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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;
public interface StructureSearchDataSource {
public static final long SEARCH_TYPE_NOT_SUPPORTED = -1L;
/**
* Returns true if idcodes and/or hash codes for this particular
* search specification are directly available by the source, i.e. without
* calculating idcodes, descriptors or hash codes on-the-fly.
* In case of search types other than substructure search the implementation needs
* to check specification.isLargestFragmentOnly(). In case of similarity
* searches the implementation needs to consider specification.getDescriptorShortName().
* @param specification
* @return
*/
public boolean isSupportedSearchType(StructureSearchSpecification specification);
/**
* This is the total number of records, whether they qualify for a structure search or not.
* @return
*/
public int getRowCount();
/**
* This is the number of individual structures within that row that a query will be checked against.
* Typically, this will be one. However, if a database contains empty structures, mixtures,
* or reactants/products of a reaction, then the row may contain multiple structures to be searched.
* @param row
* @return typically 1, but may be 0...n
*/
public int getStructureCount(int row);
/**
* Returns a number to be used in getDescriptor() to address the
* the descriptor with the given short name.
* If a descriptor of the desired kind is not available, then return -1
* as indication that it needs to be generated on-the-fly.
* @param descriptorShortName
* @return descriptor column or -1, if the descriptor is not available
*/
public int getDescriptorColumn(String descriptorShortName);
/**
* @param column
* @param row
* @param i structure index for that particular row
* @param largestFragmentOnly
* @return null if this row has no descriptor
*/
public Object getDescriptor(int column, int row, int i, boolean largestFragmentOnly);
/**
* Returns the idcode of the structure or largest fragment.
* If the code is not available, null is returned.
* This method is not supposed to calculate idcodes on-the-fly.
* @param row
* @param i structure index for that particular row
* @param largestFragmentOnly
* @return idcode of this row or null, if no structure is associated to this row
*/
public byte[] getIDCode(int row, int i, boolean largestFragmentOnly);
/**
* Returns a hash code representing the structure or its largest fragment
* without any stereo information. If this code is not available, SEARCH_TYPE_NOT_SUPPORTED
* is returned. This method is not supposed to calculate the code on-the-fly.
* @param row
* @param i structure index for that particular row
* @param largestFragmentOnly
* @return
*/
public long getNoStereoCode(int row, int i, boolean largestFragmentOnly);
/**
* Returns a hash code representing the generic tautomer of the structure or its
* largest fragment.
* If this code is not available, SEARCH_TYPE_NOT_SUPPORTED is returned.
* This method is not supposed to calculate the code on-the-fly.
* @param row
* @param i structure index for that particular row
* @param largestFragmentOnly
* @return
*/
public long getTautomerCode(int row, int i, boolean largestFragmentOnly);
/**
* Returns a hash code representing the generic tautomer of the structure or its
* largest fragment with the stereo information removed before creating the generic tautomer.
* If this code is not available, SEARCH_TYPE_NOT_SUPPORTED is returned.
* This method is not supposed to calculate the code on-the-fly.
* @param row
* @param i structure index for that particular row
* @param largestFragmentOnly
* @return
*/
public long getNoStereoTautomerCode(int row, int i, boolean largestFragmentOnly);
/**
* Returns a hash code representing the structure or its largest fragment
* without stereo information and with all unsaturated bonds converted to single bonds.
* SEARCH_TYPE_NOT_SUPPORTED is returned.
* This method is not supposed to calculate the code on-the-fly.
* @param row
* @param i structure index for that particular row
* @param largestFragmentOnly
* @return
*/
public long getBackboneCode(int row, int i, boolean largestFragmentOnly);
}