MMBuilderParameters.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.programs.moldecularmodelbuilder;
 
import java.lang.reflect.Field;
import java.util.ArrayList;
import java.util.HashMap;
 
import denoptim.exception.DENOPTIMException;
import denoptim.integration.tinker.TinkerUtils;
import denoptim.molecularmodeling.MMBuilderUtils;
import denoptim.programs.RunTimeParameters;
 
public class MMBuilderParameters extends RunTimeParameters
{
    protected boolean debug = false;
 
    protected String toolPSSROT;
 
    protected String toolXYZINT;
 
    protected String toolINTXYZ;
 
    protected boolean keepDummy = false;
 
    protected String forceFieldFile;
 
    protected String pssrotFile;
 
    protected String rsPssrotFile;
 
    protected String keyFile;
 
    protected String rsKeyFile;
 
    protected ArrayList<String> pssrotParams_Init;
 
    protected ArrayList<String> pssrotParams_Rest;
 
    protected ArrayList<String> keyFileParams;
 
    protected ArrayList<String> rsPssrotParams_Init;
 
    protected ArrayList<String> rsPssrotParams_Rest;
 
    protected ArrayList<String> rsKeyFileParams;
 
    protected int atomOrderingScheme = 1;
 
    protected HashMap<String, Integer> TINKER_MAP;
 
    protected int taskID;
 
    protected String inpSDFFile;
 
    protected String outSDFFile;
 
    protected String rcoServerHostname = "localhost";
 
    protected Integer rcoServerPort = 5972;
 
//------------------------------------------------------------------------------
    
    public MMBuilderParameters()
    {
        super(ParametersType.MMB_PARAM);
    }
 
//------------------------------------------------------------------------------
 
    public int getTaskID()
    {
        return taskID;
    }
 
//------------------------------------------------------------------------------
 
    public String getInputSDFFile()
    {
        return inpSDFFile;
    }
 
//------------------------------------------------------------------------------
 
    public String getOutputSDFFile()
    {
        return outSDFFile;
    }
 
//------------------------------------------------------------------------------
 
    public String getPSSROTTool()
    {
        return toolPSSROT;
    }
 
//------------------------------------------------------------------------------
 
    public String getXYZINTTool()
    {
        return toolXYZINT;
    }
 
//------------------------------------------------------------------------------
 
    public String getINTXYZTool()
    {
        return toolINTXYZ;
    }
 
//------------------------------------------------------------------------------
 
    public String getParamFile()
    {
        return forceFieldFile;
    }
 
//------------------------------------------------------------------------------
 
    public ArrayList<String> getInitPSSROTParams()
    {
        return pssrotParams_Init;
    }
 
//------------------------------------------------------------------------------
 
    public ArrayList<String> getRSInitPSSROTParams()
    {
        return rsPssrotParams_Init;
    }
 
//------------------------------------------------------------------------------
 
    public ArrayList<String> getRestPSSROTParams()
    {
        return pssrotParams_Rest;
    }
 
//------------------------------------------------------------------------------
 
    public ArrayList<String> getRSRestPSSROTParams()
    {
        return rsPssrotParams_Rest;
    }
 
//------------------------------------------------------------------------------
 
    public ArrayList<String> getKeyFileParams()
    {
        return keyFileParams;
    }
 
//------------------------------------------------------------------------------
 
    public boolean getKeepDummyFlag()
    {
        return keepDummy;
    }
 
//------------------------------------------------------------------------------
 
    public ArrayList<String> getRSKeyFileParams()
    {
        return rsKeyFileParams;
    }
 
//------------------------------------------------------------------------------
 
    public boolean debug()
    {
        return debug;
    }
 
//------------------------------------------------------------------------------
 
    public int getAtomOrderingScheme()
    {
        return atomOrderingScheme;
    }
 
//------------------------------------------------------------------------------
 
    public HashMap<String, Integer> getTinkerMap()
    {
        return TINKER_MAP;
    }
 
//------------------------------------------------------------------------------
 
    public String getWorkingDirectory()
    {
        return workDir;
    }
 
//------------------------------------------------------------------------------
 
    public String getRCOServerHostname() {
        return rcoServerHostname;
    }
 
//------------------------------------------------------------------------------
 
    public Integer getRCOServerPort() {
        return rcoServerPort;
    }
 
//-----------------------------------------------------------------------------
 
    public void interpretKeyword(String key, String value)
        throws DENOPTIMException
    {
        String msg = "";
        switch (key.toUpperCase())
        {
        case "TOOLPSSROT=":            
            toolPSSROT = value;
            break;
        case "TOOLXYZINT=":
            toolXYZINT = value;
            break;
        case "TOOLINTXYZ=":
            toolINTXYZ = value;
            break;
        case "FORCEFIELDFILE=":
            forceFieldFile = value;
            break;
        case "KEYFILE=":
            keyFile = value;
            break;
        case "RCKEYFILE=":
            rsKeyFile = value;
            break;
        case "VERBOSITY=":
            try
            {
                verbosity = Integer.parseInt(value);
            }
            catch (Throwable t)
            {
                msg = "Unable to understand value " + key + "'" + value + "'";
                throw new DENOPTIMException(msg);
            }
            break;
        case "DEBUG=":
            debug = true;
            break;
        case "PSSROTPARAMS=":
            pssrotFile = value;
            break;
        case "RCPSSROTPARAMS=":
            rsPssrotFile = value;
            break;
        case "KEEPDUMMYATOMS":
            keepDummy = true;
            break;
        case "ATOMORDERINGSCHEME=":
            try
            {
                atomOrderingScheme = Integer.parseInt(value);
            }
            catch (Throwable t)
            {
                msg = "Unable to understand value " + key + "'" + value + "'";
                throw new DENOPTIMException(msg);
            }
            break;
        case "INPSDF=":
            inpSDFFile = value;
            break;
        case "OUTSDF=":
            outSDFFile = value;
            break;
        case "WORKDIR=":
            workDir = value;
            break;
        case "RCOSERVERHOSTNAME=":
            rcoServerHostname = value;
            break;
        case "RCOSERVERPORT=":
            rcoServerPort = Integer.parseInt(value);
            break;
 
/*
        case "=":
            = value;
            break;
*/
 
        default:
             msg = "Keyword " + key + " is not a known keyword for the "
                     + "3d-molecular model builder. Check input files.";
            throw new DENOPTIMException(msg);
        }
    }
 
//------------------------------------------------------------------------------
 
    public void checkParameters() throws DENOPTIMException
    {
        ensureNotNull("wrkDir",workDir,"WORKDIR");
        ensureFileExists(workDir);
 
        ensureNotNull("inpSDFFile",inpSDFFile,"INPSDF");
        ensureFileExists(inpSDFFile);
 
        ensureNotNull("outSDFFile",outSDFFile,"OUTSDF");
 
        if (atomOrderingScheme < 1 || atomOrderingScheme > 2)
        {
            throw new Error("ERROR! Parameter 'atomOrderingScheme' can only "
                + "be 1 or 2");
        }
 
        checkOtherParameters();
    }
    
//------------------------------------------------------------------------------
    public String getPrintedList()
    {
        StringBuilder sb = new StringBuilder(1024);
        sb.append(" " + paramTypeName() + " ").append(NL);
        for (Field f : this.getClass().getDeclaredFields()) 
        {
            try
            {
                sb.append(f.getName()).append(" = ").append(
                            f.get(this)).append(NL);
            }
            catch (Throwable t)
            {
                sb.append("ERROR! Unable to print " + paramTypeName() 
                        + " parameters. Cause: " + t);
                break;
            }
        }
        for (RunTimeParameters otherCollector : otherParameters.values())
        {
            sb.append(otherCollector.getPrintedList());
        }
        return sb.toString();
    }
    
//------------------------------------------------------------------------------
 
    public void processParameters() throws DENOPTIMException
    {
        pssrotParams_Init = new ArrayList<>();
        pssrotParams_Rest = new ArrayList<>();
        keyFileParams = new ArrayList<>();
        rsPssrotParams_Init = new ArrayList<>();
        rsPssrotParams_Rest = new ArrayList<>();
        rsKeyFileParams = new ArrayList<>();
        
        if (keyFile!=null)
        {
            MMBuilderUtils.readKeyFileParams(keyFile, keyFileParams);
        }
        if (pssrotFile!=null)
        {
            TinkerUtils.readPSSROTParams(pssrotFile, pssrotParams_Init, 
                    pssrotParams_Rest);
        }
        if (forceFieldFile!=null)
        {
            TINKER_MAP = TinkerUtils.readTinkerAtomTypes(forceFieldFile);
        }
 
        if (otherParameters.containsKey(ParametersType.RC_PARAMS))
        {
            if (rsPssrotFile!=null)
            {
                TinkerUtils.readPSSROTParams(rsPssrotFile, rsPssrotParams_Init, 
                                                           rsPssrotParams_Rest);
            }
            if (rsKeyFile!=null)
            {
                MMBuilderUtils.readKeyFileParams(rsKeyFile, rsKeyFileParams);
            }
        }
        processOtherParameters();
    }
 
//------------------------------------------------------------------------------
}