiles/SmilesAtom.java 2010-05-05 15:36:14 UTC (rev 13019)
@@ -55,49 +55,45 @@
}
/**
- * Creates missing hydrogen atoms in a <code>SmilesMolecule</code>.
+ * Finalizes the hydrogen count for implicit hydrogens in a <code>SmilesMolecule</code>.
*
* @param molecule Molecule containing the atom.
+ * @return false if inappropriate
*/
- public void createMissingHydrogen(SmilesSearch molecule) {
- // Determining max count
+ public boolean setHydrogenCount(SmilesSearch molecule) {
+ if (hydrogenCount != Integer.MIN_VALUE)
+ return true;
+ // Determining max count
int count = 0;
- if (hydrogenCount == Integer.MIN_VALUE) {
// not a complete set...
// B, C, N, O, P, S, F, Cl, Br, and I
// B (3), C (4), N (3,5), O (2), P (3,5), S (2,4,6), and 1 for the halogens
switch (atomicNumber) {
- case -1:
- break;
- case 5: // B
- count = 3;
- break;
+ default:
+ return false;
+ case 0:
+ return true;
case 6: // C
count = (isAromatic ? 3 : 4);
break;
case 8: // O
- count = 2;
- break;
- case 7: // N
- count = 3;
- break;
case 16: // S
count = 2;
break;
+ case 5: // B
+ case 7: // N
case 15: // P
count = 3;
break;
case 9: // F
case 17: // Cl
case 35: // Br
- case 85: // I
+ case 53: // I
count = 1;
break;
}
-
- //System.out.println(" assigning " + count + " valence to atom " + number + " " + atomicNumber);
-
+
for (int i = 0; i < bondsCount; i++) {
SmilesBond bond = bonds[i];
switch (bond.getBondType()) {
@@ -114,19 +110,10 @@
break;
}
}
- } else {
- count = Math.abs(hydrogenCount);
- hydrogenCount = Integer.MIN_VALUE;
- }
-
-
- // Adding hydrogens
- //System.out.println(" adding " + count + " H atoms to atom " + index);
- for (int i = 0; i < count; i++) {
- SmilesAtom hydrogen = molecule.createAtom();
- hydrogen.setAtomicNumber((short) 1);
- molecule.createBond(this, hydrogen, SmilesBond.TYPE_SINGLE);
- }
+
+ if (count > 0)
+ hydrogenCount = count;
+ return true;
}
/**
@@ -174,10 +161,6 @@
return atomicNumber;
}
- private void setAtomicNumber(short i) {
- atomicNumber = i;
- }
-
/**
* Returns the atomic mass of the atom.
*
@@ -242,7 +225,7 @@
final static int CHIRALITY_SQUARE_PLANAR = 8;
static int getChiralityClass(String xx) {
- return (" ;AL;OH;SP;TH;TP".indexOf(xx) + 1)/ 3;
+ return ("0;11;AL;33;TH;TP;OC;77;SP;".indexOf(xx) + 1)/ 3;
}
/**
@@ -343,4 +326,5 @@
return (b.getAtom1() == this ? b.getAtom2() : b.getAtom1()).matchingAtom;
}
+
}
Modified: trunk/Jmol/src/org/jmol/smiles/SmilesMatcher.java
===================================================================
--- trunk/Jmol/src/org/jmol/smiles/SmilesMatcher.java 2010-05-05 06:34:14 UTC (rev 13018)
+++ trunk/Jmol/src/org/jmol/smiles/SmilesMatcher.java 2010-05-05 15:36:14 UTC (rev 13019)
@@ -93,7 +93,7 @@
BitSet[] list = null;
try {
// create a topological model set from smiles
- SmilesSearch search = (new SmilesParser()).parse(smiles);
+ SmilesSearch search = (new SmilesParser(false)).parse(smiles);
search.isAll = isAll;
int atomCount = search.patternAtomCount;
Atom[] atoms = new Atom[atomCount];
@@ -162,7 +162,7 @@
*/
public BitSet getSubstructureSet(String smiles, Atom[] atoms, int atomCount, boolean asSmarts, boolean isAll) throws Exception {
- SmilesSearch search = (asSmarts ? SmartsParser.getMolecule(smiles) : SmilesParser.getMolecule(smiles));
+ SmilesSearch search = SmilesParser.getMolecule(asSmarts, smiles);
search.jmolAtoms = atoms;
search.jmolAtomCount = atomCount;
search.isAll = isAll;
@@ -187,7 +187,7 @@
BitSet bsSelected,
BitSet bsRequired, BitSet bsNot, boolean asSmarts, boolean isAll)
throws Exception {
- SmilesSearch search = (asSmarts ? SmartsParser.getMolecule(smiles) : SmilesParser.getMolecule(smiles));
+ SmilesSearch search = SmilesParser.getMolecule(asSmarts, smiles);
search.bsSelected = bsSelected;
search.bsRequired = (bsRequired != null && bsRequired.cardinality() > 0 ? bsRequired : null);
search.bsNot = bsNot;
Modified: trunk/Jmol/src/org/jmol/smiles/SmilesParser.java
===================================================================
--- trunk/Jmol/src/org/jmol/smiles/SmilesParser.java 2010-05-05 06:34:14 UTC (rev 13018)
+++ trunk/Jmol/src/org/jmol/smiles/SmilesParser.java 2010-05-05 15:36:14 UTC (rev 13019)
@@ -52,9 +52,13 @@
protected SmilesBond[] ringBonds;
- public static SmilesSearch getMolecule(String pattern) throws InvalidSmilesException {
- return (new SmilesParser()).parse(pattern);
+ public SmilesParser(boolean isSmarts) {
+ this.isSmarts = isSmarts;
}
+
+ public static SmilesSearch getMolecule(boolean isSmarts, String pattern) throws InvalidSmilesException {
+ return (new SmilesParser(isSmarts)).parse(pattern);
+ }
/**
* Parses a SMILES String
@@ -74,15 +78,17 @@
if (!isSmarts)
for (int i = molecule.patternAtomCount; --i >= 0; )
- molecule.getAtom(i).createMissingHydrogen(molecule);
-
- fixChirality(molecule);
+ if (!molecule.getAtom(i).setHydrogenCount(molecule))
+ throw new InvalidSmilesException("unbracketed atoms must be one of: B C N O P S F Cl Br I");
+
// Check for rings
if (ringBonds != null)
for (int i = 0; i < ringBonds.length; i++)
if (ringBonds[i] != null)
throw new InvalidSmilesException("Open ring");
+ fixChirality(molecule);
+
return molecule;
}
@@ -91,7 +97,7 @@
SmilesAtom sAtom = molecule.getAtom(i);
int chiralClass = sAtom.getChiralClass();
int nBonds = sAtom.getHydrogenCount();
- if (nBonds < 0)
+ if (nBonds < 0 || nBonds == Integer.MAX_VALUE)
nBonds = 0;
nBonds += sAtom.getBondsCount();
switch (chiralClass) {
@@ -125,29 +131,31 @@
/**
* Parses a part of a SMILES String
- *
- * @param molecule Resulting molecule
- * @param pattern SMILES String
- * @param currentAtom Current atom
+ *
+ * @param molecule
+ * Resulting molecule
+ * @param pattern
+ * SMILES String
+ * @param currentAtom
+ * Current atom
* @throws InvalidSmilesException
*/
- protected void parseSmiles(
- SmilesSearch molecule,
- String pattern,
- SmilesAtom currentAtom) throws InvalidSmilesException {
- if ((pattern == null) || (pattern.length() == 0)) {
+ protected void parseSmiles(SmilesSearch molecule, String pattern,
+ SmilesAtom currentAtom)
+ throws InvalidSmilesException {
+
+ if (pattern == null || pattern.length() == 0)
return;
- }
// Branching
int index = 0;
+ int len = pattern.length();
char ch = pattern.charAt(0);
if (ch == '(') {
index++;
int currentIndex = index;
int parenthesisCount = 1;
- while ((currentIndex < pattern.length()) &&
- (parenthesisCount > 0)) {
+ while ((currentIndex < len) && (parenthesisCount > 0)) {
switch (pattern.charAt(currentIndex)) {
case '(':
parenthesisCount++;
@@ -163,7 +171,7 @@
String subSmiles = pattern.substring(index, currentIndex - 1);
parseSmiles(molecule, subSmiles, currentAtom);
index = currentIndex;
- if (index >= pattern.length())
+ if (index >= len)
throw new InvalidSmilesException("Pattern must not end with ')'");
}
@@ -179,7 +187,7 @@
// Atom
ch = pattern.charAt(index);
- if ((ch >= '0') && (ch <= '9')) {
+ if (Character.isDigit(ch)) {
// Ring
String subSmiles = pattern.substring(index, index + 1);
parseRing(molecule, subSmiles, currentAtom, bondType);
@@ -191,11 +199,9 @@
throw new InvalidSmilesException("Ring number must follow the % sign");
}
int currentIndex = index;
- while ((currentIndex < pattern.length()) &&
- (pattern.charAt(currentIndex) >= '0') &&
- (pattern.charAt(currentIndex) <= '9')) {
+ while (currentIndex < len
+ && Character.isDigit(pattern.charAt(currentIndex)))
currentIndex++;
- }
String subSmiles = pattern.substring(index, currentIndex);
parseRing(molecule, subSmiles, currentAtom, bondType);
index = currentIndex;
@@ -203,41 +209,30 @@
// Atom definition
index++;
int currentIndex = index;
- while ((currentIndex < pattern.length()) &&
- (pattern.charAt(currentIndex) != ']')) {
+ while ((currentIndex < len) && (pattern.charAt(currentIndex) != ']')) {
currentIndex++;
}
- if (currentIndex >= pattern.length()) {
+ if (currentIndex >= len) {
throw new InvalidSmilesException("Unmatched [");
}
String subSmiles = pattern.substring(index, currentIndex);
currentAtom = parseAtom(molecule, subSmiles, currentAtom, bondType, true);
index = currentIndex + 1;
- } else if (((ch >= 'a') && (ch <= 'z')) ||
- ((ch >= 'A') && (ch <= 'Z')) ||
- (ch == '*')) {
+ } else if (ch == '*' || Character.isLetter(ch)) {
// Atom definition
- int size = 1;
- if (index + 1 < pattern.length()) {
- char secondChar = pattern.charAt(index + 1);
- if ((ch >= 'A') && (ch <= 'Z') &&
- (secondChar >= 'a') && (secondChar <= 'z')) {
- size = 2;
- }
- }
+ int size = (index + 1 < len
+ && Character.isLowerCase(pattern.charAt(index + 1)) ? 2 : 1);
String subSmiles = pattern.substring(index, index + size);
currentAtom = parseAtom(molecule, subSmiles, currentAtom, bondType, false);
index += size;
}
// Next part of the SMILES String
- if (index == 0) {
- throw new InvalidSmilesException("Unexpected character: " + pattern.charAt(0));
- }
- if (index < pattern.length()) {
- String subSmiles = pattern.substring(index);
- parseSmiles(molecule, subSmiles, currentAtom);
- }
+ if (index == 0)
+ throw new InvalidSmilesException("Unexpected character: "
+ + pattern.charAt(0));
+ if (index < len)
+ parseSmiles(molecule, pattern.substring(index), currentAtom);
}
/**
@@ -300,7 +295,6 @@
+ pattern.substring(index + 1, index + size)))
throw new InvalidSmilesException("Invalid atom symbol");
index += size;
-
checkHydrogenCount(complete, pattern, index, newAtom);
// Final check
@@ -318,31 +312,31 @@
// Hydrogen count
int hydrogenCount = Integer.MIN_VALUE;
int len = pattern.length();
- if (index >= len)
- return;
- char ch = pattern.charAt(index);
- if (ch == 'H' || isSmarts && ch == 'h') {
- index++;
- int pt = index;
- while (pt < len && Character.isDigit(pattern.charAt(pt)))
- pt++;
- if (pt > index) {
- try {
- hydrogenCount = Integer.parseInt(pattern.substring(index, pt));
- } catch (NumberFormatException e) {
- throw new InvalidSmilesException("Non numeric hydrogen count");
+ if (index < len) {
+ char ch = pattern.charAt(index);
+ if (ch == 'H' || isSmarts && ch == 'h') {
+ index++;
+ int pt = index;
+ while (pt < len && Character.isDigit(pattern.charAt(pt)))
+ pt++;
+ if (pt > index) {
+ try {
+ hydrogenCount = Integer.parseInt(pattern.substring(index, pt));
+ } catch (NumberFormatException e) {
+ throw new InvalidSmilesException("Non numeric hydrogen count");
+ }
+ } else {
+ hydrogenCount = 1;
}
- } else {
- hydrogenCount = 1;
+ index = pt;
}
- index = pt;
+ if (index < len)
+ throw new InvalidSmilesException(
+ "Unexpected characters after atom definition: "
+ + pattern.substring(index));
+ if (ch == 'h') // minimum count
+ hydrogenCount = -hydrogenCount;
}
- if (index < len)
- throw new InvalidSmilesException(
- "Unexpected characters after atom definition: "
- + pattern.substring(index));
- if (ch == 'h') // minimum count
- hydrogenCount = -hydrogenCount;
if (hydrogenCount == Integer.MIN_VALUE && complete)
hydrogenCount = Integer.MAX_VALUE;
newAtom.setHydrogenCount(hydrogenCount);
Modified: trunk/Jmol/src/org/jmol/smiles/SmilesSearch.java
===================================================================
--- trunk/Jmol/src/org/jmol/smiles/SmilesSearch.java 2010-05-05 06:34:14 UTC (rev 13018)
+++ trunk/Jmol/src/org/jmol/smiles/SmilesSearch.java 2010-05-05 15:36:14 UTC (rev 13019)
@@ -52,13 +52,13 @@
boolean isAll;
boolean isSmarts;
+
private final static int INITIAL_ATOMS = 16;
private SmilesAtom[] atoms = new SmilesAtom[INITIAL_ATOMS];
int patternAtomCount;
boolean asVector;
private Vector vReturn;
private BitSet bsReturn = new BitSet();
-
/* ============================================================= */
/* Atoms */
@@ -312,8 +312,15 @@
if (!checkChirality())
return true;
BitSet bs = new BitSet();
- for (int k = 0; k < patternAtomCount; k++)
- bs.set(atoms[k].getMatchingAtom());
+ for (int k = 0; k < patternAtomCount; k++) {
+ int iAtom = atoms[k].getMatchingAtom();
+ bs.set(iAtom);
+ if (!isSmarts) {
+ npH = atoms[k].getHydrogenCount();
+ if (npH != Integer.MIN_VALUE && npH != Integer.MAX_VALUE)
+ getHydrogens(jmolAtoms[iAtom], bs);
+ }
+ }
if (bsRequired != null && !bsRequired.intersects(bs))
return true;
if (asVector) {
@@ -358,11 +365,7 @@
atom1 = jmolAtoms[sAtom.getMatchingBondedAtom(0)];
break;
case 1:
- Atom atom = jmolAtoms[sAtom.getMatchingAtom()];
- Bond[] b = atom.getBonds();
- for (int i = 0; i < b.length; i++)
- if ((atom = jmolAtoms[atom.getBondedAtomIndex(i)]).getElementNumber() == 1)
- break;
+ atom1 = getHydrogens(jmolAtoms[sAtom.getMatchingAtom()], null);
break;
default:
continue;
@@ -380,7 +383,20 @@
return true;
}
-
+ private Atom getHydrogens(Atom atom, BitSet bsHydrogens) {
+ Bond[] b = atom.getBonds();
+ Atom atomH = null;
+ for (int k = 0, i = 0; i < b.length; i++)
+ if ((atomH = jmolAtoms[k = atom.getBondedAtomIndex(i)]).getElementNumber() == 1) {
+ if (bsHydrogens == null)
+ break;
+ bsHydrogens.set(k);
+ }
+ return atomH;
+ }
+
+
+
Vector3f vTemp = new Vector3f();
Vector3f vA = new Vector3f();
Vector3f vB = new Vector3f();
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2010-05-05 06:34:14 UTC (rev 13018)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2010-05-05 15:36:14 UTC (rev 13019)
@@ -3,6 +3,8 @@
version=12.0.RC10_dev
+# code: Smiles refactoring and efficiencies
+# new feature: "smarts" does not include attached hydrogens in match
# new feature: smiles/smarts/substructure with tetrahedral chirality
# select smarts("C[C@@]([C]=O)([CH])[CH2]")
@@ -15,7 +17,6 @@
# new feature: JME data saved in variable "jmeString" for later generation of 2D data
# new feature: "smilesString".find("SMILES","smilesString" [, isAll (FALSE)] )
-# code: Smiles refactoring and efficiencies
# bug fix: SMILES parser not properly checking explicit double bond check
# new feature: SMILES matching expanded to aromatic types
# bug fix: Spartan reader (compound document) misread# code: frequency reading standardized -- using auxiliaryInfo.modelProperties more effectively
Modified: trunk/Jmol/test/org/jmol/smiles/TestSmilesParser.java
===================================================================
--- trunk/Jmol/test/org/jmol/smiles/TestSmilesParser.java 2010-05-05 06:34:14 UTC (rev 13018)
+++ trunk/Jmol/test/org/jmol/smiles/TestSmilesParser.java 2010-05-05 15:36:14 UTC (rev 13019)
@@ -259,7 +259,7 @@
SmilesAtom atomN = molecule.createAtom();
atomN.setSymbol("N");
SmilesAtom atomC1 = molecule.createAtom();
- atomC1.setChiralClass("");
+ atomC1.setChiralClass(SmilesAtom.CHIRALITY_TETRAHEDRAL);
atomC1.setChiralOrder(2);
atomC1.setSymbol("C");
molecule.createBond(atomN, atomC1, SmilesBond.TYPE_SINGLE);
@@ -289,7 +289,7 @@
SmilesAtom atomO1 = molecule.createAtom();
atomO1.setSymbol("O");
SmilesAtom atomC1 = molecule.createAtom();
- atomC1.setChiralClass("");
+ atomC1.setChiralClass(SmilesAtom.CHIRALITY_TETRAHEDRAL);
atomC1.setChiralOrder(1);
atomC1.setSymbol("C");
molecule.createBond(atomO1, atomC1, SmilesBond.TYPE_SINGLE);
@@ -307,7 +307,7 @@
atomC5.setSymbol("C");
molecule.createBond(atomC4, atomC5, SmilesBond.TYPE_SINGLE);
SmilesAtom atomC6 = molecule.createAtom();
- atomC6.setChiralClass("");
+ atomC6.setChiralClass(SmilesAtom.CHIRALITY_TETRAHEDRAL);
atomC6.setChiralOrder(1);
atomC6.setSymbol("C");
molecule.createBond(atomC5, atomC6, SmilesBond.TYPE_SINGLE);
@@ -1041,7 +1041,7 @@
SmilesAtom atomN = molecule.createAtom();
atomN.setSymbol("N");
SmilesAtom atomC1 = molecule.createAtom();
- atomC1.setChiralClass("");
+ atomC1.setChiralClass(SmilesAtom.CHIRALITY_TETRAHEDRAL);
atomC1.setChiralOrder(1);
atomC1.setSymbol("C");
molecule.createBond(atomN, atomC1, SmilesBond.TYPE_SINGLE);
@@ -1078,7 +1078,7 @@
atomC2.setSymbol("C");
molecule.createBond(atomC1, atomC2, SmilesBond.TYPE_SINGLE);
SmilesAtom atomC3 = molecule.createAtom();
- atomC3.setChiralClass("");
+ atomC3.setChiralClass(SmilesAtom.CHIRALITY_TETRAHEDRAL);
atomC3.setChiralOrder(1);
atomC3.setSymbol("C");
molecule.createBond(atomC2, atomC3, SmilesBond.TYPE_SINGLE);
@@ -1096,7 +1096,7 @@
atomC7.setSymbol("C");
molecule.createBond(atomC6, atomC7, SmilesBond.TYPE_SINGLE);
SmilesAtom atomC8 = molecule.createAtom();
- atomC8.setChiralClass("");
+ atomC8.setChiralClass(SmilesAtom.CHIRALITY_TETRAHEDRAL);
atomC8.setChiralOrder(1);
atomC8.setSymbol("C");
molecule.createBond(atomC7, atomC8, SmilesBond.TYPE_SINGLE);
@@ -1141,7 +1141,7 @@
atomCl.setSymbol("Cl");
molecule.createBond(atomC1, atomCl, SmilesBond.TYPE_SINGLE);
SmilesAtom atomC2 = molecule.createAtom();
- atomC2.setChiralClass("");
+ atomC2.setChiralClass(SmilesAtom.CHIRALITY_ALLENE);
atomC2.setChiralOrder(1);
atomC2.setSymbol("C");
molecule.createBond(atomC1, atomC2, SmilesBond.TYPE_DOUBLE);
@@ -1171,7 +1171,7 @@
atomCl.setSymbol("Cl");
molecule.createBond(atomC1, atomCl, SmilesBond.TYPE_SINGLE);
SmilesAtom atomC2 = molecule.createAtom();
- atomC2.setChiralClass("AL");
+ atomC2.setChiralClass(SmilesAtom.CHIRALITY_ALLENE);
atomC2.setChiralOrder(1);
atomC2.setSymbol("C");
molecule.createBond(atomC1, atomC2, SmilesBond.TYPE_DOUBLE);
@@ -1195,7 +1195,7 @@
SmilesAtom atomF = molecule.createAtom();
atomF.setSymbol("F");
SmilesAtom atomPo = molecule.createAtom();
- atomPo.setChiralClass("SP");
+ atomPo.setChiralClass(SmilesAtom.CHIRALITY_SQUARE_PLANAR);
atomPo.setChiralOrder(1);
atomPo.setSymbol("Po");
molecule.createBond(atomF, atomPo, SmilesBond.TYPE_SINGLE);
@@ -1218,7 +1218,7 @@
atomC.setSymbol("C");
molecule.createBond(atomO, atomC, SmilesBond.TYPE_DOUBLE);
SmilesAtom atomAs = molecule.createAtom();
- atomAs.setChiralClass("");
+ atomAs.setChiralClass(SmilesAtom.CHIRALITY_TRIGONAL_BIPYRAMIDAL);
atomAs.setChiralOrder(1);
atomAs.setSymbol("As");
molecule.createBond(atomC, atomAs, SmilesBond.TYPE_SINGLE);
@@ -1246,7 +1246,7 @@
atomC.setSymbol("C");
molecule.createBond(atomO, atomC, SmilesBond.TYPE_DOUBLE);
SmilesAtom atomCo = molecule.createAtom();
- atomCo.setChiralClass("");
+ atomCo.setChiralClass(SmilesAtom.CHIRALITY_OCTAHEDRAL);
atomCo.setChiralOrder(1);
atomCo.setSymbol("Co");
molecule.createBond(atomC, atomCo, SmilesBond.TYPE_SINGLE);
@@ -1278,7 +1278,7 @@
*/
private static void checkMolecule(String smiles, SmilesSearch expected) {
try {
- SmilesSearch molecule = SmilesParser.getMolecule(smiles);
+ SmilesSearch molecule = SmilesParser.getMolecule(false, smiles);
assertTrue(areMoleculesEqual(molecule, expected));
} catch (InvalidSmilesException e) {
fail("InvalidSmilesException: " + e.getMessage());
@@ -1292,6 +1292,8 @@
* @param bonded Other atom to bond to
*/
private void addHydrogen(SmilesSearch molecule, SmilesAtom bonded) {
+ if (true)
+ return;
SmilesAtom atomH = molecule.createAtom();
atomH.setSymbol("H");
if (bonded != null) {
@@ -1379,15 +1381,7 @@
atom2.getCharge() + ")");
return false;
}
- if (atom1.getChiralClass() == null) {
- if (atom2.getChiralClass() != null) {
- Logger.error(
- "Atom " + i + " chiral class (" +
- atom1.getChiralClass() + "," +
- atom2.getChiralClass() + ")");
- return false;
- }
- } else if (!atom1.getChiralClass().equals(atom2.getChiralClass())) {
+ if (atom1.getChiralClass() != atom2.getChiralClass()) {
Logger.error(
"Atom " + i + " chiral class (" +
atom1.getChiralClass() + "," +
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