lukeczapla

import org.biojava.nbio.structure.Structure;
import org.biojava.nbio.structure.StructureException;
import org.biojava.nbio.structure.StructureIO;
import org.biojava.nbio.structure.basepairs.BasePairParameters;
import org.biojava.nbio.structure.basepairs.MismatchedBasePairParameters;
import org.junit.Test;

import java.io.*;

/**

lukeczapla

<?xml version="1.0" encoding="UTF-8"?>
<project xmlns="http://maven.apache.org/POM/4.0.0"
         xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
         xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
    <modelVersion>4.0.0</modelVersion>

    <groupId>org.czapla</groupId>
    <artifactId>deeplearning</artifactId>
    <version>1.0-SNAPSHOT</version>

lukeczapla

package org.biojava.nbio.structure.secstruc;

import org.biojava.nbio.structure.*;
import org.biojava.nbio.structure.geometry.SuperPosition;
import org.biojava.nbio.structure.geometry.SuperPositionQCP;
import org.biojava.nbio.structure.io.PDBFileReader;

import javax.vecmath.Matrix4d;
import javax.vecmath.Point3d;
import java.io.ByteArrayInputStream;

lukeczapla

<?xml version="1.0" encoding="UTF-8"?>
<project xmlns="http://maven.apache.org/POM/4.0.0"
         xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
         xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
    <modelVersion>4.0.0</modelVersion>

    <groupId>org.czapla</groupId>
    <artifactId>deeplearning</artifactId>
    <version>1.0-SNAPSHOT</version>

lukeczapla

package edu.dnatools.pdbanalysis;

import edu.dnatools.calculate.NDDNA;
import org.biojava.nbio.structure.*;
import org.biojava.nbio.structure.io.PDBFileReader;
import org.nd4j.linalg.api.ndarray.INDArray;
import org.nd4j.linalg.factory.Nd4j;
import org.nd4j.linalg.inverse.InvertMatrix;
import org.nd4j.linalg.string.NDArrayStrings;
import org.slf4j.Logger;

lukeczapla

public class MatrixFun {

    public static INDArray mpow(INDArray in, int n, boolean inplace) {
        assert in.rows() == in.columns();
        if (n == 0) {
            if (inplace) return in.assign(Nd4j.eye(in.rows()));
                else return Nd4j.eye(in.rows());
        }
        INDArray temp;
        if (n < 0) {

lukeczapla

package edu.dnatools.calculate;

import org.nd4j.linalg.api.ndarray.INDArray;
import org.nd4j.linalg.eigen.Eigen;
import org.nd4j.linalg.factory.Nd4j;
import org.nd4j.linalg.indexing.NDArrayIndex;
import org.nd4j.linalg.inverse.InvertMatrix;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

lukeczapla

import org.junit.Test;
import org.nd4j.linalg.api.buffer.DataBuffer;
import org.nd4j.linalg.api.buffer.util.DataTypeUtil;
import org.nd4j.linalg.api.ndarray.INDArray;
import org.nd4j.linalg.eigen.Eigen;
import org.nd4j.linalg.factory.Nd4j;
import org.nd4j.linalg.indexing.NDArrayIndex;
import org.nd4j.linalg.inverse.InvertMatrix;
import org.nd4j.linalg.util.ArrayUtil;

lukeczapla

    /**
     * Compute generalized eigenvalues of the problem A x = L x.
     *
     * @param A symmetric Matrix A. Only the lower triangle will be considered. After execution, A will contain the eigenvectors as columns.
     * @return a vector of eigenvalues L.
     */
    public static INDArray symmetricGeneralizedEigenvalues(INDArray A) {
        INDArray eigenvalues = Nd4j.create(A.rows());
        Nd4j.getBlasWrapper().syev( 'V', 'L', A, eigenvalues );
        return eigenvalues;

lukeczapla

[INFO] Scanning for projects...
[INFO] 
[INFO] ------------------------------------------------------------------------
[INFO] Building DNAServer 1.0-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ DNAServer ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 1 resource
[INFO] Copying 2 resources