https://github.com/biomat-usp-rp/suave-software-source_v1.0

https://github.com/biomat-usp-rp/suave-software-source_v1.0

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                               ** VERSION 1.0.0 **
 
                          Santos, D. E. S.; Soares, T. A.
 

 CITATION: 

 SuAVE: A Tool for Analyzing Curvature-Dependent Properties in Chemical Interfaces
 (2020) Denys E. S. Santos, Frederico J. S. Pontes, Roberto D. Lins, Kaline Coutinho, 
 Thereza A. Soares. J. Chem. Inf. Model., v. 60(2), p. 473-484.


 DESCRIPTION: 

 The surface assessment via grid evaluation (SuAVE) software was developed to account 
 for the effect of curvature in the calculations of structural properties of chemical 
 interfaces regardless of the chemical composition, asymmetry, and level of atom coarseness. 
 It employs differential geometry techniques, enabling the representation of chemical 
 surfaces as fully differentiable. 


 Denys E. S. Santos wrote the code and conceived the algorithm and mathematical formalism. 
 Thereza A. Soares conceived the idea and supervised code development. Kaline Coutinho and  
 Roberto D. Lins revised the code and provided expertise with the equations and discussion.
 Frederico J. S. Pontes developed the atomistic simulations used to validate the software. 
 

 INSTALLATION:

 SuAVE can be compiled in any operational system, is distributed free of charge and
 it is maintained by a single developer. If you experience code issues, we kindly 
 request you to contact us at e-mail: suave.biomat@gmail.com

 ---------------------------------

 Prerequisites for installation:
 
 -> cmake installed
   
 -> gfortran installed

 -> library libquadmath installed 

 ----------------------------------

 In order to install the programs and enjoy your analysis time, please follow the steps 
 below:

 1- Download the code:

    -> From GitHub web Page (https://github.com/SuAVE-Software/source) 
       clone the repository through the following commmand:

       $ git clone https://github.com/SuAVE-Software/source.git

    -> Dowload the compiled version from SuAVE Web Page 
       (https://www.biomatsite.net/suave-software)

 2- Compile the source code:

 If you downloaded the compiled version you just need to insert the files on a 
 convenient path in order to be run. If you downloaded the source code, please compile
 it by the use of any FORTRAN compiler and the MakeFile. 
 
 ->> Enter the directory where you have downloaded the code

     $ cd ~/PATH_TO_SRC/
 
 ->> Edit makefile in order to proceed with the installation process. Edit INSTALL_PATH
     content to update the PATH where you want to place the compiled source, and also
     the FCFLAGS to adapt it to your needs.
    
     FCFLAGS = -O2 (DEFAULT)
     INSTALL_PATH = /usr/local/suave (DEFAULT)

     (The use of flags -O2 or -O3 is well accepted by this compiler and the code. It will be 
     helpful for extracting the best performance of SuAVE)
 
 ->> Once with the makefile updated, run make!
 
     $ make
	
     $ sudo make install

 ->> Insert the following directives in the .bash_profile file:

     export SUAVE=/usr/local/suave
     export PATH=$SUAVE:$PATH

 ->> Update the bash

     $ source .bash_profile

     or

     $ source .bashrc

 ->> Have fun with your analysis !


  USAGE:

 A classical use for most of SuAVE tools is exemplified below for s_dens:

 Usage: s_dens -in file.pdb -ind1 file1.ndx -ind2 file2.ndx -dens dens.ndx
 
 file.pdb ---- atomic coordinates in PDB format
 
 file.ndx ---- index file containing user-selected atoms used
               to fit the grid points to the chemical surface.
	       
 dens.ndx ---- index file containing user-selected atoms used 
               to calculate density profile.
 
 Options:
 
 -bin             defines the number of rectangular partition 
                  bins along the x- and y-axes
 
 -outer           automatically selects the 
                  surface/interface outmost atoms to fit the grid 
		  points. This option overwrites the user-selected 
		  index files.
 
 -grid            generates a PDB file containing the grid
 	          points used in the fitting for the last frame in 
		  the trajectory file.
 
 -rmsd            calculates the RMSD between the fitted
                  grid and the selected atoms in the index files. 
		  This estimates how precisely is the grid surface fitted 
		  to the chemical surface throughout the trajectory file.
 
 -coarse          generates a coarse grid over the surface
                  index atoms from which a finer grid will be generated. 
		  This recommended for surfaces defined by atoms which greatly
		  fluctuate throughout the trajectory. 
 
 -begin           first frame to use in the calculations
 
 -end             last frame to use in the calculations
 
 -skip            number of trajectory frames to be skipped
                  during the analysis 
 
 -water           used to calculate number of water
                  molecules inside the structure
 
 -map             used to generate a 2D density map for a 
                  specified group of atoms
 
 -slices          defines the number of slices along the axis
                  normal to the system used to calculate the density profile


 For more information as to the usage of each code, please use -help flag, or see the Tutorial on SuAVE
 Web page (https://www.biomatsite.net/suave-software) 

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