Commit cca7f43b authored by Alessia Vignolo's avatar Alessia Vignolo
Browse files

modified userguide

parent 5a434072
......@@ -113,14 +113,15 @@ In a Linux shell run:
\begin{center}
\textsf{python setup.py}
\end{center}
This will try to automatically guess your distribution, download and install the necessary packages accordingly,
download CGAL, compiling CGAL, patching CGAL, configuring and compiling NanoShaper as Stand Alone (.exe),
as a shared object for DelPhi, or as a Python module. You will find NanoShaper in the build folder.
%This will try to automatically guess your distribution, download and install the necessary packages accordingly,
This will list the packages needed to be installed manually, install a correct version of cmake, download CGAL, compile CGAL, patch CGAL, configure and compile NanoShaper as Stand Alone (.exe) or as a shared object for DelPhi.%, or as a Python module.
You will find NanoShaper in the build or build\_lib folder.
\subsection{Manual mode for any OS}
In order to build the full version of the software the system must have installed CGAL (for the Skin/SES support CGAL 4.2 was used), Boost libraries and cmake;
In Linux/Mac GCC is required and in Windows NanoShaper it has been tested on Visual Studio 2008/2010 but it should
work also on next versions. Building the software consists in a cmake configuration step and make; additionally patching CGAL is required (for Visual Studio 2010 also Power\_test\_3.h is required as patch); prior to building, overwrite the files contained in CGALpatch in the
In order to build the full version of the software the system must have installed CGAL (for the Skin/SES support CGAL 5.2 was used), Boost libraries and cmake2.8;
In Linux/Mac GCC is required and in Windows NanoShaper it has been tested on Visual Studio 2008/2010 but it should work also on next versions.
Building the software consists in a cmake configuration step and make; additionally patching CGAL is required (for Visual Studio 2010 also Power\_test\_3.h is required as patch);
prior to building, overwrite the files contained in CGALpatch in the
CGAL include directory where the same .h are present.
For simplicity and to minimize the number of packages to be installed use the following cmake command for CGAL:
\begin{center}
......@@ -131,16 +132,18 @@ and on a 64 bit machine perform cmake by expliciting setting the current compile
to avoid a cmake bug.\\
On a Windows system you will get a Visual Studio project and Linux/Mac a make file. Build either typing \textsf{make} or using Visual
Studio. \\
If CGAL is not present, mesh, msms and Blobby surfaces will be still available and the code should be compilable with any C++ compiler that
has boost support. If neither boost is present the same functionalities will be given but using a single execution thread; in this last case
the software does not depend on any external library except from STL containers.\\
NanoShaper can be directly used in Python: to this aim you will need the Swig package installed (Enthough Python distro already has). Rename \emph{CMakeLists\_python.txt}
into \textsf{CMakeLists.txt} and run cmake as in the previous case but this time inside \textsf{build\_python} folder. This process will generate
a project or a make file; by building the project/or performing make you will be end up with the following files: \textsf{NanoShaper.py} and
\textsf{\_NanoShaper.pyd}. You should put these files in a place where they can be reached by Python such as the same folder where
you write your script: then you can use NanoShaper classes as for any other Python package by importing
NanoShaper. In the folder \textsf{python\_example} see the file example.py
where the NanoShaper classes are used and the surface is visualized via MolFX.py script.
%NanoShaper can be directly used in Python: to this aim you will need the Swig package installed (Enthough Python distro already has). Rename \emph{CMakeLists\_python.txt}
%into \textsf{CMakeLists.txt} and run cmake as in the previous case but this time inside \textsf{build\_python} folder. This process will generate
%a project or a make file; by building the project/or performing make you will be end up with the following files: \textsf{NanoShaper.py} and
%\textsf{\_NanoShaper.pyd}. You should put these files in a place where they can be reached by Python such as the same folder where
%you write your script: then you can use NanoShaper classes as for any other Python package by importing
%NanoShaper. In the folder \textsf{python\_example} see the file example.py
%where the NanoShaper classes are used and the surface is visualized via MolFX.py script.
......@@ -273,7 +276,8 @@ The value of 2 is the default one. \\
\subsection{DelPhi interfacing}
\label{secDel}
NanoShaper can be interfaced to DelPhi when compiled as a dynamic library (.so on Linux, .dynlib on Mac, .dll on Windows). To compile NanoShaper as a shared object the user
NanoShaper can be interfaced to DelPhi when compiled as a dynamic library (.so on Linux, .dynlib on Mac, .dll on Windows).
To compile NanoShaper as a shared object the user
has to choose the \textsf{lib} option when requested by the setup.py script. Upon compilation the user must assure that the library is visible to the system. In the case of Windows it is sufficient
to put the library in the directory where DelPhi will be run or put it in the System path. On Linux the library must be put on a reachable folder; the easiest way to do that is
to let point the \textsf{LD\_LIBRARY\_PATH} environment variable to the directory that contains the library. On Mac the equivalent is \textsf{DYLD\_LIBRARY\_PATH}. \\
......
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