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a6b26253ff017bf67bd4499529d9766a94fdb8d8
rdkit/External/FreeSASA/testFreeSASA.cpp
Ric a6b26253ff Fix (most of) mem problems (#2123) 
* do not use new on loggers

* del pointers in testDistGeom

* Update Dict hasNonPOD status on bulk update

* delete new Dicts in memtest1.cpp

* fixes in MolSuppliers and testFMCS

* PeriodicTable singleton as unique_ptr

* fix EEM_arrays leak

* fix leaks in testPBF

* fix ParamCollection leak in test UFF

* fix leaks in MMFF

* clear prop dict before read in in pickler

* fix leaks in testFreeSASA

* fix leaks in test3D

* modernize Dict.h & SmilesParse.cpp

* fix leaks in testQuery

* fix leaks in testCrystalFF

* fix leaks in cxsmilesTest

* fix leaks in Catalog & mol cat test

* fix leaks in ShapeUtils & tests

* fix leaks in testSubgraphs1

* fix leaks testFingerprintGenerators

* fix leaks in Catalog/FilterCatalog

* fix leaks in graphmolqueryTest

* these changes reduce bison parse leaks

* fixed leaks in testChirality.cpp

* fix leaks + 2 tests in testMolWriter

* fix 4m leaks in substructLibraryTest

* small improvements to molTautomerTest; still leaks

* fix leaks in testRGroupDecomp

* fix leaks in test; parser still leaks

* fix leaks in itertest

* fix 4m leaks in testDepictor

* fixes in smatest; still leaking due to parser

* fixes in testSLNParse; still leaking due to parser

* flex/bison: always add atoms with ownership; smarts error cleanup

* fix leaks in testReaction

* fix leaks in testSubstructMatch

* fix leaks in resMolSupplierTest

* fix leaks in testChemTransforms + bug in ChemTransforms

* fix leaks in testPickler

* fix leaks in testMolTransform

* fix leaks in testFragCatalog

* fix leak in testSLNParse. Still leaks due to Smiles

* fixed most leaks in testMolSupplier

* pre bison fix

* fix some atom & bond parse problems; others still fail

* bison smiles & smarts, atoms & bonds more or less fixed

* fix leaks in molopstest.cpp

* fix leaks in testFingerprints, MACCS.cpp & AtomPairs.cpp

* fix leaks in moldraw2Dtest1

* fix leaks in testDescriptors

* fix leaks in testInchi

* fix leaks in testUFFForceFieldHelpers

* fix leaks in hanoiTest & new_canon.h

* fix leaks in testMMFFForceField

* fix leaks in graphmolTest1

* fix leaks in testMMFFForceFieldHelpers

* fix leaks in testDistGeomHelpers

* fix leaks in testMolAlign

* initialize occupancy & temp facto with default values

* fix leak in TautomerTransform

* updated suppressions

* fix testStructChecker

* fix logging & py tests

* fix TautomerTransform class/struct issue

* remove misplaced delete in testSLNParse

* deinit in testAvalonLib1

* fix Avalon-triggered(?) bug in StructChecker/Pattern.cpp

* fix random testMolWriter/Supplier fails

- diversify output file names to avoid clashing.
- unify Writers close/destruct behavior.
- flushing/closing in tests.

* use reset in FFs Params.cpp

* comments on testMMFFForceField

* unrequired 'if's added to mol suppliers

* correct cast in FilterCatalog.h

* use unique_ptr in MACCS Patterns

* remove unrequred if in new_canon

* update & move suppressions
2018-10-29 14:33:26 +00:00

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// Copyright (c) 2016, Novartis Institutes for BioMedical Research Inc.
// All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are
// met:
//
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
// * 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.
// * Neither the name of Novartis Institutes for BioMedical Research Inc.
// 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.
//
#include "RDFreeSASA.h"
#include <GraphMol/RDKitBase.h>
#include <GraphMol/QueryAtom.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/FileParsers/FileParsers.h>
using namespace RDKit;
struct ExpectedClasses {
unsigned int idx;
int cls;
const char *clsname;
double radius;
};
ExpectedClasses ExpectedProtor1d3z[] = {
{0, 1, "Polar", 1.64}, {1, 0, "Apolar", 1.88},
{2, 0, "Apolar", 1.61}, {3, 1, "Polar", 1.42},
{4, 0, "Apolar", 1.88}, {5, 0, "Apolar", 1.88},
{6, 1, "Polar", 1.77}, {7, 0, "Apolar", 1.88},
{8, 1, "Polar", 1.64}, {9, 0, "Apolar", 1.88},
{10, 0, "Apolar", 1.61}, {11, 1, "Polar", 1.42},
{12, 0, "Apolar", 1.88}, {13, 0, "Apolar", 1.88},
{14, 0, "Apolar", 1.61}, {15, 1, "Polar", 1.42},
{16, 1, "Polar", 1.64}, {17, 1, "Polar", 1.64},
{18, 0, "Apolar", 1.88}, {19, 0, "Apolar", 1.61},
{20, 1, "Polar", 1.42}, {21, 0, "Apolar", 1.88},
{22, 0, "Apolar", 1.88}, {23, 0, "Apolar", 1.88},
{24, 0, "Apolar", 1.88}, {25, 1, "Polar", 1.64},
{26, 0, "Apolar", 1.88}, {27, 0, "Apolar", 1.61},
{28, 1, "Polar", 1.42}, {29, 0, "Apolar", 1.88},
{30, 0, "Apolar", 1.61}, {31, 0, "Apolar", 1.76},
{32, 0, "Apolar", 1.76}, {33, 0, "Apolar", 1.76},
{34, 0, "Apolar", 1.76}, {35, 0, "Apolar", 1.76},
{36, 1, "Polar", 1.64}, {37, 0, "Apolar", 1.88},
{38, 0, "Apolar", 1.61}, {39, 1, "Polar", 1.42},
{40, 0, "Apolar", 1.88}, {41, 0, "Apolar", 1.88},
{42, 0, "Apolar", 1.88}, {43, 1, "Polar", 1.64},
{44, 0, "Apolar", 1.88}, {45, 0, "Apolar", 1.61},
{46, 1, "Polar", 1.42}, {47, 0, "Apolar", 1.88},
{48, 0, "Apolar", 1.88}, {49, 0, "Apolar", 1.88},
{50, 0, "Apolar", 1.88}, {51, 1, "Polar", 1.64},
{52, 1, "Polar", 1.64}, {53, 0, "Apolar", 1.88},
{54, 0, "Apolar", 1.61}, {55, 1, "Polar", 1.42},
{56, 0, "Apolar", 1.88}, {57, 1, "Polar", 1.46},
{58, 0, "Apolar", 1.88}, {59, 1, "Polar", 1.64},
{60, 0, "Apolar", 1.88}, {61, 0, "Apolar", 1.61},
{62, 1, "Polar", 1.42}, {63, 0, "Apolar", 1.88},
{64, 0, "Apolar", 1.88}, {65, 0, "Apolar", 1.88},
{66, 0, "Apolar", 1.88}, {67, 1, "Polar", 1.64},
{68, 0, "Apolar", 1.88}, {69, 0, "Apolar", 1.61},
{70, 1, "Polar", 1.42}, {71, 0, "Apolar", 1.88},
{72, 1, "Polar", 1.46}, {73, 0, "Apolar", 1.88},
{74, 1, "Polar", 1.64}, {75, 0, "Apolar", 1.88},
{76, 0, "Apolar", 1.61}, {77, 1, "Polar", 1.42},
{78, 1, "Polar", 1.64}, {79, 0, "Apolar", 1.88},
{80, 0, "Apolar", 1.61}, {81, 1, "Polar", 1.42},
{82, 0, "Apolar", 1.88}, {83, 0, "Apolar", 1.88},
{84, 0, "Apolar", 1.88}, {85, 0, "Apolar", 1.88},
{86, 1, "Polar", 1.64}, {87, 1, "Polar", 1.64},
{88, 0, "Apolar", 1.88}, {89, 0, "Apolar", 1.61},
{90, 1, "Polar", 1.42}, {91, 0, "Apolar", 1.88},
{92, 1, "Polar", 1.46}, {93, 0, "Apolar", 1.88},
{94, 1, "Polar", 1.64}, {95, 0, "Apolar", 1.88},
{96, 0, "Apolar", 1.61}, {97, 1, "Polar", 1.42},
{98, 0, "Apolar", 1.88}, {99, 0, "Apolar", 1.88},
{100, 0, "Apolar", 1.88}, {101, 0, "Apolar", 1.88},
{102, 1, "Polar", 1.64}, {103, 0, "Apolar", 1.88},
{104, 0, "Apolar", 1.61}, {105, 1, "Polar", 1.42},
{106, 0, "Apolar", 1.88}, {107, 1, "Polar", 1.46},
{108, 0, "Apolar", 1.88}, {109, 1, "Polar", 1.64},
{110, 0, "Apolar", 1.88}, {111, 0, "Apolar", 1.61},
{112, 1, "Polar", 1.42}, {113, 0, "Apolar", 1.88},
{114, 0, "Apolar", 1.88}, {115, 0, "Apolar", 1.88},
{116, 0, "Apolar", 1.88}, {117, 1, "Polar", 1.64},
{118, 0, "Apolar", 1.88}, {119, 0, "Apolar", 1.61},
{120, 1, "Polar", 1.42}, {121, 0, "Apolar", 1.88},
{122, 0, "Apolar", 1.88}, {123, 0, "Apolar", 1.61},
{124, 1, "Polar", 1.42}, {125, 1, "Polar", 1.46},
{126, 1, "Polar", 1.64}, {127, 0, "Apolar", 1.88},
{128, 0, "Apolar", 1.61}, {129, 1, "Polar", 1.42},
{130, 0, "Apolar", 1.88}, {131, 0, "Apolar", 1.88},
{132, 0, "Apolar", 1.88}, {133, 1, "Polar", 1.64},
{134, 0, "Apolar", 1.88}, {135, 0, "Apolar", 1.61},
{136, 1, "Polar", 1.42}, {137, 0, "Apolar", 1.88},
{138, 0, "Apolar", 1.88}, {139, 0, "Apolar", 1.61},
{140, 1, "Polar", 1.42}, {141, 1, "Polar", 1.46},
{142, 1, "Polar", 1.64}, {143, 0, "Apolar", 1.88},
{144, 0, "Apolar", 1.61}, {145, 1, "Polar", 1.42},
{146, 0, "Apolar", 1.88}, {147, 0, "Apolar", 1.88},
{148, 0, "Apolar", 1.88}, {149, 1, "Polar", 1.64},
{150, 0, "Apolar", 1.88}, {151, 0, "Apolar", 1.61},
{152, 1, "Polar", 1.42}, {153, 0, "Apolar", 1.88},
{154, 1, "Polar", 1.46}, {155, 1, "Polar", 1.64},
{156, 0, "Apolar", 1.88}, {157, 0, "Apolar", 1.61},
{158, 1, "Polar", 1.42}, {159, 0, "Apolar", 1.88},
{160, 0, "Apolar", 1.61}, {161, 1, "Polar", 1.42},
{162, 1, "Polar", 1.46}, {163, 1, "Polar", 1.64},
{164, 0, "Apolar", 1.88}, {165, 0, "Apolar", 1.61},
{166, 1, "Polar", 1.42}, {167, 0, "Apolar", 1.88},
{168, 1, "Polar", 1.46}, {169, 0, "Apolar", 1.88},
{170, 1, "Polar", 1.64}, {171, 0, "Apolar", 1.88},
{172, 0, "Apolar", 1.61}, {173, 1, "Polar", 1.42},
{174, 0, "Apolar", 1.88}, {175, 0, "Apolar", 1.88},
{176, 0, "Apolar", 1.88}, {177, 0, "Apolar", 1.88},
{178, 1, "Polar", 1.64}, {179, 0, "Apolar", 1.88},
{180, 0, "Apolar", 1.61}, {181, 1, "Polar", 1.42},
{182, 0, "Apolar", 1.88}, {183, 0, "Apolar", 1.88},
{184, 0, "Apolar", 1.61}, {185, 1, "Polar", 1.42},
{186, 1, "Polar", 1.46}, {187, 1, "Polar", 1.64},
{188, 0, "Apolar", 1.88}, {189, 0, "Apolar", 1.61},
{190, 1, "Polar", 1.42}, {191, 0, "Apolar", 1.88},
{192, 0, "Apolar", 1.61}, {193, 1, "Polar", 1.42},
{194, 1, "Polar", 1.64}, {195, 1, "Polar", 1.64},
{196, 0, "Apolar", 1.88}, {197, 0, "Apolar", 1.61},
{198, 1, "Polar", 1.42}, {199, 0, "Apolar", 1.88},
{200, 0, "Apolar", 1.88}, {201, 0, "Apolar", 1.88},
{202, 1, "Polar", 1.64}, {203, 0, "Apolar", 1.88},
{204, 0, "Apolar", 1.61}, {205, 1, "Polar", 1.42},
{206, 0, "Apolar", 1.88}, {207, 0, "Apolar", 1.88},
{208, 0, "Apolar", 1.88}, {209, 0, "Apolar", 1.88},
{210, 1, "Polar", 1.64}, {211, 1, "Polar", 1.64},
{212, 0, "Apolar", 1.88}, {213, 0, "Apolar", 1.61},
{214, 1, "Polar", 1.42}, {215, 0, "Apolar", 1.88},
{216, 1, "Polar", 1.64}, {217, 0, "Apolar", 1.88},
{218, 0, "Apolar", 1.61}, {219, 1, "Polar", 1.42},
{220, 0, "Apolar", 1.88}, {221, 0, "Apolar", 1.88},
{222, 0, "Apolar", 1.88}, {223, 0, "Apolar", 1.88},
{224, 1, "Polar", 1.64}, {225, 1, "Polar", 1.64},
{226, 0, "Apolar", 1.88}, {227, 0, "Apolar", 1.61},
{228, 1, "Polar", 1.42}, {229, 0, "Apolar", 1.88},
{230, 0, "Apolar", 1.88}, {231, 0, "Apolar", 1.88},
{232, 0, "Apolar", 1.88}, {233, 1, "Polar", 1.64},
{234, 0, "Apolar", 1.88}, {235, 0, "Apolar", 1.61},
{236, 1, "Polar", 1.42}, {237, 0, "Apolar", 1.88},
{238, 0, "Apolar", 1.88}, {239, 0, "Apolar", 1.61},
{240, 1, "Polar", 1.42}, {241, 1, "Polar", 1.64},
{242, 1, "Polar", 1.64}, {243, 0, "Apolar", 1.88},
{244, 0, "Apolar", 1.61}, {245, 1, "Polar", 1.42},
{246, 0, "Apolar", 1.88}, {247, 0, "Apolar", 1.61},
{248, 1, "Polar", 1.42}, {249, 1, "Polar", 1.46},
{250, 1, "Polar", 1.64}, {251, 0, "Apolar", 1.88},
{252, 0, "Apolar", 1.61}, {253, 1, "Polar", 1.42},
{254, 0, "Apolar", 1.88}, {255, 0, "Apolar", 1.88},
{256, 0, "Apolar", 1.88}, {257, 0, "Apolar", 1.88},
{258, 1, "Polar", 1.64}, {259, 1, "Polar", 1.64},
{260, 0, "Apolar", 1.88}, {261, 0, "Apolar", 1.61},
{262, 1, "Polar", 1.42}, {263, 0, "Apolar", 1.88},
{264, 0, "Apolar", 1.88}, {265, 0, "Apolar", 1.61},
{266, 1, "Polar", 1.42}, {267, 1, "Polar", 1.46},
{268, 1, "Polar", 1.64}, {269, 0, "Apolar", 1.88},
{270, 0, "Apolar", 1.61}, {271, 1, "Polar", 1.42},
{272, 1, "Polar", 1.64}, {273, 0, "Apolar", 1.88},
{274, 0, "Apolar", 1.61}, {275, 1, "Polar", 1.42},
{276, 0, "Apolar", 1.88}, {277, 0, "Apolar", 1.88},
{278, 0, "Apolar", 1.88}, {279, 0, "Apolar", 1.88},
{280, 1, "Polar", 1.64}, {281, 0, "Apolar", 1.88},
{282, 0, "Apolar", 1.61}, {283, 1, "Polar", 1.42},
{284, 0, "Apolar", 1.88}, {285, 0, "Apolar", 1.88},
{286, 0, "Apolar", 1.88}, {287, 1, "Polar", 1.64},
{288, 0, "Apolar", 1.88}, {289, 0, "Apolar", 1.61},
{290, 1, "Polar", 1.42}, {291, 0, "Apolar", 1.88},
{292, 0, "Apolar", 1.88}, {293, 0, "Apolar", 1.88},
{294, 1, "Polar", 1.64}, {295, 0, "Apolar", 1.88},
{296, 0, "Apolar", 1.61}, {297, 1, "Polar", 1.42},
{298, 0, "Apolar", 1.88}, {299, 0, "Apolar", 1.61},
{300, 1, "Polar", 1.42}, {301, 1, "Polar", 1.46},
{302, 1, "Polar", 1.64}, {303, 0, "Apolar", 1.88},
{304, 0, "Apolar", 1.61}, {305, 1, "Polar", 1.42},
{306, 0, "Apolar", 1.88}, {307, 0, "Apolar", 1.88},
{308, 0, "Apolar", 1.61}, {309, 1, "Polar", 1.42},
{310, 1, "Polar", 1.64}, {311, 1, "Polar", 1.64},
{312, 0, "Apolar", 1.88}, {313, 0, "Apolar", 1.61},
{314, 1, "Polar", 1.42}, {315, 0, "Apolar", 1.88},
{316, 0, "Apolar", 1.88}, {317, 0, "Apolar", 1.61},
{318, 1, "Polar", 1.42}, {319, 1, "Polar", 1.64},
{320, 1, "Polar", 1.64}, {321, 0, "Apolar", 1.88},
{322, 0, "Apolar", 1.61}, {323, 1, "Polar", 1.42},
{324, 0, "Apolar", 1.88}, {325, 0, "Apolar", 1.88},
{326, 0, "Apolar", 1.88}, {327, 1, "Polar", 1.64},
{328, 0, "Apolar", 1.61}, {329, 1, "Polar", 1.64},
{330, 1, "Polar", 1.64}, {331, 1, "Polar", 1.64},
{332, 0, "Apolar", 1.88}, {333, 0, "Apolar", 1.61},
{334, 1, "Polar", 1.42}, {335, 0, "Apolar", 1.88},
{336, 0, "Apolar", 1.88}, {337, 0, "Apolar", 1.88},
{338, 0, "Apolar", 1.88}, {339, 1, "Polar", 1.64},
{340, 0, "Apolar", 1.88}, {341, 0, "Apolar", 1.61},
{342, 1, "Polar", 1.42}, {343, 0, "Apolar", 1.88},
{344, 0, "Apolar", 1.88}, {345, 0, "Apolar", 1.88},
{346, 0, "Apolar", 1.88}, {347, 1, "Polar", 1.64},
{348, 0, "Apolar", 1.88}, {349, 0, "Apolar", 1.61},
{350, 1, "Polar", 1.42}, {351, 0, "Apolar", 1.88},
{352, 0, "Apolar", 1.61}, {353, 0, "Apolar", 1.76},
{354, 0, "Apolar", 1.76}, {355, 0, "Apolar", 1.76},
{356, 0, "Apolar", 1.76}, {357, 0, "Apolar", 1.76},
{358, 1, "Polar", 1.64}, {359, 0, "Apolar", 1.88},
{360, 0, "Apolar", 1.61}, {361, 1, "Polar", 1.42},
{362, 0, "Apolar", 1.88}, {363, 1, "Polar", 1.64},
{364, 0, "Apolar", 1.88}, {365, 0, "Apolar", 1.61},
{366, 1, "Polar", 1.42}, {367, 1, "Polar", 1.64},
{368, 0, "Apolar", 1.88}, {369, 0, "Apolar", 1.61},
{370, 1, "Polar", 1.42}, {371, 0, "Apolar", 1.88},
{372, 0, "Apolar", 1.88}, {373, 0, "Apolar", 1.88},
{374, 0, "Apolar", 1.88}, {375, 1, "Polar", 1.64},
{376, 1, "Polar", 1.64}, {377, 0, "Apolar", 1.88},
{378, 0, "Apolar", 1.61}, {379, 1, "Polar", 1.42},
{380, 0, "Apolar", 1.88}, {381, 0, "Apolar", 1.88},
{382, 0, "Apolar", 1.61}, {383, 1, "Polar", 1.42},
{384, 1, "Polar", 1.64}, {385, 1, "Polar", 1.64},
{386, 0, "Apolar", 1.88}, {387, 0, "Apolar", 1.61},
{388, 1, "Polar", 1.42}, {389, 0, "Apolar", 1.88},
{390, 0, "Apolar", 1.88}, {391, 0, "Apolar", 1.88},
{392, 0, "Apolar", 1.88}, {393, 1, "Polar", 1.64},
{394, 0, "Apolar", 1.88}, {395, 0, "Apolar", 1.61},
{396, 1, "Polar", 1.42}, {397, 0, "Apolar", 1.88},
{398, 0, "Apolar", 1.88}, {399, 0, "Apolar", 1.61},
{400, 1, "Polar", 1.42}, {401, 1, "Polar", 1.46},
{402, 1, "Polar", 1.64}, {403, 0, "Apolar", 1.88},
{404, 0, "Apolar", 1.61}, {405, 1, "Polar", 1.42},
{406, 0, "Apolar", 1.88}, {407, 0, "Apolar", 1.61},
{408, 1, "Polar", 1.42}, {409, 1, "Polar", 1.46},
{410, 1, "Polar", 1.64}, {411, 0, "Apolar", 1.88},
{412, 0, "Apolar", 1.61}, {413, 1, "Polar", 1.42},
{414, 1, "Polar", 1.64}, {415, 0, "Apolar", 1.88},
{416, 0, "Apolar", 1.61}, {417, 1, "Polar", 1.42},
{418, 0, "Apolar", 1.88}, {419, 0, "Apolar", 1.88},
{420, 0, "Apolar", 1.88}, {421, 1, "Polar", 1.64},
{422, 0, "Apolar", 1.61}, {423, 1, "Polar", 1.64},
{424, 1, "Polar", 1.64}, {425, 1, "Polar", 1.64},
{426, 0, "Apolar", 1.88}, {427, 0, "Apolar", 1.61},
{428, 1, "Polar", 1.42}, {429, 0, "Apolar", 1.88},
{430, 1, "Polar", 1.46}, {431, 0, "Apolar", 1.88},
{432, 1, "Polar", 1.64}, {433, 0, "Apolar", 1.88},
{434, 0, "Apolar", 1.61}, {435, 1, "Polar", 1.42},
{436, 0, "Apolar", 1.88}, {437, 0, "Apolar", 1.88},
{438, 0, "Apolar", 1.88}, {439, 0, "Apolar", 1.88},
{440, 1, "Polar", 1.64}, {441, 0, "Apolar", 1.88},
{442, 0, "Apolar", 1.61}, {443, 1, "Polar", 1.42},
{444, 0, "Apolar", 1.88}, {445, 1, "Polar", 1.46},
{446, 1, "Polar", 1.64}, {447, 0, "Apolar", 1.88},
{448, 0, "Apolar", 1.61}, {449, 1, "Polar", 1.42},
{450, 0, "Apolar", 1.88}, {451, 0, "Apolar", 1.61},
{452, 1, "Polar", 1.42}, {453, 1, "Polar", 1.46},
{454, 1, "Polar", 1.64}, {455, 0, "Apolar", 1.88},
{456, 0, "Apolar", 1.61}, {457, 1, "Polar", 1.42},
{458, 0, "Apolar", 1.88}, {459, 0, "Apolar", 1.61},
{460, 0, "Apolar", 1.76}, {461, 0, "Apolar", 1.76},
{462, 0, "Apolar", 1.76}, {463, 0, "Apolar", 1.76},
{464, 0, "Apolar", 1.61}, {465, 1, "Polar", 1.46},
{466, 1, "Polar", 1.64}, {467, 0, "Apolar", 1.88},
{468, 0, "Apolar", 1.61}, {469, 1, "Polar", 1.42},
{470, 0, "Apolar", 1.88}, {471, 0, "Apolar", 1.61},
{472, 1, "Polar", 1.42}, {473, 1, "Polar", 1.64},
{474, 1, "Polar", 1.64}, {475, 0, "Apolar", 1.88},
{476, 0, "Apolar", 1.61}, {477, 1, "Polar", 1.42},
{478, 0, "Apolar", 1.88}, {479, 0, "Apolar", 1.88},
{480, 0, "Apolar", 1.88}, {481, 0, "Apolar", 1.88},
{482, 1, "Polar", 1.64}, {483, 0, "Apolar", 1.88},
{484, 0, "Apolar", 1.61}, {485, 1, "Polar", 1.42},
{486, 0, "Apolar", 1.88}, {487, 0, "Apolar", 1.88},
{488, 0, "Apolar", 1.61}, {489, 1, "Polar", 1.42},
{490, 1, "Polar", 1.64}, {491, 1, "Polar", 1.64},
{492, 0, "Apolar", 1.88}, {493, 0, "Apolar", 1.61},
{494, 1, "Polar", 1.42}, {495, 0, "Apolar", 1.88},
{496, 0, "Apolar", 1.88}, {497, 0, "Apolar", 1.88},
{498, 0, "Apolar", 1.88}, {499, 1, "Polar", 1.64},
{500, 1, "Polar", 1.64}, {501, 0, "Apolar", 1.88},
{502, 0, "Apolar", 1.61}, {503, 1, "Polar", 1.42},
{504, 0, "Apolar", 1.88}, {505, 0, "Apolar", 1.88},
{506, 0, "Apolar", 1.61}, {507, 1, "Polar", 1.42},
{508, 1, "Polar", 1.46}, {509, 1, "Polar", 1.64},
{510, 0, "Apolar", 1.88}, {511, 0, "Apolar", 1.61},
{512, 1, "Polar", 1.42}, {513, 0, "Apolar", 1.88},
{514, 1, "Polar", 1.46}, {515, 1, "Polar", 1.64},
{516, 0, "Apolar", 1.88}, {517, 0, "Apolar", 1.61},
{518, 1, "Polar", 1.42}, {519, 0, "Apolar", 1.88},
{520, 1, "Polar", 1.46}, {521, 0, "Apolar", 1.88},
{522, 1, "Polar", 1.64}, {523, 0, "Apolar", 1.88},
{524, 0, "Apolar", 1.61}, {525, 1, "Polar", 1.42},
{526, 0, "Apolar", 1.88}, {527, 0, "Apolar", 1.88},
{528, 0, "Apolar", 1.88}, {529, 0, "Apolar", 1.88},
{530, 1, "Polar", 1.64}, {531, 0, "Apolar", 1.88},
{532, 0, "Apolar", 1.61}, {533, 1, "Polar", 1.42},
{534, 0, "Apolar", 1.88}, {535, 0, "Apolar", 1.61},
{536, 1, "Polar", 1.64}, {537, 0, "Apolar", 1.76},
{538, 0, "Apolar", 1.76}, {539, 1, "Polar", 1.64},
{540, 1, "Polar", 1.64}, {541, 0, "Apolar", 1.88},
{542, 0, "Apolar", 1.61}, {543, 1, "Polar", 1.42},
{544, 0, "Apolar", 1.88}, {545, 0, "Apolar", 1.88},
{546, 0, "Apolar", 1.88}, {547, 0, "Apolar", 1.88},
{548, 1, "Polar", 1.64}, {549, 0, "Apolar", 1.88},
{550, 0, "Apolar", 1.61}, {551, 1, "Polar", 1.42},
{552, 0, "Apolar", 1.88}, {553, 0, "Apolar", 1.88},
{554, 0, "Apolar", 1.88}, {555, 1, "Polar", 1.64},
{556, 0, "Apolar", 1.88}, {557, 0, "Apolar", 1.61},
{558, 1, "Polar", 1.42}, {559, 0, "Apolar", 1.88},
{560, 0, "Apolar", 1.88}, {561, 0, "Apolar", 1.88},
{562, 0, "Apolar", 1.88}, {563, 1, "Polar", 1.64},
{564, 0, "Apolar", 1.88}, {565, 0, "Apolar", 1.61},
{566, 1, "Polar", 1.42}, {567, 0, "Apolar", 1.88},
{568, 0, "Apolar", 1.88}, {569, 0, "Apolar", 1.88},
{570, 1, "Polar", 1.64}, {571, 0, "Apolar", 1.61},
{572, 1, "Polar", 1.64}, {573, 1, "Polar", 1.64},
{574, 1, "Polar", 1.64}, {575, 0, "Apolar", 1.88},
{576, 0, "Apolar", 1.61}, {577, 1, "Polar", 1.42},
{578, 0, "Apolar", 1.88}, {579, 0, "Apolar", 1.88},
{580, 0, "Apolar", 1.88}, {581, 0, "Apolar", 1.88},
{582, 1, "Polar", 1.64}, {583, 0, "Apolar", 1.88},
{584, 0, "Apolar", 1.61}, {585, 1, "Polar", 1.42},
{586, 0, "Apolar", 1.88}, {587, 0, "Apolar", 1.88},
{588, 0, "Apolar", 1.88}, {589, 1, "Polar", 1.64},
{590, 0, "Apolar", 1.61}, {591, 1, "Polar", 1.64},
{592, 1, "Polar", 1.64}, {593, 1, "Polar", 1.64},
{594, 0, "Apolar", 1.88}, {595, 0, "Apolar", 1.61},
{596, 1, "Polar", 1.42}, {597, 1, "Polar", 1.64},
{598, 0, "Apolar", 1.88}, {599, 0, "Apolar", 1.61},
{600, 1, "Polar", 1.42}, {601, 1, "Polar", 1.46}};
void testPDB() {
BOOST_LOG(rdInfoLog) << "-----------------------\n Testing FreeSASA basics"
<< std::endl;
std::string rdbase = getenv("RDBASE");
std::string fName = rdbase += "/External/FreeSASA/test_data/1d3z.pdb";
ROMol *m;
{
const bool sanitize = true;
const bool removeHs = true;
m = PDBFileToMol(fName, sanitize, removeHs);
}
std::vector<double> radii;
FreeSASA::classifyAtoms(*m, radii);
for (ROMol::AtomIterator at = m->beginAtoms(); at != m->endAtoms(); ++at) {
Atom *atom = (*at);
unsigned int idx = atom->getIdx();
TEST_ASSERT(idx == ExpectedProtor1d3z[idx].idx);
TEST_ASSERT(atom->getProp<int>(common_properties::Atom::SASAClass) ==
ExpectedProtor1d3z[idx].cls);
TEST_ASSERT(
atom->getProp<std::string>(common_properties::Atom::SASAClassName) ==
ExpectedProtor1d3z[idx].clsname);
TEST_ASSERT(radii[idx] == ExpectedProtor1d3z[idx].radius);
}
FreeSASA::SASAOpts opts;
opts.algorithm = FreeSASA::SASAOpts::ShrakeRupley;
double sasa = FreeSASA::calcSASA(*m, radii, -1, nullptr, opts);
TEST_ASSERT(fabs(sasa - 5000.340175) < 1e-5);
delete m;
{
const bool sanitize = false;
const bool removeHs = false;
m = PDBFileToMol(fName, sanitize, removeHs);
}
ROMol *mnoh = MolOps::removeHs(*m);
FreeSASA::classifyAtoms(*mnoh, radii);
sasa = FreeSASA::calcSASA(*mnoh, radii, -1, nullptr, opts);
TEST_ASSERT(fabs(sasa - 5000.340175) < 1e-5);
const QueryAtom *apolar = FreeSASA::makeFreeSasaAPolarAtomQuery();
const QueryAtom *polar = FreeSASA::makeFreeSasaPolarAtomQuery();
double apolard = FreeSASA::calcSASA(*mnoh, radii, -1, apolar, opts);
double polard = FreeSASA::calcSASA(*mnoh, radii, -1, polar, opts);
std::cerr << " polar " << polard << std::endl;
std::cerr << " apolar " << apolard << std::endl;
delete polar;
delete apolar;
delete m;
delete mnoh;
TEST_ASSERT(fabs(polard + apolard - 5000.340175) < 1e-5);
BOOST_LOG(rdInfoLog) << "Done" << std::endl;
}
int main() {
RDLog::InitLogs();
testPDB();
}
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