RingClosureParameters.java

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/*
 *   DENOPTIM
 *   Copyright (C) 2019 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.graph.rings;
 
import java.io.BufferedReader;
import java.io.File;
import java.io.IOException;
import java.io.InputStreamReader;
import java.lang.reflect.Field;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.logging.Level;
 
import denoptim.exception.DENOPTIMException;
import denoptim.files.FileUtils;
import denoptim.fragmenter.BridgeHeadFindingRule;
import denoptim.graph.APClass;
import denoptim.io.DenoptimIO;
import denoptim.logging.StaticLogger;
import denoptim.programs.RunTimeParameters;
 
 
public class RingClosureParameters extends RunTimeParameters
{
    protected boolean closeRings = false;
 
    //TODO-V3 make controllable from parameters side.
    public boolean requireCompleteRingclosure = true;
    
    protected boolean buildChelatesMode = false;
    
    protected Set<APClass> metalCoordinatingAPClasses = 
            new HashSet<APClass>();
 
    protected boolean selectFragsFromCC = false;
 
    protected int rceMode = -1;
 
    protected int maxRotBonds = 7;
 
    protected int maxRingSize = 9;
 
    protected Map<String,Integer> minRcaPerType = new HashMap<String,Integer>();
 
    protected Map<String,Integer> maxRcaPerType = new HashMap<String,Integer>();
 
    protected int minRingClosures = 0;
 
    protected int maxRingClosures = 50;
 
    protected double linearityLimit = 178.5;
 
    protected double rcTolDist = 0.33;
 
    protected double pathConfSearchExtraTol = 1.1;
 
    protected double rcMaxDot = -0.75;
 
    protected double pathConfSearchStep = 12.0;
 
    protected List<Integer> ringSizeBias = new ArrayList<Integer>()
        {
            private static final long serialVersionUID = 1L;
            {
                for (int i=0; i<maxRingSize+1; i++)
                {
                    add(0);
                }
                if (maxRingSize>=7)
                {
                        // WARNING: if the default value of maxRingSize is changed
                        // also the default content of this array has to change
                        set(5,2);
                        set(6,4);
                        set(7,1);
                }
            }
        };
 
    protected Map<String,String> ringClosabCondAsSMARTS =
                                                 new HashMap<String,String>();
 
    protected Set<String> reqElInRings = new HashSet<String>();
 
    protected String rccIndex = "";
 
    protected String rccFolder = "";
    
    private RingClosuresArchive rcArchive;
 
    protected boolean exhaustiveConfSrch = false; 
 
    protected boolean checkInterdepPaths = false;
 
    protected boolean serializeRCCs = false;
    
    protected List<BridgeHeadFindingRule> bridgeHeadFindingRules;
 
//-----------------------------------------------------------------------------
    
    public RingClosureParameters()
    {
        super(ParametersType.RC_PARAMS);
        rcArchive = new RingClosuresArchive();
 
        try
        {
            bridgeHeadFindingRules = DenoptimIO.readBridgeHesFindingRules(
                    new BufferedReader(new InputStreamReader(
                            this.getClass().getClassLoader().getResourceAsStream(
                                        "data/bridge-head_finding_rules.json"))));
        } catch (IOException e)
        {
            // should never happen
            e.printStackTrace();
        }
    }
 
//----------------------------------------------------------------------------
 
    public int getClosabilityEvalMode()
    {
        return rceMode;
    }
 
//----------------------------------------------------------------------------
 
    public int getMaxNumberRotatableBonds()
    {
        return maxRotBonds;
    }
 
//----------------------------------------------------------------------------
 
    public int getMaxRingSize()
    {
        return maxRingSize;
    }
 
//----------------------------------------------------------------------------
 
    public List<Integer> getRingSizeBias()
    {
        return ringSizeBias;
    }
    
//----------------------------------------------------------------------------
 
    public void setRingSizeBias(List<Integer> biases)
    {
        ringSizeBias = biases;
    }
 
//------------------------------------------------------------------------------
 
    public int getMinRcaPerType(String type)
    {
        if (minRcaPerType.containsKey(type))
            return minRcaPerType.get(type);
        else
            return 0;
    }
 
//------------------------------------------------------------------------------
 
    public int getMaxRcaPerType(String type)
    {
        if (maxRcaPerType.containsKey(type))
            return maxRcaPerType.get(type);
        else
            return 10000;
    }
 
//------------------------------------------------------------------------------
 
    public int getMinRingClosures()
    {
        return minRingClosures;
    }
 
//------------------------------------------------------------------------------
 
    public int getMaxRingClosures()
    {
        return maxRingClosures;
    }
 
//----------------------------------------------------------------------------
 
    public Map<String,String> getConstitutionalClosabilityConds()
    {
        return ringClosabCondAsSMARTS;
    }
    
//----------------------------------------------------------------------------
 
    public void setConstitutionalClosabilityConds(
            Map<String,String> ringClosabCondAsSMARTS)
    {
        this.ringClosabCondAsSMARTS = ringClosabCondAsSMARTS;
    }
 
//----------------------------------------------------------------------------
 
    public int getVerbosity()
    {
        return verbosity;
    }
 
//-----------------------------------------------------------------------------
 
    public void allowRingClosures(boolean value)
    {
        closeRings = value;
    }
    
//-----------------------------------------------------------------------------
 
    public boolean allowRingClosures()
    {
        return closeRings;
    }
 
//-----------------------------------------------------------------------------
 
    public boolean buildChelatesMode()
    {
        return buildChelatesMode;
    }
 
//----------------------------------------------------------------------------
 
    public boolean selectFragmentsFromClosableChains()
    {
        return selectFragsFromCC;
    }
 
//----------------------------------------------------------------------------
 
    public double getRCDistTolerance()
    {
        return rcTolDist;
    }
 
//----------------------------------------------------------------------------
 
    public double getConfPathExtraTolerance()
    {
        return pathConfSearchExtraTol;
    }
 
//----------------------------------------------------------------------------
 
    public double getRCDotPrTolerance()
    {
        return rcMaxDot;
    }
 
//----------------------------------------------------------------------------
 
    public double getLinearityLimit()
    {
        return linearityLimit;
    }
 
//----------------------------------------------------------------------------
 
    public double getPathConfSearchStep()
    {
        return pathConfSearchStep;
    }
 
//----------------------------------------------------------------------------
 
    public Set<String> getRequiredRingElements()
    {
        return reqElInRings;
    }
    
//----------------------------------------------------------------------------
 
    public List<BridgeHeadFindingRule> getBridgeHeadFindingRules()
    {
        return bridgeHeadFindingRules;
    }
 
//----------------------------------------------------------------------------
 
    public String getRCCLibraryIndexFile()
    {
        return rccIndex;
    }
 
//----------------------------------------------------------------------------
 
    public String getRCCLibraryFolder()
    {
        return rccFolder;
    }
    
//----------------------------------------------------------------------------
    
    public RingClosuresArchive getRingClosuresArchive()
    {
        return rcArchive;
    }
 
//----------------------------------------------------------------------------
 
    public boolean doExhaustiveConfSrch()
    {
        return exhaustiveConfSrch;
    }
 
//----------------------------------------------------------------------------
 
    public boolean serializeRCCs()
    {
        return serializeRCCs;
    }
 
//----------------------------------------------------------------------------
 
    public boolean checkInterdependentChains()
    {
        return checkInterdepPaths;
    }
 
//----------------------------------------------------------------------------
 
    public void interpretKeyword(String key, String value)
            throws DENOPTIMException
    {
        String msg = "";
        switch (key.toUpperCase())
        {
            case "VERBOSITY=":
                try
                {
                    verbosity = Integer.parseInt(value);
                }
                catch (Throwable t)
                {
                    msg = "Unable to understand value '" + value + "'";
                    throw new DENOPTIMException(msg);
                }
                break;
            case "CLOSERINGS":
                closeRings = true;
                break;
            case "CLOSERINGS=":
                closeRings = true;
                break;
            case "BUILDCHELATESMODE":
                buildChelatesMode = true;
                break;
            case "ORPHANAPCLASS=":
                buildChelatesMode = true;
                metalCoordinatingAPClasses.add(APClass.make(value));
                break;
            case "SELECTFRAGMENTSFROMCLOSABLECHAINS":
                selectFragsFromCC = true;
                break;
            case "EVALUATIONCLOSABILITYMODE=":
                switch (value.toUpperCase())
                {
                    case "RING_SIZE":
                        rceMode = -1;
                        break;
                        
                    case "CONSTITUTION":
                        rceMode = 0;
                        break;
                        
                    case "3D-CONFORMATION":
                        rceMode = 1;
                        break;
                        
                    case "CONSTITUTION_AND_3D-CONFORMATION":
                        rceMode = 2;
                        break;
                        
                    default:
                        msg = "Unable to understand value '" + value + "'";
                        throw new DENOPTIMException(msg);
                }
                break;
            case "MAXROTBONDS=":
                try
                {
                    maxRotBonds = Integer.parseInt(value);
                }
                catch (Throwable t)
                {
                    msg = "Unable to understand value '" + value + "'";
                    throw new DENOPTIMException(msg);
                }
                break;
            case "MAXSIZENEWRINGS=":
                try
                {
                    maxRingSize = Integer.parseInt(value);
                }
                catch (Throwable t)
                {
                    msg = "Unable to understand value '" + value + "'";
                    throw new DENOPTIMException(msg);
                }
                break;
            case "MINRCAPERTYPEPERGRAPH=":
                try
                {
                    String[] words = value.trim().split("\\s+");
                    if (words.length!=2)
                    {
                        msg = "Unable to understand value '" + value + "'";
                        throw new DENOPTIMException(msg);
                    }
                    minRcaPerType.put(words[1],Integer.parseInt(words[0]));
                }
                catch (Throwable t)
                {
                    msg = "Unable to understand value '" + value + "'";
                    throw new DENOPTIMException(msg);
                }
                break;
            case "MAXRCAPERTYPEPERGRAPH=":
                try
                {
                    String[] words = value.trim().split("\\s+");
                    if (words.length!=2)
                    {
                        msg = "Unable to understand value '" + value + "'";
                        throw new DENOPTIMException(msg);
                    }
                    maxRcaPerType.put(words[1],Integer.parseInt(words[0]));
                }
                catch (Throwable t)
                {
                    msg = "Unable to understand value '" + value + "'";
                    throw new DENOPTIMException(msg);
                }
                break;
            case "MINNUMBEROFRINGCLOSURES=":
                try
                {
                    minRingClosures = Integer.parseInt(value);
                }
                catch (Throwable t)
                {
                    msg = "Unable to understand value '" + value + "'";
                    throw new DENOPTIMException(msg);
                }
                break;
            case "MAXNUMBERRINGCLOSURES=":
                try
                {
                    maxRingClosures = Integer.parseInt(value);
                }
                catch (Throwable t)
                {
                    msg = "Unable to understand value '" + value + "'";
                    throw new DENOPTIMException(msg);
                }
                break;
            case "LINEARITYLIMIT=":
                try
                {
                    linearityLimit = Double.parseDouble(value);
                }
                catch (Throwable t)
                {
                    msg = "Unable to understand value '" + value + "'";
                    throw new DENOPTIMException(msg);
                }
                break;
            case "DISTANCETOLERANCEFACTOR=":
                try
                {
                    rcTolDist = Double.parseDouble(value);
                }
                catch (Throwable t)
                {
                    msg = "Unable to understand value '" + value + "'";
                    throw new DENOPTIMException(msg);
                }
                break;
            case "EXTRADISTANCETOLERANCEFACTOR=":
                try
                {
                    pathConfSearchExtraTol = Double.parseDouble(value);
                }
                catch (Throwable t)
                {
                    msg = "Unable to understand value '" + value + "'";
                    throw new DENOPTIMException(msg);
                }
                break;
            case "MAXDOTPROD=":
                try
                {
                    rcMaxDot = Double.parseDouble(value);
                }
                catch (Throwable t)
                {
                    msg = "Unable to understand value '" + value + "'";
                    throw new DENOPTIMException(msg);
                }
                break;
            case "CONFSEARCHSTEP=":
                try
                {
                    pathConfSearchStep = Double.parseDouble(value);
                }
                catch (Throwable t)
                {
                    msg = "Unable to understand value '" + value + "'";
                    throw new DENOPTIMException(msg);
                }
                break;
            case "RINGSIZEBIAS=":
                String[] words = value.split("\\s+");
                if (words.length != 2)
                {
                     msg = "Unable to read ring size and bias weight from "
                                 + "'" + value + "'. Expected syntax is: "
                                 + "'5 2' as to specify that 5-member rings "
                                 + "are given a weight of 2.";
                    throw new DENOPTIMException(msg);
                }
                int size = -1;
                int weight = 0;
                try
                {
                    size = Integer.parseInt(words[0]);
                } catch (Throwable t)
                {
                    throw new DENOPTIMException("Ring size must be an integer");
                }
                try
                {
                    weight = Integer.parseInt(words[1]);
                } catch (Throwable t)
                {
                    throw new DENOPTIMException("Bias weight must be an integer");
                }
                if (size < 0)
                {
                    msg = "Ring size must be >= 0";
                    throw new DENOPTIMException(msg);
                }
                if (weight < 0)
                {
                    msg = "Bias for ring size must be >= 0";
                    throw new DENOPTIMException(msg);
                }
                if (size > maxRingSize)
                {
                    for (int i=maxRingSize+1; i<size; i++)
                    {
                        ringSizeBias.add(0);
                    }
                    ringSizeBias.add(weight);
                    maxRingSize = size;
                }
                else
                {
                    ringSizeBias.set(size,weight);
                }
                break;
                
            case "CLOSABLERINGSMARTS=":
                int id = ringClosabCondAsSMARTS.size();
                ringClosabCondAsSMARTS.put("q"+id,value);
                break;
                
            case "REQUIREDELEMENTINRINGS=":
                reqElInRings.add(value);
                break;
                
            case "RCCINDEX=":
                rccIndex = value;
                break;
                
            case "RCCFOLDER=":
                serializeRCCs = true;
                rccFolder = value;
                break;
                
            case "EXHAUSTIVECONFSEARCH":
                exhaustiveConfSrch = true;
                break;
                
            case "CHECKINTERDEPENDENTCHAINS":
                checkInterdepPaths = true;
                break;
                
            case "BRIDGEHEADFINDINGRULESFILE=":
            {
                bridgeHeadFindingRules = DenoptimIO.readBridgeHesFindingRules(
                        value);
                break;
            }
                
            default:
                msg = "Keyword '" + key + "' is not a known ring closure-"
                        + "related keyword. Check input files.";
                throw new DENOPTIMException(msg);
        }
    }
 
//----------------------------------------------------------------------------
 
    public void checkParameters() throws DENOPTIMException
    {
        String msg = "";
        if (!closeRings)
        {
            msg = "The use of ring-closure related keywords "
                  + "is dependent on the activation of the ring-closing "
                  + "machinery (use " 
                  + ParametersType.RC_PARAMS.getKeywordRoot() 
                  + "CLOSERINGS keyword).";
            throw new DENOPTIMException(msg);
        }
 
        if (rceMode > 2)
        {
            msg = "Unknown ring-closure evaluation mode '" + rceMode + "' "
          + "Acceptable values are: "
          + "-1 (only ring size)"
          + "0 (only contitutional), "
          + "1 (only 3D chain), "
          + "2 (both constitutional and 3D chain). ";
            throw new DENOPTIMException(msg);
        }
 
        if (rccFolder!="" && !FileUtils.checkExists(rccFolder))
        {
            File folder = new File(rccFolder);
            try
            {
                folder.mkdir();
            }
            catch (Throwable t2)
            {
                msg = "CyclicGraphHandler can't make folder " + rccFolder
                        + ". " + t2;
                throw new DENOPTIMException(msg);
            }
        }
 
        if (buildChelatesMode && !closeRings)
        {
            msg = "To use the BuildChelates mode you need to perform "
                  + "experiments capable of closing/opening and modifying "
                  + "rings. See the "
                  + ParametersType.RC_PARAMS.getKeywordRoot() 
                  + "CLOSERINGS keyword "
                  + "and provide the related input (i.e., ring "
                  + "closing attractor fragments).";
            throw new DENOPTIMException(msg);
        }
 
        for (String type : minRcaPerType.keySet())
        {
            if (minRcaPerType.get(type) > maxRcaPerType.get(type))
            {
                msg = "Check values of max and min number of RCA for type '" 
                        + type+"'.";
                throw new DENOPTIMException(msg);
            }
        }
 
        if (minRingClosures > maxRingClosures)
        {
            msg = "Check values of minRingClosures and maxRingClosures";
            throw new DENOPTIMException(msg);
        }
 
        if (checkInterdepPaths && !exhaustiveConfSrch)
        {
            exhaustiveConfSrch = true;
        }
    
        if (exhaustiveConfSrch)
        {
            msg = "Exhaustive conformational search has been turned ON. "
              + "This is a very time consuming task!";
            StaticLogger.appLogger.log(Level.WARNING,msg);
        }
    
        if (selectFragsFromCC)
        {
            msg = "DENOPTIM can guide the selection of fragments to " 
              + "those leading to known closable chains. This "
              + "functionality is currently under development "
              + "and is fully operative only for rings "
              + "involving the scaffolds. ";
            StaticLogger.appLogger.log(Level.WARNING,msg);
        }
        checkOtherParameters();
    }
 
//----------------------------------------------------------------------------
 
    public void processParameters() throws DENOPTIMException
    {
        rcArchive = new RingClosuresArchive(this);
        processOtherParameters();
    }
    
//------------------------------------------------------------------------------
 
    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();
    }
 
//------------------------------------------------------------------------------
 
}