com.actelion.research.chem.descriptor.DescriptorConstants Maven / Gradle / Ivy
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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.
*
*/
package com.actelion.research.chem.descriptor;
import com.actelion.research.chem.SSSearcherWithIndex;
public interface DescriptorConstants {
int DESCRIPTOR_TYPE_UNKNOWN = -1;
int DESCRIPTOR_TYPE_MOLECULE = 1;
int DESCRIPTOR_TYPE_REACTION = 2;
DescriptorInfo DESCRIPTOR_FFP512 =
new DescriptorInfo("FragmentFingerprint512",
"FragFp",
SSSearcherWithIndex.cIndexVersion,
DESCRIPTOR_TYPE_MOLECULE,
true,
true,
true,
false);
DescriptorInfo DESCRIPTOR_SSSFP =
new DescriptorInfo("SSSPathFingerprint",
"SSSPathFp",
"1.0",
DESCRIPTOR_TYPE_MOLECULE,
true,
true,
true,
false);
DescriptorInfo DESCRIPTOR_PFP512 =
new DescriptorInfo("PathFingerprint512",
"PathFp",
"1.1",
DESCRIPTOR_TYPE_MOLECULE,
true,
true,
true,
false);
DescriptorInfo DESCRIPTOR_HashedCFp =
new DescriptorInfo("HashedSphericalFingerprint512",
"SphereFp",
"2.1",
DESCRIPTOR_TYPE_MOLECULE,
true,
true,
true,
true); // for the creation of up/down bonds
DescriptorInfo DESCRIPTOR_SkeletonSpheres =
new DescriptorInfo("HashedSkeletonSphereCount1024",
"SkelSpheres",
"1.1",
DESCRIPTOR_TYPE_MOLECULE,
false,
true,
true,
true); // for the creation of up/down bonds
DescriptorInfo DESCRIPTOR_ALLFRAG =
new DescriptorInfo("AllFragments1024",
"AllFragFp",
"1.0",
DESCRIPTOR_TYPE_MOLECULE,
true,
true,
true,
false);
DescriptorInfo DESCRIPTOR_OrganicFunctionalGroups =
new DescriptorInfo("FunctionalGroupTreeCount1024",
"OrgFunctions",
"1.0",
DESCRIPTOR_TYPE_MOLECULE,
false,
false,
false,
true); // for the creation of up/down bonds
DescriptorInfo DESCRIPTOR_CenteredSkeletonFragments =
new DescriptorInfo("CenteredSkeletonFragments",
"CentSkelFrags",
"1.0",
DESCRIPTOR_TYPE_MOLECULE,
false,
false,
true,
true); // for the creation of up/down bonds
DescriptorInfo DESCRIPTOR_TopoPPHistDist =
new DescriptorInfo("TopologicalPharmacophoreHistograms",
"TopPPHist",
"version",
DESCRIPTOR_TYPE_MOLECULE,
false,
false,
false,
false);
DescriptorInfo DESCRIPTOR_Flexophore =
new DescriptorInfo("Flexophore",
"Flexophore",
"5.0",
DESCRIPTOR_TYPE_MOLECULE,
false,
false,
false,
false);
DescriptorInfo DESCRIPTOR_ShapeAlign =
new DescriptorInfo("PharmacophoreEnhancedShapeAlignment",
"PheSA",
"2.1",
DESCRIPTOR_TYPE_MOLECULE,
false,
false,
false,
false);
DescriptorInfo DESCRIPTOR_ShapeAlignSingleConf =
new DescriptorInfo("PharmacophoreEnhancedShapeAlignmentSingleConfQuery",
"PheSASingleConf",
"2.1",
DESCRIPTOR_TYPE_MOLECULE,
false,
false,
false,
false);
DescriptorInfo DESCRIPTOR_ReactionFP =
new DescriptorInfo("ReactionFingerprint",
"RxnFP",
DescriptorHandlerReactionFP.cVersion,
DESCRIPTOR_TYPE_REACTION,
false, // it is a binary, but similarity calculations have a bias on reaction center bits
false,
false,
false);
DescriptorInfo DESCRIPTOR_IntegerVector =
new DescriptorInfo("IntegerVector",
"IntVec",
"1.0",
DESCRIPTOR_TYPE_UNKNOWN,
false,
true,
false,
false);
DescriptorInfo DESCRIPTOR_MAX_COMMON_SUBSTRUCT =
new DescriptorInfo("MaximumCommonSubstructure",
"Structure",
"1.0",
DESCRIPTOR_TYPE_MOLECULE,
false,
false,
true,
false);
DescriptorInfo DESCRIPTOR_SUBSTRUCT_QUERY_IN_BASE =
new DescriptorInfo("SubStructureQueryInBase",
"SSSQinB",
"1.0",
DESCRIPTOR_TYPE_MOLECULE,
false,
false,
false, // ??? TODO check
false);
DescriptorInfo DESCRIPTOR_FULL_FRAGMENT_SET =
new DescriptorInfo("FullFragmentSet",
"FullFragSet",
"1.0",
DESCRIPTOR_TYPE_MOLECULE,
true,
true,
true,
false);
DescriptorInfo DESCRIPTOR_PhysicoChemicalProperties =
new DescriptorInfo("DescriptorPhysicoChemicalProperties",
"PhysChem",
"version",
DESCRIPTOR_TYPE_MOLECULE,
false,
true,
false,
false);
DescriptorInfo DESCRIPTOR_BINARY_SKELETONSPHERES =
new DescriptorInfo("BinarySkeletonSpheres",
"BinSkelSpheres",
"10052017",
DESCRIPTOR_TYPE_MOLECULE,
true,
true,
true,
false);
DescriptorInfo DESCRIPTOR_PTREE =
new DescriptorInfo("PharmacophoreTree",
"PTree",
"1.0",
DESCRIPTOR_TYPE_MOLECULE,
false,
false,
false,
false);
DescriptorInfo[] DESCRIPTOR_LIST = {
DESCRIPTOR_FFP512,
DESCRIPTOR_PFP512,
DESCRIPTOR_ALLFRAG,
DESCRIPTOR_HashedCFp,
DESCRIPTOR_SkeletonSpheres,
DESCRIPTOR_OrganicFunctionalGroups,
DESCRIPTOR_Flexophore,
DESCRIPTOR_ReactionFP
};
DescriptorInfo[] DESCRIPTOR_EXTENDED_LIST = {
DESCRIPTOR_FFP512,
DESCRIPTOR_PFP512,
DESCRIPTOR_SSSFP,
DESCRIPTOR_ALLFRAG,
DESCRIPTOR_HashedCFp,
DESCRIPTOR_SkeletonSpheres,
DESCRIPTOR_BINARY_SKELETONSPHERES,
DESCRIPTOR_CenteredSkeletonFragments,
DESCRIPTOR_MAX_COMMON_SUBSTRUCT,
DESCRIPTOR_SUBSTRUCT_QUERY_IN_BASE,
DESCRIPTOR_TopoPPHistDist,
DESCRIPTOR_OrganicFunctionalGroups,
DESCRIPTOR_Flexophore,
DESCRIPTOR_ShapeAlign,
DESCRIPTOR_ReactionFP,
DESCRIPTOR_IntegerVector,
DESCRIPTOR_FULL_FRAGMENT_SET,
DESCRIPTOR_PhysicoChemicalProperties,
DESCRIPTOR_BINARY_SKELETONSPHERES
};
}