First commit - get 3D coords from SMILES

.gitignore

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+*.iml
+.gradle
+.idea/
+projectFilesBackup/
+/local.properties
+/.idea/workspace.xml
+/.idea/libraries
+.DS_Store
+/build
+/captures
+release/
+.externalNativeBuild
+google-services.json

app/.gitignore

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+/build

app/build.gradle

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+apply plugin: 'com.android.application'
+
+apply plugin: 'kotlin-android'
+
+apply plugin: 'kotlin-android-extensions'
+
+android {
+    compileSdkVersion 29
+    buildToolsVersion "29.0.2"
+    defaultConfig {
+        applicationId "com.plweegie.magmolecular"
+        minSdkVersion 24
+        targetSdkVersion 29
+        versionCode 1
+        versionName "1.0"
+        testInstrumentationRunner "androidx.test.runner.AndroidJUnitRunner"
+    }
+    buildTypes {
+        release {
+            minifyEnabled false
+            proguardFiles getDefaultProguardFile('proguard-android-optimize.txt'), 'proguard-rules.pro'
+        }
+    }
+    packagingOptions {
+        pickFirst 'META-INF/kotlinx-coroutines-core.kotlin_module'
+    }
+    compileOptions {
+        sourceCompatibility 1.8
+        targetCompatibility 1.8
+    }
+}
+
+dependencies {
+    implementation fileTree(dir: 'libs', include: ['*.jar'])
+    implementation"org.jetbrains.kotlin:kotlin-stdlib-jdk7:$kotlin_version"
+    implementation 'androidx.appcompat:appcompat:1.1.0'
+    implementation 'androidx.core:core-ktx:1.1.0'
+    implementation 'androidx.constraintlayout:constraintlayout:1.1.3'
+    implementation 'com.google.android.material:material:1.0.0'
+
+    implementation 'androidx.lifecycle:lifecycle-runtime-ktx:2.2.0-rc03'
+
+    implementation 'com.google.ar:core:1.14.0'
+    implementation 'com.google.ar.sceneform:core:1.14.0'
+    implementation 'com.google.ar.sceneform.ux:sceneform-ux:1.14.0'
+
+    implementation 'org.jetbrains.kotlinx:kotlinx-coroutines-core-common:1.3.1'
+    implementation 'org.jetbrains.kotlinx:kotlinx-coroutines-core:1.3.1'
+    implementation 'org.jetbrains.kotlinx:kotlinx-coroutines-android:1.3.1'
+    implementation 'org.jetbrains.kotlinx:kotlinx-coroutines-jdk8:1.3.1'
+
+    implementation 'org.openscience.cdk:cdk-core:2.3'
+    implementation 'org.openscience.cdk:cdk-interfaces:2.3'
+    implementation 'org.openscience.cdk:cdk-smiles:2.3'
+    implementation 'org.openscience.cdk:cdk-data:2.3'
+    implementation 'org.openscience.cdk:cdk-standard:2.3'
+    implementation 'org.openscience.cdk:cdk-io:2.3'
+
+    testImplementation 'junit:junit:4.12'
+    androidTestImplementation 'androidx.test.ext:junit:1.1.1'
+    androidTestImplementation 'androidx.test.espresso:espresso-core:3.2.0'
+}
+
+apply plugin: 'com.google.ar.sceneform.plugin'

app/proguard-rules.pro

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+# Add project specific ProGuard rules here.
+# You can control the set of applied configuration files using the
+# proguardFiles setting in build.gradle.
+#
+# For more details, see
+#   http://developer.android.com/guide/developing/tools/proguard.html
+
+# If your project uses WebView with JS, uncomment the following
+# and specify the fully qualified class name to the JavaScript interface
+# class:
+#-keepclassmembers class fqcn.of.javascript.interface.for.webview {
+#   public *;
+#}
+
+# Uncomment this to preserve the line number information for
+# debugging stack traces.
+#-keepattributes SourceFile,LineNumberTable
+
+# If you keep the line number information, uncomment this to
+# hide the original source file name.
+#-renamesourcefileattribute SourceFile

app/src/androidTest/java/com/plweegie/magmolecular/ExampleInstrumentedTest.kt

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+package com.plweegie.magmolecular
+
+import androidx.test.platform.app.InstrumentationRegistry
+import androidx.test.ext.junit.runners.AndroidJUnit4
+
+import org.junit.Test
+import org.junit.runner.RunWith
+
+import org.junit.Assert.*
+
+/**
+ * Instrumented test, which will execute on an Android device.
+ *
+ * See [testing documentation](http://d.android.com/tools/testing).
+ */
+@RunWith(AndroidJUnit4::class)
+class ExampleInstrumentedTest {
+    @Test
+    fun useAppContext() {
+        // Context of the app under test.
+        val appContext = InstrumentationRegistry.getInstrumentation().targetContext
+        assertEquals("com.plweegie.magmolecular", appContext.packageName)
+    }
+}

app/src/main/AndroidManifest.xml

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+<?xml version="1.0" encoding="utf-8"?>
+<manifest xmlns:android="http://schemas.android.com/apk/res/android"
+    package="com.plweegie.magmolecular">
+
+    <uses-permission android:name="android.permission.CAMERA" />
+
+    <uses-feature android:name="android.hardware.camera.ar" android:required="true" />
+
+    <application
+        android:allowBackup="true"
+        android:icon="@mipmap/ic_launcher"
+        android:label="@string/app_name"
+        android:roundIcon="@mipmap/ic_launcher_round"
+        android:supportsRtl="true"
+        android:theme="@style/AppTheme">
+        <meta-data android:name="com.google.ar.core" android:value="required" />
+        <activity android:name=".MainActivity">
+            <intent-filter>
+                <action android:name="android.intent.action.MAIN" />
+
+                <category android:name="android.intent.category.LAUNCHER" />
+            </intent-filter>
+        </activity>
+        <activity android:name=".ar.MagMolActivity" />
+    </application>
+
+</manifest>

app/src/main/java/com/plweegie/magmolecular/MainActivity.kt

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+package com.plweegie.magmolecular
+
+import androidx.appcompat.app.AppCompatActivity
+import android.os.Bundle
+import android.util.Log
+import android.widget.Toast
+import com.plweegie.magmolecular.rendering.AndroidModelBuilder3D
+import kotlinx.android.synthetic.main.activity_main.*
+import kotlinx.coroutines.*
+import org.openscience.cdk.DefaultChemObjectBuilder
+import org.openscience.cdk.exception.InvalidSmilesException
+import org.openscience.cdk.interfaces.IAtom
+import org.openscience.cdk.interfaces.IAtomContainer
+import org.openscience.cdk.smiles.SmilesParser
+import kotlin.coroutines.CoroutineContext
+
+class MainActivity : AppCompatActivity(), CoroutineScope {
+
+    private lateinit var smilesParser: SmilesParser
+    private lateinit var modelBuilder: AndroidModelBuilder3D
+    private lateinit var job: Job
+
+    override val coroutineContext: CoroutineContext
+        get() = job + Dispatchers.Main
+
+    override fun onCreate(savedInstanceState: Bundle?) {
+        super.onCreate(savedInstanceState)
+        setContentView(R.layout.activity_main)
+        job = Job()
+
+        val builder = DefaultChemObjectBuilder.getInstance()
+        smilesParser = SmilesParser(builder)
+        modelBuilder = AndroidModelBuilder3D.getInstance(builder)
+
+        get_atoms_btn?.setOnClickListener {
+            parseSmiles()
+        }
+    }
+
+    override fun onDestroy() {
+        super.onDestroy()
+        job.cancel()
+    }
+
+    private fun parseSmiles() {
+        val smiles = smiles_field?.text.toString()
+        try {
+            val atomContainer = smilesParser.parseSmiles(smiles)
+
+            launch {
+                val atoms3d = get3DCoordinates(atomContainer)
+                atoms3d.forEach {
+                    Log.d("COORDS", "${it.point3d.x}, ${it.point3d.y}, ${it.point3d.z}")
+                }
+            }
+        } catch (e: InvalidSmilesException) {
+            Toast.makeText(this, "Invalid SMILES", Toast.LENGTH_SHORT).show()
+        }
+    }
+
+    private suspend fun get3DCoordinates(atomContainer: IAtomContainer): List<IAtom> {
+        val atomContainer3D = withContext(Dispatchers.Default) {
+            modelBuilder.generate3DCoordinates(atomContainer, false)
+        }
+        return atomContainer3D.atoms().toList()
+    }
+}

app/src/main/java/com/plweegie/magmolecular/ar/MagMolActivity.kt

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+package com.plweegie.magmolecular.ar
+
+import androidx.appcompat.app.AppCompatActivity
+import com.google.ar.sceneform.ux.ArFragment
+
+
+class MagMolActivity : AppCompatActivity() {
+
+    private lateinit var arFragment: ArFragment
+
+}

app/src/main/java/com/plweegie/magmolecular/ar/MagMolFragment.kt

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+package com.plweegie.magmolecular.ar
+
+import android.content.Context
+import android.util.DisplayMetrics
+import com.google.ar.sceneform.math.Quaternion
+import com.google.ar.sceneform.math.Vector3
+import com.google.ar.sceneform.ux.*
+
+
+class MagMolFragment : ArFragment() {
+
+    companion object {
+        private val MIN_OPENGL_VERSION = 3.1
+    }
+
+    private val displayMetrics: DisplayMetrics by lazy {
+        val metrics = DisplayMetrics()
+        activity?.windowManager?.defaultDisplay?.getMetrics(metrics)
+        metrics
+    }
+
+    override fun onAttach(context: Context) {
+        super.onAttach(context)
+        //TODO add OpenGL check
+    }
+
+    override fun makeTransformationSystem(): TransformationSystem {
+
+        val transformationSystem = TransformationSystem(displayMetrics, null)
+        val gesturePointersUtility = GesturePointersUtility(displayMetrics)
+
+        val dragGestureRecognizer = DragGestureRecognizer(gesturePointersUtility)
+
+        dragGestureRecognizer.addOnGestureStartedListener {
+            val startPosition = it.position
+            var endPosition = Vector3.zero()
+
+            it.setGestureEventListener(object : BaseGesture.OnGestureEventListener<DragGesture> {
+                override fun onUpdated(gesture: DragGesture?) {
+                    endPosition = gesture?.position
+                    val angle = getRotationAngle(startPosition, endPosition)
+                    gesture?.targetNode?.localRotation = Quaternion.multiply(
+                        gesture?.targetNode?.localRotation,
+                        Quaternion.axisAngle(Vector3.up(), angle)
+                    )
+                }
+
+                override fun onFinished(gesture: DragGesture?) {}
+            })
+        }
+        transformationSystem.addGestureRecognizer(dragGestureRecognizer)
+        return transformationSystem
+    }
+
+    private fun getRotationAngle(startPosition: Vector3, endPosition: Vector3): Float {
+        val diff = endPosition.x - startPosition.x
+        return  (10 * diff) / displayMetrics.widthPixels
+    }
+}