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Open Source Chemistry Library
/*
* Copyright (c) 1997 - 2016
* Actelion Pharmaceuticals Ltd.
* Gewerbestrasse 16
* CH-4123 Allschwil, Switzerland
*
* All rights reserved.
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the above copyright notice, this
* list of conditions and the following disclaimer.
* 2. Redistributions in binary form must reproduce the above copyright notice,
* this list of conditions and the following disclaimer in the documentation
* and/or other materials provided with the distribution.
* 3. Neither the name of the the copyright holder nor the
* names of its contributors may be used to endorse or promote products
* derived from this software without specific prior written permission.
*
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
* ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
* WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
* DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
* ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
* (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
* LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
* ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
* (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
* SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*
* @author Thomas Sander
*/
package com.actelion.research.chem;
import com.actelion.research.chem.descriptor.DescriptorHelper;
import java.io.Serializable;
import java.nio.charset.StandardCharsets;
public class StructureSearchSpecification implements Serializable {
static final long serialVersionUID = 0x20120402;
private static final int TYPE_MASK = 0x0000FF;
public static final int TYPE_NO_STRUCTURE = 0x000000; // no structure search (other criteria only)
public static final int TYPE_SUBSTRUCTURE = 0x000001;
public static final int TYPE_SIMILARITY = 0x000002;
public static final int TYPE_EXACT_STRICT = 0x000003;
public static final int TYPE_EXACT_NO_STEREO = 0x000004;
public static final int TYPE_TAUTOMER = 0x000005;
public static final int TYPE_TAUTOMER_NO_STEREO = 0x000006;
public static final int TYPE_BACKBONE_NO_STEREO = 0x000007;
public static final int MODE_LARGEST_FRAGMENT_ONLY = 0x000100;
public static final int MODE_SINGLE_MATCH_ONLY = 0x000200;
private int mSearchType;
private byte[][] mIDCode;
private Object[] mDescriptor;
private String mDescriptorShortName;
private float mSimilarityThreshold;
/**
* Creates a complete specification for a substructure or similarity search
* with one or more query fragments or molecules.
* @param searchType one of TYPE_... + optionally MODE_...
* @param idcode list of query fragments/molecules
* @param descriptor null or list descriptors (in case of substructure search this should be the long FFP512)
* @param descriptorShortName in case of TYPE_SIMILARITY
* @param similarityThreshold in case of TYPE_SIMILARITY
*/
public StructureSearchSpecification(int searchType, byte[][] idcode, Object[] descriptor, String descriptorShortName, float similarityThreshold) {
mSearchType = searchType;
mIDCode = idcode;
mDescriptor = descriptor;
mDescriptorShortName = descriptorShortName;
mSimilarityThreshold = similarityThreshold;
}
/**
* Returns the search type as integer including mode flags.
* In case of TYPE_SIMILARITY use getDescriptorShortName() and
* getSimilarityThreshold() for a full search specification.
* @return one of TYPE_... and possibly MODE_LARGEST_FRAGMENT_ONLY
*
public int getSearchType() {
return mSearchType;
} */
public int getStructureCount() {
return (mIDCode == null) ? 0 : mIDCode.length;
}
/**
* Returns the (or one of the) query structures encodes as idcode.
* @param index
* @return
*/
public byte[] getIDCode(int index) {
return mIDCode[index];
}
/**
* Depending on the mode isLargestFragmentOnly() the descriptor
* is expected to be represent the whole structure or the largest fragment.
* @param index
* @return
*/
public Object getDescriptor(int index) {
return (mDescriptor == null) ? null : mDescriptor[index];
}
public boolean isSimilaritySearch() {
return (mSearchType & TYPE_MASK) == TYPE_SIMILARITY;
}
/**
* @return whether this search does not include a structure search component is uses exclusively external criteria
*/
public boolean isNoStructureSearch() {
return (mSearchType & TYPE_MASK) == TYPE_NO_STRUCTURE;
}
public boolean isSubstructureSearch() {
return (mSearchType & TYPE_MASK) == TYPE_SUBSTRUCTURE;
}
/**
* An exact search is a comparison of idcodes of
* standardized molecules with full stereo features.
* @return
*/
public boolean isExactSearch() {
return (mSearchType & TYPE_MASK) == TYPE_EXACT_STRICT;
}
/**
* A noStereo search is a hash code comparison from
* encoding stereo depleted structures.
* @return
*/
public boolean isNoStereoSearch() {
return (mSearchType & TYPE_MASK) == TYPE_EXACT_NO_STEREO;
}
/**
* A tautomer search is a hash code comparison from
* encoding generic tautomer structures.
* @return
*/
public boolean isTautomerSearch() {
return (mSearchType & TYPE_MASK) == TYPE_TAUTOMER;
}
/**
* A no-stereo-tautomer search is a hash code comparison from
* encoding stereo depleted generic tautomer structures.
* @return
*/
public boolean isNoStereoTautomerSearch() {
return (mSearchType & TYPE_MASK) == TYPE_TAUTOMER_NO_STEREO;
}
/**
* A backbone search is a hash code comparison from
* encoding stereo and unsaturation depleted structures.
* @return
*/
public boolean isBackboneSearch() {
return (mSearchType & TYPE_MASK) == TYPE_BACKBONE_NO_STEREO;
}
/**
* This setting is relevant for all search types except the substructure search.
* @return
*/
public boolean isLargestFragmentOnly() {
return (mSearchType & MODE_LARGEST_FRAGMENT_ONLY) != 0;
}
public boolean isSingleMatchOnly() {
return (mSearchType & MODE_SINGLE_MATCH_ONLY) != 0;
}
public void removeDescriptors() {
mDescriptor = null;
}
/**
*
* @param b
*/
public void setLargestFragmentOnly(boolean b) {
mSearchType &= ~MODE_LARGEST_FRAGMENT_ONLY;
if (b)
mSearchType |= MODE_LARGEST_FRAGMENT_ONLY;
}
/**
* In case of a substructure search, as default a molecule is considered a match if the query
* structure is found once or multiple times. To consider only single matches a match, call this
* method with argument true.
* @param b
*/
public void setSingleMatchOnly(boolean b) {
mSearchType &= ~MODE_SINGLE_MATCH_ONLY;
if (b)
mSearchType |= MODE_SINGLE_MATCH_ONLY;
}
public String getDescriptorShortName() {
return mDescriptorShortName;
}
public float getSimilarityThreshold() {
return mSimilarityThreshold;
}
/**
* Checks, whether this specification is correctly defining a search.
* If something is missing or inconsistent, an error message
* describing the problem is returned.
* @return null or error message
*/
public String validate() {
int count = getStructureCount();
if (count == 0)
return "No query structures defined.";
for (int i=0; i 1.0)
return "Similarity threshold out of allowed range.";
}
return null;
}
@Override
public String toString() {
int type = mSearchType & TYPE_MASK;
String typeString = ((type == TYPE_SUBSTRUCTURE) ? "substructure"
: (type == TYPE_SIMILARITY) ? "similarity/"+mDescriptorShortName+"("+mSimilarityThreshold+")"
: (type == TYPE_EXACT_STRICT) ? "exact"
: (type == TYPE_EXACT_NO_STEREO) ? "noStereo"
: (type == TYPE_TAUTOMER) ? "tautomer"
: (type == TYPE_TAUTOMER_NO_STEREO) ? "no-stereo tautomer"
: (type == TYPE_BACKBONE_NO_STEREO) ? "backbone" : "undefined")
+ (((mSearchType & MODE_LARGEST_FRAGMENT_ONLY) != 0) ? "/largestFragmentOnly":"");
return "type:"+typeString
+ (mIDCode==null?" idcodes:null":mIDCode.length==1?" idcode:"+(mIDCode[0]==null?"null":new String(mIDCode[0], StandardCharsets.UTF_8)):" idcodeCount:"+mIDCode.length)
+ (mDescriptor==null?" descriptors:null":" descriptorCount:"+mDescriptor.length);
}
}