[med-svn] [plip] 03/04: d/plipcmd.1: update man page d/plip.manpages: install d/plipcmd.1 d/copyright: add copyright information for PDB files

[Alex Mestiashvili]

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malex-guest pushed a commit to branch master
in repository plip.

commit 03e8f40f7bc73d0af9f928d6cb4ac004cb312e48
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date:   Fri Jun 5 17:13:02 2015 +0200

    d/plipcmd.1: update man page
    d/plip.manpages: install d/plipcmd.1
    d/copyright: add copyright information for PDB files
---
 debian/copyright     | 48 ++++++++++++++++++++++++++++++++++++++++++++++++
 debian/plip.manpages |  1 +
 debian/plipcmd.1     | 21 ++++++++++++---------
 3 files changed, 61 insertions(+), 9 deletions(-)

diff --git a/debian/copyright b/debian/copyright
index 327e47d..252527a 100644
--- a/debian/copyright
+++ b/debian/copyright
@@ -6,6 +6,54 @@ Files: *
 Copyright: 2015 Sebastian Salentin <sebastian.salentin at biotec.tu-dresden.de>
 License: Apache-2.0
 
+Files: plip/test/*.pdb
+Copyright: Data files contained in the PDB archive (ftp://ftp.wwpdb.org) are
+ free of all copyright restrictions and made fully and freely available for
+ both non-commercial and commercial use. Users of the data should attribute
+ the original authors of that structural data. By using the materials
+ available in the PDB archive, the user agrees to abide by the conditions
+ described in the PDB Advisory Notice.
+License:
+ ADVISORY NOTICE FOR USE OF THE PDB ARCHIVE
+ .
+ By using the materials available in this archive, the user agrees to abide
+ by the following conditions:
+ .
+ * The archival data files in the PDB archive are made freely available
+ to all users. Data files within the archive may be redistributed in original
+ form without restriction. Redistribution of modified data files using the same
+ file name as is on the FTP server is prohibited. The rules for file names are
+ detailed at http://www.wwpdb.org/wwpdb_charter.html.
+ .
+ * Data files containing PDB content may incorporate the PDB 4-letter entry
+ name (e.g. 1ABC) in standard PDB records only if they are exactly the same
+ as what is residing in the PDB archive. This does not prevent databases
+ from including PDB entry_id's as cross-references where it is clear that
+ they refer to the PDB archive. PDB records refer to the standard PDB format.
+ The distribution of modified PDB data including the records HEADER, CAVEAT,
+ REVDAT, SPRSDE, DBREF, SEQADV, and MODRES in PDB format and their mmCIF and
+ XML equivalents is not allowed.
+ .
+ * The user assumes all responsibility for insuring that intellectual property
+ claims associated with any data set deposited in the PDB archive are honored.
+ It should be understood that the PDB data files do not contain any information
+ on intellectual property claims with the exception in some cases of a reference
+ for a patent involving the structure.
+ .
+ * Any opinion, findings, and conclusions expressed in the PDB archive by the
+ authors/contributors do not necessarily reflect the views of the wwPDB.
+ .
+ * The data in the PDB archive are provided on an "as is" basis.  The wwPDB
+ nor its comprising institutions cannot be held liable to any party for direct,
+ indirect, special, incidental, or consequential damages, including lost
+ profits, arising from the use of PDB materials.
+ .
+ * Resources on this site are provided without warranty of any kind, either
+ expressed or implied. This includes but is not limited to merchantability or
+ fitness for a particular purpose. The institutions managing this site make
+ no representation that these resources will not infringe any patent or other
+ proprietary right.
+
 Files: debian/*
 Copyright: 2013 Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
 License: Apache-2.0
diff --git a/debian/plip.manpages b/debian/plip.manpages
new file mode 100644
index 0000000..ab32cc9
--- /dev/null
+++ b/debian/plip.manpages
@@ -0,0 +1 @@
+debian/plipcmd.1
diff --git a/debian/plipcmd.1 b/debian/plipcmd.1
index 9dde918..5263073 100644
--- a/debian/plipcmd.1
+++ b/debian/plipcmd.1
@@ -2,15 +2,7 @@
 .SH NAME
 plipcmd - tool to analyze and visualize protein-ligand interactions in PDB files.
 .SH SYNOPSIS
-plipcmd [\-h] (\fB\-f\fR INPUT | \fB\-i\fR PDBID) [\-o OUTPATH] [\-v] [\-p] [\-x] [\-y]
-.IP
-[\-\-maxthreads MAXTHREADS]
-.SH DESCRIPTION
-.PP
-Protein\-Ligand Interaction Profiler (PLIP) v1.1.0 is a command\-line based tool
-to analyze interactions in a protein\-ligand complex. If you are using PLIP in
-your work, please cite: Salentin,S. et al. PLIP: fully automated proteinligand interaction profiler. Nucl. Acids Res. first published online April 14,
-2015 doi:10.1093/nar/gkv315
+plipcmd [\-h] (\fB\-f\fR INPUT | \fB\-i\fR PDBID) [\-o OUTPATH] [\-v] [\-p] [\-x] [\-y] [\-\-maxthreads MAXTHREADS]
 .SH OPTIONS
 .TP
 \fB\-h\fR, \fB\-\-help\fR
@@ -37,3 +29,14 @@ Additional PyMOL session files
 \fB\-\-maxthreads\fR MAXTHREADS
 Set maximum number of main threads (number of binding
 sites processed simultaneously)
+.SH EXIT CODES
+.TP
+\fB1\fR Unspecified Error 
+.TP
+\fB2\fR Empty PDB file as input 
+.TP
+\fB3\fR Invalid PDB ID 
+.TP
+\fB4\fR PDB file can't be read by OpenBabel (due to invalid input files) 
+.TP
+\fB5\fR PDB ID is valid, but wwPDB offers no file in PDB format for download.

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