Merge branch 'master' into fix-charmm-box-vecs

libraries/irrxml/include/irrTypes.h

+// Copyright (C) 2002-2005 Nikolaus Gebhardt
+// This file is part of the "Irrlicht Engine".
+// For conditions of distribution and use, see copyright notice in irrlicht.h
+
+#ifndef __IRR_TYPES_H_INCLUDED__
+#define __IRR_TYPES_H_INCLUDED__
+
+namespace irr
+{
+
+//! 8 bit unsigned variable.
+/** This is a typedef for unsigned char, it ensures portability of the engine. */
+typedef unsigned char		u8; 
+
+//! 8 bit signed variable.
+/** This is a typedef for signed char, it ensures portability of the engine. */
+typedef signed char			s8; 
+
+//! 8 bit character variable.
+/** This is a typedef for char, it ensures portability of the engine. */
+typedef char				c8; 
+
+
+
+//! 16 bit unsigned variable.
+/** This is a typedef for unsigned short, it ensures portability of the engine. */
+typedef unsigned short		u16;
+
+//! 16 bit signed variable.
+/** This is a typedef for signed short, it ensures portability of the engine. */
+typedef signed short		s16; 
+
+
+
+//! 32 bit unsigned variable.
+/** This is a typedef for unsigned int, it ensures portability of the engine. */
+typedef unsigned int		u32;
+
+//! 32 bit signed variable.
+/** This is a typedef for signed int, it ensures portability of the engine. */
+typedef signed int			s32; 
+
+
+
+// 64 bit signed variable.
+// This is a typedef for __int64, it ensures portability of the engine. 
+// This type is currently not used by the engine and not supported by compilers
+// other than Microsoft Compilers, so it is outcommented.
+//typedef __int64				s64; 
+
+
+
+//! 32 bit floating point variable.
+/** This is a typedef for float, it ensures portability of the engine. */
+typedef float				f32; 
+
+//! 64 bit floating point variable.
+/** This is a typedef for double, it ensures portability of the engine. */
+typedef double				f64; 
+
+
+} // end namespace
+
+
+// define the wchar_t type if not already built in.
+#ifdef _MSC_VER 
+#ifndef _WCHAR_T_DEFINED
+//! A 16 bit wide character type.
+/**
+	Defines the wchar_t-type.
+	In VS6, its not possible to tell
+	the standard compiler to treat wchar_t as a built-in type, and 
+	sometimes we just don't want to include the huge stdlib.h or wchar.h,
+	so we'll use this.
+*/
+typedef unsigned short wchar_t;
+#define _WCHAR_T_DEFINED
+#endif // wchar is not defined
+#endif // microsoft compiler
+
+//! define a break macro for debugging only in Win32 mode.
+#if defined(WIN32) && defined(_MSC_VER) && defined(_DEBUG)
+#define _IRR_DEBUG_BREAK_IF( _CONDITION_ ) if (_CONDITION_) {_asm int 3}
+#else 
+#define _IRR_DEBUG_BREAK_IF( _CONDITION_ )
+#endif
+
+//! Defines a small statement to work around a microsoft compiler bug.
+/** The microsft compiler 7.0 - 7.1 has a bug:
+When you call unmanaged code that returns a bool type value of false from managed code, 
+the return value may appear as true. See 
+http://support.microsoft.com/default.aspx?kbid=823071 for details. 
+Compiler version defines: VC6.0 : 1200, VC7.0 : 1300, VC7.1 : 1310, VC8.0 : 1400*/
+#if defined(WIN32) && defined(_MSC_VER) && (_MSC_VER > 1299) && (_MSC_VER < 1400)
+#define _IRR_IMPLEMENT_MANAGED_MARSHALLING_BUGFIX __asm mov eax,100
+#else
+#define _IRR_IMPLEMENT_MANAGED_MARSHALLING_BUGFIX
+#endif // _IRR_MANAGED_MARSHALLING_BUGFIX
+
+#endif // __IRR_TYPES_H_INCLUDED__
+

libraries/irrxml/readme.txt

+==========================================================================
+irrXML 1.2
+==========================================================================
+
+  Welcome to irrXML
+
+  Content of this file:
+
+  1. Directory structure overview
+  2. How to use
+  3. Requirements
+  5. License
+  6. Contact
+
+
+
+==========================================================================
+1. Directory structure overview
+==========================================================================
+
+  You will find some directories after decompressing the archive in which
+  came the SDK. These are:
+  
+  \doc         Documentation of irrXML.
+  \example     A short example showing how to use the parser with solution
+               and make files.
+  \src         The source code of irrXML.   
+
+==========================================================================
+2. How to use
+==========================================================================
+
+  For Linux/Unix users: Simply go into the directory /example and run
+  'make'. This will create a sample project using irrXML.
+  
+  Windows users: Just add the source files to your project. That's all. 
+  For more information see the documentation in the \doc directory.
+    
+  Alternatively, you could compile irrXML as .lib, after this you would
+  only need to use the irrXML.h header file, nothing more.
+
+
+==========================================================================
+3. Requirements
+==========================================================================
+
+  You can use one of the following compilers/IDEs to develop applications
+  with irrXML. However, other compilers/IDEs make work  as well, 
+  we simply didn't test them. 
+  
+  * gcc 3.2
+  * gcc 3.3
+  * Visual Studio 6.0
+  * Visual Studio.NET (7.0)
+  * Visual Studio.NET 2003 (7.1)
+  * Visual Studio.NET 2005 (8.0)
+  * DevC++ 4.9 & gcc (project files included)
+ 
+==========================================================================
+5. License
+==========================================================================
+
+  The license of irrXML is based on the zlib/libpng license.
+  Even though this license does not require you to mention that you are
+  using the Irrlicht Engine in your product, an acknowledgement
+  would be highly appreciated.
+
+  The irrXML License
+  ===========================
+
+  Copyright (C) 2002-2005 Nikolaus Gebhardt
+
+  This software is provided 'as-is', without any express or implied
+  warranty.  In no event will the authors be held liable for any damages
+  arising from the use of this software.
+
+  Permission is granted to anyone to use this software for any purpose,
+  including commercial applications, and to alter it and redistribute it
+  freely, subject to the following restrictions:
+
+  1. The origin of this software must not be misrepresented; you must not
+     claim that you wrote the original software. If you use this software
+     in a product, an acknowledgment in the product documentation would be
+     appreciated but is not required.
+  2. Altered source versions must be plainly marked as such, and must not be
+     misrepresented as being the original software.
+  3. This notice may not be removed or altered from any source distribution.
+  
+
+  
+==========================================================================
+6. Contact
+==========================================================================
+
+  If you have problems, questions or suggestions, please visit the 
+  official homepage of irrXML:
+  
+  http://xml.irrlicht3d.org
+  
+  You will find forums, patches, documentation, and other stuff
+  which will help you out.
+  
+  If want to contact the author of the engine, please send an email to
+  Nikolaus Gebhardt:
+  
+  irrlicht@users.sourceforge.net
+
+
+  
+    
\ No newline at end of file

libraries/irrxml/src/irrXML.cpp

+// Copyright (C) 2002-2005 Nikolaus Gebhardt
+// This file is part of the "Irrlicht Engine" and the "irrXML" project.
+// For conditions of distribution and use, see copyright notice in irrlicht.h and/or irrXML.h
+
+#include "irrXML.h"
+#include "irrString.h"
+#include "irrArray.h"
+#include "fast_atof.h"
+#include "CXMLReaderImpl.h"
+
+namespace irr
+{
+namespace io
+{
+
+//! Implementation of the file read callback for ordinary files
+class CFileReadCallBack : public IFileReadCallBack
+{
+public:
+
+	//! construct from filename
+	CFileReadCallBack(const char* filename)
+		: File(0), Size(0), Close(true)
+	{
+		// open file
+		File = fopen(filename, "rb");
+
+		if (File)
+			getFileSize();
+	}
+
+	//! construct from FILE pointer
+	CFileReadCallBack(FILE* file)
+		: File(file), Size(0), Close(false)
+	{
+		if (File)
+			getFileSize();
+	}
+
+	//! destructor
+	virtual ~CFileReadCallBack()
+	{
+		if (Close && File)
+			fclose(File);
+	}
+
+	//! Reads an amount of bytes from the file.
+	virtual int read(void* buffer, int sizeToRead)
+	{
+		if (!File)
+			return 0;
+
+		return (int)fread(buffer, 1, sizeToRead, File);
+	}
+
+	//! Returns size of file in bytes
+	virtual int getSize()
+	{
+		return Size;
+	}
+
+private:
+
+	//! retrieves the file size of the open file
+	void getFileSize()
+	{
+		fseek(File, 0, SEEK_END);
+		Size = ftell(File);
+		fseek(File, 0, SEEK_SET);
+	}
+
+	FILE* File;
+	int Size;
+	bool Close;
+
+}; // end class CFileReadCallBack
+
+
+
+// FACTORY FUNCTIONS:
+
+
+//! Creates an instance of an UFT-8 or ASCII character xml parser. 
+IrrXMLReader* createIrrXMLReader(const char* filename)
+{
+	return new CXMLReaderImpl<char, IXMLBase>(new CFileReadCallBack(filename)); 
+}
+
+
+//! Creates an instance of an UFT-8 or ASCII character xml parser. 
+IrrXMLReader* createIrrXMLReader(FILE* file)
+{
+	return new CXMLReaderImpl<char, IXMLBase>(new CFileReadCallBack(file)); 
+}
+
+
+//! Creates an instance of an UFT-8 or ASCII character xml parser. 
+IrrXMLReader* createIrrXMLReader(IFileReadCallBack* callback)
+{
+	return new CXMLReaderImpl<char, IXMLBase>(callback, false); 
+}
+
+
+//! Creates an instance of an UTF-16 xml parser. 
+IrrXMLReaderUTF16* createIrrXMLReaderUTF16(const char* filename)
+{
+	return new CXMLReaderImpl<char16, IXMLBase>(new CFileReadCallBack(filename)); 
+}
+
+
+//! Creates an instance of an UTF-16 xml parser. 
+IrrXMLReaderUTF16* createIrrXMLReaderUTF16(FILE* file)
+{
+	return new CXMLReaderImpl<char16, IXMLBase>(new CFileReadCallBack(file)); 
+}
+
+
+//! Creates an instance of an UTF-16 xml parser. 
+IrrXMLReaderUTF16* createIrrXMLReaderUTF16(IFileReadCallBack* callback)
+{
+	return new CXMLReaderImpl<char16, IXMLBase>(callback, false); 
+}
+
+
+//! Creates an instance of an UTF-32 xml parser. 
+IrrXMLReaderUTF32* createIrrXMLReaderUTF32(const char* filename)
+{
+	return new CXMLReaderImpl<char32, IXMLBase>(new CFileReadCallBack(filename)); 
+}
+
+
+//! Creates an instance of an UTF-32 xml parser. 
+IrrXMLReaderUTF32* createIrrXMLReaderUTF32(FILE* file)
+{
+	return new CXMLReaderImpl<char32, IXMLBase>(new CFileReadCallBack(file)); 
+}
+
+
+//! Creates an instance of an UTF-32 xml parser. 
+IrrXMLReaderUTF32* createIrrXMLReaderUTF32(IFileReadCallBack* callback)
+{
+	return new CXMLReaderImpl<char32, IXMLBase>(callback, false); 
+}
+
+
+} // end namespace io
+} // end namespace irr

serialization/include/openmm/serialization/XmlSerializer.h

@@ -9,7 +9,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2010-2014 Stanford University and the Authors.      *
+ * Portions copyright (c) 2010-2015 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -38,8 +38,6 @@
 #include "openmm/internal/windowsExport.h"
 #include <iosfwd>
 
-class TiXmlElement;
-
 namespace OpenMM {
 
 /**
@@ -77,10 +75,10 @@ public:
         return reinterpret_cast<T*>(deserializeStream(stream));
     }
 private:
+    class StreamReader;
     static void serialize(const SerializationNode& node, std::ostream& stream);
     static void* deserializeStream(std::istream& stream);
     static void encodeNode(const SerializationNode& node, std::ostream& stream, int depth);
-    static void decodeNode(SerializationNode& node, const TiXmlElement& element);
 };
 
 } // namespace OpenMM

serialization/src/XmlSerializer.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2010-2014 Stanford University and the Authors.      *
+ * Portions copyright (c) 2010-2015 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -30,10 +30,81 @@
  * -------------------------------------------------------------------------- */
 
 #include "openmm/serialization/XmlSerializer.h"
-#include "tinyxml.h"
+#include "irrXML.h"
+#include <cstring>
+#include <iostream>
+#include <map>
 
 using namespace OpenMM;
 using namespace std;
+using namespace irr;
+using namespace io;
+
+/**
+ * Apply XML encoding to a string.  This is adapted from TinyXML (written by Lee Thomason).
+ */
+static void encodeString(const string& str, string* outString) {
+    static map<char, string> entities;
+    static bool hasInitialized = false;
+    if (!hasInitialized) {
+        hasInitialized = true;
+	entities['&'] = "&amp;";
+	entities['<'] = "&lt;";
+	entities['>'] = "&gt;";
+	entities['\"'] = "&quot;";
+	entities['\''] = "&apos;";
+    }
+
+    int i=0;
+
+    while (i<(int)str.length()) {
+        unsigned char c = (unsigned char) str[i];
+
+        if (c == '&' 
+             && i < ((int)str.length() - 2)
+             && str[i+1] == '#'
+             && str[i+2] == 'x') {
+            // Hexadecimal character reference.
+            // Pass through unchanged.
+            // &#xA9;	-- copyright symbol, for example.
+            //
+            // The -1 is a bug fix from Rob Laveaux. It keeps
+            // an overflow from happening if there is no ';'.
+            // There are actually 2 ways to exit this loop -
+            // while fails (error case) and break (semicolon found).
+            // However, there is no mechanism (currently) for
+            // this function to return an error.
+            while (i<(int)str.length()-1) {
+                outString->append(str.c_str() + i, 1);
+                ++i;
+                if (str[i] == ';')
+                    break;
+            }
+        }
+        else if (entities.find(c) != entities.end()) {
+            outString->append(entities[c]);
+            ++i;
+        }
+        else if (c < 32) {
+            // Easy pass at non-alpha/numeric/symbol
+            // Below 32 is symbolic.
+            char buf[ 32 ];
+
+            snprintf(buf, sizeof(buf), "&#x%02X;", (unsigned) (c & 0xff));
+
+            //*ME:	warning C4267: convert 'size_t' to 'int'
+            //*ME:	Int-Cast to make compiler happy ...
+            outString->append(buf, (int)strlen(buf));
+            ++i;
+        }
+        else {
+            //char realc = (char) c;
+            //outString->append(&realc, 1);
+            *outString += (char) c;	// somewhat more efficient function call.
+            ++i;
+        }
+    }
+}
 
 void XmlSerializer::serialize(const SerializationNode& node, std::ostream& stream) {
     stream << "<?xml version=\"1.0\" ?>\n";
@@ -47,8 +118,8 @@ void XmlSerializer::encodeNode(const SerializationNode& node, std::ostream& stre
     const map<string, string>& properties = node.getProperties();
     for (map<string, string>::const_iterator iter = properties.begin(); iter != properties.end(); ++iter) {
         string name, value;
-        TiXmlBase::EncodeString(iter->first, &name);
-        TiXmlBase::EncodeString(iter->second, &value);
+        encodeString(iter->first, &name);
+        encodeString(iter->second, &value);
         stream << ' ' << name << "=\"" << value << '\"';
     }
     const vector<SerializationNode>& children = node.getChildren();
@@ -64,20 +135,64 @@ void XmlSerializer::encodeNode(const SerializationNode& node, std::ostream& stre
     }
 }
 
+/**
+ * Adapter class to let irrXML read a C++ stream.
+ */
+class XmlSerializer::StreamReader : public IFileReadCallBack {
+public:
+    StreamReader(std::istream& stream) : stream(stream) {
+        stream.seekg(0, ios_base::end);
+        size = stream.tellg();
+        stream.seekg(0);
+    }
+    int read(void* buffer, int sizeToRead) {
+        stream.read((char*) buffer, sizeToRead);
+        return stream.gcount();
+    }
+    int getSize() {
+        return size;
+    }
+private:
+    std::istream& stream;
+    int size;
+};
+
+/**
+ * Process an XML node, storing its content into a SerializationNode.
+ */
+static void decodeNode(SerializationNode& node, IrrXMLReader& xml) {
+    for (int i = 0; i < xml.getAttributeCount(); i++)
+        node.setStringProperty(xml.getAttributeName(i), xml.getAttributeValue(i));
+    if (xml.isEmptyElement())
+        return;
+    while (xml.read()) {
+        switch (xml.getNodeType()) {
+            case EXN_ELEMENT:
+            {
+                SerializationNode& childNode = node.createChildNode(xml.getNodeName());
+                decodeNode(childNode, xml);
+                break;
+            }
+            case EXN_ELEMENT_END:
+                return;
+        }
+    }
+}
+
 void* XmlSerializer::deserializeStream(std::istream& stream) {
-    TiXmlDocument doc;
-    stream >> doc;
     SerializationNode root;
-    decodeNode(root, *doc.FirstChildElement());
+    StreamReader reader(stream);
+    IrrXMLReader* xml = createIrrXMLReader(&reader);
+    
+    // Find the root node in the file.
+    
+    while (xml->read() && xml->getNodeType() != EXN_ELEMENT)
+        ;
+    decodeNode(root, *xml);
+    delete xml;
+    
+    // Process the SerializationNodes.
+    
     const SerializationProxy& proxy = SerializationProxy::getProxy(root.getStringProperty("type"));
     return proxy.deserialize(root);
 }
-
-void XmlSerializer::decodeNode(SerializationNode& node, const TiXmlElement& element) {
-    for (const TiXmlAttribute* attribute = element.FirstAttribute(); attribute != NULL; attribute = attribute->Next())
-        node.setStringProperty(attribute->NameTStr(), attribute->ValueStr());
-    for (const TiXmlElement* child = element.FirstChildElement(); child != NULL; child = child->NextSiblingElement()) {
-        SerializationNode& childNode = node.createChildNode(child->ValueTStr());
-        decodeNode(childNode, *child);
-    }
-}
\ No newline at end of file

serialization/src/tinyxmlerror.cpp

-/*
-www.sourceforge.net/projects/tinyxml
-Original code (2.0 and earlier )copyright (c) 2000-2006 Lee Thomason (www.grinninglizard.com)
-
-This software is provided 'as-is', without any express or implied 
-warranty. In no event will the authors be held liable for any 
-damages arising from the use of this software.
-
-Permission is granted to anyone to use this software for any 
-purpose, including commercial applications, and to alter it and 
-redistribute it freely, subject to the following restrictions:
-
-1. The origin of this software must not be misrepresented; you must
-not claim that you wrote the original software. If you use this
-software in a product, an acknowledgment in the product documentation
-would be appreciated but is not required.
-
-2. Altered source versions must be plainly marked as such, and
-must not be misrepresented as being the original software.
-
-3. This notice may not be removed or altered from any source
-distribution.
-*/
-
-#include "tinyxml.h"
-
-// The goal of the seperate error file is to make the first
-// step towards localization. tinyxml (currently) only supports
-// english error messages, but the could now be translated.
-//
-// It also cleans up the code a bit.
-//
-
-const char* TiXmlBase::errorString[ TIXML_ERROR_STRING_COUNT ] =
-{
-	"No error",
-	"Error",
-	"Failed to open file",
-	"Error parsing Element.",
-	"Failed to read Element name",
-	"Error reading Element value.",
-	"Error reading Attributes.",
-	"Error: empty tag.",
-	"Error reading end tag.",
-	"Error parsing Unknown.",
-	"Error parsing Comment.",
-	"Error parsing Declaration.",
-	"Error document empty.",
-	"Error null (0) or unexpected EOF found in input stream.",
-	"Error parsing CDATA.",
-	"Error when TiXmlDocument added to document, because TiXmlDocument can only be at the root.",
-};

wrappers/python/CMakeLists.txt

@@ -54,10 +54,12 @@ foreach(SUBDIR ${SUBDIRS})
         "${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.sh"
         "${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.xml"
         "${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.pdb"
+        "${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.pdbx"
         "${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.prmtop"
         "${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.prm"
         "${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.inpcrd"
         "${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.crd"
+        "${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.gro"
         "${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.parm7"
         "${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.rst7"
         "${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.ncrst"

wrappers/python/simtk/openmm/app/dcdfile.py

@@ -77,14 +77,17 @@ class DCDFile(object):
         header += struct.pack('<4i', 164, 4, len(list(topology.atoms())), 4)
         file.write(header)
 
-    def writeModel(self, positions, unitCellDimensions=None):
+    def writeModel(self, positions, unitCellDimensions=None, periodicBoxVectors=None):
         """Write out a model to the DCD file.
 
+        The periodic box can be specified either by the unit cell dimensions (for a rectangular box), or the full set of box
+        vectors (for an arbitrary triclinic box).  If neither is specified, the box vectors specified in the Topology will be
+        used.  Regardless of the value specified, no dimensions will be written if the Topology does not represent a periodic system.
+
         Parameters:
          - positions (list) The list of atomic positions to write
-         - unitCellDimensions (Vec3=None) The dimensions of the crystallographic unit cell.  If None, the dimensions specified in
-           the Topology will be used.  Regardless of the value specified, no dimensions will be written if the Topology does not
-           represent a periodic system.
+         - unitCellDimensions (Vec3=None) The dimensions of the crystallographic unit cell.
+         - periodicBoxVectors (tuple of Vec3=None) The vectors defining the periodic box.
         """
         if len(list(self._topology.atoms())) != len(positions):
             raise ValueError('The number of positions must match the number of atoms')
@@ -107,12 +110,22 @@ class DCDFile(object):
         # Write the data.
 
         file.seek(0, os.SEEK_END)
-        boxSize = self._topology.getUnitCellDimensions()
-        if boxSize is not None:
-            if unitCellDimensions is not None:
-                boxSize = unitCellDimensions
-            size = boxSize.value_in_unit(angstroms)
-            file.write(struct.pack('<i6di', 48, size[0], 0, size[1], 0, 0, size[2], 48))
+        boxVectors = self._topology.getPeriodicBoxVectors()
+        if boxVectors is not None:
+            if getPeriodicBoxVectors is not None:
+                boxVectors = getPeriodicBoxVectors
+            elif unitCellDimensions is not None:
+                if is_quantity(unitCellDimensions):
+                    unitCellDimensions = unitCellDimensions.value_in_unit(nanometers)
+                boxVectors = (Vec3(unitCellDimensions[0], 0, 0), Vec3(0, unitCellDimensions[1], 0), Vec3(0, 0, unitCellDimensions[2]))*nanometers
+            (a_length, b_length, c_length, alpha, beta, gamma) = computeLengthsAndAngles(boxVectors)
+            a_length = a_length.value_in_unit(angstroms)
+            b_length = b_length.value_in_unit(angstroms)
+            c_length = c_length.value_in_unit(angstroms)
+            angle1 = math.sin(math.pi/2-gamma)
+            angle2 = math.sin(math.pi/2-beta)
+            angle3 = math.sin(math.pi/2-alpha)
+            file.write(struct.pack('<i6di', 48, a_length, angle1, b_length, angle2, angle3, c_length, 48))
         length = struct.pack('<i', 4*len(positions))
         for i in range(3):
             file.write(length)

wrappers/python/simtk/openmm/app/forcefield.py

@@ -6,7 +6,7 @@ Simbios, the NIH National Center for Physics-Based Simulation of
 Biological Structures at Stanford, funded under the NIH Roadmap for
 Medical Research, grant U54 GM072970. See https://simtk.org.
 
-Portions copyright (c) 2012-2014 Stanford University and the Authors.
+Portions copyright (c) 2012-2015 Stanford University and the Authors.
 Authors: Peter Eastman, Mark Friedrichs
 Contributors:
 
@@ -403,9 +403,9 @@ class ForceField(object):
 
         # Set periodic boundary conditions.
 
-        boxSize = topology.getUnitCellDimensions()
-        if boxSize is not None:
-            sys.setDefaultPeriodicBoxVectors((boxSize[0], 0, 0), (0, boxSize[1], 0), (0, 0, boxSize[2]))
+        boxVectors = topology.getPeriodicBoxVectors()
+        if boxVectors is not None:
+            sys.setDefaultPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2])
         elif nonbondedMethod is not NoCutoff and nonbondedMethod is not CutoffNonPeriodic:
             raise ValueError('Requested periodic boundary conditions for a Topology that does not specify periodic box dimensions')
 

wrappers/python/simtk/openmm/app/gromacsgrofile.py

@@ -6,7 +6,7 @@ Simbios, the NIH National Center for Physics-Based Simulation of
 Biological Structures at Stanford, funded under the NIH Roadmap for
 Medical Research, grant U54 GM072970. See https://simtk.org.
 
-Portions copyright (c) 2012 Stanford University and the Authors.
+Portions copyright (c) 2012-2015 Stanford University and the Authors.
 Authors: Lee-Ping Wang, Peter Eastman
 Contributors:
 
@@ -89,6 +89,18 @@ def _is_gro_box(line):
     else:
         return 0
 
+def _construct_box_vectors(line):
+    """Create the periodic box vectors based on the values stored in the file.
+
+    @param[in] line The line containing the description
+    """
+
+    sline = line.split()
+    values = [float(i) for i in sline]
+    if len(sline) == 3:
+        return (Vec3(values[0], 0, 0), Vec3(0, values[1], 0), Vec3(0, 0, values[2]))*nanometers
+    return (Vec3(values[0], values[3], values[4]), Vec3(values[5], values[1], values[6]), Vec3(values[7], values[8], values[2]))*nanometers
+
 class GromacsGroFile(object):
     """GromacsGroFile parses a Gromacs .gro file and constructs a set of atom positions from it.
 
@@ -140,7 +152,7 @@ class GromacsGroFile(object):
                 xyz.append(Vec3(pos[0], pos[1], pos[2]))
             elif _is_gro_box(line) and ln == na + 2:
                 sline = line.split()
-                boxes.append(tuple([float(i) for i in sline])*nanometers)
+                boxes.append(_construct_box_vectors(line))
                 xyzs.append(xyz*nanometers)
                 xyz = []
                 ln = -1
@@ -160,7 +172,7 @@ class GromacsGroFile(object):
         ## A list containing the name of the residue that each atom belongs to
         self.residueNames = resname
         self._positions = xyzs
-        self._unitCellDimensions = boxes
+        self._periodicBoxVectors = boxes
         self._numpyPositions = None
 
     def getNumFrames(self):
@@ -182,10 +194,21 @@ class GromacsGroFile(object):
             return self._numpyPositions[frame]
         return self._positions[frame]
 
+    def getPeriodicBoxVectors(self, frame=0):
+        """Get the vectors defining the periodic box.
+
+        Parameters:
+         - frame (int=0) the index of the frame for which to get the box vectors
+        """
+        return self._periodicBoxVectors[frame]
+
     def getUnitCellDimensions(self, frame=0):
         """Get the dimensions of the crystallographic unit cell.
 
         Parameters:
          - frame (int=0) the index of the frame for which to get the unit cell dimensions
         """
-        return self._unitCellDimensions[frame]
+        xsize = self._periodicBoxVectors[frame][0][0].value_in_unit(nanometers)
+        ysize = self._periodicBoxVectors[frame][1][1].value_in_unit(nanometers)
+        zsize = self._periodicBoxVectors[frame][2][2].value_in_unit(nanometers)
+        return Vec3(xsize, ysize, zsize)*nanometers

wrappers/python/simtk/openmm/app/gromacstopfile.py

@@ -6,7 +6,7 @@ Simbios, the NIH National Center for Physics-Based Simulation of
 Biological Structures at Stanford, funded under the NIH Roadmap for
 Medical Research, grant U54 GM072970. See https://simtk.org.
 
-Portions copyright (c) 2012-2014 Stanford University and the Authors.
+Portions copyright (c) 2012-2015 Stanford University and the Authors.
 Authors: Peter Eastman
 Contributors:
 
@@ -358,12 +358,14 @@ class GromacsTopFile(object):
             raise ValueError('Unsupported function type in [ cmaptypes ] line: '+line);
         self._cmapTypes[tuple(fields[:5])] = fields
 
-    def __init__(self, file, unitCellDimensions=None, includeDir=None, defines=None):
+    def __init__(self, file, periodicBoxVectors=None, unitCellDimensions=None, includeDir=None, defines=None):
         """Load a top file.
 
         Parameters:
          - file (string) the name of the file to load
-         - unitCellDimensions (Vec3=None) the dimensions of the crystallographic unit cell
+         - periodicBoxVectors (tuple of Vec3=None) the vectors defining the periodic box
+         - unitCellDimensions (Vec3=None) the dimensions of the crystallographic unit cell.  For
+           non-rectangular unit cells, specify periodicBoxVectors instead.
          - includeDir (string=None) A directory in which to look for other files
            included from the top file. If not specified, we will attempt to locate a gromacs
            installation on your system. When gromacs is installed in /usr/local, this will resolve
@@ -403,7 +405,12 @@ class GromacsTopFile(object):
         top = Topology()
         ## The Topology read from the prmtop file
         self.topology = top
-        top.setUnitCellDimensions(unitCellDimensions)
+        if periodicBoxVectors is not None:
+            if unitCellDimensions is not None:
+                raise ValueError("specify either periodicBoxVectors or unitCellDimensions, but not both")
+            top.setPeriodicBoxVectors(periodicBoxVectors)
+        else:
+            top.setUnitCellDimensions(unitCellDimensions)
         PDBFile._loadNameReplacementTables()
         for moleculeName, moleculeCount in self._molecules:
             if moleculeName not in self._moleculeTypes:

wrappers/python/simtk/openmm/app/internal/pdbstructure.py

@@ -8,7 +8,7 @@ Simbios, the NIH National Center for Physics-Based Simulation of
 Biological Structures at Stanford, funded under the NIH Roadmap for
 Medical Research, grant U54 GM072970. See https://simtk.org.
 
-Portions copyright (c) 2012-2013 Stanford University and the Authors.
+Portions copyright (c) 2012-2015 Stanford University and the Authors.
 Authors: Christopher M. Bruns
 Contributors: Peter Eastman
 
@@ -37,8 +37,10 @@ __version__ = "1.0"
 from simtk.openmm.vec3 import Vec3
 import simtk.unit as unit
 from .. import element
+from unitcell import computePeriodicBoxVectors
 import warnings
 import sys
+import math
 
 class PdbStructure(object):
     """
@@ -137,7 +139,7 @@ class PdbStructure(object):
         self._current_model = None
         self.default_model = None
         self.models_by_number = {}
-        self._unit_cell_dimensions = None
+        self._periodic_box_vectors = None
         self.sequences = []
         self.modified_residues = []
         # read file
@@ -170,7 +172,13 @@ class PdbStructure(object):
                 self._current_model._current_chain._add_ter_record()
                 self._reset_residue_numbers()
             elif (pdb_line.find("CRYST1") == 0):
-                self._unit_cell_dimensions = Vec3(float(pdb_line[6:15]), float(pdb_line[15:24]), float(pdb_line[24:33]))*unit.angstroms
+                a_length = float(pdb_line[6:15])*0.1
+                b_length = float(pdb_line[15:24])*0.1
+                c_length = float(pdb_line[24:33])*0.1
+                alpha = float(pdb_line[33:40])*math.pi/180.0
+                beta = float(pdb_line[40:47])*math.pi/180.0
+                gamma = float(pdb_line[47:54])*math.pi/180.0
+                self._periodic_box_vectors = computePeriodicBoxVectors(a_length, b_length, c_length, alpha, beta, gamma)
             elif (pdb_line.find("CONECT") == 0):
                 atoms = [int(pdb_line[6:11])]
                 for pos in (11,16,21,26):
@@ -187,7 +195,7 @@ class PdbStructure(object):
             elif (pdb_line.find("MODRES") == 0):
                 self.modified_residues.append(ModifiedResidue(pdb_line[16], int(pdb_line[18:22]), pdb_line[12:15].strip(), pdb_line[24:27].strip()))
         self._finalize()
-    
+
     def _reset_atom_numbers(self):
         self._atom_numbers_are_hex = False
         self._next_atom_number = 1
@@ -283,9 +291,9 @@ class PdbStructure(object):
         for model in self.models:
             model._finalize()
 
-    def get_unit_cell_dimensions(self):
-        """Get the dimensions of the crystallographic unit cell (may be None)."""
-        return self._unit_cell_dimensions
+    def get_periodic_box_vectors(self):
+        """Get the vectors defining the crystallographic unit cell (may be None)."""
+        return self._periodic_box_vectors
 
 
 class Sequence(object):

wrappers/python/simtk/openmm/app/internal/unitcell.py

+"""
+unitcell.py: Routines for converting between different representations of the periodic unit cell.
+
+This is part of the OpenMM molecular simulation toolkit originating from
+Simbios, the NIH National Center for Physics-Based Simulation of
+Biological Structures at Stanford, funded under the NIH Roadmap for
+Medical Research, grant U54 GM072970. See https://simtk.org.
+
+Portions copyright (c) 2015 Stanford University and the Authors.
+Authors: Peter Eastman
+Contributors:
+
+Permission is hereby granted, free of charge, to any person obtaining a
+copy of this software and associated documentation files (the "Software"),
+to deal in the Software without restriction, including without limitation
+the rights to use, copy, modify, merge, publish, distribute, sublicense,
+and/or sell copies of the Software, and to permit persons to whom the
+Software is furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,
+DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR
+OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE
+USE OR OTHER DEALINGS IN THE SOFTWARE.
+"""
+__author__ = "Peter Eastman"
+__version__ = "1.0"
+
+from simtk.openmm import Vec3
+from simtk.unit import nanometers, is_quantity, norm, dot
+import math
+
+
+def computePeriodicBoxVectors(a_length, b_length, c_length, alpha, beta, gamma):
+    """Convert lengths and angles to periodic box vectors.
+    
+    Lengths should be given in nanometers and angles in radians.
+    """
+
+    # Compute the vectors.
+
+    a = [a_length, 0, 0]
+    b = [b_length*math.cos(gamma), b_length*math.sin(gamma), 0]
+    cx = c_length*math.cos(beta)
+    cy = c_length*(math.cos(alpha)-math.cos(beta)*math.cos(gamma))/math.sin(gamma)
+    cz = math.sqrt(c_length*c_length-cx*cx-cy*cy)
+    c = [cx, cy, cz]
+
+    # If any elements are very close to 0, set them to exactly 0.
+
+    for i in range(3):
+        if abs(a[i]) < 1e-6:
+            a[i] = 0.0
+        if abs(b[i]) < 1e-6:
+            b[i] = 0.0
+        if abs(c[i]) < 1e-6:
+            c[i] = 0.0
+    a = Vec3(*a)
+    b = Vec3(*b)
+    c = Vec3(*c)
+
+    # Make sure they're in the reduced form required by OpenMM.
+
+    c = c - b*round(c[1]/b[1])
+    c = c - a*round(c[0]/a[0])
+    b = b - a*round(b[0]/a[0])
+    return (a, b, c)*nanometers
+
+def computeLengthsAndAngles(periodicBoxVectors):
+    """Convert periodic box vectors to lengths and angles.
+
+    Lengths are returned in nanometers and angles in radians.
+    """
+
+    (a, b, c) = vectors.value_in_unit(nanometers)
+    a_length = norm(a)
+    b_length = norm(b)
+    c_length = norm(c)
+    alpha = math.acos(dot(b, c)/(b_length*c_length))
+    beta = math.acos(dot(c, a)/(c_length*a_length))
+    gamma = math.acos(dot(a, b)/(a_length*b_length))
+    return (a_length, b_length, c_length, alpha, beta, gamma)

wrappers/python/simtk/openmm/app/modeller.py

@@ -6,7 +6,7 @@ Simbios, the NIH National Center for Physics-Based Simulation of
 Biological Structures at Stanford, funded under the NIH Roadmap for
 Medical Research, grant U54 GM072970. See https://simtk.org.
 
-Portions copyright (c) 2012-2013 Stanford University and the Authors.
+Portions copyright (c) 2012-2015 Stanford University and the Authors.
 Authors: Peter Eastman
 Contributors:
 
@@ -94,7 +94,7 @@ class Modeller(object):
         # Copy over the existing model.
 
         newTopology = Topology()
-        newTopology.setUnitCellDimensions(deepcopy(self.topology.getUnitCellDimensions()))
+        newTopology.setPeriodicBoxVectors(self.topology.getPeriodicBoxVectors())
         newAtoms = {}
         newPositions = []*nanometer
         for chain in self.topology.chains():
@@ -140,7 +140,7 @@ class Modeller(object):
          - toDelete (list) a list of Atoms, Residues, Chains, and bonds (specified as tuples of Atoms) to delete
         """
         newTopology = Topology()
-        newTopology.setUnitCellDimensions(deepcopy(self.topology.getUnitCellDimensions()))
+        newTopology.setPeriodicBoxVectors(self.topology.getPeriodicBoxVectors())
         newAtoms = {}
         newPositions = []*nanometer
         deleteSet = set(toDelete)
@@ -189,7 +189,7 @@ class Modeller(object):
         else:
             raise ValueError('Unknown water model: %s' % model)
         newTopology = Topology()
-        newTopology.setUnitCellDimensions(deepcopy(self.topology.getUnitCellDimensions()))
+        newTopology.setPeriodicBoxVectors(self.topology.getPeriodicBoxVectors())
         newAtoms = {}
         newPositions = []*nanometer
         for chain in self.topology.chains():
@@ -240,7 +240,7 @@ class Modeller(object):
         self.topology = newTopology
         self.positions = newPositions
 
-    def addSolvent(self, forcefield, model='tip3p', boxSize=None, padding=None, positiveIon='Na+', negativeIon='Cl-', ionicStrength=0*molar):
+    def addSolvent(self, forcefield, model='tip3p', boxSize=None, boxVectors=None, padding=None, positiveIon='Na+', negativeIon='Cl-', ionicStrength=0*molar):
         """Add solvent (both water and ions) to the model to fill a rectangular box.
 
         The algorithm works as follows:
@@ -250,15 +250,17 @@ class Modeller(object):
            randomly selecting a water molecule and replacing it with the ion.
         4. Ion pairs are added to give the requested total ionic strength.
 
-        The box size can be specified in three ways.  First, you can explicitly give a box size to use.  Alternatively, you can
+        The box size can be specified in four ways.  First, you can explicitly give the vectors defining the periodic box to
+        use.  Alternatively, for a rectangular box you can simply give the dimensions of the unit cell.  Third, you can
         give a padding distance.  The largest dimension of the solute (along the x, y, or z axis) is determined, and a cubic
-        box of size (largest dimension)+2*padding is used.  Finally, if neither a box size nor a padding distance is specified,
-        the existing Topology's unit cell dimensions are used.
+        box of size (largest dimension)+2*padding is used.  Finally, if neither box vectors, box size, nor padding distance is specified,
+        the existing Topology's box vectors are used.
 
         Parameters:
          - forcefield (ForceField) the ForceField to use for determining van der Waals radii and atomic charges
          - model (string='tip3p') the water model to use.  Supported values are 'tip3p', 'spce', 'tip4pew', and 'tip5p'.
          - boxSize (Vec3=None) the size of the box to fill with water
+         - boxVectors (tuple of Vec3=None) the vectors defining the periodic box to fill with water
          - padding (distance=None) the padding distance to use
          - positiveIon (string='Na+') the type of positive ion to add.  Allowed values are 'Cs+', 'K+', 'Li+', 'Na+', and 'Rb+'
          - negativeIon (string='Cl-') the type of negative ion to add.  Allowed values are 'Cl-', 'Br-', 'F-', and 'I-'. Be aware
@@ -268,18 +270,28 @@ class Modeller(object):
         """
         # Pick a unit cell size.
 
-        if boxSize is not None:
+        if boxVectors is not None:
+            if is_quantity(boxVectors[0]):
+                boxVectors = (boxVectors[0].value_in_unit(nanometer), boxVectors[1].value_in_unit(nanometer), boxVectors[2].value_in_unit(nanometer))
+            box = Vec3(boxVectors[0][0], boxVectors[1][1], boxVectors[2][2])
+            vectors = boxVectors
+        elif boxSize is not None:
             if is_quantity(boxSize):
                 boxSize = boxSize.value_in_unit(nanometer)
-            box = Vec3(boxSize[0], boxSize[1], boxSize[2])*nanometer
+            box = Vec3(boxSize[0], boxSize[1], boxSize[2])
+            vectors = (Vec3(boxSize[0], 0, 0), Vec3(0, boxSize[1], 0), Vec3(0, 0, boxSize[2]))
         elif padding is not None:
+            if is_quantity(padding):
+                padding = padding.value_in_unit(nanometer)
             maxSize = max(max((pos[i] for pos in self.positions))-min((pos[i] for pos in self.positions)) for i in range(3))
+            maxSize = maxSize.value_in_unit(nanometer)
             box = (maxSize+2*padding)*Vec3(1, 1, 1)
+            vectors = (Vec3(maxSize+2*padding, 0, 0), Vec3(0, maxSize+2*padding, 0), Vec3(0, 0, maxSize+2*padding))
         else:
-            box = self.topology.getUnitCellDimensions()
+            box = self.topology.getUnitCellDimensions().value_in_unit(nanometer)
+            vectors = self.topology.getPeriodicBoxVectors().value_in_unit(nanometer)
             if box is None:
-                raise ValueError('Neither the box size nor padding was specified, and the Topology does not define unit cell dimensions')
-        box = box.value_in_unit(nanometer)
+                raise ValueError('Neither the box size, box vectors, nor padding was specified, and the Topology does not define unit cell dimensions')
         invBox = Vec3(1.0/box[0], 1.0/box[1], 1.0/box[2])
 
         # Identify the ion types.
@@ -331,7 +343,7 @@ class Modeller(object):
         # Copy the solute over.
 
         newTopology = Topology()
-        newTopology.setUnitCellDimensions(box)
+        newTopology.setPeriodicBoxVectors(vectors*nanometer)
         newAtoms = {}
         newPositions = []*nanometer
         for chain in self.topology.chains():
@@ -378,7 +390,9 @@ class Modeller(object):
 
         def periodicDistance(pos1, pos2):
             delta = pos1-pos2
-            delta = [delta[i]-floor(delta[i]*invBox[i]+0.5)*box[i] for i in range(3)]
+            delta -= vectors[2]*floor(delta[2]*invBox[2]+0.5)
+            delta -= vectors[1]*floor(delta[1]*invBox[1]+0.5)
+            delta -= vectors[0]*floor(delta[0]*invBox[0]+0.5)
             return norm(delta)
 
         # Find the list of water molecules to add.
@@ -472,7 +486,6 @@ class Modeller(object):
                     for atom2 in molAtoms:
                         if atom2.element == elem.hydrogen:
                             newTopology.addBond(atom1, atom2)
-        newTopology.setUnitCellDimensions(deepcopy(box)*nanometer)
         self.topology = newTopology
         self.positions = newPositions
 
@@ -610,7 +623,7 @@ class Modeller(object):
         # Loop over residues.
 
         newTopology = Topology()
-        newTopology.setUnitCellDimensions(deepcopy(self.topology.getUnitCellDimensions()))
+        newTopology.setPeriodicBoxVectors(self.topology.getPeriodicBoxVectors())
         newAtoms = {}
         newPositions = []*nanometer
         newIndices = []
@@ -883,7 +896,7 @@ class Modeller(object):
         # Create the new Topology.
 
         newTopology = Topology()
-        newTopology.setUnitCellDimensions(deepcopy(self.topology.getUnitCellDimensions()))
+        newTopology.setPeriodicBoxVectors(self.topology.getPeriodicBoxVectors())
         newAtoms = {}
         newPositions = []*nanometer
         for chain in self.topology.chains():

wrappers/python/simtk/openmm/app/pdbfile.py

@@ -6,7 +6,7 @@ Simbios, the NIH National Center for Physics-Based Simulation of
 Biological Structures at Stanford, funded under the NIH Roadmap for
 Medical Research, grant U54 GM072970. See https://simtk.org.
 
-Portions copyright (c) 2012 Stanford University and the Authors.
+Portions copyright (c) 2012-2015 Stanford University and the Authors.
 Authors: Peter Eastman
 Contributors:
 
@@ -40,7 +40,7 @@ from datetime import date
 from simtk.openmm import Vec3, Platform
 from simtk.openmm.app.internal.pdbstructure import PdbStructure
 from simtk.openmm.app import Topology
-from simtk.unit import nanometers, angstroms, is_quantity, norm, Quantity
+from simtk.unit import nanometers, angstroms, is_quantity, norm, Quantity, dot
 import element as elem
 try:
     import numpy
@@ -142,7 +142,7 @@ class PDBFile(object):
             self._positions.append(coords*nanometers)
         ## The atom positions read from the PDB file.  If the file contains multiple frames, these are the positions in the first frame.
         self.positions = self._positions[0]
-        self.topology.setUnitCellDimensions(pdb.get_unit_cell_dimensions())
+        self.topology.setPeriodicBoxVectors(pdb.get_periodic_box_vectors())
         self.topology.createStandardBonds()
         self.topology.createDisulfideBonds(self.positions)
         self._numpyPositions = None
@@ -250,10 +250,16 @@ class PDBFile(object):
          - file (file=stdout) A file to write the file to
         """
         print >>file, "REMARK   1 CREATED WITH OPENMM %s, %s" % (Platform.getOpenMMVersion(), str(date.today()))
-        boxSize = topology.getUnitCellDimensions()
-        if boxSize is not None:
-            size = boxSize.value_in_unit(angstroms)
-            print >>file, "CRYST1%9.3f%9.3f%9.3f  90.00  90.00  90.00 P 1           1 " % size
+        vectors = topology.getPeriodicBoxVectors()
+        if vectors is not None:
+            (a, b, c) = vectors.value_in_unit(angstroms)
+            a_length = norm(a)
+            b_length = norm(b)
+            c_length = norm(c)
+            alpha = math.acos(dot(b, c)/(b_length*c_length))*180.0/math.pi
+            beta = math.acos(dot(c, a)/(c_length*a_length))*180.0/math.pi
+            gamma = math.acos(dot(a, b)/(a_length*b_length))*180.0/math.pi
+            print >>file, "CRYST1%9.3f%9.3f%9.3f%7.2f%7.2f%7.2f P 1           1 " % (a_length, b_length, c_length, alpha, beta, gamma)
 
     @staticmethod
     def writeModel(topology, positions, file=sys.stdout, modelIndex=None):

wrappers/python/simtk/openmm/app/pdbxfile.py

@@ -6,7 +6,7 @@ Simbios, the NIH National Center for Physics-Based Simulation of
 Biological Structures at Stanford, funded under the NIH Roadmap for
 Medical Research, grant U54 GM072970. See https://simtk.org.
 
-Portions copyright (c) 2014 Stanford University and the Authors.
+Portions copyright (c) 2014-2015 Stanford University and the Authors.
 Authors: Peter Eastman
 Contributors:
 
@@ -33,8 +33,10 @@ __version__ = "1.0"
 
 import os
 import sys
+import math
 from simtk.openmm import Vec3
 from simtk.openmm.app.internal.pdbx.reader.PdbxReader import PdbxReader
+from simtk.openmm.app.internal.unitcell import computePeriodicBoxVectors
 from simtk.openmm.app import Topology
 from simtk.unit import nanometers, angstroms, is_quantity, norm, Quantity
 import element as elem
@@ -145,8 +147,9 @@ class PDBxFile(object):
         cell = block.getObj('cell')
         if cell is not None and cell.getRowCount() > 0:
             row = cell.getRow(0)
-            cellSize = [float(row[cell.getAttributeIndex(attribute)]) for attribute in ('length_a', 'length_b', 'length_c')]*angstroms
-            self.topology.setUnitCellDimensions(cellSize)
+            (a, b, c) = [float(row[cell.getAttributeIndex(attribute)])*0.1 for attribute in ('length_a', 'length_b', 'length_c')]
+            (alpha, beta, gamma) = [float(row[cell.getAttributeIndex(attribute)])*math.pi/180.0 for attribute in ('angle_alpha', 'angle_beta', 'angle_gamma')]
+            self.topology.setPeriodicBoxVectors(computePeriodicBoxVectors(a, b, c, alpha, beta, gamma))
 
         # Add bonds based on struct_conn records.