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91 lines
2.0 KiB
Groff
91 lines
2.0 KiB
Groff
.\" Process this file with
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.\" groff -man -Tascii foo.1
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.\"
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.TH DPOCKET 1 "JANUARY 2009" Linux "User Manuals"
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.SH NAME
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dpocket \- calculate descriptors on protein pockets.
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.SH SYNOPSIS
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.B dpocket -f
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.I pdb-list
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.B [OPTIONS]
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.SH DESCRIPTION
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.B dpocket
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is a program written to calculate descriptors on protein pockets.
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It takes as basic input a file containing a list pf pdb file
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name/path, with an associated ligand represented by its resname
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in the pdb ( 3letter code). Both should be separated by a tabulation.
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.I PATH/1BXO.pdb GTD
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.I PATH/1BBC.pdb GTE
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.I ...
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Three file are created as output. One contains all pockets explicitely
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defined using one of the two methods available for this explicit definition.
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The two others contains all pockets as found by fpocket algorithm. One contain
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all pockets that match either the overlap or the distance criteria, and the
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other contains all pockets that does not match any of these criteria.
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See the documentation for more details on output, methods, and on descriprots
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currently availables.
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.SH OPTIONS SPECIFIC TO DPOCKET
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.IP -o
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.I dout_file
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.B [string]
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Prefix of the output files. Otherwise, output files are writen
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in the current directory, having the default prefix.
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.B DEFAULT: dpout
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.IP -e
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.B [no value needed]
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Use the first explicit interface definition (default): we define the
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explicit pocket as being all atoms contacted by alpha spheres situated
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at a distance of d A° from any ligand atom.
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.B DEFAULT: used
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.IP -E
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.B [no value needed]
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Use the second explicit interface definition: we define the
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explicit pocket as being all atoms situated
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at a distance of d A° from any ligand atom.
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.B DEFAULT: not used
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.IP -d
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.I dist
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.B [float]
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Distance used by the explicit pocket definition.
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.B DEFAULT: 4.0
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.SH OPTIONS SPECIFIC TO FPOCKET
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.B Use man fpocket.
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.SH BUGS
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.SH AUTHOR
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.BR Developpers:
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Peter Schmidtke <pschmidtke@mmb.pcb.ub.es>
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Vincent Le Guilloux <vincent.le-guilloux@univ-orleans.fr>
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.BR Supervisor:
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Pierre Tuffery
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.SH "SEE ALSO"
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.BR fpocket (1),
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.BR tpocket (1),
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