Molby - A Molecular Modeling Software

Fork

========================================================

                     Molby

    An Interactive Molecular Modeling Software
        with Integrated Ruby Interpreter
  
          Version 0.5.6.2 build 20110823

                  Toshi Nagata

========================================================

1. What is it?

Molby is an application to visualize and build molecular models interactively through 3D display. It provides the following capability:

- Viewing molecular models in either ball-and-stick or "line" display.
- Interactive modification of molecular models by mouse operation.
- Viewing and editing atomic coordinates and other parameters in numeric tables.
- Importing and exporting structure/coordinate data for other program packages such as Gaussian, GAMESS, NAMD and SHELX.
- Embedded Ruby interpreter for automated processing of molecular models.

2. Supported Platforms

Molby runs on Mac OS X (10.4 and later) and Microsoft Windows (XP and later). Executable binaries are provided for both platforms (Molby.dmg for Mac, SetupMolby.exe for Windows).

3. Copyright and License

Molby is a copyrighted product of Toshi Nagata.

       Copyright (C) 2009-2010 Toshi Nagata

Molby includes (more technically: is statically linked to) the following softwares, which are copyrighted products as described below:

- wxWidgets 2.8.9: Copyright (C) 1992-2008 Julian Smart, Robert Roebling, Vadim Zeitlin and other members of the wxWidgets team. Portions (c) 1996 Artificial Intelligence Applications Institute
- Ruby 1.8.7: Copyright (C) 1993-2009 Yukihiro Matsumoto
- CLAPACK: Copyright (c) 1992-2008 The University of Tennessee.
- AmberTools 1.3: Copyright (c) Junmei Wang, Ross C. Walker, Michael F. Crowley, Scott Brozell and David A. Case

Molby is distributed under the GNU General Public License (version 2). See the file COPYING for more details.

4. How to Use

The document in HTML format is available. Try the tutorial to get familiar with Molby.

5. How to Build

The information in this section is only for those who want to build Molby from the source. If you use the binary distribution, you do not need to read this section.

Building Molby is somewhat complicated because you need static libraries of wxWidgets and Ruby (and CLAPACK in Windows). The procedures are described below for each platform.

(1) Mac OS X

(i) Xcode, gfortran

Install Xcode, if you have not done so yet. The Xcode project included in the source distribution is for Xcode 3.0 and later, thus you need Mac OS 10.5. It may work with Xcode 2.5 on Mac OS 10.4, but this have not been tested.

To build AmberTools, you need to have gfortran installed. The author uses a binary build available at the "R for Mac OS X" website (http://r.research.att.com/tools/, gfortran-4.2.3.dmg).

We need static linking of libgfortran.a. For that purpose, the following modification should be done after installation of gfortran.

% cd /usr/local/lib
% sudo cp libgfortran.a libgfortran-static.a  #  Copy as a different name
% sudo strip -S libgfortran-static.a  #  Remove the symbols
% sudo ranlib libgfortran-static.a

The last two lines are necessary to avoid linker warnings saying "Can't find atom for N_GSYM stabs."

(ii) wxWidgets

Get wxMac-2.8.9.tar.gz from the wxWidgets page in sourceforge.net (http://sourceforge.net/projects/wxwindows/files/). Newer versions may work, but they are not tested.

Unpack wxMac-2.8.9.tar.gz. Move the resulting directory wxMac-2.8.9 to $HOME/Development, and rename it to wxMac (or make a symbolic link). The console commands will be as follows:
$ mkdir -p $HOME/Development
$ cd $HOME/Development
$ mv somewhere/wxMac-2.8.9.tar.gz ./
$ tar xvzf wxMac-2.8.9.tar.gz
$ ln -s wxMac-2.8.9 wxMac

If you want to place wxMac in another place (and/or another name) than $HOME/Development, you will need to change the build settings in Xcode.

Build wxMac. The commands will be as follows. Take care of the configure options.
$ cd $HOME/Development/wxMac
$ mkdir osx-build
$ cd osx-build
$ ../configure --with-macos-sdk=/Developer/SDKs/MacOSX10.4u.sdk --with-macosx-version-min=10.4 --enable-universal_binary --disable-shared --with-opengl --enable-unicode --with-libjpeg=builtin --with-libpng=builtin --with-regex=builtin --with-libtiff=builtin --with-zlib=builtin --with-expat=builtin
$ make
(You do not need to do "sudo make install".)

(iii) Ruby

Get ruby-1.8.7-p160.tar.gz from the Molby source distribution site. Unpack it, and move the resulting directory ruby-1.8.7-p160 to $HOME/Development. Rename it to ruby-1.8.7-static (or make a symbolic link).
$ cd $HOME/Development
$ mv somewhere/ruby-1.8.7-p160.tar.gz ./
$ tar xvzf ruby-1.8.7-p160.tar.gz
$ ln -s ruby-1.8.7-p160 ruby-1.8.7-static

If you want to place ruby-1.8.7-static in another place (and/or another name) than $HOME/Development, you will need to change the build settings in Xcode.

Patch the Ruby source.
$ cd $HOME/Development/ruby-1.8.7-static
$ patch --backup -p1 < $MOLBY/ruby-1.8.7-p160-tn.patch
($MOLBY is the location of the Molby source.)

Build Ruby with --disable-shared option.
$ CFLAGS='-isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -arch i386 -arch ppc -O2' ./configure --disable-shared --disable-thread
$ make

(iv) Build on Xcode

Open xcode-build/Molby.xcodeproj, and build. Note that there are two configurations, Debug and Release. In the "Release" build, the Ruby scripts update_version.rb and Documents/makedoc.rb are executed before compilation; update_version.rb modifies the version strings in the source files (by looking up the file Version), and makedoc.rb creates the HTML docments in the doc directory.

(2) Windows

The Windows binary is built by using MinGW/MSYS. If you use VC++ or Cygwin, you need to help yourself. I use Windows only occasionally, so there may be errors and misunderstandings in the following descriptions. Feedback is welcome!

(i) MinGW, MSYS, gfortran

Install MinGW and MSYS. The author uses MinGW-5.1.4 and MSYS-1.0.11.

To build AmberTools, you need to have gfortran installed. The author has experienced problems with the gfortran of MinGW, and instead is using the binary build taken from http://quatramaran.ens.fr/~coudert/gfortran/ (version 4.5.0, 20090421, trunk revision 146519).

(ii) wxWidgets

Get wxMSW-2.8.9.tar.gz from the wxWidgets page in sourceforge.net (http://sourceforge.net/projects/wxwindows/files/). Newer versions may work, but they are not tested.

Unpack wxMSW-2.8.9.tar.gz. Move the resulting directory wxMSW-2.8.9 to $HOME (the home directory of the MinGW The console commands will be as follows:
$ cd $HOME
$ mv somewhere/wxMSW-2.8.9.tar.gz ./
$ tar xvzf wxMSW-2.8.9.tar.gz

Build wxMSW. The commands will be as follows. Take care of the configure options.
$ cd $HOME/wxMSW-2.8.9
$ mkdir msw-build
$ cd msw-build
$ ../configure --with-msw --with-opengl --disable-shared --enable-unicode --with-libjpeg=builtin --with-zlib=builtin
$ make
(You do not need to do "sudo make install".)

(iii) Ruby

Get ruby-1.8.7-p160.tar.gz from the Molby source distribution site. Unpack it, and move the resulting directory ruby-1.8.7-p160 to $HOME. Rename it to ruby-1.8.7-static.
$ cd $HOME
$ mv somewhere/ruby-1.8.7-p160.tar.gz ./
$ tar xvzf ruby-1.8.7-p160.tar.gz
$ mv ruby-1.8.7-p160 ruby-1.8.7-static

Patch the Ruby source.
$ cd $HOME/ruby-1.8.7-static
$ patch --backup -p1 < $MOLBY/ruby-1.8.7-p160-tn.patch
($MOLBY is the location of the Molby source.)

Build Ruby with --disable-shared option.
$ ./configure --disable-shared --disable-thread
$ make

(iv) CLAPACK

Get clapack-3.1.1.1.tar.gz from the CLAPACK official site (http://www.netlib.org/clapack/) and unpack it. (clapack-3.2.1 may cause trouble because it uses symbolic links.)
$ cd $HOME
$ mv somewhere/clapack-3.1.1.1.tgz ./
$ tar xvzf clapack-3.1.1.1.tgz

Patch the clapack source.
$ patch -p0 <$MOLBY/clapack-3.1.1.1-mingw.patch

Build CLAPACK.
$ cd CLAPACK-3.1.1.1
$ make

Modify libf2c.a, so that the 'main' entry does not interfere the main program.
$ cd F2CLIBS
$ cp libf2c.a libf2c_nomain.a
$ ar d libf2c_nomain.a main.o
$ cd ..

Copy the library and header files to /lib/clapack.
$ mkdir /lib/clapack
$ cp F2CLIBS/libf2c_nomain.a /lib/clapack
$ cp blasMinGW.a /lib/clapack/libblas.a
$ cp lapackMinGW.a /lib/clapack/liblapack.a
$ cp INCLUDE/f2c.h INCLUDE/blaswrap.h INCLUDE/clapack.h /lib/clapack

(v) Inno Setup 5

Install Inno Setup 5 (http://www.jrsoftware.org/isinfo.php). This is necessary to create the Molby Installer.

(vi) Build

Now you can start building Molby! Go to the project directory and do make.
$ cd somewhere/Molby/msw-build
$ make
$ make setup  #  To make the installer


2010.1.21.
2010.1.31. Added notice on AmberTools1.3
2010.4.29. Update description for MinGW/MSYS
2011.8.3.  Added notice on static linking of libgfortran for Mac

Toshi Nagata