From c30256c6f52451e0472555220dad57e55ef7015b Mon Sep 17 00:00:00 2001 From: John May Date: Sun, 16 Oct 2016 12:04:22 +0100 Subject: [PATCH 01/16] Improved API for atom creation. --- .../main/java/org/openscience/cdk/Atom.java | 155 +++++++++++++++- .../java/org/openscience/cdk/AtomTest.java | 86 +++++++++ .../java/org/openscience/cdk/silent/Atom.java | 171 +++++++++++++++++- .../org/openscience/cdk/silent/AtomTest.java | 85 +++++++++ 4 files changed, 482 insertions(+), 15 deletions(-) diff --git a/base/data/src/main/java/org/openscience/cdk/Atom.java b/base/data/src/main/java/org/openscience/cdk/Atom.java index 58c87d376b..5dd1389380 100644 --- a/base/data/src/main/java/org/openscience/cdk/Atom.java +++ b/base/data/src/main/java/org/openscience/cdk/Atom.java @@ -22,6 +22,7 @@ */ package org.openscience.cdk; +import org.openscience.cdk.config.Elements; import org.openscience.cdk.interfaces.IAtom; import org.openscience.cdk.interfaces.IElement; import org.openscience.cdk.tools.periodictable.PeriodicTable; @@ -113,15 +114,67 @@ public Atom() { } /** - * Constructs an Atom from a String containing an element symbol. + * Create a new atom with of the specified element. * - * @param elementSymbol The String describing the element for the Atom + * @param elem atomic number */ - public Atom(String elementSymbol) { - this(new Element(elementSymbol, PeriodicTable.getAtomicNumber(elementSymbol))); - this.formalCharge = 0; + public Atom(int elem) { + this(elem, 0, 0); } + /** + * Create a new atom with of the specified element and hydrogen count. + * + * @param elem atomic number + * @param hcnt hydrogen count + */ + public Atom(int elem, int hcnt) { + this(elem, hcnt, 0); + } + + /** + * Create a new atom with of the specified element, hydrogen count, and formal charge. + * + * @param elem atomic number + * @param hcnt hydrogen count + * @param fchg formal charge + */ + public Atom(int elem, int hcnt, int fchg) { + super((String)null); + setAtomicNumber(elem); + setSymbol(Elements.ofNumber(elem).symbol()); + setImplicitHydrogenCount(hcnt); + setFormalCharge(fchg); + } + + /** + * Constructs an Atom from a string containing an element symbol and optionally + * the atomic mass, hydrogen count, and formal charge. The symbol grammar allows + * easy construction from common symbols, for example: + * + * 
+     *     new Atom("NH+");   // nitrogen cation with one hydrogen
+     *     new Atom("OH");    // hydroxy
+     *     new Atom("O-");    // oxygen anion
+     *     new Atom("13CH3"); // methyl isotope 13
+     *
+ * + * 
+     *     atom := {mass}? {symbol} {hcnt}? {fchg}?
+     *     mass := \d+
+     *     hcnt := 'H' \d+
+     *     fchg := '+' \d+? | '-' \d+?
+     *
+ * + * @param symbol string with the element symbol + */ + public Atom(String symbol) { + super((String)null); + if (!parseAtomSymbol(this, symbol)) + throw new IllegalArgumentException("Cannot pass atom symbol: " + symbol); + } + + /** * Constructs an Atom from an Element and a Point3d. * @@ -452,4 +505,96 @@ public IAtom clone() throws CloneNotSupportedException { return (IAtom) clone; } + + private static boolean isUpper(char c) { + return c >= 'A' && c <= 'Z'; + } + + private static boolean isLower(char c) { + return c >= 'a' && c <= 'z'; + } + + private static boolean isDigit(char c) { + return c >= '0' && c <= '9'; + } + + private static boolean parseAtomSymbol(IAtom atom, String str) { + final int len = str.length(); + int pos = 0; + + int mass = -1; + int anum = 0; + int hcnt = 0; + int chg = 0; + + // optional mass + if (pos < len && isDigit(str.charAt(pos))) { + mass = (str.charAt(pos++) - '0'); + while (pos < len && isDigit(str.charAt(pos))) + mass = 10 * mass + (str.charAt(pos++) - '0'); + } + + // atom symbol + if (pos < len && isUpper(str.charAt(pos))) { + int beg = pos; + pos++; + while (pos < len && isLower(str.charAt(pos))) + pos++; + Elements elem = Elements.ofString(str.substring(beg, pos)); + if (elem == Elements.Unknown) + return false; + anum = elem.number(); + + // optional fields after atom symbol + while (pos < len) { + switch (str.charAt(pos)) { + case 'H': + pos++; + if (pos < len && isDigit(str.charAt(pos))) { + while (pos < len && isDigit(str.charAt(pos))) + hcnt = 10 * hcnt + (str.charAt(pos++) - '0'); + } else { + hcnt = 1; + } + break; + case '+': + pos++; + if (pos < len && isDigit(str.charAt(pos))) { + chg = (str.charAt(pos++) - '0'); + while (pos < len && isDigit(str.charAt(pos))) + chg = 10 * chg + (str.charAt(pos++) - '0'); + } else { + chg = +1; + } + break; + case '-': + pos++; + if (pos < len && isDigit(str.charAt(pos))) { + chg = (str.charAt(pos++) - '0'); + while (pos < len && isDigit(str.charAt(pos))) + chg = 10 * chg + (str.charAt(pos++) - '0'); + chg *= -1; + } else { + chg = -1; + } + break; + default: + return false; + } + } + } else { + return false; + } + + if (mass < 0) + atom.setMassNumber(null); + else + atom.setMassNumber(mass); + atom.setAtomicNumber(anum); + atom.setSymbol(Elements.ofNumber(anum).symbol()); + atom.setImplicitHydrogenCount(hcnt); + atom.setFormalCharge(chg); + + return pos == len && len > 0; + } } diff --git a/base/data/src/test/java/org/openscience/cdk/AtomTest.java b/base/data/src/test/java/org/openscience/cdk/AtomTest.java index d8fb64f9e8..6a1542ed7f 100644 --- a/base/data/src/test/java/org/openscience/cdk/AtomTest.java +++ b/base/data/src/test/java/org/openscience/cdk/AtomTest.java @@ -77,6 +77,92 @@ public void testAtom_String() { Assert.assertNull(a.getFractionalPoint3d()); } + @Test + public void testAtom_NH4plus_direct() { + IAtom a = new Atom(7, 4, +1); + Assert.assertEquals("N", a.getSymbol()); + Assert.assertEquals((Integer) 7, a.getAtomicNumber()); + Assert.assertEquals((Integer) 4, a.getImplicitHydrogenCount()); + Assert.assertEquals((Integer) 1, a.getFormalCharge()); + Assert.assertNull(a.getPoint2d()); + Assert.assertNull(a.getPoint3d()); + Assert.assertNull(a.getFractionalPoint3d()); + } + + @Test + public void testAtom_CH3_direct() { + IAtom a = new Atom(6, 3); + Assert.assertEquals("C", a.getSymbol()); + Assert.assertEquals((Integer) 6, a.getAtomicNumber()); + Assert.assertEquals((Integer) 3, a.getImplicitHydrogenCount()); + Assert.assertEquals((Integer) 0, a.getFormalCharge()); + Assert.assertNull(a.getPoint2d()); + Assert.assertNull(a.getPoint3d()); + Assert.assertNull(a.getFractionalPoint3d()); + } + + @Test + public void testAtom_Cl_direct() { + IAtom a = new Atom(17); + Assert.assertEquals("Cl", a.getSymbol()); + Assert.assertEquals((Integer) 17, a.getAtomicNumber()); + Assert.assertEquals((Integer) 0, a.getImplicitHydrogenCount()); + Assert.assertEquals((Integer) 0, a.getFormalCharge()); + Assert.assertNull(a.getPoint2d()); + Assert.assertNull(a.getPoint3d()); + Assert.assertNull(a.getFractionalPoint3d()); + } + + @Test + public void testAtom_NH4plus() { + IAtom a = new Atom("NH4+"); + Assert.assertEquals("N", a.getSymbol()); + Assert.assertEquals((Integer) 7, a.getAtomicNumber()); + Assert.assertEquals((Integer) 4, a.getImplicitHydrogenCount()); + Assert.assertEquals((Integer) 1, a.getFormalCharge()); + Assert.assertNull(a.getPoint2d()); + Assert.assertNull(a.getPoint3d()); + Assert.assertNull(a.getFractionalPoint3d()); + } + + @Test + public void testAtom_Ominus() { + IAtom a = new Atom("O-"); + Assert.assertEquals("O", a.getSymbol()); + Assert.assertEquals((Integer) 8, a.getAtomicNumber()); + Assert.assertEquals((Integer) 0, a.getImplicitHydrogenCount()); + Assert.assertEquals(Integer.valueOf(-1), a.getFormalCharge()); + Assert.assertNull(a.getPoint2d()); + Assert.assertNull(a.getPoint3d()); + Assert.assertNull(a.getFractionalPoint3d()); + } + + @Test + public void testAtom_Ca2plus() { + IAtom a = new Atom("Ca+2"); + Assert.assertEquals("Ca", a.getSymbol()); + Assert.assertEquals((Integer) 20, a.getAtomicNumber()); + Assert.assertEquals((Integer) 0, a.getImplicitHydrogenCount()); + Assert.assertEquals(Integer.valueOf(+2), a.getFormalCharge()); + Assert.assertNull(a.getPoint2d()); + Assert.assertNull(a.getPoint3d()); + Assert.assertNull(a.getFractionalPoint3d()); + } + + @Test + public void testAtom_13CH3() { + IAtom a = new Atom("13CH3"); + Assert.assertEquals("C", a.getSymbol()); + Assert.assertEquals((Integer) 13, a.getMassNumber()); + Assert.assertEquals((Integer) 6, a.getAtomicNumber()); + Assert.assertEquals((Integer) 3, a.getImplicitHydrogenCount()); + Assert.assertEquals((Integer) 0, a.getFormalCharge()); + Assert.assertNull(a.getPoint2d()); + Assert.assertNull(a.getPoint3d()); + Assert.assertNull(a.getFractionalPoint3d()); + } + + /** * Method to test the Atom(String symbol, javax.vecmath.Point3d point3D) method. */ diff --git a/base/silent/src/main/java/org/openscience/cdk/silent/Atom.java b/base/silent/src/main/java/org/openscience/cdk/silent/Atom.java index ed4c5dd085..e31506d1f8 100644 --- a/base/silent/src/main/java/org/openscience/cdk/silent/Atom.java +++ b/base/silent/src/main/java/org/openscience/cdk/silent/Atom.java @@ -28,6 +28,7 @@ import javax.vecmath.Point3d; import org.openscience.cdk.CDKConstants; +import org.openscience.cdk.config.Elements; import org.openscience.cdk.interfaces.IAtom; import org.openscience.cdk.interfaces.IElement; import org.openscience.cdk.tools.periodictable.PeriodicTable; @@ -115,21 +116,72 @@ public Atom() { } /** - * Constructs an Atom from a String containing an element symbol. + * Create a new atom with of the specified element. * - * @param elementSymbol The String describing the element for the Atom + * @param elem atomic number */ - public Atom(String elementSymbol) { - this(new Element(elementSymbol, PeriodicTable.getAtomicNumber(elementSymbol))); - this.formalCharge = 0; + public Atom(int elem) { + this(elem, 0, 0); } /** - * Constructs an Atom from an Element and a Point3d. - * - * @param elementSymbol The symbol of the atom - * @param point3d The 3D coordinates of the atom - */ + * Create a new atom with of the specified element and hydrogen count. + * + * @param elem atomic number + * @param hcnt hydrogen count + */ + public Atom(int elem, int hcnt) { + this(elem, hcnt, 0); + } + + /** + * Create a new atom with of the specified element, hydrogen count, and formal charge. + * + * @param elem atomic number + * @param hcnt hydrogen count + * @param fchg formal charge + */ + public Atom(int elem, int hcnt, int fchg) { + super((String)null); + setAtomicNumber(elem); + setSymbol(Elements.ofNumber(elem).symbol()); + setImplicitHydrogenCount(hcnt); + setFormalCharge(fchg); + } + + /** + * Constructs an Atom from a string containing an element symbol and optionally + * the atomic mass, hydrogen count, and formal charge. The symbol grammar allows + * easy construction from common symbols, for example: + * + * 
+     *     new Atom("NH+");   // nitrogen cation with one hydrogen
+     *     new Atom("OH");    // hydroxy
+     *     new Atom("O-");    // oxygen anion
+     *     new Atom("13CH3"); // methyl isotope 13
+     *
+ * + * 
+     *     atom := {mass}? {symbol} {hcnt}? {fchg}?
+     *     mass := \d+
+     *     hcnt := 'H' \d+
+     *     fchg := '+' \d+? | '-' \d+?
+     *
+ * + * @param symbol string with the element symbol + */ + public Atom(String symbol) { + super((String)null); + if (!parseAtomSymbol(this, symbol)) + throw new IllegalArgumentException("Cannot pass atom symbol: " + symbol); + } + + /** + * Constructs an Atom from an Element and a Point3d. + * + * @param elementSymbol The symbol of the atom + * @param point3d The 3D coordinates of the atom + */ public Atom(String elementSymbol, Point3d point3d) { this(elementSymbol); this.point3d = point3d; @@ -448,4 +500,103 @@ public IAtom clone() throws CloneNotSupportedException { return (IAtom) clone; } + private static boolean isUpper(char c) { + return c >= 'A' && c <= 'Z'; + } + + private static boolean isLower(char c) { + return c >= 'a' && c <= 'z'; + } + + private static boolean isDigit(char c) { + return c >= '0' && c <= '9'; + } + + private static boolean parseAtomSymbol(IAtom atom, String str) { + + Elements elem = Elements.ofString(str); + if (elem != Elements.Unknown) { + atom.setAtomicNumber(elem.number()); + atom.setSymbol(elem.symbol()); + return true; + } + + final int len = str.length(); + int pos = 0; + + int mass = -1; + int anum = 0; + int hcnt = 0; + int chg = 0; + + // optional mass + if (pos < len && isDigit(str.charAt(pos))) { + mass = (str.charAt(pos++) - '0'); + while (pos < len && isDigit(str.charAt(pos))) + mass = 10 * mass + (str.charAt(pos++) - '0'); + } + + // atom symbol + if (pos < len && isUpper(str.charAt(pos))) { + int beg = pos; + pos++; + while (pos < len && isLower(str.charAt(pos))) + pos++; + elem = Elements.ofString(str.substring(beg, pos)); + if (elem == Elements.Unknown) + return false; + anum = elem.number(); + + // optional fields after atom symbol + while (pos < len) { + switch (str.charAt(pos)) { + case 'H': + pos++; + if (pos < len && isDigit(str.charAt(pos))) { + while (pos < len && isDigit(str.charAt(pos))) + hcnt = 10 * hcnt + (str.charAt(pos++) - '0'); + } else { + hcnt = 1; + } + break; + case '+': + pos++; + if (pos < len && isDigit(str.charAt(pos))) { + chg = (str.charAt(pos++) - '0'); + while (pos < len && isDigit(str.charAt(pos))) + chg = 10 * chg + (str.charAt(pos++) - '0'); + } else { + chg = +1; + } + break; + case '-': + pos++; + if (pos < len && isDigit(str.charAt(pos))) { + chg = (str.charAt(pos++) - '0'); + while (pos < len && isDigit(str.charAt(pos))) + chg = 10 * chg + (str.charAt(pos++) - '0'); + chg *= -1; + } else { + chg = -1; + } + break; + default: + return false; + } + } + } else { + return false; + } + + if (mass < 0) + atom.setMassNumber(null); + else + atom.setMassNumber(mass); + atom.setAtomicNumber(anum); + atom.setSymbol(Elements.ofNumber(anum).symbol()); + atom.setImplicitHydrogenCount(hcnt); + atom.setFormalCharge(chg); + + return pos == len && len > 0; + } } diff --git a/base/silent/src/test/java/org/openscience/cdk/silent/AtomTest.java b/base/silent/src/test/java/org/openscience/cdk/silent/AtomTest.java index abdfa1228d..92d9e93c0d 100644 --- a/base/silent/src/test/java/org/openscience/cdk/silent/AtomTest.java +++ b/base/silent/src/test/java/org/openscience/cdk/silent/AtomTest.java @@ -71,6 +71,91 @@ public void testAtom_String() { Assert.assertNull(a.getFractionalPoint3d()); } + @Test + public void testAtom_NH4plus_direct() { + IAtom a = new Atom(7, 4, +1); + Assert.assertEquals("N", a.getSymbol()); + Assert.assertEquals((Integer) 7, a.getAtomicNumber()); + Assert.assertEquals((Integer) 4, a.getImplicitHydrogenCount()); + Assert.assertEquals((Integer) 1, a.getFormalCharge()); + Assert.assertNull(a.getPoint2d()); + Assert.assertNull(a.getPoint3d()); + Assert.assertNull(a.getFractionalPoint3d()); + } + + @Test + public void testAtom_CH3_direct() { + IAtom a = new Atom(6, 3); + Assert.assertEquals("C", a.getSymbol()); + Assert.assertEquals((Integer) 6, a.getAtomicNumber()); + Assert.assertEquals((Integer) 3, a.getImplicitHydrogenCount()); + Assert.assertEquals((Integer) 0, a.getFormalCharge()); + Assert.assertNull(a.getPoint2d()); + Assert.assertNull(a.getPoint3d()); + Assert.assertNull(a.getFractionalPoint3d()); + } + + @Test + public void testAtom_Cl_direct() { + IAtom a = new Atom(17); + Assert.assertEquals("Cl", a.getSymbol()); + Assert.assertEquals((Integer) 17, a.getAtomicNumber()); + Assert.assertEquals((Integer) 0, a.getImplicitHydrogenCount()); + Assert.assertEquals((Integer) 0, a.getFormalCharge()); + Assert.assertNull(a.getPoint2d()); + Assert.assertNull(a.getPoint3d()); + Assert.assertNull(a.getFractionalPoint3d()); + } + + @Test + public void testAtom_NH4plus() { + IAtom a = new Atom("NH4+"); + Assert.assertEquals("N", a.getSymbol()); + Assert.assertEquals((Integer) 7, a.getAtomicNumber()); + Assert.assertEquals((Integer) 4, a.getImplicitHydrogenCount()); + Assert.assertEquals((Integer) 1, a.getFormalCharge()); + Assert.assertNull(a.getPoint2d()); + Assert.assertNull(a.getPoint3d()); + Assert.assertNull(a.getFractionalPoint3d()); + } + + @Test + public void testAtom_Ominus() { + IAtom a = new Atom("O-"); + Assert.assertEquals("O", a.getSymbol()); + Assert.assertEquals((Integer) 8, a.getAtomicNumber()); + Assert.assertEquals((Integer) 0, a.getImplicitHydrogenCount()); + Assert.assertEquals(Integer.valueOf(-1), a.getFormalCharge()); + Assert.assertNull(a.getPoint2d()); + Assert.assertNull(a.getPoint3d()); + Assert.assertNull(a.getFractionalPoint3d()); + } + + @Test + public void testAtom_Ca2plus() { + IAtom a = new Atom("Ca+2"); + Assert.assertEquals("Ca", a.getSymbol()); + Assert.assertEquals((Integer) 20, a.getAtomicNumber()); + Assert.assertEquals((Integer) 0, a.getImplicitHydrogenCount()); + Assert.assertEquals(Integer.valueOf(+2), a.getFormalCharge()); + Assert.assertNull(a.getPoint2d()); + Assert.assertNull(a.getPoint3d()); + Assert.assertNull(a.getFractionalPoint3d()); + } + + @Test + public void testAtom_13CH3() { + IAtom a = new Atom("13CH3"); + Assert.assertEquals("C", a.getSymbol()); + Assert.assertEquals((Integer) 13, a.getMassNumber()); + Assert.assertEquals((Integer) 6, a.getAtomicNumber()); + Assert.assertEquals((Integer) 3, a.getImplicitHydrogenCount()); + Assert.assertEquals((Integer) 0, a.getFormalCharge()); + Assert.assertNull(a.getPoint2d()); + Assert.assertNull(a.getPoint3d()); + Assert.assertNull(a.getFractionalPoint3d()); + } + @Test public void testAtom_String_Point3d() { Point3d point3d = new Point3d(1.0, 2.0, 3.0); From b3861ca1345db4207e4e615c71e78fc853a09a6f Mon Sep 17 00:00:00 2001 From: John May Date: Sun, 16 Oct 2016 18:15:11 +0100 Subject: [PATCH 02/16] Handle R atoms. --- base/data/src/main/java/org/openscience/cdk/Atom.java | 4 ++++ .../silent/src/main/java/org/openscience/cdk/silent/Atom.java | 4 ++++ 2 files changed, 8 insertions(+) diff --git a/base/data/src/main/java/org/openscience/cdk/Atom.java b/base/data/src/main/java/org/openscience/cdk/Atom.java index 5dd1389380..75e6518238 100644 --- a/base/data/src/main/java/org/openscience/cdk/Atom.java +++ b/base/data/src/main/java/org/openscience/cdk/Atom.java @@ -532,6 +532,10 @@ private static boolean parseAtomSymbol(IAtom atom, String str) { mass = (str.charAt(pos++) - '0'); while (pos < len && isDigit(str.charAt(pos))) mass = 10 * mass + (str.charAt(pos++) - '0'); + } else if ("R".equals(str)) { + atom.setAtomicNumber(0); + atom.setSymbol("R"); + return true; } // atom symbol diff --git a/base/silent/src/main/java/org/openscience/cdk/silent/Atom.java b/base/silent/src/main/java/org/openscience/cdk/silent/Atom.java index e31506d1f8..d599e9c48b 100644 --- a/base/silent/src/main/java/org/openscience/cdk/silent/Atom.java +++ b/base/silent/src/main/java/org/openscience/cdk/silent/Atom.java @@ -519,6 +519,10 @@ private static boolean parseAtomSymbol(IAtom atom, String str) { atom.setAtomicNumber(elem.number()); atom.setSymbol(elem.symbol()); return true; + } else if ("R".equals(str)) { + atom.setAtomicNumber(0); + atom.setSymbol("R"); + return true; } final int len = str.length(); From 65438a67315db005e544c9def32d611afd3ba1ac Mon Sep 17 00:00:00 2001 From: John May Date: Sun, 16 Oct 2016 18:15:30 +0100 Subject: [PATCH 03/16] Logger needs to be static - logging can happen in super class. --- .../src/main/java/org/openscience/cdk/debug/DebugAtom.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/base/datadebug/src/main/java/org/openscience/cdk/debug/DebugAtom.java b/base/datadebug/src/main/java/org/openscience/cdk/debug/DebugAtom.java index 2de7e8ec3e..66493b3b09 100644 --- a/base/datadebug/src/main/java/org/openscience/cdk/debug/DebugAtom.java +++ b/base/datadebug/src/main/java/org/openscience/cdk/debug/DebugAtom.java @@ -45,7 +45,7 @@ public class DebugAtom extends Atom implements IAtom { private static final long serialVersionUID = 188945429187084868L; - ILoggingTool logger = LoggingToolFactory.createLoggingTool(DebugAtom.class); + private static final ILoggingTool logger = LoggingToolFactory.createLoggingTool(DebugAtom.class); public DebugAtom() { super(); From dbc91c15a9eae4f3d2e681bfce25b5a72c7e73a0 Mon Sep 17 00:00:00 2001 From: John May Date: Sun, 16 Oct 2016 18:17:37 +0100 Subject: [PATCH 04/16] PDB atom semantics. --- .../src/main/java/org/openscience/cdk/protein/data/PDBAtom.java | 1 + .../src/main/java/org/openscience/cdk/silent/PDBAtom.java | 2 +- 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/base/data/src/main/java/org/openscience/cdk/protein/data/PDBAtom.java b/base/data/src/main/java/org/openscience/cdk/protein/data/PDBAtom.java index 997c433b23..221642035e 100644 --- a/base/data/src/main/java/org/openscience/cdk/protein/data/PDBAtom.java +++ b/base/data/src/main/java/org/openscience/cdk/protein/data/PDBAtom.java @@ -110,6 +110,7 @@ record = null; oxt = false; hetAtom = false; + super.hydrogenCount = null; super.charge = Double.valueOf(0.0); super.formalCharge = Integer.valueOf(0); } diff --git a/base/silent/src/main/java/org/openscience/cdk/silent/PDBAtom.java b/base/silent/src/main/java/org/openscience/cdk/silent/PDBAtom.java index 0127910d66..3085c361c2 100644 --- a/base/silent/src/main/java/org/openscience/cdk/silent/PDBAtom.java +++ b/base/silent/src/main/java/org/openscience/cdk/silent/PDBAtom.java @@ -108,7 +108,7 @@ record = null; oxt = false; hetAtom = false; - + super.hydrogenCount = null; super.charge = Double.valueOf(0.0); super.formalCharge = Integer.valueOf(0); } From 54d5de893bf13c8658bf59333997d0dc0c514d55 Mon Sep 17 00:00:00 2001 From: John May Date: Sun, 16 Oct 2016 18:20:02 +0100 Subject: [PATCH 05/16] These are not valid atom symbols. --- .../org/openscience/cdk/atomtype/CDKAtomTypeMatcherTest.java | 2 +- .../java/org/openscience/cdk/config/AtomTypeFactoryTest.java | 2 +- .../java/org/openscience/cdk/AbstractChemObjectBuilderTest.java | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/base/test-core/src/test/java/org/openscience/cdk/atomtype/CDKAtomTypeMatcherTest.java b/base/test-core/src/test/java/org/openscience/cdk/atomtype/CDKAtomTypeMatcherTest.java index 608619864c..6a75014964 100644 --- a/base/test-core/src/test/java/org/openscience/cdk/atomtype/CDKAtomTypeMatcherTest.java +++ b/base/test-core/src/test/java/org/openscience/cdk/atomtype/CDKAtomTypeMatcherTest.java @@ -124,7 +124,7 @@ public void testDummy() throws Exception { @Test public void testNonExistingType() throws Exception { IAtomContainer mol = new AtomContainer(); - IAtom atom = new Atom("Error"); + IAtom atom = new Atom(); mol.addAtom(atom); CDKAtomTypeMatcher matcher = CDKAtomTypeMatcher.getInstance(DefaultChemObjectBuilder.getInstance()); IAtomType type = matcher.findMatchingAtomType(mol, atom); diff --git a/base/test-core/src/test/java/org/openscience/cdk/config/AtomTypeFactoryTest.java b/base/test-core/src/test/java/org/openscience/cdk/config/AtomTypeFactoryTest.java index c35df280b8..3213e5a70a 100644 --- a/base/test-core/src/test/java/org/openscience/cdk/config/AtomTypeFactoryTest.java +++ b/base/test-core/src/test/java/org/openscience/cdk/config/AtomTypeFactoryTest.java @@ -235,7 +235,7 @@ public void testGetAtomTypeFromJmol() throws Exception { @Test public void testConfigure_IAtom() throws Exception { IAtomType atomType; - IAtom atom = new org.openscience.cdk.Atom("X"); + IAtom atom = new org.openscience.cdk.Atom(); atom.setAtomTypeName("C.ar"); AtomTypeFactory factory = AtomTypeFactory.getInstance("org/openscience/cdk/config/data/mol2_atomtypes.xml", new ChemObject().getBuilder()); diff --git a/base/test-interfaces/src/test/java/org/openscience/cdk/AbstractChemObjectBuilderTest.java b/base/test-interfaces/src/test/java/org/openscience/cdk/AbstractChemObjectBuilderTest.java index 0b6dfb36f8..40c65c28ab 100644 --- a/base/test-interfaces/src/test/java/org/openscience/cdk/AbstractChemObjectBuilderTest.java +++ b/base/test-interfaces/src/test/java/org/openscience/cdk/AbstractChemObjectBuilderTest.java @@ -495,7 +495,7 @@ public void testNewPseudoAtom_String_Point3d() { @Test public void testNewPDBAtom_String_Point3d() { IChemObjectBuilder builder = rootObject.getBuilder(); - IPDBAtom atom = builder.newInstance(IPDBAtom.class, "Foo", new Point3d(1, 2, 3)); + IPDBAtom atom = builder.newInstance(IPDBAtom.class, "C", new Point3d(1, 2, 3)); Assert.assertNotNull(atom); } From 07050d8966c1dda92d47fcc52ffce8c59e404b81 Mon Sep 17 00:00:00 2001 From: John May Date: Sun, 16 Oct 2016 18:21:29 +0100 Subject: [PATCH 06/16] Systematic errors with PDB code. Atom IDs being wrongly set as symbol, the pdb_atomtypes.xml shows the correct config. --- .../org/openscience/cdk/BioPolymerTest.java | 10 ++-- .../java/org/openscience/cdk/StrandTest.java | 10 ++-- .../cdk/protein/data/PDBPolymerTest.java | 14 +++--- .../cdk/silent/BioPolymerTest.java | 10 ++-- .../cdk/silent/PDBPolymerTest.java | 14 +++--- .../openscience/cdk/silent/StrandTest.java | 10 ++-- .../cdk/AbstractChemObjectBuilderTest.java | 4 +- .../interfaces/AbstractBioPolymerTest.java | 46 ++++++++--------- .../interfaces/AbstractPDBPolymerTest.java | 50 +++++++++---------- .../cdk/interfaces/AbstractPolymerTest.java | 34 ++++++------- .../cdk/interfaces/AbstractStrandTest.java | 32 ++++++------ 11 files changed, 117 insertions(+), 117 deletions(-) diff --git a/base/data/src/test/java/org/openscience/cdk/BioPolymerTest.java b/base/data/src/test/java/org/openscience/cdk/BioPolymerTest.java index 8a55618d09..2b2b26592d 100644 --- a/base/data/src/test/java/org/openscience/cdk/BioPolymerTest.java +++ b/base/data/src/test/java/org/openscience/cdk/BioPolymerTest.java @@ -66,11 +66,11 @@ public void testBioPolymer() { oMono2.setMonomerName(new String("HOH")); IMonomer oMono3 = oBioPolymer.getBuilder().newInstance(IMonomer.class); oMono3.setMonomerName(new String("GLYA16")); - IAtom oAtom1 = oBioPolymer.getBuilder().newInstance(IAtom.class, "C1"); - IAtom oAtom2 = oBioPolymer.getBuilder().newInstance(IAtom.class, "C2"); - IAtom oAtom3 = oBioPolymer.getBuilder().newInstance(IAtom.class, "C3"); - IAtom oAtom4 = oBioPolymer.getBuilder().newInstance(IAtom.class, "C4"); - IAtom oAtom5 = oBioPolymer.getBuilder().newInstance(IAtom.class, "C5"); + IAtom oAtom1 = oBioPolymer.getBuilder().newInstance(IAtom.class, "C"); + IAtom oAtom2 = oBioPolymer.getBuilder().newInstance(IAtom.class, "C"); + IAtom oAtom3 = oBioPolymer.getBuilder().newInstance(IAtom.class, "C"); + IAtom oAtom4 = oBioPolymer.getBuilder().newInstance(IAtom.class, "C"); + IAtom oAtom5 = oBioPolymer.getBuilder().newInstance(IAtom.class, "C"); oBioPolymer.addAtom(oAtom1); oBioPolymer.addAtom(oAtom2, oStrand1); diff --git a/base/data/src/test/java/org/openscience/cdk/StrandTest.java b/base/data/src/test/java/org/openscience/cdk/StrandTest.java index 3a009d4ac5..18c76ff030 100644 --- a/base/data/src/test/java/org/openscience/cdk/StrandTest.java +++ b/base/data/src/test/java/org/openscience/cdk/StrandTest.java @@ -64,11 +64,11 @@ public void testStrand() { oMono2.setMonomerName(new String("HOH")); IMonomer oMono3 = oStrand.getBuilder().newInstance(IMonomer.class); oMono3.setMonomerName(new String("GLYA16")); - IAtom oAtom1 = oStrand.getBuilder().newInstance(IAtom.class, "C1"); - IAtom oAtom2 = oStrand.getBuilder().newInstance(IAtom.class, "C2"); - IAtom oAtom3 = oStrand.getBuilder().newInstance(IAtom.class, "C3"); - IAtom oAtom4 = oStrand.getBuilder().newInstance(IAtom.class, "C4"); - IAtom oAtom5 = oStrand.getBuilder().newInstance(IAtom.class, "C5"); + IAtom oAtom1 = oStrand.getBuilder().newInstance(IAtom.class, "C"); + IAtom oAtom2 = oStrand.getBuilder().newInstance(IAtom.class, "C"); + IAtom oAtom3 = oStrand.getBuilder().newInstance(IAtom.class, "C"); + IAtom oAtom4 = oStrand.getBuilder().newInstance(IAtom.class, "C"); + IAtom oAtom5 = oStrand.getBuilder().newInstance(IAtom.class, "C"); oStrand.addAtom(oAtom1); oStrand.addAtom(oAtom2); diff --git a/base/data/src/test/java/org/openscience/cdk/protein/data/PDBPolymerTest.java b/base/data/src/test/java/org/openscience/cdk/protein/data/PDBPolymerTest.java index 21f57e7b9c..b0533aeadb 100644 --- a/base/data/src/test/java/org/openscience/cdk/protein/data/PDBPolymerTest.java +++ b/base/data/src/test/java/org/openscience/cdk/protein/data/PDBPolymerTest.java @@ -68,11 +68,11 @@ public void testPDBPolymer() { oMono2.setMonomerName(new String("HOH")); IMonomer oMono3 = pdbPolymer.getBuilder().newInstance(IMonomer.class); oMono3.setMonomerName(new String("GLYA16")); - IPDBAtom oPDBAtom1 = pdbPolymer.getBuilder().newInstance(IPDBAtom.class, "C1"); - IPDBAtom oPDBAtom2 = pdbPolymer.getBuilder().newInstance(IPDBAtom.class, "C2"); - IPDBAtom oPDBAtom3 = pdbPolymer.getBuilder().newInstance(IPDBAtom.class, "C3"); - IPDBAtom oPDBAtom4 = pdbPolymer.getBuilder().newInstance(IPDBAtom.class, "C4"); - IPDBAtom oPDBAtom5 = pdbPolymer.getBuilder().newInstance(IPDBAtom.class, "C5"); + IPDBAtom oPDBAtom1 = pdbPolymer.getBuilder().newInstance(IPDBAtom.class, "C"); + IPDBAtom oPDBAtom2 = pdbPolymer.getBuilder().newInstance(IPDBAtom.class, "C"); + IPDBAtom oPDBAtom3 = pdbPolymer.getBuilder().newInstance(IPDBAtom.class, "C"); + IPDBAtom oPDBAtom4 = pdbPolymer.getBuilder().newInstance(IPDBAtom.class, "C"); + IPDBAtom oPDBAtom5 = pdbPolymer.getBuilder().newInstance(IPDBAtom.class, "C"); pdbPolymer.addAtom(oPDBAtom1); pdbPolymer.addAtom(oPDBAtom2, oStrand1); @@ -117,8 +117,8 @@ public void testGetMonomerNamesInSequentialOrder() { oMono1.setMonomerName("TRP279"); IMonomer oMono2 = pdbPolymer.getBuilder().newInstance(IMonomer.class); oMono2.setMonomerName("CYS280"); - IPDBAtom oPDBAtom2 = pdbPolymer.getBuilder().newInstance(IPDBAtom.class, "C2"); - IPDBAtom oPDBAtom3 = pdbPolymer.getBuilder().newInstance(IPDBAtom.class, "C3"); + IPDBAtom oPDBAtom2 = pdbPolymer.getBuilder().newInstance(IPDBAtom.class, "C"); + IPDBAtom oPDBAtom3 = pdbPolymer.getBuilder().newInstance(IPDBAtom.class, "C"); pdbPolymer.addAtom(oPDBAtom2, oMono1, oStrand1); pdbPolymer.addAtom(oPDBAtom3, oMono2, oStrand1); Assert.assertNotNull(pdbPolymer.getAtom(0)); diff --git a/base/silent/src/test/java/org/openscience/cdk/silent/BioPolymerTest.java b/base/silent/src/test/java/org/openscience/cdk/silent/BioPolymerTest.java index ff95de07e8..23d106b183 100644 --- a/base/silent/src/test/java/org/openscience/cdk/silent/BioPolymerTest.java +++ b/base/silent/src/test/java/org/openscience/cdk/silent/BioPolymerTest.java @@ -64,11 +64,11 @@ public void testBioPolymer() { oMono2.setMonomerName(new String("HOH")); IMonomer oMono3 = oBioPolymer.getBuilder().newInstance(IMonomer.class); oMono3.setMonomerName(new String("GLYA16")); - IAtom oAtom1 = oBioPolymer.getBuilder().newInstance(IAtom.class, "C1"); - IAtom oAtom2 = oBioPolymer.getBuilder().newInstance(IAtom.class, "C2"); - IAtom oAtom3 = oBioPolymer.getBuilder().newInstance(IAtom.class, "C3"); - IAtom oAtom4 = oBioPolymer.getBuilder().newInstance(IAtom.class, "C4"); - IAtom oAtom5 = oBioPolymer.getBuilder().newInstance(IAtom.class, "C5"); + IAtom oAtom1 = oBioPolymer.getBuilder().newInstance(IAtom.class, "C"); + IAtom oAtom2 = oBioPolymer.getBuilder().newInstance(IAtom.class, "C"); + IAtom oAtom3 = oBioPolymer.getBuilder().newInstance(IAtom.class, "C"); + IAtom oAtom4 = oBioPolymer.getBuilder().newInstance(IAtom.class, "C"); + IAtom oAtom5 = oBioPolymer.getBuilder().newInstance(IAtom.class, "C"); oBioPolymer.addAtom(oAtom1); oBioPolymer.addAtom(oAtom2, oStrand1); diff --git a/base/silent/src/test/java/org/openscience/cdk/silent/PDBPolymerTest.java b/base/silent/src/test/java/org/openscience/cdk/silent/PDBPolymerTest.java index d95136bccb..0a423ff4ff 100644 --- a/base/silent/src/test/java/org/openscience/cdk/silent/PDBPolymerTest.java +++ b/base/silent/src/test/java/org/openscience/cdk/silent/PDBPolymerTest.java @@ -66,11 +66,11 @@ public void testPDBPolymer() { oMono2.setMonomerName(new String("HOH")); IMonomer oMono3 = pdbPolymer.getBuilder().newInstance(IMonomer.class); oMono3.setMonomerName(new String("GLYA16")); - IPDBAtom oPDBAtom1 = pdbPolymer.getBuilder().newInstance(IPDBAtom.class, "C1"); - IPDBAtom oPDBAtom2 = pdbPolymer.getBuilder().newInstance(IPDBAtom.class, "C2"); - IPDBAtom oPDBAtom3 = pdbPolymer.getBuilder().newInstance(IPDBAtom.class, "C3"); - IPDBAtom oPDBAtom4 = pdbPolymer.getBuilder().newInstance(IPDBAtom.class, "C4"); - IPDBAtom oPDBAtom5 = pdbPolymer.getBuilder().newInstance(IPDBAtom.class, "C5"); + IPDBAtom oPDBAtom1 = pdbPolymer.getBuilder().newInstance(IPDBAtom.class, "C"); + IPDBAtom oPDBAtom2 = pdbPolymer.getBuilder().newInstance(IPDBAtom.class, "C"); + IPDBAtom oPDBAtom3 = pdbPolymer.getBuilder().newInstance(IPDBAtom.class, "C"); + IPDBAtom oPDBAtom4 = pdbPolymer.getBuilder().newInstance(IPDBAtom.class, "C"); + IPDBAtom oPDBAtom5 = pdbPolymer.getBuilder().newInstance(IPDBAtom.class, "C"); pdbPolymer.addAtom(oPDBAtom1); pdbPolymer.addAtom(oPDBAtom2, oStrand1); @@ -115,8 +115,8 @@ public void testGetMonomerNamesInSequentialOrder() { oMono1.setMonomerName("TRP279"); IMonomer oMono2 = pdbPolymer.getBuilder().newInstance(IMonomer.class); oMono2.setMonomerName("CYS280"); - IPDBAtom oPDBAtom2 = pdbPolymer.getBuilder().newInstance(IPDBAtom.class, "C2"); - IPDBAtom oPDBAtom3 = pdbPolymer.getBuilder().newInstance(IPDBAtom.class, "C3"); + IPDBAtom oPDBAtom2 = pdbPolymer.getBuilder().newInstance(IPDBAtom.class, "C"); + IPDBAtom oPDBAtom3 = pdbPolymer.getBuilder().newInstance(IPDBAtom.class, "C"); pdbPolymer.addAtom(oPDBAtom2, oMono1, oStrand1); pdbPolymer.addAtom(oPDBAtom3, oMono2, oStrand1); Assert.assertNotNull(pdbPolymer.getAtom(0)); diff --git a/base/silent/src/test/java/org/openscience/cdk/silent/StrandTest.java b/base/silent/src/test/java/org/openscience/cdk/silent/StrandTest.java index e3f7cca65e..8124f77125 100644 --- a/base/silent/src/test/java/org/openscience/cdk/silent/StrandTest.java +++ b/base/silent/src/test/java/org/openscience/cdk/silent/StrandTest.java @@ -59,11 +59,11 @@ public void testStrand() { oMono2.setMonomerName(new String("HOH")); IMonomer oMono3 = oStrand.getBuilder().newInstance(IMonomer.class); oMono3.setMonomerName(new String("GLYA16")); - IAtom oAtom1 = oStrand.getBuilder().newInstance(IAtom.class, "C1"); - IAtom oAtom2 = oStrand.getBuilder().newInstance(IAtom.class, "C2"); - IAtom oAtom3 = oStrand.getBuilder().newInstance(IAtom.class, "C3"); - IAtom oAtom4 = oStrand.getBuilder().newInstance(IAtom.class, "C4"); - IAtom oAtom5 = oStrand.getBuilder().newInstance(IAtom.class, "C5"); + IAtom oAtom1 = oStrand.getBuilder().newInstance(IAtom.class, "C"); + IAtom oAtom2 = oStrand.getBuilder().newInstance(IAtom.class, "C"); + IAtom oAtom3 = oStrand.getBuilder().newInstance(IAtom.class, "C"); + IAtom oAtom4 = oStrand.getBuilder().newInstance(IAtom.class, "C"); + IAtom oAtom5 = oStrand.getBuilder().newInstance(IAtom.class, "C"); oStrand.addAtom(oAtom1); oStrand.addAtom(oAtom2); diff --git a/base/test-interfaces/src/test/java/org/openscience/cdk/AbstractChemObjectBuilderTest.java b/base/test-interfaces/src/test/java/org/openscience/cdk/AbstractChemObjectBuilderTest.java index 40c65c28ab..dca12cd38c 100644 --- a/base/test-interfaces/src/test/java/org/openscience/cdk/AbstractChemObjectBuilderTest.java +++ b/base/test-interfaces/src/test/java/org/openscience/cdk/AbstractChemObjectBuilderTest.java @@ -418,14 +418,14 @@ public void testNewPDBAtom_IElement() { @Test public void testNewPDBAtom_String() { IChemObjectBuilder builder = rootObject.getBuilder(); - IPDBAtom atom = builder.newInstance(IPDBAtom.class, "O.3"); + IPDBAtom atom = builder.newInstance(IPDBAtom.class, "O"); Assert.assertNotNull(atom); } @Test public void testNewPDBAtom_String_Point3D() { IChemObjectBuilder builder = rootObject.getBuilder(); - IPDBAtom atom = builder.newInstance(IPDBAtom.class, "O.3", new Point3d(1, 2, 3)); + IPDBAtom atom = builder.newInstance(IPDBAtom.class, "O", new Point3d(1, 2, 3)); Assert.assertNotNull(atom); } diff --git a/base/test-interfaces/src/test/java/org/openscience/cdk/interfaces/AbstractBioPolymerTest.java b/base/test-interfaces/src/test/java/org/openscience/cdk/interfaces/AbstractBioPolymerTest.java index d6ad4bf16f..0c9e068807 100644 --- a/base/test-interfaces/src/test/java/org/openscience/cdk/interfaces/AbstractBioPolymerTest.java +++ b/base/test-interfaces/src/test/java/org/openscience/cdk/interfaces/AbstractBioPolymerTest.java @@ -46,9 +46,9 @@ public void testGetMonomerCount() { oMono1.setMonomerName(new String("TRP279")); IMonomer oMono2 = oBioPolymer.getBuilder().newInstance(IMonomer.class); oMono2.setMonomerName(new String("HOH")); - IAtom oAtom1 = oBioPolymer.getBuilder().newInstance(IAtom.class, "C1"); - IAtom oAtom2 = oBioPolymer.getBuilder().newInstance(IAtom.class, "C2"); - IAtom oAtom3 = oBioPolymer.getBuilder().newInstance(IAtom.class, "C3"); + IAtom oAtom1 = oBioPolymer.getBuilder().newInstance(IAtom.class, "C"); + IAtom oAtom2 = oBioPolymer.getBuilder().newInstance(IAtom.class, "C"); + IAtom oAtom3 = oBioPolymer.getBuilder().newInstance(IAtom.class, "C"); oBioPolymer.addAtom(oAtom1); oBioPolymer.addAtom(oAtom2, oMono1, oStrand1); oBioPolymer.addAtom(oAtom3, oMono2, oStrand2); @@ -76,9 +76,9 @@ public void testGetMonomerNames() { oMono1.setMonomerName(new String("TRP279")); IMonomer oMono2 = oBioPolymer.getBuilder().newInstance(IMonomer.class); oMono2.setMonomerName(new String("HOH")); - IAtom oAtom1 = oBioPolymer.getBuilder().newInstance(IAtom.class, "C1"); - IAtom oAtom2 = oBioPolymer.getBuilder().newInstance(IAtom.class, "C2"); - IAtom oAtom3 = oBioPolymer.getBuilder().newInstance(IAtom.class, "C3"); + IAtom oAtom1 = oBioPolymer.getBuilder().newInstance(IAtom.class, "C"); + IAtom oAtom2 = oBioPolymer.getBuilder().newInstance(IAtom.class, "C"); + IAtom oAtom3 = oBioPolymer.getBuilder().newInstance(IAtom.class, "C"); oBioPolymer.addAtom(oAtom1); oBioPolymer.addAtom(oAtom2, oMono1, oStrand1); oBioPolymer.addAtom(oAtom3, oMono2, oStrand2); @@ -106,9 +106,9 @@ public void testGetMonomer_String_String() { oMono1.setMonomerName(new String("TRP279")); IMonomer oMono2 = oBioPolymer.getBuilder().newInstance(IMonomer.class); oMono2.setMonomerName(new String("HOH")); - IAtom oAtom1 = oBioPolymer.getBuilder().newInstance(IAtom.class, "C1"); - IAtom oAtom2 = oBioPolymer.getBuilder().newInstance(IAtom.class, "C2"); - IAtom oAtom3 = oBioPolymer.getBuilder().newInstance(IAtom.class, "C3"); + IAtom oAtom1 = oBioPolymer.getBuilder().newInstance(IAtom.class, "C"); + IAtom oAtom2 = oBioPolymer.getBuilder().newInstance(IAtom.class, "C"); + IAtom oAtom3 = oBioPolymer.getBuilder().newInstance(IAtom.class, "C"); oBioPolymer.addAtom(oAtom1, oMono1, oStrand1); oBioPolymer.addAtom(oAtom2, oMono1, oStrand1); oBioPolymer.addAtom(oAtom3, oMono2, oStrand2); @@ -122,8 +122,8 @@ public void testGetMonomer_String_String() { public void testAddAtom_IAtom() { IBioPolymer oBioPolymer = (IBioPolymer) newChemObject(); - IAtom oAtom1 = oBioPolymer.getBuilder().newInstance(IAtom.class, "C1"); - IAtom oAtom2 = oBioPolymer.getBuilder().newInstance(IAtom.class, "C2"); + IAtom oAtom1 = oBioPolymer.getBuilder().newInstance(IAtom.class, "C"); + IAtom oAtom2 = oBioPolymer.getBuilder().newInstance(IAtom.class, "C"); oBioPolymer.addAtom(oAtom1); oBioPolymer.addAtom(oAtom2); @@ -137,9 +137,9 @@ public void testAddAtom_IAtom_IStrand() { oStrand1.setStrandName("A"); IMonomer oMono1 = oBioPolymer.getBuilder().newInstance(IMonomer.class); oMono1.setMonomerName(new String("TRP279")); - IAtom oAtom1 = oBioPolymer.getBuilder().newInstance(IAtom.class, "C1"); - IAtom oAtom2 = oBioPolymer.getBuilder().newInstance(IAtom.class, "C2"); - IAtom oAtom3 = oBioPolymer.getBuilder().newInstance(IAtom.class, "C3"); + IAtom oAtom1 = oBioPolymer.getBuilder().newInstance(IAtom.class, "C"); + IAtom oAtom2 = oBioPolymer.getBuilder().newInstance(IAtom.class, "C"); + IAtom oAtom3 = oBioPolymer.getBuilder().newInstance(IAtom.class, "C"); oBioPolymer.addAtom(oAtom1, oStrand1); oBioPolymer.addAtom(oAtom2, oStrand1); oBioPolymer.addAtom(oAtom3, oMono1, oStrand1); @@ -156,8 +156,8 @@ public void testAddAtom_IAtom_IMonomer_IStrand() { oStrand1.setStrandName("A"); IMonomer oMono1 = oBioPolymer.getBuilder().newInstance(IMonomer.class); oMono1.setMonomerName(new String("TRP279")); - IAtom oAtom1 = oBioPolymer.getBuilder().newInstance(IAtom.class, "C1"); - IAtom oAtom2 = oBioPolymer.getBuilder().newInstance(IAtom.class, "C2"); + IAtom oAtom1 = oBioPolymer.getBuilder().newInstance(IAtom.class, "C"); + IAtom oAtom2 = oBioPolymer.getBuilder().newInstance(IAtom.class, "C"); oBioPolymer.addAtom(oAtom1, oMono1, oStrand1); oBioPolymer.addAtom(oAtom2, oMono1, oStrand1); oBioPolymer.addAtom(oAtom1, null, oStrand1); @@ -173,7 +173,7 @@ public void testGetStrandCount() { oStrand1.setStrandName("A"); IMonomer oMono1 = oBioPolymer.getBuilder().newInstance(IMonomer.class); oMono1.setMonomerName(new String("TRP279")); - IAtom oAtom1 = oBioPolymer.getBuilder().newInstance(IAtom.class, "C1"); + IAtom oAtom1 = oBioPolymer.getBuilder().newInstance(IAtom.class, "C"); oBioPolymer.addAtom(oAtom1, oMono1, oStrand1); Assert.assertEquals(1, oBioPolymer.getStrandCount()); @@ -186,7 +186,7 @@ public void testGetStrand_String() { oStrand1.setStrandName("A"); IMonomer oMono1 = oBioPolymer.getBuilder().newInstance(IMonomer.class); oMono1.setMonomerName(new String("TRP279")); - IAtom oAtom1 = oBioPolymer.getBuilder().newInstance(IAtom.class, "C1"); + IAtom oAtom1 = oBioPolymer.getBuilder().newInstance(IAtom.class, "C"); oBioPolymer.addAtom(oAtom1, oMono1, oStrand1); Assert.assertEquals(oStrand1, oBioPolymer.getStrand("A")); @@ -203,8 +203,8 @@ public void testGetStrandNames() { oMono1.setMonomerName(new String("TRP279")); IMonomer oMono2 = oBioPolymer.getBuilder().newInstance(IMonomer.class); oMono2.setMonomerName(new String("GLY123")); - IAtom oAtom1 = oBioPolymer.getBuilder().newInstance(IAtom.class, "C1"); - IAtom oAtom2 = oBioPolymer.getBuilder().newInstance(IAtom.class, "C2"); + IAtom oAtom1 = oBioPolymer.getBuilder().newInstance(IAtom.class, "C"); + IAtom oAtom2 = oBioPolymer.getBuilder().newInstance(IAtom.class, "C"); oBioPolymer.addAtom(oAtom1, oMono1, oStrand1); oBioPolymer.addAtom(oAtom2, oMono2, oStrand2); Map strands = new Hashtable(); @@ -221,7 +221,7 @@ public void testRemoveStrand_String() { oStrand1.setStrandName("A"); IMonomer oMono1 = oBioPolymer.getBuilder().newInstance(IMonomer.class); oMono1.setMonomerName(new String("TRP279")); - IAtom oAtom1 = oBioPolymer.getBuilder().newInstance(IAtom.class, "C1"); + IAtom oAtom1 = oBioPolymer.getBuilder().newInstance(IAtom.class, "C"); oBioPolymer.addAtom(oAtom1, oMono1, oStrand1); Assert.assertTrue(oBioPolymer.getStrandNames().contains(oStrand1.getStrandName())); @@ -242,8 +242,8 @@ public void testGetStrands() { oMono1.setMonomerName(new String("TRP279")); IMonomer oMono2 = oBioPolymer.getBuilder().newInstance(IMonomer.class); oMono2.setMonomerName(new String("GLY123")); - IAtom oAtom1 = oBioPolymer.getBuilder().newInstance(IAtom.class, "C1"); - IAtom oAtom2 = oBioPolymer.getBuilder().newInstance(IAtom.class, "C2"); + IAtom oAtom1 = oBioPolymer.getBuilder().newInstance(IAtom.class, "C"); + IAtom oAtom2 = oBioPolymer.getBuilder().newInstance(IAtom.class, "C"); oBioPolymer.addAtom(oAtom1, oMono1, oStrand1); oBioPolymer.addAtom(oAtom2, oMono2, oStrand2); Map strands = new Hashtable(); diff --git a/base/test-interfaces/src/test/java/org/openscience/cdk/interfaces/AbstractPDBPolymerTest.java b/base/test-interfaces/src/test/java/org/openscience/cdk/interfaces/AbstractPDBPolymerTest.java index c1b8fbe3dc..6fefc87b7e 100644 --- a/base/test-interfaces/src/test/java/org/openscience/cdk/interfaces/AbstractPDBPolymerTest.java +++ b/base/test-interfaces/src/test/java/org/openscience/cdk/interfaces/AbstractPDBPolymerTest.java @@ -63,9 +63,9 @@ public void testGetMonomerCount() { oMono1.setMonomerName(new String("TRP279")); IMonomer oMono2 = pdbPolymer.getBuilder().newInstance(IMonomer.class); oMono2.setMonomerName(new String("HOH")); - IPDBAtom oPDBAtom1 = pdbPolymer.getBuilder().newInstance(IPDBAtom.class, "C1"); - IPDBAtom oPDBAtom2 = pdbPolymer.getBuilder().newInstance(IPDBAtom.class, "C2"); - IPDBAtom oPDBAtom3 = pdbPolymer.getBuilder().newInstance(IPDBAtom.class, "C3"); + IPDBAtom oPDBAtom1 = pdbPolymer.getBuilder().newInstance(IPDBAtom.class, "C"); + IPDBAtom oPDBAtom2 = pdbPolymer.getBuilder().newInstance(IPDBAtom.class, "C"); + IPDBAtom oPDBAtom3 = pdbPolymer.getBuilder().newInstance(IPDBAtom.class, "C"); pdbPolymer.addAtom(oPDBAtom1); pdbPolymer.addAtom(oPDBAtom2, oMono1, oStrand1); pdbPolymer.addAtom(oPDBAtom3, oMono2, oStrand2); @@ -93,9 +93,9 @@ public void testGetMonomerNames() { oMono1.setMonomerName(new String("TRP279")); IMonomer oMono2 = pdbPolymer.getBuilder().newInstance(IMonomer.class); oMono2.setMonomerName(new String("HOH")); - IPDBAtom oPDBAtom1 = pdbPolymer.getBuilder().newInstance(IPDBAtom.class, "C1"); - IPDBAtom oPDBAtom2 = pdbPolymer.getBuilder().newInstance(IPDBAtom.class, "C2"); - IPDBAtom oPDBAtom3 = pdbPolymer.getBuilder().newInstance(IPDBAtom.class, "C3"); + IPDBAtom oPDBAtom1 = pdbPolymer.getBuilder().newInstance(IPDBAtom.class, "C"); + IPDBAtom oPDBAtom2 = pdbPolymer.getBuilder().newInstance(IPDBAtom.class, "C"); + IPDBAtom oPDBAtom3 = pdbPolymer.getBuilder().newInstance(IPDBAtom.class, "C"); pdbPolymer.addAtom(oPDBAtom1); pdbPolymer.addAtom(oPDBAtom2, oMono1, oStrand1); pdbPolymer.addAtom(oPDBAtom3, oMono2, oStrand2); @@ -124,9 +124,9 @@ public void testGetMonomer_String_String() { oMono1.setMonomerName(new String("TRP279")); IMonomer oMono2 = pdbPolymer.getBuilder().newInstance(IMonomer.class); oMono2.setMonomerName(new String("HOH")); - IPDBAtom oPDBAtom1 = pdbPolymer.getBuilder().newInstance(IPDBAtom.class, "C1"); - IPDBAtom oPDBAtom2 = pdbPolymer.getBuilder().newInstance(IPDBAtom.class, "C2"); - IPDBAtom oPDBAtom3 = pdbPolymer.getBuilder().newInstance(IPDBAtom.class, "C3"); + IPDBAtom oPDBAtom1 = pdbPolymer.getBuilder().newInstance(IPDBAtom.class, "C"); + IPDBAtom oPDBAtom2 = pdbPolymer.getBuilder().newInstance(IPDBAtom.class, "C"); + IPDBAtom oPDBAtom3 = pdbPolymer.getBuilder().newInstance(IPDBAtom.class, "C"); pdbPolymer.addAtom(oPDBAtom1, oMono1, oStrand1); pdbPolymer.addAtom(oPDBAtom2, oMono1, oStrand1); pdbPolymer.addAtom(oPDBAtom3, oMono2, oStrand2); @@ -139,8 +139,8 @@ public void testGetMonomer_String_String() { public void testAddAtom_IPDBAtom() { IPDBPolymer pdbPolymer = (IPDBPolymer) newChemObject(); - IPDBAtom oPDBAtom1 = pdbPolymer.getBuilder().newInstance(IPDBAtom.class, "C1"); - IPDBAtom oPDBAtom2 = pdbPolymer.getBuilder().newInstance(IPDBAtom.class, "C2"); + IPDBAtom oPDBAtom1 = pdbPolymer.getBuilder().newInstance(IPDBAtom.class, "C"); + IPDBAtom oPDBAtom2 = pdbPolymer.getBuilder().newInstance(IPDBAtom.class, "C"); pdbPolymer.addAtom(oPDBAtom1); pdbPolymer.addAtom(oPDBAtom2); @@ -154,9 +154,9 @@ public void testAddAtom_IPDBAtom_IStrand() { oStrand1.setStrandName("A"); IPDBMonomer oMono1 = pdbPolymer.getBuilder().newInstance(IPDBMonomer.class); oMono1.setMonomerName(new String("TRP279")); - IPDBAtom oPDBAtom1 = pdbPolymer.getBuilder().newInstance(IPDBAtom.class, "C1"); - IPDBAtom oPDBAtom2 = pdbPolymer.getBuilder().newInstance(IPDBAtom.class, "C2"); - IPDBAtom oPDBAtom3 = pdbPolymer.getBuilder().newInstance(IPDBAtom.class, "C3"); + IPDBAtom oPDBAtom1 = pdbPolymer.getBuilder().newInstance(IPDBAtom.class, "C"); + IPDBAtom oPDBAtom2 = pdbPolymer.getBuilder().newInstance(IPDBAtom.class, "C"); + IPDBAtom oPDBAtom3 = pdbPolymer.getBuilder().newInstance(IPDBAtom.class, "C"); pdbPolymer.addAtom(oPDBAtom1, oStrand1); pdbPolymer.addAtom(oPDBAtom2, oStrand1); pdbPolymer.addAtom(oPDBAtom3, oMono1, oStrand1); @@ -173,9 +173,9 @@ public void testAddAtom_IPDBAtom_IMonomer_IStrand() { oStrand1.setStrandName("A"); IPDBMonomer oMono1 = pdbPolymer.getBuilder().newInstance(IPDBMonomer.class); oMono1.setMonomerName(new String("TRP279")); - IPDBAtom oPDBAtom1 = pdbPolymer.getBuilder().newInstance(IPDBAtom.class, "C1"); - IPDBAtom oPDBAtom2 = pdbPolymer.getBuilder().newInstance(IPDBAtom.class, "C2"); - IPDBAtom oPDBAtom3 = pdbPolymer.getBuilder().newInstance(IPDBAtom.class, "C3"); + IPDBAtom oPDBAtom1 = pdbPolymer.getBuilder().newInstance(IPDBAtom.class, "C"); + IPDBAtom oPDBAtom2 = pdbPolymer.getBuilder().newInstance(IPDBAtom.class, "C"); + IPDBAtom oPDBAtom3 = pdbPolymer.getBuilder().newInstance(IPDBAtom.class, "C"); pdbPolymer.addAtom(oPDBAtom1, oStrand1); pdbPolymer.addAtom(oPDBAtom2, oStrand1); pdbPolymer.addAtom(oPDBAtom3, oMono1, oStrand1); @@ -192,7 +192,7 @@ public void testAddAtom_IPDBAtom_IMonomer() { oMono1.setMonomerName(new String("TRP279")); IStrand oStrand1 = pdbPolymer.getBuilder().newInstance(IStrand.class); oStrand1.setStrandName("A"); - IPDBAtom oPDBAtom1 = pdbPolymer.getBuilder().newInstance(IPDBAtom.class, "C1"); + IPDBAtom oPDBAtom1 = pdbPolymer.getBuilder().newInstance(IPDBAtom.class, "C"); pdbPolymer.addAtom(oPDBAtom1, oMono1, oStrand1); Assert.assertEquals(1, pdbPolymer.getMonomer("TRP279", "A").getAtomCount()); @@ -206,7 +206,7 @@ public void testGetStrandCount() { oStrand1.setStrandName("A"); IMonomer oMono1 = pdbPolymer.getBuilder().newInstance(IMonomer.class); oMono1.setMonomerName(new String("TRP279")); - IPDBAtom oPDBAtom1 = pdbPolymer.getBuilder().newInstance(IPDBAtom.class, "C1"); + IPDBAtom oPDBAtom1 = pdbPolymer.getBuilder().newInstance(IPDBAtom.class, "C"); pdbPolymer.addAtom(oPDBAtom1, oMono1, oStrand1); Assert.assertEquals(1, pdbPolymer.getStrandCount()); @@ -220,7 +220,7 @@ public void testGetStrand_String() { oStrand1.setStrandName("A"); IMonomer oMono1 = pdbPolymer.getBuilder().newInstance(IMonomer.class); oMono1.setMonomerName(new String("TRP279")); - IPDBAtom oPDBAtom1 = pdbPolymer.getBuilder().newInstance(IPDBAtom.class, "C1"); + IPDBAtom oPDBAtom1 = pdbPolymer.getBuilder().newInstance(IPDBAtom.class, "C"); pdbPolymer.addAtom(oPDBAtom1, oMono1, oStrand1); Assert.assertEquals(oStrand1, pdbPolymer.getStrand("A")); @@ -238,8 +238,8 @@ public void testGetStrandNames() { oMono1.setMonomerName(new String("TRP279")); IMonomer oMono2 = pdbPolymer.getBuilder().newInstance(IMonomer.class); oMono2.setMonomerName(new String("GLY123")); - IPDBAtom oPDBAtom1 = pdbPolymer.getBuilder().newInstance(IPDBAtom.class, "C1"); - IPDBAtom oPDBAtom2 = pdbPolymer.getBuilder().newInstance(IPDBAtom.class, "C2"); + IPDBAtom oPDBAtom1 = pdbPolymer.getBuilder().newInstance(IPDBAtom.class, "C"); + IPDBAtom oPDBAtom2 = pdbPolymer.getBuilder().newInstance(IPDBAtom.class, "C"); pdbPolymer.addAtom(oPDBAtom1, oMono1, oStrand1); pdbPolymer.addAtom(oPDBAtom2, oMono2, oStrand2); Map strands = new Hashtable(); @@ -257,7 +257,7 @@ public void testRemoveStrand_String() { oStrand1.setStrandName("A"); IMonomer oMono1 = pdbPolymer.getBuilder().newInstance(IMonomer.class); oMono1.setMonomerName(new String("TRP279")); - IPDBAtom oPDBAtom1 = pdbPolymer.getBuilder().newInstance(IPDBAtom.class, "C1"); + IPDBAtom oPDBAtom1 = pdbPolymer.getBuilder().newInstance(IPDBAtom.class, "C"); pdbPolymer.addAtom(oPDBAtom1, oMono1, oStrand1); Assert.assertTrue(pdbPolymer.getStrandNames().contains(oStrand1.getStrandName())); @@ -279,8 +279,8 @@ public void testGetStrands() { oMono1.setMonomerName(new String("TRP279")); IMonomer oMono2 = pdbPolymer.getBuilder().newInstance(IMonomer.class); oMono2.setMonomerName(new String("GLY123")); - IPDBAtom oPDBAtom1 = pdbPolymer.getBuilder().newInstance(IPDBAtom.class, "C1"); - IPDBAtom oPDBAtom2 = pdbPolymer.getBuilder().newInstance(IPDBAtom.class, "C2"); + IPDBAtom oPDBAtom1 = pdbPolymer.getBuilder().newInstance(IPDBAtom.class, "C"); + IPDBAtom oPDBAtom2 = pdbPolymer.getBuilder().newInstance(IPDBAtom.class, "C"); pdbPolymer.addAtom(oPDBAtom1, oMono1, oStrand1); pdbPolymer.addAtom(oPDBAtom2, oMono2, oStrand2); Map strands = new Hashtable(); diff --git a/base/test-interfaces/src/test/java/org/openscience/cdk/interfaces/AbstractPolymerTest.java b/base/test-interfaces/src/test/java/org/openscience/cdk/interfaces/AbstractPolymerTest.java index b4a3eeed5e..7889551b19 100644 --- a/base/test-interfaces/src/test/java/org/openscience/cdk/interfaces/AbstractPolymerTest.java +++ b/base/test-interfaces/src/test/java/org/openscience/cdk/interfaces/AbstractPolymerTest.java @@ -43,8 +43,8 @@ public abstract class AbstractPolymerTest extends AbstractMoleculeTest { public void testAddAtom_IAtom() { IPolymer oPolymer = (IPolymer) newChemObject(); - IAtom oAtom1 = oPolymer.getBuilder().newInstance(IAtom.class, "C1"); - IAtom oAtom2 = oPolymer.getBuilder().newInstance(IAtom.class, "C2"); + IAtom oAtom1 = oPolymer.getBuilder().newInstance(IAtom.class, "C"); + IAtom oAtom2 = oPolymer.getBuilder().newInstance(IAtom.class, "C"); oPolymer.addAtom(oAtom1); oPolymer.addAtom(oAtom2); @@ -58,9 +58,9 @@ public void testAddAtom_IAtom_IMonomer() { IMonomer oMono1 = oPolymer.getBuilder().newInstance(IMonomer.class); oMono1.setMonomerName(new String("TRP279")); IMonomer oMono2 = null; - IAtom oAtom1 = oPolymer.getBuilder().newInstance(IAtom.class, "C1"); - IAtom oAtom2 = oPolymer.getBuilder().newInstance(IAtom.class, "C2"); - IAtom oAtom3 = oPolymer.getBuilder().newInstance(IAtom.class, "C3"); + IAtom oAtom1 = oPolymer.getBuilder().newInstance(IAtom.class, "C"); + IAtom oAtom2 = oPolymer.getBuilder().newInstance(IAtom.class, "C"); + IAtom oAtom3 = oPolymer.getBuilder().newInstance(IAtom.class, "C"); oPolymer.addAtom(oAtom1); oPolymer.addAtom(oAtom2, oMono1); @@ -88,9 +88,9 @@ public void testGetMonomerCount() { oMono1.setMonomerName(new String("TRP279")); IMonomer oMono2 = oPolymer.getBuilder().newInstance(IMonomer.class); oMono2.setMonomerName(new String("HOH")); - IAtom oAtom1 = oPolymer.getBuilder().newInstance(IAtom.class, "C1"); - IAtom oAtom2 = oPolymer.getBuilder().newInstance(IAtom.class, "C2"); - IAtom oAtom3 = oPolymer.getBuilder().newInstance(IAtom.class, "C3"); + IAtom oAtom1 = oPolymer.getBuilder().newInstance(IAtom.class, "C"); + IAtom oAtom2 = oPolymer.getBuilder().newInstance(IAtom.class, "C"); + IAtom oAtom3 = oPolymer.getBuilder().newInstance(IAtom.class, "C"); oPolymer.addAtom(oAtom1); oPolymer.addAtom(oAtom2, oMono1); oPolymer.addAtom(oAtom3, oMono2); @@ -107,9 +107,9 @@ public void testGetMonomer_String() { oMono1.setMonomerName(new String("TRP279")); IMonomer oMono2 = oPolymer.getBuilder().newInstance(IMonomer.class); oMono2.setMonomerName(new String("HOH")); - IAtom oAtom1 = oPolymer.getBuilder().newInstance(IAtom.class, "C1"); - IAtom oAtom2 = oPolymer.getBuilder().newInstance(IAtom.class, "C2"); - IAtom oAtom3 = oPolymer.getBuilder().newInstance(IAtom.class, "C3"); + IAtom oAtom1 = oPolymer.getBuilder().newInstance(IAtom.class, "C"); + IAtom oAtom2 = oPolymer.getBuilder().newInstance(IAtom.class, "C"); + IAtom oAtom3 = oPolymer.getBuilder().newInstance(IAtom.class, "C"); oPolymer.addAtom(oAtom1, oMono1); oPolymer.addAtom(oAtom2, oMono1); oPolymer.addAtom(oAtom3, oMono2); @@ -128,9 +128,9 @@ public void testGetMonomerNames() { oMono1.setMonomerName(new String("TRP279")); IMonomer oMono2 = oPolymer.getBuilder().newInstance(IMonomer.class); oMono2.setMonomerName(new String("HOH")); - IAtom oAtom1 = oPolymer.getBuilder().newInstance(IAtom.class, "C1"); - IAtom oAtom2 = oPolymer.getBuilder().newInstance(IAtom.class, "C2"); - IAtom oAtom3 = oPolymer.getBuilder().newInstance(IAtom.class, "C3"); + IAtom oAtom1 = oPolymer.getBuilder().newInstance(IAtom.class, "C"); + IAtom oAtom2 = oPolymer.getBuilder().newInstance(IAtom.class, "C"); + IAtom oAtom3 = oPolymer.getBuilder().newInstance(IAtom.class, "C"); oPolymer.addAtom(oAtom1); oPolymer.addAtom(oAtom2, oMono1); oPolymer.addAtom(oAtom3, oMono2); @@ -150,7 +150,7 @@ public void testRemoveMonomer_String() { IPolymer oPolymer = (IPolymer) newChemObject(); IMonomer oMono1 = oPolymer.getBuilder().newInstance(IMonomer.class); oMono1.setMonomerName(new String("TRP279")); - IAtom oAtom1 = oPolymer.getBuilder().newInstance(IAtom.class, "C1"); + IAtom oAtom1 = oPolymer.getBuilder().newInstance(IAtom.class, "C"); oPolymer.addAtom(oAtom1, oMono1); Assert.assertTrue(oPolymer.getMonomerNames().contains(oMono1.getMonomerName())); Assert.assertEquals(1, oPolymer.getAtomCount()); @@ -171,8 +171,8 @@ public void testToString() { oMono1.setMonomerName(new String("TRP279")); IMonomer oMono2 = polymer.getBuilder().newInstance(IMonomer.class); oMono2.setMonomerName(new String("HOH")); - IAtom oAtom2 = polymer.getBuilder().newInstance(IAtom.class, "C2"); - IAtom oAtom3 = polymer.getBuilder().newInstance(IAtom.class, "C3"); + IAtom oAtom2 = polymer.getBuilder().newInstance(IAtom.class, "C"); + IAtom oAtom3 = polymer.getBuilder().newInstance(IAtom.class, "C"); polymer.addAtom(oAtom2, oMono1); polymer.addAtom(oAtom3, oMono2); Map monomers = new Hashtable(); diff --git a/base/test-interfaces/src/test/java/org/openscience/cdk/interfaces/AbstractStrandTest.java b/base/test-interfaces/src/test/java/org/openscience/cdk/interfaces/AbstractStrandTest.java index 56aad594a9..f1726ab657 100644 --- a/base/test-interfaces/src/test/java/org/openscience/cdk/interfaces/AbstractStrandTest.java +++ b/base/test-interfaces/src/test/java/org/openscience/cdk/interfaces/AbstractStrandTest.java @@ -77,8 +77,8 @@ public void testSetStrandType_String() { @Override public void testAddAtom_IAtom() { IStrand oStrand = (IStrand) newChemObject(); - IAtom oAtom1 = oStrand.getBuilder().newInstance(IAtom.class, "C1"); - IAtom oAtom2 = oStrand.getBuilder().newInstance(IAtom.class, "C2"); + IAtom oAtom1 = oStrand.getBuilder().newInstance(IAtom.class, "C"); + IAtom oAtom2 = oStrand.getBuilder().newInstance(IAtom.class, "C"); oStrand.addAtom(oAtom1); oStrand.addAtom(oAtom2); @@ -90,9 +90,9 @@ public void testAddAtom_IAtom_IMonomer() { IStrand oStrand = (IStrand) newChemObject(); IMonomer oMono1 = oStrand.getBuilder().newInstance(IMonomer.class); oMono1.setMonomerName(new String("TRP279")); - IAtom oAtom1 = oStrand.getBuilder().newInstance(IAtom.class, "C1"); - IAtom oAtom2 = oStrand.getBuilder().newInstance(IAtom.class, "C2"); - IAtom oAtom3 = oStrand.getBuilder().newInstance(IAtom.class, "C3"); + IAtom oAtom1 = oStrand.getBuilder().newInstance(IAtom.class, "C"); + IAtom oAtom2 = oStrand.getBuilder().newInstance(IAtom.class, "C"); + IAtom oAtom3 = oStrand.getBuilder().newInstance(IAtom.class, "C"); oStrand.addAtom(oAtom1); oStrand.addAtom(oAtom2); oStrand.addAtom(oAtom3, oMono1); @@ -108,8 +108,8 @@ public void testGetMonomerCount() { oMono1.setMonomerName(new String("TRP279")); IMonomer oMono2 = oStrand.getBuilder().newInstance(IMonomer.class); oMono2.setMonomerName(new String("HOH")); - IAtom oAtom2 = oStrand.getBuilder().newInstance(IAtom.class, "C2"); - IAtom oAtom3 = oStrand.getBuilder().newInstance(IAtom.class, "C3"); + IAtom oAtom2 = oStrand.getBuilder().newInstance(IAtom.class, "C"); + IAtom oAtom3 = oStrand.getBuilder().newInstance(IAtom.class, "C"); oStrand.addAtom(oAtom2, oMono1); oStrand.addAtom(oAtom3, oMono2); @@ -123,8 +123,8 @@ public void testGetMonomer_String() { oMono1.setMonomerName(new String("TRP279")); IMonomer oMono2 = oStrand.getBuilder().newInstance(IMonomer.class); oMono2.setMonomerName(new String("HOH")); - IAtom oAtom2 = oStrand.getBuilder().newInstance(IAtom.class, "C2"); - IAtom oAtom3 = oStrand.getBuilder().newInstance(IAtom.class, "C3"); + IAtom oAtom2 = oStrand.getBuilder().newInstance(IAtom.class, "C"); + IAtom oAtom3 = oStrand.getBuilder().newInstance(IAtom.class, "C"); oStrand.addAtom(oAtom2, oMono1); oStrand.addAtom(oAtom3, oMono2); @@ -140,8 +140,8 @@ public void testGetMonomerNames() { oMono1.setMonomerName(new String("TRP279")); IMonomer oMono2 = oStrand.getBuilder().newInstance(IMonomer.class); oMono2.setMonomerName(new String("HOH")); - IAtom oAtom2 = oStrand.getBuilder().newInstance(IAtom.class, "C2"); - IAtom oAtom3 = oStrand.getBuilder().newInstance(IAtom.class, "C3"); + IAtom oAtom2 = oStrand.getBuilder().newInstance(IAtom.class, "C"); + IAtom oAtom3 = oStrand.getBuilder().newInstance(IAtom.class, "C"); oStrand.addAtom(oAtom2, oMono1); oStrand.addAtom(oAtom3, oMono2); Map monomers = new Hashtable(); @@ -168,7 +168,7 @@ public void testRemoveMonomer_String() { IStrand oStrand = (IStrand) newChemObject(); IMonomer oMono1 = oStrand.getBuilder().newInstance(IMonomer.class); oMono1.setMonomerName(new String("TRP279")); - IAtom oAtom1 = oStrand.getBuilder().newInstance(IAtom.class, "C1"); + IAtom oAtom1 = oStrand.getBuilder().newInstance(IAtom.class, "C"); oStrand.addAtom(oAtom1, oMono1); Assert.assertTrue(oStrand.getMonomerNames().contains(oMono1.getMonomerName())); Assert.assertEquals(1, oStrand.getAtomCount()); @@ -184,8 +184,8 @@ public void testGetMonomers() { oMono1.setMonomerName(new String("TRP279")); IMonomer oMono2 = oStrand.getBuilder().newInstance(IMonomer.class); oMono2.setMonomerName(new String("HOH")); - IAtom oAtom2 = oStrand.getBuilder().newInstance(IAtom.class, "C2"); - IAtom oAtom3 = oStrand.getBuilder().newInstance(IAtom.class, "C3"); + IAtom oAtom2 = oStrand.getBuilder().newInstance(IAtom.class, "C"); + IAtom oAtom3 = oStrand.getBuilder().newInstance(IAtom.class, "C"); oStrand.addAtom(oAtom2, oMono1); oStrand.addAtom(oAtom3, oMono2); Map monomers = new Hashtable(); @@ -210,8 +210,8 @@ public void testToString() { oMono1.setMonomerName(new String("TRP279")); IMonomer oMono2 = oStrand.getBuilder().newInstance(IMonomer.class); oMono2.setMonomerName(new String("HOH")); - IAtom oAtom2 = oStrand.getBuilder().newInstance(IAtom.class, "C2"); - IAtom oAtom3 = oStrand.getBuilder().newInstance(IAtom.class, "C3"); + IAtom oAtom2 = oStrand.getBuilder().newInstance(IAtom.class, "C"); + IAtom oAtom3 = oStrand.getBuilder().newInstance(IAtom.class, "C"); oStrand.addAtom(oAtom2, oMono1); oStrand.addAtom(oAtom3, oMono2); Map monomers = new Hashtable(); From e498c63650767d2938b6ddd55d90ffd92a92113d Mon Sep 17 00:00:00 2001 From: John May Date: Sun, 16 Oct 2016 18:43:30 +0100 Subject: [PATCH 07/16] More debug atoms needing static loggers. --- .../main/java/org/openscience/cdk/debug/DebugFragmentAtom.java | 2 +- .../src/main/java/org/openscience/cdk/debug/DebugPDBAtom.java | 2 +- .../main/java/org/openscience/cdk/debug/DebugPseudoAtom.java | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/base/datadebug/src/main/java/org/openscience/cdk/debug/DebugFragmentAtom.java b/base/datadebug/src/main/java/org/openscience/cdk/debug/DebugFragmentAtom.java index df2517afe1..210415c1d3 100644 --- a/base/datadebug/src/main/java/org/openscience/cdk/debug/DebugFragmentAtom.java +++ b/base/datadebug/src/main/java/org/openscience/cdk/debug/DebugFragmentAtom.java @@ -51,7 +51,7 @@ public class DebugFragmentAtom extends FragmentAtom { private static final long serialVersionUID = 0L; - ILoggingTool logger = LoggingToolFactory.createLoggingTool(DebugFragmentAtom.class); + private static final ILoggingTool logger = LoggingToolFactory.createLoggingTool(DebugFragmentAtom.class); public DebugFragmentAtom() { super(); diff --git a/base/datadebug/src/main/java/org/openscience/cdk/debug/DebugPDBAtom.java b/base/datadebug/src/main/java/org/openscience/cdk/debug/DebugPDBAtom.java index 1881fccd87..86e3582af0 100644 --- a/base/datadebug/src/main/java/org/openscience/cdk/debug/DebugPDBAtom.java +++ b/base/datadebug/src/main/java/org/openscience/cdk/debug/DebugPDBAtom.java @@ -37,7 +37,7 @@ public class DebugPDBAtom extends PDBAtom implements IPDBAtom { private static final long serialVersionUID = -2432127382224382452L; - ILoggingTool logger = LoggingToolFactory.createLoggingTool(DebugPDBAtom.class); + private static final ILoggingTool logger = LoggingToolFactory.createLoggingTool(DebugPDBAtom.class); public DebugPDBAtom(IElement element) { super(element); diff --git a/base/datadebug/src/main/java/org/openscience/cdk/debug/DebugPseudoAtom.java b/base/datadebug/src/main/java/org/openscience/cdk/debug/DebugPseudoAtom.java index 00c5642a1e..35a85ff9d6 100644 --- a/base/datadebug/src/main/java/org/openscience/cdk/debug/DebugPseudoAtom.java +++ b/base/datadebug/src/main/java/org/openscience/cdk/debug/DebugPseudoAtom.java @@ -45,7 +45,7 @@ public class DebugPseudoAtom extends PseudoAtom implements IPseudoAtom { private static final long serialVersionUID = -5935090219383862070L; - ILoggingTool logger = LoggingToolFactory.createLoggingTool(DebugPseudoAtom.class); + private static final ILoggingTool logger = LoggingToolFactory.createLoggingTool(DebugPseudoAtom.class); public DebugPseudoAtom() { super(); From ecc2c9d358a68bf017f74156826906cbd1e8993e Mon Sep 17 00:00:00 2001 From: John May Date: Sun, 16 Oct 2016 18:43:53 +0100 Subject: [PATCH 08/16] More Atom Id usage --- .../org/openscience/cdk/debug/DebugBioPolymerTest.java | 10 +++++----- .../org/openscience/cdk/debug/DebugPDBPolymerTest.java | 10 +++++----- .../org/openscience/cdk/debug/DebugStrandTest.java | 10 +++++----- 3 files changed, 15 insertions(+), 15 deletions(-) diff --git a/base/datadebug/src/test/java/org/openscience/cdk/debug/DebugBioPolymerTest.java b/base/datadebug/src/test/java/org/openscience/cdk/debug/DebugBioPolymerTest.java index 63907a162a..914646741a 100644 --- a/base/datadebug/src/test/java/org/openscience/cdk/debug/DebugBioPolymerTest.java +++ b/base/datadebug/src/test/java/org/openscience/cdk/debug/DebugBioPolymerTest.java @@ -64,11 +64,11 @@ public void testDebugBioPolymer() { oMono2.setMonomerName(new String("HOH")); IMonomer oMono3 = oBioPolymer.getBuilder().newInstance(IMonomer.class); oMono3.setMonomerName(new String("GLYA16")); - IAtom oAtom1 = oBioPolymer.getBuilder().newInstance(IAtom.class, "C1"); - IAtom oAtom2 = oBioPolymer.getBuilder().newInstance(IAtom.class, "C2"); - IAtom oAtom3 = oBioPolymer.getBuilder().newInstance(IAtom.class, "C3"); - IAtom oAtom4 = oBioPolymer.getBuilder().newInstance(IAtom.class, "C4"); - IAtom oAtom5 = oBioPolymer.getBuilder().newInstance(IAtom.class, "C5"); + IAtom oAtom1 = oBioPolymer.getBuilder().newInstance(IAtom.class, "C"); + IAtom oAtom2 = oBioPolymer.getBuilder().newInstance(IAtom.class, "C"); + IAtom oAtom3 = oBioPolymer.getBuilder().newInstance(IAtom.class, "C"); + IAtom oAtom4 = oBioPolymer.getBuilder().newInstance(IAtom.class, "C"); + IAtom oAtom5 = oBioPolymer.getBuilder().newInstance(IAtom.class, "C"); oBioPolymer.addAtom(oAtom1); oBioPolymer.addAtom(oAtom2, oStrand1); diff --git a/base/datadebug/src/test/java/org/openscience/cdk/debug/DebugPDBPolymerTest.java b/base/datadebug/src/test/java/org/openscience/cdk/debug/DebugPDBPolymerTest.java index ab80e69908..781e19a706 100644 --- a/base/datadebug/src/test/java/org/openscience/cdk/debug/DebugPDBPolymerTest.java +++ b/base/datadebug/src/test/java/org/openscience/cdk/debug/DebugPDBPolymerTest.java @@ -64,11 +64,11 @@ public void testDebugPDBPolymer() { oMono2.setMonomerName(new String("HOH")); IMonomer oMono3 = pdbPolymer.getBuilder().newInstance(IMonomer.class); oMono3.setMonomerName(new String("GLYA16")); - IPDBAtom oPDBAtom1 = pdbPolymer.getBuilder().newInstance(IPDBAtom.class, "C1"); - IPDBAtom oPDBAtom2 = pdbPolymer.getBuilder().newInstance(IPDBAtom.class, "C2"); - IPDBAtom oPDBAtom3 = pdbPolymer.getBuilder().newInstance(IPDBAtom.class, "C3"); - IPDBAtom oPDBAtom4 = pdbPolymer.getBuilder().newInstance(IPDBAtom.class, "C4"); - IPDBAtom oPDBAtom5 = pdbPolymer.getBuilder().newInstance(IPDBAtom.class, "C5"); + IPDBAtom oPDBAtom1 = pdbPolymer.getBuilder().newInstance(IPDBAtom.class, "C"); + IPDBAtom oPDBAtom2 = pdbPolymer.getBuilder().newInstance(IPDBAtom.class, "C"); + IPDBAtom oPDBAtom3 = pdbPolymer.getBuilder().newInstance(IPDBAtom.class, "C"); + IPDBAtom oPDBAtom4 = pdbPolymer.getBuilder().newInstance(IPDBAtom.class, "C"); + IPDBAtom oPDBAtom5 = pdbPolymer.getBuilder().newInstance(IPDBAtom.class, "C"); pdbPolymer.addAtom(oPDBAtom1); pdbPolymer.addAtom(oPDBAtom2, oStrand1); diff --git a/base/datadebug/src/test/java/org/openscience/cdk/debug/DebugStrandTest.java b/base/datadebug/src/test/java/org/openscience/cdk/debug/DebugStrandTest.java index 340a72659c..26466fa23a 100644 --- a/base/datadebug/src/test/java/org/openscience/cdk/debug/DebugStrandTest.java +++ b/base/datadebug/src/test/java/org/openscience/cdk/debug/DebugStrandTest.java @@ -59,11 +59,11 @@ public void testDebugStrand() { oMono2.setMonomerName(new String("HOH")); IMonomer oMono3 = oStrand.getBuilder().newInstance(IMonomer.class); oMono3.setMonomerName(new String("GLYA16")); - IAtom oAtom1 = oStrand.getBuilder().newInstance(IAtom.class, "C1"); - IAtom oAtom2 = oStrand.getBuilder().newInstance(IAtom.class, "C2"); - IAtom oAtom3 = oStrand.getBuilder().newInstance(IAtom.class, "C3"); - IAtom oAtom4 = oStrand.getBuilder().newInstance(IAtom.class, "C4"); - IAtom oAtom5 = oStrand.getBuilder().newInstance(IAtom.class, "C5"); + IAtom oAtom1 = oStrand.getBuilder().newInstance(IAtom.class, "C"); + IAtom oAtom2 = oStrand.getBuilder().newInstance(IAtom.class, "C"); + IAtom oAtom3 = oStrand.getBuilder().newInstance(IAtom.class, "C"); + IAtom oAtom4 = oStrand.getBuilder().newInstance(IAtom.class, "C"); + IAtom oAtom5 = oStrand.getBuilder().newInstance(IAtom.class, "C"); oStrand.addAtom(oAtom1); oStrand.addAtom(oAtom2); From c47d87e905e61ea09c35523bca6908e5dee2b775 Mon Sep 17 00:00:00 2001 From: John May Date: Sun, 16 Oct 2016 18:44:28 +0100 Subject: [PATCH 09/16] Avoid invalid atom symbols, X is an atom type id! --- .../org/openscience/cdk/atomtype/SybylAtomTypeMatcherTest.java | 2 +- storage/io/src/main/java/org/openscience/cdk/io/Mol2Reader.java | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/base/test-atomtype/src/test/java/org/openscience/cdk/atomtype/SybylAtomTypeMatcherTest.java b/base/test-atomtype/src/test/java/org/openscience/cdk/atomtype/SybylAtomTypeMatcherTest.java index 74cd9aeb28..e069d1ba95 100644 --- a/base/test-atomtype/src/test/java/org/openscience/cdk/atomtype/SybylAtomTypeMatcherTest.java +++ b/base/test-atomtype/src/test/java/org/openscience/cdk/atomtype/SybylAtomTypeMatcherTest.java @@ -191,7 +191,7 @@ public void testAtomTyping4() throws Exception { @Test public void testNonExistingType() throws Exception { IAtomContainer mol = new AtomContainer(); - IAtom atom = new Atom("Error"); + IAtom atom = new Atom(); mol.addAtom(atom); SybylAtomTypeMatcher matcher = SybylAtomTypeMatcher.getInstance(mol.getBuilder()); IAtomType type = matcher.findMatchingAtomType(mol, atom); diff --git a/storage/io/src/main/java/org/openscience/cdk/io/Mol2Reader.java b/storage/io/src/main/java/org/openscience/cdk/io/Mol2Reader.java index d818270a86..e886b62de7 100644 --- a/storage/io/src/main/java/org/openscience/cdk/io/Mol2Reader.java +++ b/storage/io/src/main/java/org/openscience/cdk/io/Mol2Reader.java @@ -316,7 +316,7 @@ private IAtomContainer readMolecule(IAtomContainer molecule) throws CDKException if (ATOM_TYPE_ALIASES.containsKey(atomTypeStr)) atomTypeStr = ATOM_TYPE_ALIASES.get(atomTypeStr); - IAtom atom = molecule.getBuilder().newInstance(IAtom.class, "X"); + IAtom atom = molecule.getBuilder().newInstance(IAtom.class); IAtomType atomType; try { atomType = atFactory.getAtomType(atomTypeStr); From 89814e73886f435cc3e397da74774148d5836c29 Mon Sep 17 00:00:00 2001 From: John May Date: Sun, 16 Oct 2016 18:44:41 +0100 Subject: [PATCH 10/16] Hydrogen semantics have changed. --- .../org/openscience/cdk/templates/TestMoleculeFactory.java | 2 ++ .../cdk/tools/manipulator/AtomContainerManipulatorTest.java | 6 ++++-- .../org/openscience/cdk/tools/CDKHydrogenAdderTest.java | 2 +- 3 files changed, 7 insertions(+), 3 deletions(-) diff --git a/base/data/src/test/java/org/openscience/cdk/templates/TestMoleculeFactory.java b/base/data/src/test/java/org/openscience/cdk/templates/TestMoleculeFactory.java index 29b37c6c22..49d296c1d0 100644 --- a/base/data/src/test/java/org/openscience/cdk/templates/TestMoleculeFactory.java +++ b/base/data/src/test/java/org/openscience/cdk/templates/TestMoleculeFactory.java @@ -1870,6 +1870,8 @@ public static IAtomContainer makeGappedCyclophaneLike() { private static void configureAtoms(IAtomContainer mol) { try { + for (IAtom atom : mol.atoms()) + atom.setImplicitHydrogenCount(null); Isotopes.getInstance().configureAtoms(mol); } catch (Exception exc) { logger.error("Could not configure molecule!"); diff --git a/base/test-standard/src/test/java/org/openscience/cdk/tools/manipulator/AtomContainerManipulatorTest.java b/base/test-standard/src/test/java/org/openscience/cdk/tools/manipulator/AtomContainerManipulatorTest.java index f17858b83b..00966ec4b5 100644 --- a/base/test-standard/src/test/java/org/openscience/cdk/tools/manipulator/AtomContainerManipulatorTest.java +++ b/base/test-standard/src/test/java/org/openscience/cdk/tools/manipulator/AtomContainerManipulatorTest.java @@ -565,7 +565,9 @@ public void testGetTotalExactMass_IAtomContainer() throws Exception { @Test(expected = IllegalArgumentException.class) public void getNaturalExactMassNeedsHydrogens() { IAtomContainer mol = new AtomContainer(); - mol.addAtom(new Atom("C")); + IAtom atom = new Atom("C"); + atom.setImplicitHydrogenCount(null); + mol.addAtom(atom); AtomContainerManipulator.getNaturalExactMass(mol); } @@ -1031,7 +1033,7 @@ public void testAnonymise() throws Exception { assertThat(anonymous.getAtom(0).getSymbol(), is("C")); assertThat(anonymous.getAtom(2).getSymbol(), is("C")); assertNull(anonymous.getAtom(1).getAtomTypeName()); - assertNull(anonymous.getAtom(4).getImplicitHydrogenCount()); + assertThat(anonymous.getAtom(4).getImplicitHydrogenCount(), is(0)); assertFalse(anonymous.getAtom(3).getFlag(CDKConstants.ISAROMATIC)); assertFalse(anonymous.getBond(1).getFlag(CDKConstants.ISAROMATIC)); diff --git a/base/test-valencycheck/src/test/java/org/openscience/cdk/tools/CDKHydrogenAdderTest.java b/base/test-valencycheck/src/test/java/org/openscience/cdk/tools/CDKHydrogenAdderTest.java index 05f1858bcb..44b41066c1 100644 --- a/base/test-valencycheck/src/test/java/org/openscience/cdk/tools/CDKHydrogenAdderTest.java +++ b/base/test-valencycheck/src/test/java/org/openscience/cdk/tools/CDKHydrogenAdderTest.java @@ -214,7 +214,7 @@ public void testSulphur() throws Exception { Assert.assertNotNull(type); AtomTypeManipulator.configure(atom, type); - Assert.assertNull(atom.getImplicitHydrogenCount()); + Assert.assertNotEquals((Integer) 2, atom.getImplicitHydrogenCount()); adder.addImplicitHydrogens(mol); Assert.assertEquals(1, mol.getAtomCount()); Assert.assertNotNull(atom.getImplicitHydrogenCount()); From 5b3ddd257508468783a7c057f460232d95b8d180 Mon Sep 17 00:00:00 2001 From: John May Date: Sun, 16 Oct 2016 19:03:14 +0100 Subject: [PATCH 11/16] More bad atom symbols again. --- .../java/org/openscience/cdk/io/cml/CMLRoundTripTest.java | 3 ++- .../java/org/openscience/cdk/smiles/CDKToBeamTest.java | 8 ++++---- 2 files changed, 6 insertions(+), 5 deletions(-) diff --git a/storage/libiocml/src/test/java/org/openscience/cdk/io/cml/CMLRoundTripTest.java b/storage/libiocml/src/test/java/org/openscience/cdk/io/cml/CMLRoundTripTest.java index 77c7846e3f..4a31f58064 100644 --- a/storage/libiocml/src/test/java/org/openscience/cdk/io/cml/CMLRoundTripTest.java +++ b/storage/libiocml/src/test/java/org/openscience/cdk/io/cml/CMLRoundTripTest.java @@ -508,7 +508,7 @@ public void testReaction() throws Exception { IAtomContainer product = reaction.getBuilder().newInstance(IAtomContainer.class); product.setID("product"); - atom = reaction.getBuilder().newInstance(IAtom.class, "X"); + atom = reaction.getBuilder().newInstance(IAtom.class, "R"); product.addAtom(atom); reaction.addProduct(product); @@ -725,6 +725,7 @@ public void testAtomProperties() throws Exception { public void testUnsetHydrogenCount() throws Exception { IAtomContainer mol = new AtomContainer(); Atom atom = new Atom("C"); + atom.setImplicitHydrogenCount(null); Assert.assertNull(atom.getImplicitHydrogenCount()); mol.addAtom(atom); diff --git a/storage/smiles/src/test/java/org/openscience/cdk/smiles/CDKToBeamTest.java b/storage/smiles/src/test/java/org/openscience/cdk/smiles/CDKToBeamTest.java index 725f1fbd2c..1744526375 100644 --- a/storage/smiles/src/test/java/org/openscience/cdk/smiles/CDKToBeamTest.java +++ b/storage/smiles/src/test/java/org/openscience/cdk/smiles/CDKToBeamTest.java @@ -85,7 +85,7 @@ public void noSymbol() throws Exception { @Test public void unknownSymbol() throws Exception { - IAtom a = new Atom("ALA"); + IAtom a = new PseudoAtom("ALA"); a.setImplicitHydrogenCount(0); assertThat(new CDKToBeam().toBeamAtom(a).element(), is(Element.Unknown)); } @@ -165,9 +165,9 @@ public void defaultIsotope() throws Exception { // the hydrogens are set to null @Test public void pseudoAtom_nullH() throws Exception { - assertThat(new CDKToBeam().toBeamAtom(new Atom("R")).hydrogens(), is(0)); - assertThat(new CDKToBeam().toBeamAtom(new Atom("*")).hydrogens(), is(0)); - assertThat(new CDKToBeam().toBeamAtom(new Atom("R1")).hydrogens(), is(0)); + assertThat(new CDKToBeam().toBeamAtom(new PseudoAtom("R")).hydrogens(), is(0)); + assertThat(new CDKToBeam().toBeamAtom(new PseudoAtom("*")).hydrogens(), is(0)); + assertThat(new CDKToBeam().toBeamAtom(new PseudoAtom("R1")).hydrogens(), is(0)); } @SuppressWarnings("unchecked") From 3c5d2241b132be0d52851d7ff2b446c8d521f21b Mon Sep 17 00:00:00 2001 From: John May Date: Sun, 16 Oct 2016 19:03:40 +0100 Subject: [PATCH 12/16] Hydrogen count semantics change - defaults to zero with provided symbol. --- .../cdk/inchi/InChIGeneratorFactoryTest.java | 2 ++ .../cdk/inchi/InChIGeneratorTest.java | 32 +++++++++---------- 2 files changed, 18 insertions(+), 16 deletions(-) diff --git a/storage/inchi/src/test/java/org/openscience/cdk/inchi/InChIGeneratorFactoryTest.java b/storage/inchi/src/test/java/org/openscience/cdk/inchi/InChIGeneratorFactoryTest.java index 12ea6a951c..e78adf1760 100644 --- a/storage/inchi/src/test/java/org/openscience/cdk/inchi/InChIGeneratorFactoryTest.java +++ b/storage/inchi/src/test/java/org/openscience/cdk/inchi/InChIGeneratorFactoryTest.java @@ -177,6 +177,8 @@ public void testInChIGenerator_AromaticBonds() throws CDKException { try { // create a fairly complex aromatic molecule IAtomContainer tetrazole = TestMoleculeFactory.makeTetrazole(); + for (IAtom atom : tetrazole.atoms()) + atom.setImplicitHydrogenCount(null); AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(tetrazole); Aromaticity.cdkLegacy().apply(tetrazole); diff --git a/storage/inchi/src/test/java/org/openscience/cdk/inchi/InChIGeneratorTest.java b/storage/inchi/src/test/java/org/openscience/cdk/inchi/InChIGeneratorTest.java index 3fbe70b908..91590be3d5 100644 --- a/storage/inchi/src/test/java/org/openscience/cdk/inchi/InChIGeneratorTest.java +++ b/storage/inchi/src/test/java/org/openscience/cdk/inchi/InChIGeneratorTest.java @@ -81,7 +81,7 @@ protected InChIGeneratorFactory getFactory() throws Exception { @Test public void testGetInchiFromChlorineAtom() throws Exception { IAtomContainer ac = new AtomContainer(); - ac.addAtom(new Atom("Cl")); + ac.addAtom(new Atom("ClH")); InChIGenerator gen = getFactory().getInChIGenerator(ac, "FixedH"); Assert.assertEquals(gen.getReturnStatus(), INCHI_RET.OKAY); Assert.assertEquals("InChI=1/ClH/h1H", gen.getInchi()); @@ -153,7 +153,7 @@ public void testGetInchiFromLithiumIon() throws Exception { @Test public void testGetInchiFromChlorine37Atom() throws Exception { IAtomContainer ac = new AtomContainer(); - IAtom a = new Atom("Cl"); + IAtom a = new Atom("ClH"); a.setMassNumber(37); ac.addAtom(a); InChIGenerator gen = getFactory().getInChIGenerator(ac, "FixedH"); @@ -394,7 +394,7 @@ public void zeroHydrogenCount() throws Exception { @Test public void testGetStandardInchiFromChlorineAtom() throws Exception { IAtomContainer ac = new AtomContainer(); - ac.addAtom(new Atom("Cl")); + ac.addAtom(new Atom("ClH")); InChIGenerator gen = getFactory().getInChIGenerator(ac); Assert.assertEquals(INCHI_RET.OKAY, gen.getReturnStatus()); Assert.assertEquals("InChI=1S/ClH/h1H", gen.getInchi()); @@ -424,7 +424,7 @@ public void testGetStandardInchiFromLithiumIon() throws Exception { @Test public void testGetStandardInchiFromChlorine37Atom() throws Exception { IAtomContainer ac = new AtomContainer(); - IAtom a = new Atom("Cl"); + IAtom a = new Atom("ClH"); a.setMassNumber(37); ac.addAtom(a); InChIGenerator gen = getFactory().getInChIGenerator(ac); @@ -738,11 +738,11 @@ public void bug1295() throws Exception { @Test public void r_penta_2_3_diene_impl_h() throws Exception { IAtomContainer m = new AtomContainer(5, 4, 0, 0); + m.addAtom(new Atom("CH3")); + m.addAtom(new Atom("CH")); m.addAtom(new Atom("C")); - m.addAtom(new Atom("C")); - m.addAtom(new Atom("C")); - m.addAtom(new Atom("C")); - m.addAtom(new Atom("C")); + m.addAtom(new Atom("CH")); + m.addAtom(new Atom("CH3")); m.addBond(0, 1, IBond.Order.SINGLE); m.addBond(1, 2, IBond.Order.DOUBLE); m.addBond(2, 3, IBond.Order.DOUBLE); @@ -767,11 +767,11 @@ public void r_penta_2_3_diene_impl_h() throws Exception { @Test public void s_penta_2_3_diene_impl_h() throws Exception { IAtomContainer m = new AtomContainer(5, 4, 0, 0); + m.addAtom(new Atom("CH3")); + m.addAtom(new Atom("CH")); m.addAtom(new Atom("C")); - m.addAtom(new Atom("C")); - m.addAtom(new Atom("C")); - m.addAtom(new Atom("C")); - m.addAtom(new Atom("C")); + m.addAtom(new Atom("CH")); + m.addAtom(new Atom("CH3")); m.addBond(0, 1, IBond.Order.SINGLE); m.addBond(1, 2, IBond.Order.DOUBLE); m.addBond(2, 3, IBond.Order.DOUBLE); @@ -797,11 +797,11 @@ public void s_penta_2_3_diene_impl_h() throws Exception { @Test public void r_penta_2_3_diene_expl_h() throws Exception { IAtomContainer m = new AtomContainer(5, 4, 0, 0); + m.addAtom(new Atom("CH3")); m.addAtom(new Atom("C")); m.addAtom(new Atom("C")); m.addAtom(new Atom("C")); - m.addAtom(new Atom("C")); - m.addAtom(new Atom("C")); + m.addAtom(new Atom("CH3")); m.addAtom(new Atom("H")); m.addAtom(new Atom("H")); m.addBond(0, 1, IBond.Order.SINGLE); @@ -831,11 +831,11 @@ public void r_penta_2_3_diene_expl_h() throws Exception { @Test public void s_penta_2_3_diene_expl_h() throws Exception { IAtomContainer m = new AtomContainer(5, 4, 0, 0); + m.addAtom(new Atom("CH3")); m.addAtom(new Atom("C")); m.addAtom(new Atom("C")); m.addAtom(new Atom("C")); - m.addAtom(new Atom("C")); - m.addAtom(new Atom("C")); + m.addAtom(new Atom("CH3")); m.addAtom(new Atom("H")); m.addAtom(new Atom("H")); m.addBond(0, 1, IBond.Order.SINGLE); From c887ff3a59416b07ce32193731defc364ed31554 Mon Sep 17 00:00:00 2001 From: John May Date: Sun, 16 Oct 2016 19:17:35 +0100 Subject: [PATCH 13/16] Correct more test with bad atom symbols and symbol visibility due to hcount. --- .../org/openscience/cdk/renderer/SymbolVisibilityTest.java | 2 ++ .../openscience/cdk/renderer/color/CDK2DAtomColorsTest.java | 3 ++- .../org/openscience/cdk/renderer/color/CDKAtomColorsTest.java | 3 ++- .../org/openscience/cdk/renderer/color/CPKAtomColorsTest.java | 3 ++- .../cdk/renderer/color/PartialAtomicChargeColorsTest.java | 3 ++- .../org/openscience/cdk/renderer/color/RasmolColorsTest.java | 3 ++- 6 files changed, 12 insertions(+), 5 deletions(-) diff --git a/display/render/src/test/java/org/openscience/cdk/renderer/SymbolVisibilityTest.java b/display/render/src/test/java/org/openscience/cdk/renderer/SymbolVisibilityTest.java index 73b223f66a..afd55fe694 100644 --- a/display/render/src/test/java/org/openscience/cdk/renderer/SymbolVisibilityTest.java +++ b/display/render/src/test/java/org/openscience/cdk/renderer/SymbolVisibilityTest.java @@ -77,6 +77,8 @@ public void iupacMethylPreferred() { public void iupacMethylAcceptable() { IAtom a1 = new Atom("C"); IAtom a2 = new Atom("C"); + a1.setImplicitHydrogenCount(null); + a1.setImplicitHydrogenCount(null); IBond bond = new Bond(a1, a2); a1.setPoint2d(new Point2d(0, 0)); a2.setPoint2d(new Point2d(0, 0)); diff --git a/display/render/src/test/java/org/openscience/cdk/renderer/color/CDK2DAtomColorsTest.java b/display/render/src/test/java/org/openscience/cdk/renderer/color/CDK2DAtomColorsTest.java index c2fc5d5381..ce3bad2231 100644 --- a/display/render/src/test/java/org/openscience/cdk/renderer/color/CDK2DAtomColorsTest.java +++ b/display/render/src/test/java/org/openscience/cdk/renderer/color/CDK2DAtomColorsTest.java @@ -27,6 +27,7 @@ import org.junit.Test; import org.openscience.cdk.Atom; import org.openscience.cdk.CDKTestCase; +import org.openscience.cdk.PseudoAtom; import org.openscience.cdk.interfaces.IAtom; /** @@ -51,7 +52,7 @@ public void testGetDefaultAtomColor() { CDK2DAtomColors colors = new CDK2DAtomColors(); Assert.assertNotNull(colors); - IAtom imaginary = new Atom("Ix"); + IAtom imaginary = new PseudoAtom("Ix"); Assert.assertEquals(new Color(0, 0, 0), colors.getAtomColor(imaginary, Color.BLACK)); } } diff --git a/display/render/src/test/java/org/openscience/cdk/renderer/color/CDKAtomColorsTest.java b/display/render/src/test/java/org/openscience/cdk/renderer/color/CDKAtomColorsTest.java index 794efaf088..a7fd7a914e 100644 --- a/display/render/src/test/java/org/openscience/cdk/renderer/color/CDKAtomColorsTest.java +++ b/display/render/src/test/java/org/openscience/cdk/renderer/color/CDKAtomColorsTest.java @@ -28,6 +28,7 @@ import org.junit.Test; import org.openscience.cdk.Atom; import org.openscience.cdk.CDKTestCase; +import org.openscience.cdk.PseudoAtom; import org.openscience.cdk.interfaces.IAtom; /** @@ -52,7 +53,7 @@ public void testGetDefaultAtomColor() { CDKAtomColors colors = new CDKAtomColors(); Assert.assertNotNull(colors); - IAtom imaginary = new Atom("Ix"); + IAtom imaginary = new PseudoAtom("Ix"); Assert.assertEquals(Color.ORANGE, colors.getAtomColor(imaginary, Color.ORANGE)); } } diff --git a/display/render/src/test/java/org/openscience/cdk/renderer/color/CPKAtomColorsTest.java b/display/render/src/test/java/org/openscience/cdk/renderer/color/CPKAtomColorsTest.java index b9aec342da..055af29120 100644 --- a/display/render/src/test/java/org/openscience/cdk/renderer/color/CPKAtomColorsTest.java +++ b/display/render/src/test/java/org/openscience/cdk/renderer/color/CPKAtomColorsTest.java @@ -28,6 +28,7 @@ import org.junit.Test; import org.openscience.cdk.Atom; import org.openscience.cdk.CDKTestCase; +import org.openscience.cdk.PseudoAtom; import org.openscience.cdk.interfaces.IAtom; /** @@ -48,7 +49,7 @@ public void testGetDefaultAtomColor() { CPKAtomColors colors = new CPKAtomColors(); Assert.assertNotNull(colors); - IAtom imaginary = new Atom("Ix"); + IAtom imaginary = new PseudoAtom("Ix"); Assert.assertEquals(Color.ORANGE, colors.getAtomColor(imaginary, Color.ORANGE)); } } diff --git a/display/render/src/test/java/org/openscience/cdk/renderer/color/PartialAtomicChargeColorsTest.java b/display/render/src/test/java/org/openscience/cdk/renderer/color/PartialAtomicChargeColorsTest.java index eafd8b1c30..e0f6098464 100644 --- a/display/render/src/test/java/org/openscience/cdk/renderer/color/PartialAtomicChargeColorsTest.java +++ b/display/render/src/test/java/org/openscience/cdk/renderer/color/PartialAtomicChargeColorsTest.java @@ -27,6 +27,7 @@ import org.junit.Test; import org.openscience.cdk.Atom; import org.openscience.cdk.CDKTestCase; +import org.openscience.cdk.PseudoAtom; import org.openscience.cdk.interfaces.IAtom; /** @@ -51,7 +52,7 @@ public void testGetDefaultAtomColor() { PartialAtomicChargeColors colors = new PartialAtomicChargeColors(); Assert.assertNotNull(colors); - IAtom imaginary = new Atom("Ix"); + IAtom imaginary = new PseudoAtom("Ix"); Assert.assertEquals(Color.ORANGE, colors.getAtomColor(imaginary, Color.ORANGE)); } } diff --git a/display/render/src/test/java/org/openscience/cdk/renderer/color/RasmolColorsTest.java b/display/render/src/test/java/org/openscience/cdk/renderer/color/RasmolColorsTest.java index 0946e51943..14711c6976 100644 --- a/display/render/src/test/java/org/openscience/cdk/renderer/color/RasmolColorsTest.java +++ b/display/render/src/test/java/org/openscience/cdk/renderer/color/RasmolColorsTest.java @@ -27,6 +27,7 @@ import org.openscience.cdk.Atom; import org.openscience.cdk.CDKTestCase; +import org.openscience.cdk.PseudoAtom; import org.openscience.cdk.interfaces.IAtom; /** @@ -51,7 +52,7 @@ public void testGetDefaultAtomColor() { RasmolColors colors = new RasmolColors(); Assert.assertNotNull(colors); - IAtom imaginary = new Atom("Ix"); + IAtom imaginary = new PseudoAtom("Ix"); Assert.assertEquals(Color.ORANGE, colors.getAtomColor(imaginary, Color.ORANGE)); } From f65dcc93d38329abe5f5fc9c1ee872ee467e9b5b Mon Sep 17 00:00:00 2001 From: John May Date: Wed, 19 Oct 2016 12:45:12 +0100 Subject: [PATCH 14/16] More robust parsing of atom symbols. --- .../org/openscience/cdk/io/PDBReader.java | 78 +++++++------------ 1 file changed, 29 insertions(+), 49 deletions(-) diff --git a/storage/pdb/src/main/java/org/openscience/cdk/io/PDBReader.java b/storage/pdb/src/main/java/org/openscience/cdk/io/PDBReader.java index a52f2b324b..4ac41df1f2 100644 --- a/storage/pdb/src/main/java/org/openscience/cdk/io/PDBReader.java +++ b/storage/pdb/src/main/java/org/openscience/cdk/io/PDBReader.java @@ -104,8 +104,6 @@ public class PDBReader extends DefaultChemObjectReader { */ private List bondsFromConnectRecords; - private static AtomTypeFactory pdbFactory; - /** * A mapping between HETATM 3-letter codes + atomNames to CDK atom type * names; for example "RFB.N13" maps to "N.planar3". @@ -139,7 +137,6 @@ public PDBReader(InputStream oIn) { public PDBReader(Reader oIn) { _oInput = new BufferedReader(oIn); initIOSettings(); - pdbFactory = null; hetDictionary = null; cdkAtomTypeFactory = null; } @@ -194,16 +191,6 @@ public boolean accepts(Class classObject) { @Override public T read(T oObj) throws CDKException { if (oObj instanceof IChemFile) { - if (pdbFactory == null) { - try { - pdbFactory = AtomTypeFactory.getInstance("org/openscience/cdk/config/data/pdb_atomtypes.xml", - ((IChemFile) oObj).getBuilder()); - } catch (Exception exception) { - logger.debug(exception); - throw new CDKException("Could not setup list of PDB atom types! " + exception.getMessage(), - exception); - } - } return (T) readChemFile((IChemFile) oObj); } else { throw new CDKException("Only supported is reading of ChemFile objects."); @@ -483,7 +470,7 @@ else if ("HELIX ".equalsIgnoreCase(cCol)) { } // ignore all other commands } } while (_oInput.ready() && (cRead != null)); - } catch (IOException | IllegalArgumentException e) { + } catch (IOException | IllegalArgumentException | CDKException e) { logger.error("Found a problem at line:"); logger.error(cRead); logger.error("01234567890123456789012345678901234567890123456789012345678901234567890123456789"); @@ -559,6 +546,20 @@ private boolean createBondsWithRebondTool(IAtomContainer molecule) { return true; } + private static boolean isUpper(char c) { + return c >= 'A' && c <= 'Z'; + } + + private String parseAtomSymbol(String str) { + if (str == null || str.isEmpty()) + return null; + int pos = 0; + final int len = str.length(); + while (pos < len && isUpper(str.charAt(pos))) + pos++; + return str.substring(0, pos); + } + /** * Creates an Atom and sets properties to their values from * the ATOM or HETATM record. If the line is shorter than 80 characters, the @@ -569,7 +570,7 @@ private boolean createBondsWithRebondTool(IAtomContainer molecule) { * @return the Atom created from the record. * @throws RuntimeException if the line is too short (less than 59 characters). */ - private PDBAtom readAtom(String cLine, int lineLength) { + private PDBAtom readAtom(String cLine, int lineLength) throws CDKException { // a line can look like (two in old format, then two in new format): // // 1 2 3 4 5 6 7 @@ -586,62 +587,41 @@ private PDBAtom readAtom(String cLine, int lineLength) { if (lineLength < 59) { throw new RuntimeException("PDBReader error during readAtom(): line too short"); } - String elementSymbol; - if (cLine.length() > 78) { - elementSymbol = cLine.substring(76, 78).trim(); - if (elementSymbol.length() == 0) { - elementSymbol = cLine.substring(12, 14).trim(); - } - } else { - elementSymbol = cLine.substring(12, 14).trim(); - } - if (elementSymbol.length() == 2) { - // ensure that the second char is lower case - if (Character.isDigit(elementSymbol.charAt(0))) { - elementSymbol = elementSymbol.substring(1); - } else { - elementSymbol = elementSymbol.charAt(0) + elementSymbol.substring(1).toLowerCase(); - } - } + boolean isHetatm = cLine.substring(0, 6).equals("HETATM"); + String atomName = cLine.substring(12, 16).trim(); + String resName = cLine.substring(17, 20).trim(); + String symbol = parseAtomSymbol(atomName); - String rawAtomName = cLine.substring(12, 16).trim(); - String resName = cLine.substring(17, 20).trim(); - boolean isHetatm; - try { - IAtomType type = pdbFactory.getAtomType(resName + "." + rawAtomName); - elementSymbol = type.getSymbol(); - isHetatm = false; - } catch (NoSuchAtomTypeException e) { - logger.error("Did not recognize PDB atom type: " + resName + "." + rawAtomName); - isHetatm = true; - } - PDBAtom oAtom = new PDBAtom(elementSymbol, new Point3d(Double.parseDouble(cLine.substring(30, 38)), + if (symbol == null) + handleError("Cannot parse symbol from " + atomName); + + PDBAtom oAtom = new PDBAtom(symbol, new Point3d(Double.parseDouble(cLine.substring(30, 38)), Double.parseDouble(cLine.substring(38, 46)), Double.parseDouble(cLine.substring(46, 54)))); if (useHetDictionary.isSet() && isHetatm) { - String cdkType = typeHetatm(resName, rawAtomName); + String cdkType = typeHetatm(resName, atomName); oAtom.setAtomTypeName(cdkType); if (cdkType != null) { try { cdkAtomTypeFactory.configure(oAtom); } catch (CDKException cdke) { - logger.warn("Could not configure", resName, " ", rawAtomName); + logger.warn("Could not configure", resName, " ", atomName); } } } oAtom.setRecord(cLine); oAtom.setSerial(Integer.parseInt(cLine.substring(6, 11).trim())); - oAtom.setName(rawAtomName.trim()); + oAtom.setName(atomName.trim()); oAtom.setAltLoc(cLine.substring(16, 17).trim()); oAtom.setResName(resName); oAtom.setChainID(cLine.substring(21, 22).trim()); oAtom.setResSeq(cLine.substring(22, 26).trim()); oAtom.setICode(cLine.substring(26, 27).trim()); if (useHetDictionary.isSet() && isHetatm) { - oAtom.setID(oAtom.getResName() + "." + rawAtomName); + oAtom.setID(oAtom.getResName() + "." + atomName); } else { - oAtom.setAtomTypeName(oAtom.getResName() + "." + rawAtomName); + oAtom.setAtomTypeName(oAtom.getResName() + "." + atomName); } if (lineLength >= 59) { String frag = cLine.substring(54, Math.min(lineLength, 60)).trim(); From 6c8f009c7ee66bed85711de5614c05119b556782 Mon Sep 17 00:00:00 2001 From: John May Date: Wed, 19 Oct 2016 17:06:01 +0100 Subject: [PATCH 15/16] Parse hydrogen isotopes. --- base/data/src/main/java/org/openscience/cdk/Atom.java | 10 ++++++++++ .../src/main/java/org/openscience/cdk/silent/Atom.java | 10 ++++++++++ 2 files changed, 20 insertions(+) diff --git a/base/data/src/main/java/org/openscience/cdk/Atom.java b/base/data/src/main/java/org/openscience/cdk/Atom.java index 75e6518238..53478a7844 100644 --- a/base/data/src/main/java/org/openscience/cdk/Atom.java +++ b/base/data/src/main/java/org/openscience/cdk/Atom.java @@ -536,6 +536,16 @@ private static boolean parseAtomSymbol(IAtom atom, String str) { atom.setAtomicNumber(0); atom.setSymbol("R"); return true; + } else if ("D".equals(str)) { + atom.setAtomicNumber(1); + atom.setMassNumber(2); + atom.setSymbol("H"); + return true; + } else if ("T".equals(str)) { + atom.setAtomicNumber(1); + atom.setMassNumber(3); + atom.setSymbol("H"); + return true; } // atom symbol diff --git a/base/silent/src/main/java/org/openscience/cdk/silent/Atom.java b/base/silent/src/main/java/org/openscience/cdk/silent/Atom.java index d599e9c48b..5844434808 100644 --- a/base/silent/src/main/java/org/openscience/cdk/silent/Atom.java +++ b/base/silent/src/main/java/org/openscience/cdk/silent/Atom.java @@ -523,6 +523,16 @@ private static boolean parseAtomSymbol(IAtom atom, String str) { atom.setAtomicNumber(0); atom.setSymbol("R"); return true; + } else if ("D".equals(str)) { + atom.setAtomicNumber(1); + atom.setMassNumber(2); + atom.setSymbol("H"); + return true; + } else if ("T".equals(str)) { + atom.setAtomicNumber(1); + atom.setMassNumber(3); + atom.setSymbol("H"); + return true; } final int len = str.length(); From f3c112bcd59b1ef30f5d9700e2818cc9aeb98f06 Mon Sep 17 00:00:00 2001 From: John May Date: Wed, 19 Oct 2016 17:26:39 +0100 Subject: [PATCH 16/16] Much more robust PDB atom symbol parsing. --- .../org/openscience/cdk/io/PDBReader.java | 56 +++++++++++++++++-- 1 file changed, 51 insertions(+), 5 deletions(-) diff --git a/storage/pdb/src/main/java/org/openscience/cdk/io/PDBReader.java b/storage/pdb/src/main/java/org/openscience/cdk/io/PDBReader.java index 4ac41df1f2..10ac6a0951 100644 --- a/storage/pdb/src/main/java/org/openscience/cdk/io/PDBReader.java +++ b/storage/pdb/src/main/java/org/openscience/cdk/io/PDBReader.java @@ -40,6 +40,7 @@ import org.openscience.cdk.CDKConstants; import org.openscience.cdk.DefaultChemObjectBuilder; import org.openscience.cdk.config.AtomTypeFactory; +import org.openscience.cdk.config.Elements; import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.exception.NoSuchAtomTypeException; import org.openscience.cdk.graph.rebond.RebondTool; @@ -549,15 +550,60 @@ private boolean createBondsWithRebondTool(IAtomContainer molecule) { private static boolean isUpper(char c) { return c >= 'A' && c <= 'Z'; } + private static boolean isLower(char c) { + return c >= 'a' && c <= 'z'; + } + private static boolean isDigit(char c) { + return c >= '0' && c <= '9'; + } private String parseAtomSymbol(String str) { + if (str == null || str.isEmpty()) return null; - int pos = 0; + final int len = str.length(); - while (pos < len && isUpper(str.charAt(pos))) - pos++; - return str.substring(0, pos); + + StringBuilder sym = new StringBuilder(); + + // try grabbing from end of line + + if (len > 76 && isUpper(str.charAt(76))) { + sym.append(str.charAt(76)); + if (len > 77 && isUpper(str.charAt(77))) + sym.append(Character.toLowerCase(str.charAt(77))); + else if (len > 77 && isLower(str.charAt(77))) + sym.append(Character.toLowerCase(str.charAt(77))); + } else if (len > 76 &&str.charAt(76) == ' ') { + if (len > 77 && isUpper(str.charAt(77))) + sym.append(str.charAt(77)); + } + + if (sym.length() > 0) + return sym.toString(); + + // try getting from PDB atom name + if (len > 13 && isUpper(str.charAt(13))) { + if (str.charAt(12) == ' ') { + sym.append(str.charAt(13)); + if (isLower(str.charAt(14))) + sym.append(str.charAt(14)); + } else if (isUpper(str.charAt(12))) { + if (str.charAt(0) == 'A' && str.charAt(12) == 'H') { + sym.append('H'); // ATOM record H is always H + } else { + sym.append(str.charAt(12)); + sym.append(Character.toLowerCase(str.charAt(13))); + } + } else if (isDigit(str.charAt(12))) { + sym.append(str.charAt(13)); + } + } + + if (sym.length() > 0) + return sym.toString(); + + return null; } /** @@ -591,7 +637,7 @@ private PDBAtom readAtom(String cLine, int lineLength) throws CDKException { boolean isHetatm = cLine.substring(0, 6).equals("HETATM"); String atomName = cLine.substring(12, 16).trim(); String resName = cLine.substring(17, 20).trim(); - String symbol = parseAtomSymbol(atomName); + String symbol = parseAtomSymbol(cLine); if (symbol == null) handleError("Cannot parse symbol from " + atomName);