Merge pull request #25 from rcsb/v1.0.1

Version 1.0.1 of mmtf-java

Author: abradle

CHANGELOG.md

@@ -58,3 +58,8 @@ All notable changes to this project will be documented in this file, following t
 
 ### Added
  - API function to get a byte array from the URL
+
+
+## v1.0.1 - 2016-08-18
+### Changed
+ - Added saccharides to the reduced format

README.md

@@ -1,7 +1,7 @@
 [![Build Status](https://travis-ci.org/rcsb/mmtf-java.svg?branch=master)](https://travis-ci.org/rcsb/mmtf-java)
 [![Coverage Status](https://coveralls.io/repos/github/rcsb/mmtf-java/badge.svg?branch=master)](https://coveralls.io/github/rcsb/mmtf-java?branch=master)
 [![Dependency Status](https://www.versioneye.com/user/projects/56feb8e5fcd19a0039f1553c/badge.svg?style=flat)](https://www.versioneye.com/user/projects/56feb8e5fcd19a0039f1553c)
-[![Version](http://img.shields.io/badge/version-1.0.0-blue.svg?style=flat)](https://github.com/rcsb/mmtf-java/) [![License](http://img.shields.io/badge/license-Apache 2.0-blue.svg?style=flat)](https://github.com/rcsb/mmtf-java/blob/master/LICENSE.txt)
+[![Version](http://img.shields.io/badge/version-1.0.1-blue.svg?style=flat)](https://github.com/rcsb/mmtf-java/) [![License](http://img.shields.io/badge/license-Apache 2.0-blue.svg?style=flat)](https://github.com/rcsb/mmtf-java/blob/master/LICENSE.txt)
 [![Changelog](https://img.shields.io/badge/changelog--lightgrey.svg?style=flat)](https://github.com/rcsb/mmtf-java/blob/master/CHANGELOG.md)
 
 
@@ -16,12 +16,12 @@ The alpha release is available on Maven central.
 		<dependency>
 			<groupId>org.rcsb</groupId>
 			<artifactId>mmtf-codec</artifactId>
-			<version>1.0.0</version>
+			<version>1.0.1</version>
 		</dependency>
         <dependency>
             <groupId>org.rcsb</groupId>
             <artifactId>mmtf-api</artifactId>
-            <version>1.0.0</version>
+            <version>1.0.1</version>
         </dependency>
 ```
 

mmtf-api/pom.xml

@@ -3,7 +3,7 @@
 	<parent>
 		<groupId>org.rcsb</groupId>
 		<artifactId>mmtf</artifactId>
-		<version>1.0.1-SNAPSHOT</version>
+		<version>1.0.2-SNAPSHOT</version>
 	</parent>
 	<artifactId>mmtf-api</artifactId>
 	<packaging>jar</packaging>

mmtf-codec/pom.xml

@@ -3,7 +3,7 @@
 	<parent>
 		<groupId>org.rcsb</groupId>
 		<artifactId>mmtf</artifactId>
-		<version>1.0.1-SNAPSHOT</version>
+		<version>1.0.2-SNAPSHOT</version>
 	</parent>
 	<artifactId>mmtf-codec</artifactId>
 	<packaging>jar</packaging>
@@ -19,12 +19,12 @@
 		<dependency>
 			<groupId>org.rcsb</groupId>
 			<artifactId>mmtf-api</artifactId>
-			<version>1.0.1-SNAPSHOT</version>
+			<version>1.0.2-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>org.rcsb</groupId>
 			<artifactId>mmtf-serialization</artifactId>
-			<version>1.0.1-SNAPSHOT</version>
+			<version>1.0.2-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>commons-lang</groupId>

mmtf-codec/src/main/java/org/rcsb/mmtf/encoder/ReducedEncoder.java

@@ -166,6 +166,10 @@ private static List<Integer> getIndicesToAdd(StructureDataInterface structureDat
 				if(atomName.equals(PHOSPHATE_NAME) && elementName.equals(PHOSPHATE_ELEMENT)){
 					outList.add(i);
 				}
+				// Check if it's a saccharide
+				if(structureDataInterface.getGroupChemCompType(groupType).toUpperCase().contains("SACCHARIDE")) {
+					outList.add(i);
+				}
 			}
 		}
 		// Check if it's a non-polymer 

mmtf-serialization/pom.xml

@@ -3,7 +3,7 @@
 	<parent>
 		<groupId>org.rcsb</groupId>
 		<artifactId>mmtf</artifactId>
-                <version>1.0.1-SNAPSHOT</version>
+                <version>1.0.2-SNAPSHOT</version>
 	</parent>
 	<artifactId>mmtf-serialization</artifactId>
 	<packaging>jar</packaging>

pom.xml

@@ -13,7 +13,7 @@
 	<groupId>org.rcsb</groupId>
 	<artifactId>mmtf</artifactId>
 	<packaging>pom</packaging>
-	<version>1.0.1-SNAPSHOT</version>
+	<version>1.0.2-SNAPSHOT</version>
 	<name>mmtf</name>
 	<description>MMTF is a compressed, fast and useful format for serving macromolecular data.
     </description>