make iostreams optional

2026-06-03 21:44:30 +08:00 · 2019-05-08 17:33:17 +02:00
parent 89f769cd88
commit 17828cc2c9
8 changed files with 131 additions and 117 deletions
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -54,6 +54,7 @@ option(RDK_BUILD_MOLINTERCHANGE_SUPPORT "build in support for CommonChem molecul
 option(RDK_BUILD_YAEHMOP_SUPPORT "build support for the YAeHMOP wrapper" OFF)
 option(RDK_INSTALL_DEV_COMPONENT "install libraries and headers" ON)
 option(RDK_USE_BOOST_REGEX "use boost::regex instead of std::regex (needed for systems with g++-4.8)" OFF)
+option(RDK_USE_BOOST_IOSTREAMS "use boost::iostreams" ON)
 if(NOT MSVC)
  if(RDK_OPTIMIZE_NATIVE)
      set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -mpopcnt")
--- a/Code/GraphMol/FileParsers/CMakeLists.txt
+++ b/Code/GraphMol/FileParsers/CMakeLists.txt
@@ -2,6 +2,7 @@
 remove_definitions(-DRDKIT_GRAPHMOL_BUILD)
 add_definitions(-DRDKIT_FILEPARSERS_BUILD)

+if(RDK_USE_BOOST_IOSTREAMS)
 if(WIN32)
  find_package(Boost 1.56.0 COMPONENTS system iostreams REQUIRED)
  find_package(Boost 1.56.0 COMPONENTS zlib)
@@ -16,6 +17,7 @@ else()
     add_definitions("-DBOOST_IOSTREAMS_DYN_LINK")
  endif()
 endif()
+endif(RDK_USE_BOOST_IOSTREAMS)

 if(RDK_BUILD_COORDGEN_SUPPORT)
    include_directories(${maeparser_INCLUDE_DIRS})
--- a/Code/GraphMol/FileParsers/testMolSupplier.cpp
+++ b/Code/GraphMol/FileParsers/testMolSupplier.cpp
@@ -129,7 +129,7 @@ int testMolSup() {
    }
    TEST_ASSERT(ok);
  }
-#endif // RDK_BUILD_COORDGEN_SUPPORT
+#endif  // RDK_BUILD_COORDGEN_SUPPORT
  return 1;
 }

@@ -319,10 +319,11 @@ void testSmilesSupFromText() {
  // this was a delightful boundary condition:
  BOOST_LOG(rdErrorLog)
      << "------------------------------------------------------" << std::endl;
-  text = "CC\n"
-         "CCC\n"
-         "CCOC\n"
-         "CCCCOC";
+  text =
+      "CC\n"
+      "CCC\n"
+      "CCOC\n"
+      "CCCCOC";
  {
    nSup2.setData(text, " ", 0, -1, false, true);
    //  BOOST_LOG(rdErrorLog) << "SIZE: " << nSup2.length() << std::endl;
@@ -395,11 +396,12 @@ void testSmilesSupFromText() {
  }
  // --------------
  // basics:
-  text = "Id SMILES Column_2\n"
-         "mol-1 C 1.0\n"
-         "mol-2 CC 4.0\n"
-         "mol-3 CCC 9.0\n"
-         "mol-4 CCCC 16.0\n";
+  text =
+      "Id SMILES Column_2\n"
+      "mol-1 C 1.0\n"
+      "mol-2 CC 4.0\n"
+      "mol-3 CCC 9.0\n"
+      "mol-4 CCCC 16.0\n";
 #if 1
  nSup2.setData(text, " ", 1, 0, true, true);
  mol = nSup2[3];
@@ -412,10 +414,11 @@ void testSmilesSupFromText() {
  delete mol;

  // ensure that we can call setData a second time:
-  text = "Id SMILES Column_2\n"
-         "mol-1 C 1.0\n"
-         "mol-2 CC 4.0\n"
-         "mol-3 CCC 9.0\n";
+  text =
+      "Id SMILES Column_2\n"
+      "mol-1 C 1.0\n"
+      "mol-2 CC 4.0\n"
+      "mol-3 CCC 9.0\n";
  nSup2.setData(text, " ", 1, 0, true, true);
  CHECK_INVARIANT(nSup2.length() == 3, "");
  mol = nSup2[2];
@@ -426,11 +429,12 @@ void testSmilesSupFromText() {
  delete mol;

  // now test for failure handling:
-  text = "Id SMILES Column_2\n"
-         "mol-1 C 1.0\n"
-         "mol-2 CC 4.0\n"
-         "mol-3 fail 9.0\n"
-         "mol-4 CCCC 16.0\n";
+  text =
+      "Id SMILES Column_2\n"
+      "mol-1 C 1.0\n"
+      "mol-2 CC 4.0\n"
+      "mol-3 fail 9.0\n"
+      "mol-4 CCCC 16.0\n";
  nSup2.setData(text, " ", 1, 0, true, true);
  mol = nSup2[3];
  //  BOOST_LOG(rdErrorLog) << "SIZE: " << nSup2.length() << std::endl;
@@ -448,10 +452,11 @@ void testSmilesSupFromText() {
 #endif

  // issue 114, no \n at EOF:
-  text = "Id SMILES Column_2\n"
-         "mol-1 C 1.0\n"
-         "mol-2 CC 4.0\n"
-         "mol-4 CCCC 16.0\n";
+  text =
+      "Id SMILES Column_2\n"
+      "mol-1 C 1.0\n"
+      "mol-2 CC 4.0\n"
+      "mol-4 CCCC 16.0\n";
  nSup2.setData(text, " ", 1, 0, true, true);
  //  BOOST_LOG(rdErrorLog) << "SIZE: " << nSup2.length() << std::endl;
  TEST_ASSERT(nSup2.length() == 3);
@@ -464,10 +469,11 @@ void testSmilesSupFromText() {
  TEST_ASSERT(nSup2.atEnd());
  delete mol;

-  text = "Id SMILES Column_2\n"
-         "mol-1 C 1.0\n"
-         "mol-2 CC 4.0\n"
-         "mol-4 CCCC 16.0";
+  text =
+      "Id SMILES Column_2\n"
+      "mol-1 C 1.0\n"
+      "mol-2 CC 4.0\n"
+      "mol-4 CCCC 16.0";
  nSup2.setData(text, " ", 1, 0, true, true);
  //  BOOST_LOG(rdErrorLog) << "SIZE: " << nSup2.length() << std::endl;
  TEST_ASSERT(nSup2.length() == 3);
@@ -488,9 +494,10 @@ void testSmilesSupFromText() {
  }
  TEST_ASSERT(failed);

-  text = "mol-1 C 1.0\n"
-         "mol-2 CC 4.0\n"
-         "mol-4 CCCC 16.0";
+  text =
+      "mol-1 C 1.0\n"
+      "mol-2 CC 4.0\n"
+      "mol-4 CCCC 16.0";
  nSup2.setData(text, " ", 1, 0, false, true);
  //  BOOST_LOG(rdErrorLog) << "SIZE: " << nSup2.length() << std::endl;
  TEST_ASSERT(nSup2.length() == 3);
@@ -502,9 +509,10 @@ void testSmilesSupFromText() {
  TEST_ASSERT(mname == "16.0");
  delete mol;

-  text = "C\n"
-         "CC\n"
-         "CCCC";
+  text =
+      "C\n"
+      "CC\n"
+      "CCCC";
  nSup2.setData(text, " ", 0, -1, false, true);
  //  BOOST_LOG(rdErrorLog) << "SIZE: " << nSup2.length() << std::endl;
  TEST_ASSERT(nSup2.length() == 3);
@@ -516,10 +524,11 @@ void testSmilesSupFromText() {
  // this was a delightful boundary condition:
  BOOST_LOG(rdErrorLog)
      << "------------------------------------------------------" << std::endl;
-  text = "CC\n"
-         "CCC\n"
-         "CCOC\n"
-         "CCCCOC";
+  text =
+      "CC\n"
+      "CCC\n"
+      "CCOC\n"
+      "CCCCOC";
  nSup2.setData(text, " ", 0, -1, false, true);
  //  BOOST_LOG(rdErrorLog) << "SIZE: " << nSup2.length() << std::endl;
  mol = nSup2.next();
@@ -541,10 +550,11 @@ void testSmilesSupFromText() {
  BOOST_LOG(rdErrorLog)
      << "------------------------------------------------------" << std::endl;
  // this was a delightful boundary condition:
-  text = "CC\n"
-         "CCC\n"
-         "CCOC\n"
-         "CCCCOC";
+  text =
+      "CC\n"
+      "CCC\n"
+      "CCOC\n"
+      "CCCCOC";
  nSup2.setData(text, " ", 0, -1, false, true);
  //  BOOST_LOG(rdErrorLog) << "SIZE: " << nSup2.length() << std::endl;
  failed = false;
@@ -571,12 +581,13 @@ void testSmilesSupFromText() {
  TEST_ASSERT(nDone == nSup2.length());

  // ensure that we can call setData a second time:
-  text = "Id SMILES Column_2\n"
-         "# comment, ignore\n"
-         "mol-1 C 1.0\n"
-         "mol-2 CC 4.0\n"
-         "mol-3 CCC 9.0\n"
-         "mol-4 CCCC 16.0\n";
+  text =
+      "Id SMILES Column_2\n"
+      "# comment, ignore\n"
+      "mol-1 C 1.0\n"
+      "mol-2 CC 4.0\n"
+      "mol-3 CCC 9.0\n"
+      "mol-4 CCCC 16.0\n";
  nSup2.setData(text, " ", 1, 0, true, true);
  mol = nSup2[2];
  mol->getProp(common_properties::_Name, mname);
@@ -593,12 +604,13 @@ void testSmilesSupFromText() {
  delete mol;

  // this was a delightful boundary condition:
-  text = "CC\n"
-         "CCC\n"
-         "CCOC\n"
-         "CCCCOC\n"
-         "\n"
-         "\n";
+  text =
+      "CC\n"
+      "CCC\n"
+      "CCOC\n"
+      "CCCCOC\n"
+      "\n"
+      "\n";
  nSup2.setData(text, " ", 0, -1, false, true);
  TEST_ASSERT(nSup2.length() == 4);
  nSup2.reset();
@@ -837,9 +849,10 @@ void testSuppliersEmptyFile() {

 void testCisTrans() {
  std::string text;
-  text = "mol-1 ClC(C)=C(Br)C\n"
-         "mol-2 C1=COC=CC1C(Cl)=C(Br)C\n"
-         "mol-3 C1=COC=CC1\\C(Cl)=C(Br)\\C";
+  text =
+      "mol-1 ClC(C)=C(Br)C\n"
+      "mol-2 C1=COC=CC1C(Cl)=C(Br)C\n"
+      "mol-3 C1=COC=CC1\\C(Cl)=C(Br)\\C";
  SmilesMolSupplier smiSup;
  smiSup.setData(text, " ", 1, 0, false, true);

@@ -1076,18 +1089,19 @@ int testTDTSupplier3() {

  TDTMolSupplier suppl;

-  data = "$SMI<Cc1nnc(N)nc1C>\n"
-         "CAS<17584-12-2>\n"
-         "|\n"
-         "$SMI<Cc1n[nH]c(=O)nc1N>\n"
-         "CAS<~>\n"
-         "|\n"
-         "$SMI<Cc1n[nH]c(=O)[nH]c1=O>\n"
-         "CAS<932-53-6>\n"
-         "|\n"
-         "$SMI<Cc1nnc(NN)nc1O>\n"
-         "CAS<~>\n"
-         "|\n";
+  data =
+      "$SMI<Cc1nnc(N)nc1C>\n"
+      "CAS<17584-12-2>\n"
+      "|\n"
+      "$SMI<Cc1n[nH]c(=O)nc1N>\n"
+      "CAS<~>\n"
+      "|\n"
+      "$SMI<Cc1n[nH]c(=O)[nH]c1=O>\n"
+      "CAS<932-53-6>\n"
+      "|\n"
+      "$SMI<Cc1nnc(NN)nc1O>\n"
+      "CAS<~>\n"
+      "|\n";
  suppl.setData(data, "CAS");

  i = 0;
@@ -1268,8 +1282,7 @@ void testSDSupplierFromTextStrLax1() {
    while (!reader.atEnd()) {
      ROMol *mol = reader.next();
      TEST_ASSERT(mol->hasProp(common_properties::_Name));
-      if (i == 0)
-        TEST_ASSERT(!mol->hasProp("ID"));
+      if (i == 0) TEST_ASSERT(!mol->hasProp("ID"));
      TEST_ASSERT(!mol->hasProp("ANOTHER_PROPERTY"));
      i++;
      delete mol;
@@ -1358,10 +1371,11 @@ void testSDSupplierFromTextStrLax2() {
      mol->getProp("ID", s);
      TEST_ASSERT(s == "Lig1");
      mol->getProp("ANOTHER_PROPERTY", s);
-      TEST_ASSERT(s == "No blank line before dollars\n"
-                       "$$$$\n"
-                       "Structure1\n"
-                       "csChFnd70/05230312262D");
+      TEST_ASSERT(s ==
+                  "No blank line before dollars\n"
+                  "$$$$\n"
+                  "Structure1\n"
+                  "csChFnd70/05230312262D");
      i++;
      delete mol;
    }
@@ -1403,8 +1417,7 @@ void testSDSupplierStrLax1() {
    while (!reader.atEnd()) {
      ROMol *mol = reader.next();
      TEST_ASSERT(mol->hasProp(common_properties::_Name));
-      if (i == 0)
-        TEST_ASSERT(!mol->hasProp("ID"));
+      if (i == 0) TEST_ASSERT(!mol->hasProp("ID"));
      TEST_ASSERT(!mol->hasProp("ANOTHER_PROPERTY"));
      i++;
      delete mol;
@@ -1446,10 +1459,11 @@ void testSDSupplierStrLax2() {
      mol->getProp("ID", s);
      TEST_ASSERT(s == "Lig1");
      mol->getProp("ANOTHER_PROPERTY", s);
-      TEST_ASSERT(s == "No blank line before dollars\n"
-                       "$$$$\n"
-                       "Structure1\n"
-                       "csChFnd70/05230312262D");
+      TEST_ASSERT(s ==
+                  "No blank line before dollars\n"
+                  "$$$$\n"
+                  "Structure1\n"
+                  "csChFnd70/05230312262D");
      i++;
      delete mol;
    }
@@ -1569,8 +1583,7 @@ void testIssue381() {
  count = 0;
  while (!sdsup->atEnd()) {
    nmol = sdsup->next();
-    if (nmol)
-      delete nmol;
+    if (nmol) delete nmol;
    count++;
  }
  TEST_ASSERT(sdsup->atEnd());
@@ -1592,12 +1605,10 @@ void testSetStreamIndices() {
  std::streampos pos = 0;
  std::string line;
  while (notEof) {
-    if (addIndex)
-      pos = ifs.tellg();
+    if (addIndex) pos = ifs.tellg();
    notEof = (std::getline(ifs, line) ? true : false);
    if (notEof) {
-      if (addIndex)
-        indices.push_back(pos);
+      if (addIndex) indices.push_back(pos);
      addIndex = (line.substr(0, 4) == "$$$$");
    }
  }
@@ -1615,8 +1626,7 @@ void testSetStreamIndices() {
  count = 0;
  while (!sdsup->atEnd()) {
    nmol = sdsup->next();
-    if (nmol)
-      delete nmol;
+    if (nmol) delete nmol;
    count++;
  }
  TEST_ASSERT(sdsup->atEnd());
@@ -2074,7 +2084,7 @@ int testForwardSDSupplier() {
    }
    TEST_ASSERT(i == 16);
  }
-
+#ifdef RDK_USE_BOOST_IOSTREAMS
  // make sure the boost::iostreams are working
  {
    io::filtering_istream strm;
@@ -2084,10 +2094,8 @@ int testForwardSDSupplier() {
    while (!strm.eof()) {
      std::string line;
      std::getline(strm, line);
-      if (!strm.eof())
-        ++i;
-      if (i > 1000)
-        break;
+      if (!strm.eof()) ++i;
+      if (i > 1000) break;
    }
    TEST_ASSERT(i == 998);
  }
@@ -2097,10 +2105,8 @@ int testForwardSDSupplier() {
    while (!strm.eof()) {
      std::string line;
      std::getline(strm, line);
-      if (!strm.eof())
-        ++i;
-      if (i > 1000)
-        break;
+      if (!strm.eof()) ++i;
+      if (i > 1000) break;
    }
    TEST_ASSERT(i == 997);
  }
@@ -2121,6 +2127,7 @@ int testForwardSDSupplier() {
    }
    TEST_ASSERT(i == 16);
  }
+#endif

 #ifdef RDK_BUILD_COORDGEN_SUPPORT
  // Now test that Maestro parsing of gz files works
@@ -2136,10 +2143,8 @@ int testForwardSDSupplier() {
    while (!strm.eof()) {
      std::string line;
      std::getline(strm, line);
-      if (!strm.eof())
-        ++i;
-      if (i > 1700)
-        break;
+      if (!strm.eof()) ++i;
+      if (i > 1700) break;
    }
    TEST_ASSERT(i == 1663);
  }
@@ -2150,10 +2155,8 @@ int testForwardSDSupplier() {
    while (!strm.eof()) {
      std::string line;
      std::getline(strm, line);
-      if (!strm.eof())
-        ++i;
-      if (i > 1700)
-        break;
+      if (!strm.eof()) ++i;
+      if (i > 1700) break;
    }
    TEST_ASSERT(i == 1663);
  }
@@ -2172,8 +2175,7 @@ int testForwardSDSupplier() {
    }
    TEST_ASSERT(i == 16);
  }
-#endif // RDK_BUILD_COORDGEN_SUPPORT
-
+#endif  // RDK_BUILD_COORDGEN_SUPPORT

  return 1;
 }
@@ -2329,7 +2331,7 @@ void testGitHub2285() {
  std::vector<std::string> smiles;
  {
    SDMolSupplier sdsup(fname);
-    while(!sdsup.atEnd()) {
+    while (!sdsup.atEnd()) {
      ROMol *nmol = sdsup.next();
      TEST_ASSERT(nmol);
      smiles.push_back(MolToSmiles(*nmol));
@@ -2339,7 +2341,7 @@ void testGitHub2285() {
  {
    SDMolSupplier sdsup(fname, true, false);
    int i = 0;
-    while(!sdsup.atEnd()) {
+    while (!sdsup.atEnd()) {
      ROMol *nmol = sdsup.next();
      TEST_ASSERT(nmol);
      ROMol *m = MolOps::removeHs(*nmol);
@@ -2347,7 +2349,7 @@ void testGitHub2285() {
      delete nmol;
      delete m;
    }
-    TEST_ASSERT(i>0);
+    TEST_ASSERT(i > 0);
  }
 }

--- a/Code/JavaWrappers/CMakeLists.txt
+++ b/Code/JavaWrappers/CMakeLists.txt
@@ -37,7 +37,7 @@ foreach(swigRDKitLib ${swigRDKitLibList})
 endforeach()
 set(swigRDKitLibs "${swigRDKitLibs}${Boost_SERIALIZATION_LIBRARY};")

-
+if(RDK_USE_BOOST_IOSTREAMS)
 if(WIN32)
  find_package(Boost 1.56.0 COMPONENTS system iostreams REQUIRED)  
  set(swigRDKitLibs "${swigRDKitLibs}${Boost_IOSTREAMS_LIBRARY};${Boost_SYSTEM_LIBRARY};")
@@ -50,6 +50,7 @@ else()
  find_package(Boost 1.56.0 COMPONENTS system iostreams REQUIRED)
  set(swigRDKitLibs "${swigRDKitLibs}${Boost_IOSTREAMS_LIBRARY};${Boost_SYSTEM_LIBRARY};")
 endif()
+endif(RDK_USE_BOOST_IOSTREAMS)



--- a/Code/RDGeneral/RDConfig.h.cmake
+++ b/Code/RDGeneral/RDConfig.h.cmake
@@ -10,6 +10,7 @@

 // RDKit configuration options
 #cmakedefine RDK_USE_BOOST_SERIALIZATION
+#cmakedefine RDK_USE_BOOST_IOSTREAMS

 #cmakedefine RDK_OPTIMIZE_NATIVE
 #ifdef RDK_OPTIMIZE_NATIVE
--- a/Code/RDStreams/CMakeLists.txt
+++ b/Code/RDStreams/CMakeLists.txt
@@ -1,3 +1,5 @@
+if(RDK_USE_BOOST_IOSTREAMS)
+
 find_package(Boost 1.56.0 COMPONENTS system iostreams REQUIRED)
 set (link_iostreams ${Boost_LIBRARIES})
 if (NOT Boost_USE_STATIC_LIBS)
@@ -12,6 +14,7 @@ if (WIN32)
 endif()

 add_definitions(-DRDKIT_RDSTREAMS_BUILD)
+endif(RDK_USE_BOOST_IOSTREAMS)
 rdkit_library(RDStreams streams.cpp
              LINK_LIBRARIES ${Boost_LIBRARIES} ${link_iostreams} ${zlib_lib}
              DEST RDStreams)
--- a/Code/RDStreams/streams.cpp
+++ b/Code/RDStreams/streams.cpp
@@ -1,11 +1,12 @@
 #include "streams.h"
+#ifdef RDK_USE_BOOST_IOSTREAMS

-namespace RDKit
-{
-gzstream::gzstream(const std::string &fname) :
-    boost::iostreams::filtering_istream(),
-    is(fname.c_str(), std::ios_base::binary) {
+namespace RDKit {
+gzstream::gzstream(const std::string &fname)
+    : boost::iostreams::filtering_istream(),
+      is(fname.c_str(), std::ios_base::binary) {
  push(boost::iostreams::gzip_decompressor());
  push(is);
 }
-}
+}  // namespace RDKit
+#endif
--- a/Code/RDStreams/streams.h
+++ b/Code/RDStreams/streams.h
@@ -1,5 +1,7 @@
 //
 #include <RDGeneral/export.h>
+#ifdef RDK_USE_BOOST_IOSTREAMS
+
 #include <boost/iostreams/device/file.hpp>
 #include <boost/iostreams/filtering_stream.hpp>
 #include <boost/iostreams/filter/gzip.hpp>
@@ -14,3 +16,4 @@ class RDKIT_RDSTREAMS_EXPORT gzstream
  gzstream(const std::string &fname);
 };
 }  // namespace RDKit
+#endif