DENOPTIMConstants.java

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/*
 *   DENOPTIM
 *   Copyright (C) 2019 Vishwesh Venkatraman <vishwesh.venkatraman@ntnu.no> and
 *   Marco Foscato <marco.foscato@uib.no>
 * 
 *   This program is free software: you can redistribute it and/or modify
 *   it under the terms of the GNU Affero General Public License as published
 *   by the Free Software Foundation, either version 3 of the License, or
 *   (at your option) any later version.
 *
 *   This program is distributed in the hope that it will be useful,
 *   but WITHOUT ANY WARRANTY; without even the implied warranty of
 *   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 *   GNU Affero General Public License for more details.
 *
 *   You should have received a copy of the GNU Affero General Public License
 *   along with this program.  If not, see <http://www.gnu.org/licenses/>.
 */
 
package denoptim.constants;
 
import java.io.File;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Map;
import java.util.Set;
 
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
 
import denoptim.exception.DENOPTIMException;
import denoptim.files.FileFormat;
import denoptim.files.FileUtils;
import denoptim.graph.APClass;
import denoptim.graph.AttachmentPoint;
import denoptim.graph.Edge.BondType;
import denoptim.graph.Vertex;
import denoptim.graph.rings.RingClosingAttractor;
 
 
public final class DENOPTIMConstants 
{
    public static final String EOL = System.getProperty("line.separator");
 
    public static final String FSEP = System.getProperty("file.separator");
 
    public static final File GLOBALCONFIG = ensureConfigFolderExists();
    private static File ensureConfigFolderExists()
    {
        File configFolder = new File(
                System.getProperty("user.home") + FSEP + ".denoptim");
        try
        {
            if (!configFolder.exists())
            {
                boolean wasMade = FileUtils.createDirectory(
                        configFolder.getAbsolutePath());
                if (!wasMade)
                {
                    throw new DENOPTIMException("ERROR: could not make "
                            + "configuration folder '" 
                            + configFolder.getAbsolutePath() + "'");
                }
            }
        } catch (Throwable t)
        {
            t.printStackTrace();
            String msg = "ERROR: unable to make configuration folder '"  
                    + configFolder.getAbsolutePath() + "'";
            System.err.println(msg);
            throw new Error(msg);
        }
        return configFolder;
    }
    
    public static final File RECENTFILESLIST = new File(
            GLOBALCONFIG.getAbsoluteFile() + FSEP + "recent_files_list");
 
    public static final Map<String, Integer> VALENCE_MAP = createMap();
    private static Map<String, Integer> createMap()
    {
        Map<String, Integer> result = new HashMap<>();
        result.put("C", 4);
        result.put("N", 3);
        result.put("S", 6);
        result.put("As", 5);
        result.put("Cd", 2);
        result.put("Hg", 2);
        result.put("Zn", 2);
        result.put("B", 3);
        result.put("Si", 4);
        result.put("Ge", 4);
        result.put("Se", 6);
        result.put("Te", 6);
        result.put("Sb", 5);
        result.put("Sn", 4);
        result.put("Cl", 1);
        result.put("Br", 1);
        result.put("F", 1);
        result.put("I", 1);
        result.put("P", 5);
        result.put("O", 2);
        return Collections.unmodifiableMap(result);
    };
    
    public static final Set<String> ORGANIC_SUBSET_ELEMENTS = 
                    new HashSet<>(Arrays.asList(new String[] {"C",  
                        "N", "S", "O", "P", "F", "Br", "Cl", "I", "B"}
                    ));
 
    public static final Set<String> ALL_ELEMENTS = 
                    new HashSet<>(Arrays.asList(new String[] {"H", "He",
                    "Li", "Be", "B", "C", "N", "O", "F", "Ne",
                    "Na", "Mg", "Al", "SiP", "S", "Cl", "Ar",
                    "K", "Ca", "Ga", "Ge", "As", "Se", "Br", "Kr",
                    "Rb", "Sr", "In", "Sn", "Sb", "Te", "I", "Xe",
                    "Cs", "Ba", "Tl", "Pb", "Bi", "Po", "At", "Rn",
                    "Fr", "Ra",
                    "Sc", "Ti", "V", "Cr", "Mn", "Fe", "Co", "Ni",
                "Cu", "Zn",
                    "Y", "Zr", "Nb", "Mo", "Tc", "Ru", "Rh", "Pd", 
                "Ag", "Cd",
                    "La", "Hf", "Ta", "W", "Re", "Os", "Ir", "Pt", 
                "Au", "Hg",
                    "Ac", "Ce", "Pr", "Nd", "Pm", "Sm", "Eu", "Gd",
                "Tb", "Dy",
                    "Ho", "Er", "Tm", "Yb", "Lu", "Th", "Pa", "U", 
                "Np", "Pu",
                    "Am", "Cm", "Bk", "Cf", "Es", "Fm", "Md", "No",
                "Lr"}));
    
    public static ArrayList<String> ALL_METALS = new ArrayList<String>(
            Arrays.asList("Li", "Na", "K", "Rb", "Cs", "Fr",
            "Be", "Mg", "Ca", "Sr", "Ba", "Ra",
            "Al", "Ga", "In", "Tl", 
            "Ge", "Sn", "Pb", 
            "Sb", "Bi", 
            "Po",
            "Sc", "Ti", "V", "Cr", "Mn", "Fe", "Co", "Ni", "Cu", "Zn",
            "Y", "Zr", "Nb", "Mo", "Tc", "Ru", "Rh", "Pd", "Ag", "Cd",
            "Hf", "Ta", "W", "Re", "Os", "Ir", "Pt", "Au", "Hg",
            "La", "Ce", "Pr", "Nd", "Pm", "Sm", "Eu", "Gd", "Tb", "Dy", "Ho", "Er",
            "Tm", "Yb", "Lu",
            "Ac", "Th", "Pa", "U", "Np", "Pu", "Am", "Cm", "Bk", "Cf", "Es", "Fm", 
            "Md", "No", "Lr"));
    
    public static final Set<String> ALLOWED_ELEMENTS = 
                    new HashSet<>(Arrays.asList(new String[] {"C", "H", 
                        "N", "S", "O", "P", "F", "Br", "Cl", "I", "B", "As", 
                        "Si", "Sn", "Cd", "Hg", "Zn", "Te", "Ge", "Sb", "Se"}
                    ));
 
    public static final Set<String> ALLOWED_EXTENSIONS = 
                    new HashSet<>(Arrays.asList(new String[] {".txt", 
            ".sdf", ".mol"}
                    ));
    
    public static final String APCMAPCOMPRULE = "RCN";
    
    public static final String APCMAPAP2BO = "RBO";
    
    public static final String APCMAPFORBIDDENEND = "DEL";
    
    public static final String APCMAPCAPPING = "CAP";
    
    public static final String APCMAPIGNORE = "#";
    
    public static final String GAGENDIRNAMEROOT = "Gen";
    
    public static final String GAGENSUMMARYHEADER = "#Name               "
            + "GraphId             UID                           "
            + "Fitness        Source";
    
    public static final String FSEIDXNAMEROOT = "FSE-Level_";
    
    public static final String SERGFILENAMEROOT = "dg_";
    
    public static final String SERGFILENAMEEXT = "json";
    
    public static final String FITFILENAMEPREFIX = "M";
    
    public static final String FITFILENAMEEXTIN = "_inp.sdf";
    
    public static final String FITFILENAMEEXTOUT = "_out.sdf";
    
    public static final String CANDIDATE2DEXTENSION = ".png";    
    
    public static final String UNREADABLEFILEPOSTFIX = "_UNREADABLE";
    
    public static final String GRAPHFORMATSTRING = "STRING";
    
    public static final String GRAPHFORMATBYTE = "BYTE";
    
    
    public static final double INVPI = 1.0/Math.sqrt(Math.PI * 2);
    
    
    public static final int MOLDIGITS = 8;
 
    public static final String GCODETAG = "GCODE";
    
    public static final String GRAPHTAG = "GraphENC";
    
    public static final String GRAPHJSONTAG = "GraphJson";
    
    public static final String VERTEXJSONTAG = "VertexJson";
    
    public static final String PROVENANCE = "Provenance";
 
    public static final String APSTAG = "ATTACHMENT_POINTS";
    
    public static final String MOLERRORTAG = "MOL_ERROR";
    
    public static final String FITNESSTAG = "FITNESS";
    
    public static final String SMILESTAG = "SMILES";
    
    public static final String UNIQUEIDTAG = "UID";
    
    public static final String INCHIKEYTAG = "InChi";
    
    public static final String PARENTGRAPHTAG = "ParentGraph";  
    
    public static final String GRAPHLEVELTAG = "GraphLevel";
 
    public static final String DUMMYATMSYMBOL = "Du";
    
    public static final String ATMPROPAPS = "ATTACHMENT_POINTS";
 
    public static final String ATMPROPVERTEXID = "DENOPTIMVertexID";
    
    public static final String ATMPROPVERTEXPATH = "ATMPROPVERTEXPATH";
    
    public static final String ATMPROPORIGINALATMID = "DENOPTIMAtomPosition";
 
    public static final String BONDPROPROTATABLE = "DENOPTIMRotable";
 
    public static final Object RCAPROPAPCTORCA = "RCAPROPAPCTORCA";
    
    public static final Object RCAPROPCHORDBNDTYP = "RCAPROPCHORDBNDTYP";
    
    public static final Object RCAPROPRINGUSER = "RCAPROPRINGUSER";
    
    public static final double FLOATCOMPARISONTOLERANCE = 0.000000001;
    
    public static final String SEPARATORAPPROPATMS = " ";
    
    public static final String SEPARATORAPPROPAPS = ",";
    
    public static final String SEPARATORAPPROPAAP = "#";
    
    public static final String SEPARATORAPPROPSCL = ":";
    
    public static final String SEPARATORAPPROPXYZ = "%";
 
    public static final Object MOLPROPAPxVID = "APsPerVertexID";
 
    public static final Object MOLPROPAPxEDGE = "APsPerEdge";
    
    public static final Object MOLPROPAPxATOM = "APsPerAtom";
    
    public static final Object MOLPROPAPxBOND = "APsPerBond";
 
    public static final Object STOREDVID = "OLDVERTEXID";
    
    public static final Object LINKAPS = "LINKTOGRAPHSAP";
 
    public static final Object APORIGINALLENGTH = "ORIGINALLENGTH";
    
    public static final Object VRTSYMMSETID = "VRTSYMMSETID";
 
    public static final Object GRAPHBRANCHID = "GRAPHBRANCHID";
    
    public static final String CUTRULKEYWORD = "CTR";
 
    public static final Object FORMULASTR = "FORMULASTR";
 
    public static final Object ISOMORPHICFAMILYID = "ISOMORPHICFAMILYID";
    
    public static final String MWSLOTFRAGSFILENAMEROOT = "MWSlot_";
    
    public static final String MWSLOTFRAGSUNQFILENANEEND = "_Unq";
    
    public static final String MWSLOTFRAGSALLFILENANEEND = "_All";
    
    public static final FileFormat TMPFRAGFILEFORMAT = FileFormat.VRTXSDF;
    
}