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https://github.com/unixjunkie/fconv

optimal superposition of small molcules (mirror of http://pc1664.pharmazie.uni-marburg.de/drugscore/fconv_download.php)
https://github.com/unixjunkie/fconv

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optimal superposition of small molcules (mirror of http://pc1664.pharmazie.uni-marburg.de/drugscore/fconv_download.php)

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README 

        

#============================================================================

# fconv; format conversion, manipulation, and feature computaion

#        of molecular data

#

# Copyright (C) 2007, 2008, 2009, 2010, 2011, 2012 Gerd Neudert

#

# fconv is free software; you can redistribute it and/or modify it under the

# terms of the GNU General Public License as published by the Free Software

# Foundation; either version 3 of the License, or (at your option) any later

# version.

#

# This program is distributed in the hope that it will be useful, but WITHOUT

# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or

# FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for

# more details.

#

# You should have received a copy of the GNU General Public License along

# with this program; if not, see .

#----------------------------------------------------------------------------

#

# author:      Gerd Neudert

#              gneudert(place_at_here)web.de

# supervisor:  Prof. Dr. Gerhard Klebe

#              klebe(place_at_here)staff.uni-marburg.de

# Department of Pharmaceutical Chemistry, Philipps-University of Marburg

#

# We acknowledge the Cambridge Crystallographic Data Centre (CCDC) for

# the permission to use CSD-derived data for bond lengths and bond angles,

# as found in 'ELEMENT_DATA_new_GN.cpp'.

# 

# fconv is a program, intended for parsing and manipulating multiple aspects

# and properties of molecular data. Typical tasks are: Conversion and error

# correction of multiple formats such as PDB, MOL2, SDF, DLG and CIF,

# extracting ligands from PDB as MOL2, automatic or ligand-based cavity

# detection, rmsd calculation and clustering, substructure searches,

# functional alignment and structural superposition, building of crystal

# packings, adding hydrogens, calculation of various properties like the

# number of rotatable bonds, molecular weights or vdW-volumes. The atom type

# classification is based on a consistent assignment of internal atom types,

# which are more differentiated compared to e.g. Sybyl atom types. Apart

# from the predefined mapping of these types onto Sybyl types, the user is

# able to assign own mappings by providing modified template files.

#----------------------------------------------------------------------------

#

# The program is developed since 2007, but I decided to make it open source

# just in 2010 as part of the publication. I appreciate the idea behind free

# software, especially in the field of scientific research. Nevertheless,

# at the moment of publication the documentation inside the code demands

# significant improvement. Furthermore, this program is just a side product

# of my PhD thesis. While having a robust understanding of good programming

# practise nowadays, at the beginning of my PhD I was completely new to C++.

# Thus, there are many parts in the code showing an ugly style and not

# regarding preferable programming rules.

# It's also up to you, to help on improving fconv. I would appreciate, if

# people contact me and share their opinions and changes.

# I am currently using gcc 4.5.x on Ubuntu.

# The code compiles without any errors or warnings with options

# '-pedantic -Wall -O2' on Linux, Windows and MacOS.

# Use '-D_LINUX_OS' if compiling on a linux system.

# 

# Gerd Neudert, Marburg 27.09.2010

#----------------------------------------------------------------------------



 -->  Please see INSTALL.txt for informations on how to compile fconv



 -->  If you have downloaded precompiled binaries, there is only a single

      executable file and you can just start using it.



 -->  fconv should be completely self explaining (Just start it).

       Be sure to READ the HELP carefully (fconv -h) as there is the

       possibility to overwrite your files!



 -->  If you encounter any problems please contact me:



                'gneudert(place_at_here)web.de'



      Please also supply any files you have problems with.

      I would be also pleased for any suggestions on how to improve 'fconv'



 -->  Check for new versions on 'www.agklebe.de'



 -->  Next planned:

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

   -> reworking the complete commandline interface (to get more consistence

       and less confusion)

   -> reworking the complete programming interface

   -> conversion for different contour maps (e.g. acnt, cnt, grd, map)



Have fun,

27.09.2011, Gerd Neudert