001/*
002 *                    BioJava development code
003 *
004 * This code may be freely distributed and modified under the
005 * terms of the GNU Lesser General Public Licence.  This should
006 * be distributed with the code.  If you do not have a copy,
007 * see:
008 *
009 *      http://www.gnu.org/copyleft/lesser.html
010 *
011 * Copyright for this code is held jointly by the individual
012 * authors.  These should be listed in @author doc comments.
013 *
014 * For more information on the BioJava project and its aims,
015 * or to join the biojava-l mailing list, visit the home page
016 * at:
017 *
018 *      http://www.biojava.org/
019 *
020 */
021package org.biojava.nbio.structure.domain.pdp;
022
023public class PDPParameters {
024        public static final int MAXLEN = 3200;
025        public static final int MAXDOM = 30;
026        public static final int MAX_CUTS = 80;
027        public static final int MAXSIZE = 350;
028        public static final int MIN_DOMAIN_LENGTH = 35;
029        public static final int ENDS = 12 ;
030        public static final int ENDSEND = 9;
031        public static final float RG1 = 1.0f;
032        public static final float RG  = 0.0f;
033        public static final float TD1 = 40.f;
034        public static final float TD  = 25.f;
035        public static final float DBL = .05f;
036        public static final int MAXCONT = 900;
037
038        public static final float CUT_OFF_VALUE=.50f; /* decide to cut */
039        public static final float CUT_OFF_VALUE1=.29f; /* decide to combine */
040        public static final float CUT_OFF_VALUE2=.44f; /* decide to double cut */
041        public static final float CUT_OFF_VALUE1S=.19f; /* decide to combine small domains */
042        public static final float CUT_OFF_VALUE1M=.21f; /* decide to combine medium domains */
043
044
045}