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johnmayegonw
johnmay
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egonw
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Formatting only - to make changes easier to follow
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‎storage/inchi/src/main/java/org/openscience/cdk/inchi/InChIGenerator.java

Lines changed: 10 additions & 11 deletions
Original file line numberDiff line numberDiff line change
@@ -98,7 +98,6 @@
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* </b>
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*
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* @author Sam Adams
101-
*
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* @cdk.module inchi
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* @cdk.githash
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*/
@@ -123,10 +122,10 @@ public class InChIGenerator {
123122
* <p>Reads atoms, bonds etc from atom container and converts to format
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* InChI library requires, then calls the library.
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*
126-
* @param atomContainer AtomContainer to generate InChI for.
125+
* @param atomContainer AtomContainer to generate InChI for.
127126
* @param ignoreAromaticBonds if aromatic bonds should be treated as bonds of type single and double
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* @throws org.openscience.cdk.exception.CDKException if there is an
129-
* error during InChI generation
128+
* error during InChI generation
130129
*/
131130
protected InChIGenerator(IAtomContainer atomContainer, boolean ignoreAromaticBonds) throws CDKException {
132131
this(atomContainer, Collections.singletonList(INCHI_OPTION.AuxNone), ignoreAromaticBonds);
@@ -138,10 +137,10 @@ protected InChIGenerator(IAtomContainer atomContainer, boolean ignoreAromaticBon
138137
* <p>Reads atoms, bonds etc from atom container and converts to format
139138
* InChI library requires, then calls the library.
140139
*
141-
* @param atomContainer AtomContainer to generate InChI for.
142-
* @param options Space delimited string of options to pass to InChI library.
143-
* Each option may optionally be preceded by a command line
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* switch (/ or -).
140+
* @param atomContainer AtomContainer to generate InChI for.
141+
* @param options Space delimited string of options to pass to InChI library.
142+
* Each option may optionally be preceded by a command line
143+
* switch (/ or -).
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* @param ignoreAromaticBonds if aromatic bonds should be treated as bonds of type single and double
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* @throws CDKException
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*/
@@ -162,8 +161,8 @@ protected InChIGenerator(IAtomContainer atomContainer, String options, boolean i
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* <p>Reads atoms, bonds etc from atom container and converts to format
163162
* InChI library requires, then calls the library.
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*
165-
* @param atomContainer AtomContainer to generate InChI for.
166-
* @param options List of INCHI_OPTION.
164+
* @param atomContainer AtomContainer to generate InChI for.
165+
* @param options List of INCHI_OPTION.
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* @param ignoreAromaticBonds if aromatic bonds should be treated as bonds of type single and double
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* @throws CDKException
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*/
@@ -183,7 +182,7 @@ protected InChIGenerator(IAtomContainer atomContainer, List<INCHI_OPTION> option
183182
* InChI library requires, then places call for the library to generate
184183
* the InChI.
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*
186-
* @param atomContainer AtomContainer to generate InChI for.
185+
* @param atomContainer AtomContainer to generate InChI for.
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* @throws CDKException
188187
*/
189188
private void generateInchiFromCDKAtomContainer(IAtomContainer atomContainer, boolean ignore) throws CDKException {
@@ -285,7 +284,7 @@ private void generateInchiFromCDKAtomContainer(IAtomContainer atomContainer, boo
285284

286285
// Get bond order
287286
INCHI_BOND_TYPE order;
288-
Order bo = bond.getOrder();
287+
Order bo = bond.getOrder();
289288
if (!ignore && bond.getFlag(CDKConstants.ISAROMATIC)) {
290289
order = INCHI_BOND_TYPE.ALTERN;
291290
} else if (bo == Order.SINGLE) {

‎storage/inchi/src/main/java/org/openscience/cdk/inchi/InChIGeneratorFactory.java

Lines changed: 23 additions & 24 deletions
Original file line numberDiff line numberDiff line change
@@ -60,7 +60,6 @@
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* </ul>
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*
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* @author Sam Adams
63-
*
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* @cdk.module inchi
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* @cdk.githash
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*/
@@ -71,7 +70,7 @@ public class InChIGeneratorFactory {
7170
/**
7271
* If the CDK aromaticity flag should be ignored and the bonds treated solely as single and double bonds.
7372
*/
74-
private boolean ignoreAromaticBonds = true;
73+
private boolean ignoreAromaticBonds = true;
7574

7675
/**
7776
* <p>Constructor for InChIGeneratorFactory. Ensures that native code
@@ -94,7 +93,7 @@ private InChIGeneratorFactory() throws CDKException {
9493
*
9594
* @return the one <code>InChIGeneratorFactory</code> instance
9695
* @throws CDKException if unable to load native code when attempting
97-
* to create the factory
96+
* to create the factory
9897
*/
9998
public static InChIGeneratorFactory getInstance() throws CDKException {
10099
synchronized (InChIGeneratorFactory.class) {
@@ -110,14 +109,14 @@ public static InChIGeneratorFactory getInstance() throws CDKException {
110109
* INCHI_BOND_TYPE.ALTERN is considered special in contrast to single, double, and triple bonds,
111110
* and is not bulletproof. If the molecule has clearly defined single and double bonds,
112111
* the option can be used to force the class not to use the alternating bond type.
113-
*
112+
* <p>
114113
* http://www.inchi-trust.org/fileadmin/user_upload/html/inchifaq/inchi-faq.html#16.3
115114
*
116115
* @param ignore if aromatic bonds should be treated as bonds of type single and double
117116
* @deprecated "the use of aromatic bonds is strongly discouraged" - InChI
118-
* FAQ, the InChI will fail for many compounds if ignore
119-
* aromatic bonds is not enabled and the compound have aromatic
120-
* flags.
117+
* FAQ, the InChI will fail for many compounds if ignore
118+
* aromatic bonds is not enabled and the compound have aromatic
119+
* flags.
121120
*/
122121
@Deprecated
123122
public void setIgnoreAromaticBonds(boolean ignore) {
@@ -139,7 +138,7 @@ public boolean getIgnoreAromaticBonds() {
139138
* generated by this method, please use {@link #getInChIGenerator(IAtomContainer, List)}
140139
* with no options specified if you would like to generate AuxInfo.
141140
*
142-
* @param container AtomContainer to generate InChI for.
141+
* @param container AtomContainer to generate InChI for.
143142
* @return the InChI generator object
144143
* @throws CDKException if the generator cannot be instantiated
145144
*/
@@ -150,8 +149,8 @@ public InChIGenerator getInChIGenerator(IAtomContainer container) throws CDKExce
150149
/**
151150
* Gets InChI generator for CDK IAtomContainer.
152151
*
153-
* @param container AtomContainer to generate InChI for.
154-
* @param options String of options for InChI generation.
152+
* @param container AtomContainer to generate InChI for.
153+
* @param options String of options for InChI generation.
155154
* @return the InChI generator object
156155
* @throws CDKException if the generator cannot be instantiated
157156
*/
@@ -162,10 +161,10 @@ public InChIGenerator getInChIGenerator(IAtomContainer container, String options
162161
/**
163162
* Gets InChI generator for CDK IAtomContainer.
164163
*
165-
* @param container AtomContainer to generate InChI for.
166-
* @param options List of options (net.sf.jniinchi.INCHI_OPTION) for InChI generation.
164+
* @param container AtomContainer to generate InChI for.
165+
* @param options List of options (net.sf.jniinchi.INCHI_OPTION) for InChI generation.
167166
* @return the InChI generator object
168-
* @throws CDKException if the generator cannot be instantiated
167+
* @throws CDKException if the generator cannot be instantiated
169168
*/
170169
public InChIGenerator getInChIGenerator(IAtomContainer container, List<INCHI_OPTION> options) throws CDKException {
171170
if (options == null) throw new IllegalArgumentException("Null options");
@@ -175,10 +174,10 @@ public InChIGenerator getInChIGenerator(IAtomContainer container, List<INCHI_OPT
175174
/**
176175
* Gets structure generator for an InChI string.
177176
*
178-
* @param inchi InChI to generate structure from.
177+
* @param inchi InChI to generate structure from.
179178
* @param builder the builder to use
180-
* @return the InChI structure generator object
181-
* @throws CDKException if the generator cannot be instantiated
179+
* @return the InChI structure generator object
180+
* @throws CDKException if the generator cannot be instantiated
182181
*/
183182
public InChIToStructure getInChIToStructure(String inchi, IChemObjectBuilder builder) throws CDKException {
184183
return (new InChIToStructure(inchi, builder));
@@ -187,11 +186,11 @@ public InChIToStructure getInChIToStructure(String inchi, IChemObjectBuilder bui
187186
/**
188187
* <p>Gets structure generator for an InChI string.
189188
*
190-
* @param inchi InChI to generate structure from.
189+
* @param inchi InChI to generate structure from.
191190
* @param builder the builder to employ
192-
* @param options String of options for structure generation.
193-
* @return the InChI structure generator object
194-
* @throws CDKException if the generator cannot be instantiated
191+
* @param options String of options for structure generation.
192+
* @return the InChI structure generator object
193+
* @throws CDKException if the generator cannot be instantiated
195194
*/
196195
public InChIToStructure getInChIToStructure(String inchi, IChemObjectBuilder builder, String options)
197196
throws CDKException {
@@ -201,11 +200,11 @@ public InChIToStructure getInChIToStructure(String inchi, IChemObjectBuilder bui
201200
/**
202201
* <p>Gets structure generator for an InChI string.
203202
*
204-
* @param inchi InChI to generate structure from.
205-
* @param options List of options (net.sf.jniinchi.INCHI_OPTION) for structure generation.
203+
* @param inchi InChI to generate structure from.
204+
* @param options List of options (net.sf.jniinchi.INCHI_OPTION) for structure generation.
206205
* @param builder the builder to employ
207-
* @return the InChI structure generator object
208-
* @throws CDKException if the generator cannot be instantiated
206+
* @return the InChI structure generator object
207+
* @throws CDKException if the generator cannot be instantiated
209208
*/
210209
public InChIToStructure getInChIToStructure(String inchi, IChemObjectBuilder builder, List<String> options)
211210
throws CDKException {

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