Welcome to Enantiomers discovery program - SAICS
================================================

This program is able to identify two molecular geometries as enantiomeric structures.
For this one only needs the cartesian coordinates of the two systems in the XYZ format
(http://en.wikipedia.org/wiki/XYZ_file_format) or you can use openbabel (http://openbabel.org/)
to convert almost any type of chemical file format to the XYZ format. See the user manual of
openbabel for more details. 

Usage:
./saics 1.xyz 2.xyz

Options:
By using option "rmsd" the program only calculates the rmsd between the two
structures, without testing for enantiomers. Example of use:
./saics -rmsd 1.xyz 2.xyz

Example output:
 =============================================================================
 == This program is offered ''as is''. If you use this program, please cite ==
 == the paper, which this program is part of the Supporting Information.    ==
 =============================================================================

 Input files: simple-R.xyz simple-S.xyz

 Superimposition of structure 1 and structure 2
 rmsd1=   1.2745494266159172     
 nrots1=          50

 Superimposition of structure 1 and mirror image of structure 2
 rmsd2=  1.09343996739599399E-004
 nrots2=          50

 --- Structure simple-R.xyz and simple-S.xyz are enantiomers ---



Compiling and testing
=====================
To compile and test the program, you will need:

1) bash shell (only needed for testing)
2) make (tested with gnu make)
3) A fortran 90/95 compiler (tested with ifort and gfortran)

Compilation:

1) You make choose the compiler you want to use, by editing the Makefile and changing 
the line corresponding to the fortran compiler (the default is using gfortran):
F90=gfortran or ifort

After testing the program in your environment, you should alter the compilation flags (F90FLAGS),
and recompile for a better performance of the program (-O2 is the suggested optimization level).

2) issue the command 'make' and and executable named "saics" will be produced

3) to test the program just 'make test' and several tests (described in the paper) will be performed.


Coimbra, 2th of February 2012


This version writes two files with containing the geometries with the smallest RMSD.
example:
./saics struct1.xyz struct2.xyz will write the new files:
centered_struct1.xyz  containing the first structure centered in the center of mass
best_rmsd_struct2.xyz containing the best superposition between the two structures
These structures can then be used to create figures or just to visualize the results.

Coimbra, 16th of February 2012