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- update AvalonTools to version 2.0.4a (#5796)
- update config files in Data to the same version as in AvalonTools - fix a bug in AvalonTools.cpp causing the last character of the optString bassed to initCheckMol() to be deleted - add a test to confirm the bug is fixed Co-authored-by: Tosco, Paolo <paolo.tosco@novartis.com>
This commit is contained in:
Paolo Tosco
GitHub
@@ -1,4 +1,4 @@
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606 ! _N10_, 12.Dec.2008 incl. Sandoz R-...; C-C(=O)-D,T.
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607 ! _N10_, 12.Dec.2008 incl. Sandoz R-...; C-C(=O)-D,T.
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/* 00 */ "Li,Na,K,Rb,Cs,Fr,Tl+1"
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/* 00 */ "Be,Mg,Ca,Sr,Ba,Ra,Sn,Pb+2"
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/* 00 */ "Al,Ga,In,Tl,Sb,Bi,Fe+3"
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@@ -309,6 +309,7 @@
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/* 03C*/ "C(-C+1)(-C)(-C)"
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/* 03 */ "C(-I+1)(-C)(-C)"
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/* 03 */ "C(-N+1)(-N+1)(-C)"
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/* 03 */ "@C(=C)(-O)(-O-1)"
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/* 03 */ "C(=C)(-B)(-B,C,N,O,S)"
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/* 03 */ "C(=C)(-C,Si,Ge,Sn,Pb)(-C,Si,Ge,Sn,Pb,O,S,Se,Te,N,P,As,F,Cl,Br,I,D,T)"
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/* 03 */ "C(=C)(-O,S,Se,Te,N,P,F,Cl,Br,I)(-O,S,Se,Te,N,P,F,Cl,Br,I)"
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@@ -1,9 +1,9 @@
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# Parameter file for STRUCHK 2.0
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# for use with CORDAT
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#
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ta \apps\chemistry\checkfgs.trn # augmented atom transformations
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ta StandardFiles/checkfgs.trn # augmented atom transformations
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or # create data fields with STRUCHK results
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ca \apps\chemistry\checkfgs.chk # table of allowed augmented atoms
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ca StandardFiles/checkfgs.chk # table of allowed augmented atoms
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cc # check for atom collisions
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cl 3 # collision limit is 3% of bond length
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cs # check stereo conventions
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@@ -79,7 +79,7 @@
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/*F123*/ "C(-C)(-O-1)(-N+1)" --> "C(-C)(-O)(-N+1)" prot.
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/*F203*/ "C(=C)(-N-1)(-C,N)" --> "C(=C)(-N)(-C,N)" prot.
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/*F213*/ "C(=C)(-O,S-1)(-C)" --> "C(=C)(-O,S)(-C)" prot. enol C
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/*F223*/ "C(=C)(-O-1)(-N,O,S)" --> "C(-C)(=O)(-N,O,S)" prot. enol Het.
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/*F223*/ "!@C(=C)(-O-1)(-N,O,S)" --> "C(-C)(=O)(-N,O,S)" prot. enol Het.
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/*F233*/ "C(=C)(-S-1)(-N,S)" --> "C(-C)(=S)(-N,S)" prot. enol
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/*F243*/ "C(=C)(-O-1)(-N+1)" --> "C(-C)(=O)(-N+1)" prot. enol
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/*F303*/ "C(=N)(-C,N,O,S-1)(-C,N,O,S)" --> "C(=N)(-C,N,O,S)(-C,N,O,S)" prot.
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10
External/AvalonTools/AvalonTools.cpp
vendored
10
External/AvalonTools/AvalonTools.cpp
vendored
@@ -349,7 +349,7 @@ void getAvalonCountFP(const std::string &data, bool isSmiles,
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reaccsToCounts(mp, res, bitFlags, isQuery, nBits);
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FreeMolecule(mp);
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} else {
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BOOST_LOG(rdErrorLog) << "ERROR: no fingeprint generated for molecule."
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BOOST_LOG(rdErrorLog) << "ERROR: no fingerprint generated for molecule."
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<< std::endl;
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}
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}
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@@ -368,7 +368,7 @@ void getAvalonFP(const std::string &data, bool isSmiles, ExplicitBitVect &res,
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reaccsToFingerprint(mp, res, bitFlags, isQuery, resetVect, nBytes);
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FreeMolecule(mp);
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} else {
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BOOST_LOG(rdErrorLog) << "ERROR: no fingeprint generated for molecule."
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BOOST_LOG(rdErrorLog) << "ERROR: no fingerprint generated for molecule."
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<< std::endl;
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}
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}
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@@ -387,7 +387,7 @@ void getAvalonFP(const std::string &data, bool isSmiles,
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reaccsToFingerprint(mp, res, bitFlags, isQuery, resetVect, nBytes);
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FreeMolecule(mp);
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} else {
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BOOST_LOG(rdErrorLog) << "ERROR: no fingeprint generated for molecule."
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BOOST_LOG(rdErrorLog) << "ERROR: no fingerprint generated for molecule."
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<< std::endl;
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}
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}
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@@ -438,8 +438,8 @@ int initCheckMol(const std::string &optString) {
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// n.b. always add a cr to the end for safety
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auto *optBuffer = new char[optString.size() + 2];
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optString.copy(optBuffer, optString.size());
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optBuffer[optString.size() - 1] = '\n';
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optBuffer[optString.size()] = '\0';
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optBuffer[optString.size()] = '\n';
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optBuffer[optString.size() + 1] = '\0';
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int res = InitCheckMol(optBuffer);
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delete[] optBuffer;
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return res;
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4
External/AvalonTools/CMakeLists.txt
vendored
4
External/AvalonTools/CMakeLists.txt
vendored
@@ -2,7 +2,7 @@ if(NOT RDK_BUILD_AVALON_SUPPORT)
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return()
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endif(NOT RDK_BUILD_AVALON_SUPPORT)
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set(AVALON_VERSION "2.0.2")
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set(AVALON_VERSION "2.0.4a")
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if(NOT DEFINED AVALONTOOLS_DIR)
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set(AVALONTOOLS_DIR "${CMAKE_CURRENT_SOURCE_DIR}/ava-formake-AvalonToolkit_${AVALON_VERSION}")
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set(fileToCheck "${AVALONTOOLS_DIR}/src/main/C/common/reaccsio.c")
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@@ -25,7 +25,7 @@ if(needDownload)
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set(AVALONTOOLS_URL "https://github.com/rohdebe1/ava-formake/archive/refs/tags/AvalonToolkit_${AVALON_VERSION}.tar.gz")
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endif()
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if(NOT DEFINED AVALONTOOLS_MD5SUM)
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set(AVALONTOOLS_MD5SUM "fc188383a8896802e948c977b73dbe71")
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set(AVALONTOOLS_MD5SUM "8e0fdedce0d93bdbc1e3c6ab3ae5c6cf")
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endif()
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if(NOT DEFINED AVALONTOOLS_BASE)
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string(REGEX REPLACE "^.*/" "" AVALONTOOLS_BASE "${AVALONTOOLS_URL}")
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25
External/AvalonTools/test1.cpp
vendored
25
External/AvalonTools/test1.cpp
vendored
@@ -529,6 +529,30 @@ void testNoAtomCTAB() {
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TEST_ASSERT(res.empty());
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}
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void testBigMoleculeNoNewlineInInitString() {
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BOOST_LOG(rdInfoLog) << "testing molecule with >150 atoms when "
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"init string has no newline"
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<< std::endl;
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std::string pathName = getenv("RDBASE");
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pathName += "/Data/struchk/";
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std::stringstream struchk_init;
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struchk_init << "-ta " << pathName << "checkfgs.trn\n"
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<< "-tm\n"
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"-or\n"
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"-ca " << pathName << "checkfgs.chk\n"
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<< "-cc\n"
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"-cl 3\n"
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"-cs\n"
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"-cn 999";
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int errs = AvalonTools::initCheckMol(struchk_init.str());
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TEST_ASSERT(!errs);
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std::string bigMol =
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"CC(C)CC(C(=O)NC(CCSC)C(=O)NC(CC(=O)N)C(=O)NC(C(C)O)C(=O)O)NC(=O)C(CC1=CNC2=CC=CC=C21)NC(=O)C(CCC(=O)N)NC(=O)C(C(C)C)NC(=O)C(CC3=CC=CC=C3)NC(=O)C(CC(=O)O)NC(=O)C(CCC(=O)N)NC(=O)C(C)NC(=O)C(CCCNC(=N)N)NC(=O)C(CCCNC(=N)N)NC(=O)C(CO)NC(=O)C(CC(=O)O)NC(=O)C(CC(C)C)NC(=O)C(CC4=CC=C(C=C4)O)NC(=O)C(CCCCN)NC(=O)C(CO)NC(=O)C(CC5=CC=C(C=C5)O)NC(=O)C(CC(=O)O)NC(=O)C(CO)NC(=O)C(C(C)O)NC(=O)C(CC6=CC=CC=C6)NC(=O)C(C(C)O)NC(=O)CNC(=O)C(CCC(=O)N)NC(=O)C(CO)NC(=O)C(CC7=CN=CN7)N";
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RDKit::ROMOL_SPTR m = AvalonTools::checkMol(errs, bigMol, true);
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AvalonTools::closeCheckMolFiles();
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TEST_ASSERT(errs == 0);
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}
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int main() {
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RDLog::InitLogs();
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#if 1
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@@ -549,6 +573,7 @@ int main() {
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testGithub4075();
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testGithub4330();
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testNoAtomCTAB();
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testBigMoleculeNoNewlineInInitString();
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return 0;
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}
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