PROGRAM RECON

Version 5.5

Created by N. Sukumar and C. M. Breneman
© 2002, Rensselaer Polytechnic Institute, Troy, New York

INTRODUCTION:

RECON is an algorithm for the rapid reconstruction of molecular charge densities and charge density-based electronic properties of molecules, using atomic charge density fragments. The method is based on the quantum theory of atoms in molecules. A library of atomic charge density fragments has been built in a form that allows for the rapid retrieval of the fragments and molecular assembly. Associated with each atomic charge density fragment in the library is a surface file and a data file. The surface file is a numerical representation of the 3-dimensional shape of the atomic charge density. The data file contains information describing important topological features of the atomic charge density, which is used to orient the atomic charge density fragments into their proper molecular space orientations. The data file also contains atomic charge density-based descriptors encoding electronic and structural information relevant to the chemistry of intermolecular interactions.

User Documentation

This release includes the following files:

Recon5-5 (executable element)
README.html (this documentation)
Java class/jar files (for GUI)

and a DATA directory containing:

TAE.LIST (list of transferable atom equivalents)
bond (list of standard single bond lengths)
and atomic data files as listed in TAE.LIST

SETUP:

Setup varies with the platform. On UNIX and Linux platforms you need to define an environment variable recon4_root which points to the location of the RECON DATA directory referred to above. A trailing slash is expected in the pathname!

To run the Java GUI, java should be in your path.

On Windows platforms, edit the RECON.BAT file to give the locations of java, perl and RECON in your path. The location of the RECON DATA folder is specified in the REM line (edit this path, but DO NOT remove the REM line; it is NOT optional). Please try to give short, DOS-friendly pathnames, without spaces or special characters if you want to avoid problems!

Description of recon.inp Input file structure:

RECON5-5 is designed to read geometry inputs in several formats: .PDB, .MOL2, .COM, .DRA, .QCS or .SDF FILES or any combination of these formats. SMILES strings are also accepted as input.

The first line of recon.inp contains a string of integer Input Flags (free-format): nfile, icheck, iprint, istt, iovr

nfile is used for file type specification; default=automatic file type recognition (from file extension). Otherwise enter the number corresponding to the geometry file type:

0 : Default (Automatic fily type recognition)

Brookhaven PDB
Tripos MOL2
GAUSSIAN .COM FILE (Z-matrix format only)
SIMS .DRA FILE
QCS format
SDF file format
SMILES strings

<0 : Multi-molecule input file read from recon.inp

icheck is used to select the geometry routine; default=no geometry

QSPR Indices
QSPR Indices and Molecular Geometry

iprint is for individual molecule file printing; default=no (Suppress individual molecular file printing). This option can also be used to generate (or turn off) entirely silent RECON runs. (The default varies with the platform: for UNIX and Linux, silent run is the default, so that very large datasets can be run in the background, while for Windows, the default is to print each molecule name to the console).

istt is to suppress atom type visitation statistics; default=print

iovr is for connectivity override. For iovr>0, the connectivity information contained in the PDB, MOL2 or SIMS .DRA file is ignored and a distance criterion is used to determine the atomic neighbors. (This is also the procedure followed in case of GAUSSIAN .COM files - the distance cutoffs for bonding are taken from the "bond" file, with a 5% tolerance). iovr<0 is used to force RECON to take alphanumeric molecule names in SD files (the default for SD files is serial, numeric molecule names).

In subsequent lines, enter the names of the files from which the molecular geometries are to be read (one filename per line).

List of output files:

The following output files are produced by default:

recon.ff: Descriptor file
recon.stt: Cummulative statistics
recon.err: Error file

If any atom types are not found in the library and need to be generated, you will find this information in the error file. (Use the Atomtyper program to generate these new atom types). The .stt file reports the total number of times each atomtype was encountered in the database (input list). If the print option (iprint) is turned on, RECON produces output files, for each input molecule, with the following extensions:

.qmf (QSAR metafile)
.sum (Surface Properties summary for each atom)
.stt (Atomtype hit statistics)
.err (error file, in case of errors)

REFERENCES:

N. Sukumar and Curt M. Breneman, "QTAIM in Drug Discovery and Protein Modeling" in "The Quantum Theory of Atoms in Molecules: From Solid State to DNA and Drug Design" C.F. Matta & R.J. Boyd, Eds. (Wiley-VCH, 2007)
Richard F. W. Bader, "Atoms in Molecules: A Quantum Theory" Int. Ser. Mon. Chem. (Clarendon, Oxford, 1990)
C. M. Breneman and L. W. Weber, "Transferable Atom Equivalents. Assembling Accurate Electrostatic Potential Fields for Large Molecules from Ab Initio and PROAIMS Results on Model Systems" in "The Application of Charge Density Research to Chemistry and Drug Design" G. A. Jeffrey and J. F. Piniella, Eds. (Plenum, 1991)
C. M. Breneman and T. Thompson, "Modeling the Hydrogen Bond with Transferable Atom Equivalents" in "Modeling the Hydrogen Bond" D. Smith, Ed., ACS Symp. Ser., pp.152-174, Washington, D.C. (1993)
C. M. Breneman, T. R. Thompson, M. Rhem and M. Dung, "Electron Density Modeling of Large Systems Using the Transferable Atom Equivalent Method" Computers & Chemistry, 19(3), 161 (1995)
M. O. Rhem, "RECON: An Algorithm for Molecular Charge Density Reconstruction Using Atomic Charge Density Fragments" Ph.D. Dissertation, (Rensselaer Polytechnic Institute, Troy, 1996)
C. M. Breneman and J. A. Moore, "The Rotational Barrier of an Enaminonitrile. Charge and Energy Redistribution During Rotation About the C-N Bond" Structural Chemistry, 8(1), 13-19 (1997)
C. M. Breneman and M. Rhem, "A QSPR Analysis of HPLC Column Capacity Factors for a set of High-Energy Materials Using Electronic Van der Waals Surface Property Descriptors Computed by the Transferable Atom Equivalent Method" J. Comput. Chem., 18(2), 182-197 (1997)
J. A. Moore, P. G. Mehta and C. M. Breneman, Internal Rotation in Enaminonitriles. Investigation by Dynamic NMR Spectroscopy and Molecular Modeling" Structural Chemistry, 8(1), 21-37 (1997)
N. Sukumar, C. Breneman, K. Bennett, M. Embrechts, M. Sundling and L. Lockwood, "The TAE/RECON Method in Large Database Mining, QSAR and ADME: A Progress Report on the DDASSL Project", Pacifichem 2000 - fourth International Chemical Congress of Pacific Basin Societies, Honolulu, Hawaii, December 2000
C. B. Mazza, N. Sukumar, C. M. Breneman and S. Cramer, "Prediction of Protein Retention in Ion-Exchange Systems using Molecular Descriptors obtained from Crystal Structure" Anal. Chem., 73, 5457-5461 (2001)
M. Song, C. M. Breneman, J. Bi, N. Sukumar, K. P. Bennett, S. Cramer and N. Tugcu, "Prediction of Protein Retention Times in Anion-exchange Chromatography Systems using Support Vector Regression" J. Chem. Inf. Comp. Sci., 42, 1347-1357 (2002)
C. M. Breneman, K. P. Bennett, M. Embrechts, S. Cramer, M. Song, J. Bi and N. Sukumar, "Descriptor Generation, Selection and Model Building in Quantitative Structure-Property Analysis" in "Experimental Design for Combinatorial and High Throughput Materials Development, James N. Cawse, ed. (John Wiley, New York, 2002), pp.203-238
C. E. Whitehead, N. Sukumar, C. M. Breneman and M. D. Ryan, "Transferable Atom Equivalent Multi-Centered Multipole Expansion Method" J. Comp. Chem., 24, 512-529 (2003)
Curt M. Breneman , C. Matthew Sundling , N. Sukumar, Lingling Shen , William P. Katt and Mark J. Embrechts, "New developments in PEST shape/property hybrid descriptors" J. Comput. aided Mol. Design (In Press, 2003)
DDDASSL Project homepage
Fuzzy Bar Code representations of DNA-protein interactions

DDDASSL group PUBLICATIONS

USER SUPPORT:

Curt M. Breneman, Tel: (518) 276-2678
N. Sukumar, Tel: 276-2835
Department of Chemistry
Cogswell Labs # 319-A
Rensselaer Polytechnic Institute
Troy, New York 12180-3590
Fax: (518) 276-4045

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