Merge pull request #1 from ccsb-scripps/boost_upgrade

Remove deprecated Boost features and improve compiling for newer Boost versions

.gitignore

@@ -0,0 +1 @@
+*.o

build/linux/debug/Makefile

@@ -1,8 +1,8 @@
-BASE=/usr/local
-BOOST_VERSION=1_41
+BASE=/usr
+BOOST_VERSION=
 BOOST_INCLUDE = $(BASE)/include
 C_PLATFORM=-static -pthread
-GPP=/usr/local/bin/g++
+GPP=/usr/bin/g++
 C_OPTIONS= -g
 BOOST_LIB_VERSION=
 

build/linux/release/Makefile

@@ -1,8 +1,8 @@
-BASE=/usr/local
-BOOST_VERSION=1_41
+BASE=/usr
+BOOST_VERSION=
 BOOST_INCLUDE = $(BASE)/include
 C_PLATFORM=-static -pthread
-GPP=/usr/local/bin/g++
+GPP=/usr/bin/g++
 C_OPTIONS= -O3 -DNDEBUG
 BOOST_LIB_VERSION=
 

build/mac/debug/Makefile

@@ -1,8 +1,8 @@
 BASE=/usr/local
-BOOST_VERSION=1_41
+BOOST_VERSION=1_71
 BOOST_INCLUDE = $(BASE)/include
-C_PLATFORM=-arch i386 -arch ppc -isysroot /Developer/SDKs/MacOSX10.5.sdk -mmacosx-version-min=10.4
-GPP=/usr/bin/g++
+C_PLATFORM=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
+GPP=clang++
 C_OPTIONS= -g
 BOOST_LIB_VERSION=
 

build/mac/release/Makefile

@@ -1,9 +1,9 @@
 BASE=/usr/local
-BOOST_VERSION=1_41
+BOOST_VERSION=1_71
 BOOST_INCLUDE = $(BASE)/include
-C_PLATFORM=-arch i386 -arch ppc -isysroot /Developer/SDKs/MacOSX10.5.sdk -mmacosx-version-min=10.4
-GPP=/usr/bin/g++
-C_OPTIONS= -O3 -DNDEBUG
+C_PLATFORM=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
+GPP=clang++
+C_OPTIONS= -O2 -DNDEBUG
 BOOST_LIB_VERSION=
 
 include ../../makefile_common

build/makefile_common

@@ -10,7 +10,16 @@ CC = ${GPP} ${C_PLATFORM} -ansi -Wno-long-long ${C_OPTIONS} $(INCFLAGS)
 
 LDFLAGS = -L$(BASE)/lib -L.
 
-LIBS = -l boost_system${BOOST_LIB_VERSION} -l boost_thread${BOOST_LIB_VERSION} -l boost_serialization${BOOST_LIB_VERSION} -l boost_filesystem${BOOST_LIB_VERSION} -l boost_program_options${BOOST_LIB_VERSION}#-l pthread
+# test if boost_thread-mt exists, this is
+# necessary as some versions of boost only
+# install libboost_thread-mt, but not
+# libboost_thread (e.g. macOS)
+$(shell echo "int main(){ return 0; }" > linktest.cpp)
+$(shell $(GPP) $(LDFLAGS) -l boost_thread-mt linktest.cpp -o linktest >/dev/null 2>&1)
+threadmt:=$(shell if [ -f ./linktest ]; then echo "-mt"; rm ./linktest; fi;)
+$(shell rm ./linktest.cpp)
+
+LIBS = -l boost_system${BOOST_LIB_VERSION} -l boost_thread${threadmt}${BOOST_LIB_VERSION} -l boost_serialization${BOOST_LIB_VERSION} -l boost_filesystem${BOOST_LIB_VERSION} -l boost_program_options${BOOST_LIB_VERSION}#-l pthread
 
 .SUFFIXES: .cpp .o
 

src/lib/array3d.h

@@ -1,77 +1,77 @@
-/*
-
-   Copyright (c) 2006-2010, The Scripps Research Institute
-
-   Licensed under the Apache License, Version 2.0 (the "License");
-   you may not use this file except in compliance with the License.
-   You may obtain a copy of the License at
-
-       http://www.apache.org/licenses/LICENSE-2.0
-
-   Unless required by applicable law or agreed to in writing, software
-   distributed under the License is distributed on an "AS IS" BASIS,
-   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-   See the License for the specific language governing permissions and
-   limitations under the License.
-
-   Author: Dr. Oleg Trott <ot14@columbia.edu>, 
-           The Olson Lab, 
-           The Scripps Research Institute
-
-*/
-
-#ifndef VINA_ARRAY3D_H
-#define VINA_ARRAY3D_H
-
-#include <exception> // std::bad_alloc
-#include "common.h"
-
-inline sz checked_multiply(sz i, sz j) {
-	if(i == 0 || j == 0) return 0;
-	const sz tmp = i * j;
-	if(tmp < i || tmp < j || tmp / i != j)
-		throw std::bad_alloc(); // can't alloc if the size makes sz wrap around
-	return tmp;
-}
-
-inline sz checked_multiply(sz i, sz j, sz k) {
-	return checked_multiply(checked_multiply(i, j), k);
-}
-
-template<typename T>
-class array3d {
-	sz m_i, m_j, m_k;
-	std::vector<T> m_data;
-	friend class boost::serialization::access;
-	template<typename Archive>
-	void serialize(Archive& ar, const unsigned version) {
-		ar & m_i;
-		ar & m_j;
-		ar & m_k;
-		ar & m_data;
-	}
-public:
-	array3d() : m_i(0), m_j(0), m_k(0) {}
-	array3d(sz i, sz j, sz k) : m_i(i), m_j(j), m_k(k), m_data(checked_multiply(i, j, k)) {}
-	sz dim0() const { return m_i; }
-	sz dim1() const { return m_j; }
-	sz dim2() const { return m_k; }
-	sz dim(sz i) const {
-		switch(i) {
-			case 0: return m_i;
-			case 1: return m_j;
-			case 2: return m_k;
-			default: assert(false); return 0; // to get rid of the warning
-		}
-	}
-	void resize(sz i, sz j, sz k) { // data is essentially garbled
-		m_i = i;
-		m_j = j;
-		m_k = k;
-		m_data.resize(checked_multiply(i, j, k));
-	}
-	T&       operator()(sz i, sz j, sz k)       { return m_data[i + m_i*(j + m_j*k)]; }
-	const T& operator()(sz i, sz j, sz k) const { return m_data[i + m_i*(j + m_j*k)]; }
-};
-
-#endif
+/*
+
+   Copyright (c) 2006-2010, The Scripps Research Institute
+
+   Licensed under the Apache License, Version 2.0 (the "License");
+   you may not use this file except in compliance with the License.
+   You may obtain a copy of the License at
+
+       http://www.apache.org/licenses/LICENSE-2.0
+
+   Unless required by applicable law or agreed to in writing, software
+   distributed under the License is distributed on an "AS IS" BASIS,
+   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+   See the License for the specific language governing permissions and
+   limitations under the License.
+
+   Author: Dr. Oleg Trott <ot14@columbia.edu>, 
+           The Olson Lab, 
+           The Scripps Research Institute
+
+*/
+
+#ifndef VINA_ARRAY3D_H
+#define VINA_ARRAY3D_H
+
+#include <exception> // std::bad_alloc
+#include "common.h"
+
+inline sz checked_multiply(sz i, sz j) {
+	if(i == 0 || j == 0) return 0;
+	const sz tmp = i * j;
+	if(tmp < i || tmp < j || tmp / i != j)
+		throw std::bad_alloc(); // can't alloc if the size makes sz wrap around
+	return tmp;
+}
+
+inline sz checked_multiply(sz i, sz j, sz k) {
+	return checked_multiply(checked_multiply(i, j), k);
+}
+
+template<typename T>
+class array3d {
+	sz m_i, m_j, m_k;
+	std::vector<T> m_data;
+	friend class boost::serialization::access;
+	template<typename Archive>
+	void serialize(Archive& ar, const unsigned version) {
+		ar & m_i;
+		ar & m_j;
+		ar & m_k;
+		ar & m_data;
+	}
+public:
+	array3d() : m_i(0), m_j(0), m_k(0) {}
+	array3d(sz i, sz j, sz k) : m_i(i), m_j(j), m_k(k), m_data(checked_multiply(i, j, k)) {}
+	sz dim0() const { return m_i; }
+	sz dim1() const { return m_j; }
+	sz dim2() const { return m_k; }
+	sz dim(sz i) const {
+		switch(i) {
+			case 0: return m_i;
+			case 1: return m_j;
+			case 2: return m_k;
+			default: assert(false); return 0; // to get rid of the warning
+		}
+	}
+	void resize(sz i, sz j, sz k) { // data is essentially garbled
+		m_i = i;
+		m_j = j;
+		m_k = k;
+		m_data.resize(checked_multiply(i, j, k));
+	}
+	T&       operator()(sz i, sz j, sz k)       { return m_data[i + m_i*(j + m_j*k)]; }
+	const T& operator()(sz i, sz j, sz k) const { return m_data[i + m_i*(j + m_j*k)]; }
+};
+
+#endif

src/lib/atom.h

@@ -1,78 +1,78 @@
-/*
-
-   Copyright (c) 2006-2010, The Scripps Research Institute
-
-   Licensed under the Apache License, Version 2.0 (the "License");
-   you may not use this file except in compliance with the License.
-   You may obtain a copy of the License at
-
-       http://www.apache.org/licenses/LICENSE-2.0
-
-   Unless required by applicable law or agreed to in writing, software
-   distributed under the License is distributed on an "AS IS" BASIS,
-   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-   See the License for the specific language governing permissions and
-   limitations under the License.
-
-   Author: Dr. Oleg Trott <ot14@columbia.edu>, 
-           The Olson Lab, 
-           The Scripps Research Institute
-
-*/
-
-#ifndef VINA_ATOM_H
-#define VINA_ATOM_H
-
-#include "atom_base.h"
-
-struct atom_index {
-	sz i;
-	bool in_grid;
-	atom_index() : i(max_sz), in_grid(false) {}
-	atom_index(sz i_, bool in_grid_) : i(i_), in_grid(in_grid_) {}
-private:
-	friend class boost::serialization::access;
-	template<class Archive> 
-	void serialize(Archive& ar, const unsigned version) {
-		ar & i;
-		ar & in_grid;
-	}
-};
-
-inline bool operator==(const atom_index& i, const atom_index& j) {
-	return i.i == j.i && i.in_grid == j.in_grid;
-}
-
-struct bond {
-	atom_index connected_atom_index;
-	fl length;
-	bool rotatable;
-	bond() : length(0), rotatable(false) {}
-	bond(const atom_index& connected_atom_index_, fl length_, bool rotatable_) : connected_atom_index(connected_atom_index_), length(length_), rotatable(rotatable_) {}
-private:
-	friend class boost::serialization::access;
-	template<class Archive> 
-	void serialize(Archive& ar, const unsigned version) {
-		ar & connected_atom_index;
-		ar & length;
-		ar & rotatable;
-	}
-};
-
-struct atom : public atom_base {
-    vec coords;
-	std::vector<bond> bonds;
-	atom() : coords(max_vec) {}
-private:
-	friend class boost::serialization::access;
-	template<class Archive> 
-	void serialize(Archive& ar, const unsigned version) {
-		ar & boost::serialization::base_object<atom_base>(*this);
-		ar & coords;
-		ar & bonds;
-	}
-};
-
-typedef std::vector<atom> atomv;
-
-#endif
+/*
+
+   Copyright (c) 2006-2010, The Scripps Research Institute
+
+   Licensed under the Apache License, Version 2.0 (the "License");
+   you may not use this file except in compliance with the License.
+   You may obtain a copy of the License at
+
+       http://www.apache.org/licenses/LICENSE-2.0
+
+   Unless required by applicable law or agreed to in writing, software
+   distributed under the License is distributed on an "AS IS" BASIS,
+   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+   See the License for the specific language governing permissions and
+   limitations under the License.
+
+   Author: Dr. Oleg Trott <ot14@columbia.edu>, 
+           The Olson Lab, 
+           The Scripps Research Institute
+
+*/
+
+#ifndef VINA_ATOM_H
+#define VINA_ATOM_H
+
+#include "atom_base.h"
+
+struct atom_index {
+	sz i;
+	bool in_grid;
+	atom_index() : i(max_sz), in_grid(false) {}
+	atom_index(sz i_, bool in_grid_) : i(i_), in_grid(in_grid_) {}
+private:
+	friend class boost::serialization::access;
+	template<class Archive> 
+	void serialize(Archive& ar, const unsigned version) {
+		ar & i;
+		ar & in_grid;
+	}
+};
+
+inline bool operator==(const atom_index& i, const atom_index& j) {
+	return i.i == j.i && i.in_grid == j.in_grid;
+}
+
+struct bond {
+	atom_index connected_atom_index;
+	fl length;
+	bool rotatable;
+	bond() : length(0), rotatable(false) {}
+	bond(const atom_index& connected_atom_index_, fl length_, bool rotatable_) : connected_atom_index(connected_atom_index_), length(length_), rotatable(rotatable_) {}
+private:
+	friend class boost::serialization::access;
+	template<class Archive> 
+	void serialize(Archive& ar, const unsigned version) {
+		ar & connected_atom_index;
+		ar & length;
+		ar & rotatable;
+	}
+};
+
+struct atom : public atom_base {
+    vec coords;
+	std::vector<bond> bonds;
+	atom() : coords(max_vec) {}
+private:
+	friend class boost::serialization::access;
+	template<class Archive> 
+	void serialize(Archive& ar, const unsigned version) {
+		ar & boost::serialization::base_object<atom_base>(*this);
+		ar & coords;
+		ar & bonds;
+	}
+};
+
+typedef std::vector<atom> atomv;
+
+#endif