Update man page

install html page in Windows/CCP4 Added changelog file

Update man page
install html page in Windows/CCP4 Added changelog file
72b541e2 · Maarten L. Hekkelman · 4fdaafea · 72b541e2 · 72b541e2 · 72b541e2
Commit 72b541e2 authored Aug 31, 2021 by Maarten L. Hekkelman
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CMakeLists.txt
+7 -2

README.md
+12 -4

changelog
+5 -0

doc/mkdssp.1
+1 -1

doc/mkdssp.html
+119 -0

doc/mkdssp.pdf
+0 -0

No files found.
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -172,8 +172,13 @@ install(TARGETS ${PROJECT_NAME}
 # manual
-install(FILES doc/mkdssp.1
+if(UNIX)
-	DESTINATION ${CMAKE_INSTALL_DATADIR}/man/man1)
+	install(FILES doc/mkdssp.1
+		DESTINATION ${CMAKE_INSTALL_DATADIR}/man/man1)
+elseif(MSVC AND EXISTS "${CCP4}/html")
+	install(FILES doc/mkdssp.html
+		DESTINATION ${CCP4}/html)
+endif()
 # test

--- a/README.md
+++ b/README.md
@@ -32,12 +32,20 @@ Make sure you install [libcif++](https://github.com/PDB-REDO/libcifpp) first bef
 After that, building should be as easy as typing:
 ```
-./configure
+git clone https://github.com/PBD-REDO/dssp.git
-make
+cd dssp
-sudo make install
+mkdir build
+cd build
+cmake ..
+cmake --build . --config Release
+ctest -C Release
+cmake --install .
 ```
+This will install the `mkdssp` program in `$HOME/.local/bin`. If you want to
+install elsewhere, specify the prefix with the [CMAKE_INSTALL_PREFIX](https://cmake.org/cmake/help/v3.21/variable/CMAKE_INSTALL_PREFIX.html) variable.
 Usage
 -----
-See `man mkdssp` for more info.
+See [manual page](doc/mkdssp.pdf) for more info.
--- a/changelog
+++ b/changelog
+Version 4.0.0
+- Write the secondary structure information as an annotation to an mmCIF file
+  (old format is still available as an option)
+- Added the recognition of Poly-Proline helices
+- Switch from GNU configure to cmake as the build environment
--- a/doc/mkdssp.1
+++ b/doc/mkdssp.1
-.TH mkdssp 1 "2020-11-23" "version 1.0.0" "User Commands"
+.TH mkdssp 1 "2021-08-31" "version 4.0.0" "User Commands"
 .if n .ad l
 .nh
 .SH NAME

--- a/doc/mkdssp.html
+++ b/doc/mkdssp.html
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+<HTML><HEAD><TITLE>Man page of mkdssp</TITLE>
+</HEAD><BODY>
+<H1>mkdssp</H1>
+Section: User Commands (1)<BR>Updated: 2021-08-31<BR><A HREF="#index">Index</A>
+<A HREF="/cgi-bin/man/man2html">Return to Main Contents</A><HR>
+<A NAME="lbAB">&nbsp;</A>
+<H2>NAME</H2>
+mkdssp - Assign secondary structure to proteins
+<A NAME="lbAC">&nbsp;</A>
+<H2>SYNOPSIS</H2>
+mkdssp [OPTION] input [output]
+<A NAME="lbAD">&nbsp;</A>
+<H2>DESCRIPTION</H2>
+The DSSP program was designed by Wolfgang Kabsch and Chris Sander to
+standardize secondary structure assignment. DSSP is a database of
+secondary structure assignments (and much more) for all protein entries
+in the Protein Data Bank (PDB). mkdssp is the program that calculates
+DSSP entries from PDB entries. mkdssp does <B>not</B> predict secondary structure.
+<P>
+The original DSSP program wrote output in a fixed format, this version
+by default writes annotated mmCIF files, storing the secondary structure
+information in the _struct_conf category.
+<P>
+Since version 4.0 the mkdssp program also assigns PPII helices.
+<A NAME="lbAE">&nbsp;</A>
+<H2>OPTIONS</H2>
+The input file can be either mmCIF or PDB format and the file may be
+gzip or bzip2 compressed. Note that input files must be formatted correctly.
+E.g. PDB files must have a CRYST1 record. More info:
+<A HREF="https://www.wwpdb.org/documentation/file-format-content/format33/sect8.html#CRYST1">https://www.wwpdb.org/documentation/file-format-content/format33/sect8.html#CRYST1</A>
+<P>
+The output is optional, if omitted the output is written to <I>stdout</I>. If
+the name of the output file ends with either <I>.gz</I> or <I>.bz2</I> the
+output is compressed accordingly.
+<DL COMPACT>
+<DT><B>--output-format</B>=[dssp|mmcif]<DD>
+If an output file is specified, the extension of the filename is used to
+choose to output format, but if it is unclear, mmcif is the default. Use
+this option to force output in either the old fixed column DSSP format or
+the new annotated mmCIF format.
+<DT><B>--min-pp-stretch</B><DD>
+This option can be used to define the minimal number of residues with PHI/PSI
+angles within the range required to assing a PP helix.
+<DT><B>--write-other</B><DD>
+By default the new format does not write the structure information for OTHER.
+Use this flag to change that.
+</DL>
+<A NAME="lbAF">&nbsp;</A>
+<H2>DETAILS</H2>
+The DSSP algorithm assings secondary structure based on the energy calculated
+for H-bonds.
+<BR>
+<B>Table&nbsp;1.&nbsp;Secondary&nbsp;Structures&nbsp;recognized</B>
+<TABLE BORDER>
+<TR VALIGN=top><TD ALIGN=center><B>DSSP Code</B></TD><TD ALIGN=center><B>mmCIF Code</B></TD><TD ALIGN=center><B>Description</B><BR></TD></TR>
+<TR VALIGN=top><TD>H</TD><TD>HELX_RH_AL_P</TD><TD>Alphahelix<BR></TD></TR>
+<TR VALIGN=top><TD>B</TD><TD>STRN</TD><TD>Betabridge<BR></TD></TR>
+<TR VALIGN=top><TD>E</TD><TD>STRN</TD><TD>Strand<BR></TD></TR>
+<TR VALIGN=top><TD>G</TD><TD>HELX_RH_3T_P</TD><TD>Helix_3<BR></TD></TR>
+<TR VALIGN=top><TD>I</TD><TD>HELX_RH_PI_P</TD><TD>Helix_5<BR></TD></TR>
+<TR VALIGN=top><TD>P</TD><TD>HELX_LH_PP_P</TD><TD>Helix_PPII<BR></TD></TR>
+<TR VALIGN=top><TD>T</TD><TD>TURN_TY1_P</TD><TD>Turn<BR></TD></TR>
+<TR VALIGN=top><TD>S</TD><TD>BEND</TD><TD>Bend<BR></TD></TR>
+<TR VALIGN=top><TD>
+' ' (space)
+</TD><TD>OTHER</TD><TD>Loop<BR></TD></TR>
+</TABLE>
+<A NAME="lbAG">&nbsp;</A>
+<H2>BUGS</H2>
+The mmCIF format currently lacks a lot of information that was available
+in the old format like information about the bridge pairs or the span
+of the various helices recognized. Also the accessibility information
+is left out.
+<P>
+If you think this information should be part of the output, please contact
+the author.
+<A NAME="lbAH">&nbsp;</A>
+<H2>AUTHOR</H2>
+Written by Maarten L. Hekkelman &lt;<A HREF="mailto:maarten@hekkelman.com">maarten@hekkelman.com</A>&gt;
+<A NAME="lbAI">&nbsp;</A>
+<H2>REPORTING BUGS</H2>
+Report bugs at <A HREF="https://github.com/PDB-REDO/dssp/issues">https://github.com/PDB-REDO/dssp/issues</A>
+<P>
+<HR>
+<A NAME="index">&nbsp;</A><H2>Index</H2>
+<DL>
+<DT><A HREF="#lbAB">NAME</A><DD>
+<DT><A HREF="#lbAC">SYNOPSIS</A><DD>
+<DT><A HREF="#lbAD">DESCRIPTION</A><DD>
+<DT><A HREF="#lbAE">OPTIONS</A><DD>
+<DT><A HREF="#lbAF">DETAILS</A><DD>
+<DT><A HREF="#lbAG">BUGS</A><DD>
+<DT><A HREF="#lbAH">AUTHOR</A><DD>
+<DT><A HREF="#lbAI">REPORTING BUGS</A><DD>
+</DL>
+<HR>
+This document was created by
+<A HREF="/cgi-bin/man/man2html">man2html</A>,
+using the manual pages.<BR>
+Time: 13:29:37 GMT, August 31, 2021
+</BODY>
+</HTML>
--- a/doc/mkdssp.pdf
+++ b/doc/mkdssp.pdf