From 9b4390f452c62baa24d90ab165d478be3f9658f5 Mon Sep 17 00:00:00 2001 From: arcan1s Date: Mon, 5 Aug 2013 06:42:23 +0400 Subject: [PATCH] Release mm_trj2pdb-1.0.1 --- mm_trj/src/read_gmx.c | 2 +- mm_trj2pdb/AUTHORS | 3 + mm_trj2pdb/CMakeLists.txt | 32 + mm_trj2pdb/COPYING | 341 ++++++ mm_trj2pdb/INSTALL | 14 + mm_trj2pdb/README | 13 + mm_trj2pdb/logo.png | Bin 0 -> 3478 bytes mm_trj2pdb/mm_trj2pdb.cmake | 32 + mm_trj2pdb/mm_trj2pdb.doxygen | 1889 +++++++++++++++++++++++++++++++++ mm_trj2pdb/src/CMakeLists.txt | 29 + mm_trj2pdb/src/Makefile | 20 + mm_trj2pdb/src/add_main.c | 93 ++ mm_trj2pdb/src/add_main.h | 22 + mm_trj2pdb/src/coords.c | 354 ++++++ mm_trj2pdb/src/coords.h | 16 + mm_trj2pdb/src/main.c | 255 +++++ mm_trj2pdb/src/messages.c | 119 +++ mm_trj2pdb/src/messages.h | 14 + mm_trj2pdb/src/print_struct.c | 69 ++ mm_trj2pdb/src/print_struct.h | 15 + 20 files changed, 3331 insertions(+), 1 deletion(-) create mode 100644 mm_trj2pdb/AUTHORS create mode 100644 mm_trj2pdb/CMakeLists.txt create mode 100644 mm_trj2pdb/COPYING create mode 100644 mm_trj2pdb/INSTALL create mode 100644 mm_trj2pdb/README create mode 100755 mm_trj2pdb/logo.png create mode 100644 mm_trj2pdb/mm_trj2pdb.cmake create mode 100644 mm_trj2pdb/mm_trj2pdb.doxygen create mode 100644 mm_trj2pdb/src/CMakeLists.txt create mode 100644 mm_trj2pdb/src/Makefile create mode 100644 mm_trj2pdb/src/add_main.c create mode 100644 mm_trj2pdb/src/add_main.h create mode 100644 mm_trj2pdb/src/coords.c create mode 100644 mm_trj2pdb/src/coords.h create mode 100644 mm_trj2pdb/src/main.c create mode 100644 mm_trj2pdb/src/messages.c create mode 100644 mm_trj2pdb/src/messages.h create mode 100644 mm_trj2pdb/src/print_struct.c create mode 100644 mm_trj2pdb/src/print_struct.h diff --git a/mm_trj/src/read_gmx.c b/mm_trj/src/read_gmx.c index 260c5fa..fa47af6 100644 --- a/mm_trj/src/read_gmx.c +++ b/mm_trj/src/read_gmx.c @@ -15,7 +15,7 @@ int translate_coords (const float coords, const float cell, float *trans) /** * @brief funtion that translates coordinate * @code - * + * translate_coords (coords[3*i+j], cell[j], trans); * @endcode * * @param coords coordinate diff --git a/mm_trj2pdb/AUTHORS b/mm_trj2pdb/AUTHORS new file mode 100644 index 0000000..2c0d60a --- /dev/null +++ b/mm_trj2pdb/AUTHORS @@ -0,0 +1,3 @@ +Current developers: + +Evgeniy Alekseev aka arcanis diff --git a/mm_trj2pdb/CMakeLists.txt b/mm_trj2pdb/CMakeLists.txt new file mode 100644 index 0000000..bf3402e --- /dev/null +++ b/mm_trj2pdb/CMakeLists.txt @@ -0,0 +1,32 @@ +cmake_minimum_required (VERSION 2.8) + +cmake_policy(SET CMP0003 OLD) +cmake_policy(SET CMP0011 NEW) +cmake_policy(SET CMP0015 NEW) + +# set project name +set (PROJECT mm_trj2pdb) +# set additional cmake file +include (${PROJECT}.cmake) + + +# additional options +OPTION (WITH_DEBUG_MODE "Build with debug mode" OFF) +OPTION (ADD_INCLUDE "Add include files" OFF) + +# set libraries +set (LIBRARIES) + foreach (LIBRARY ${LIBRARIES}) + find_library ("${LIBRARY}_FOUND" ${LIBRARY}) + message (STATUS "Check the ${LIBRARY} is installed: " ${${LIBRARY}_FOUND}) + if ("${${LIBRARY}_FOUND}" STREQUAL "${LIBRARY}_FOUND-NOTFOUND") + message (STATUS "Adding library sources") + add_subdirectory (../${LIBRARY} lib/${LIBRARY}) + endif () + endforeach () + +# additional targets +set (TARGETS "") +set (HEADERS "") + +add_subdirectory (${${PROJECT}_SOURCE_DIR}) \ No newline at end of file diff --git a/mm_trj2pdb/COPYING b/mm_trj2pdb/COPYING new file mode 100644 index 0000000..eb47f5d --- /dev/null +++ b/mm_trj2pdb/COPYING @@ -0,0 +1,341 @@ + GNU GENERAL PUBLIC LICENSE + Version 2, June 1991 + + Copyright (C) 1989, 1991 Free Software Foundation, Inc. + 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA + + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The licenses for most software are designed to take away your +freedom to share and change it. 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It is safest +to attach them to the start of each source file to most effectively +convey the exclusion of warranty; and each file should have at least +the "copyright" line and a pointer to where the full notice is found. + + + Copyright (C) 19yy + + This program 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 2 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, write to the Free Software + Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA + + +Also add information on how to contact you by electronic and paper mail. + +If the program is interactive, make it output a short notice like this +when it starts in an interactive mode: + + Gnomovision version 69, Copyright (C) 19yy name of author + Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'. + This is free software, and you are welcome to redistribute it + under certain conditions; type `show c' for details. + +The hypothetical commands `show w' and `show c' should show the appropriate +parts of the General Public License. Of course, the commands you use may +be called something other than `show w' and `show c'; they could even be +mouse-clicks or menu items--whatever suits your program. + +You should also get your employer (if you work as a programmer) or your +school, if any, to sign a "copyright disclaimer" for the program, if +necessary. Here is a sample; alter the names: + + Yoyodyne, Inc., hereby disclaims all copyright interest in the program + `Gnomovision' (which makes passes at compilers) written by James Hacker. + + , 1 April 1989 + Ty Coon, President of Vice + +This General Public License does not permit incorporating your program into +proprietary programs. If your program is a subroutine library, you may +consider it more useful to permit linking proprietary applications with the +library. If this is what you want to do, use the GNU Library General +Public License instead of this License. diff --git a/mm_trj2pdb/INSTALL b/mm_trj2pdb/INSTALL new file mode 100644 index 0000000..cbd6143 --- /dev/null +++ b/mm_trj2pdb/INSTALL @@ -0,0 +1,14 @@ +CMakeFlags: + -DCMAKE_INSTALL_PREFIX= - install prefix (default is '/usr/local') + -DADD_INCLUDE=1 - install include files (default is disable) + -DWITH_DEBUG_MODE=1 - compile with flag '-g' (default is disable) + +Install for Linux: + mkdir build && cd build + cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=Release ../ + make + make install +Install for Windows: + create project file using 'cmake' + compile project +You may also download compiled executable file for Win_x86. diff --git a/mm_trj2pdb/README b/mm_trj2pdb/README new file mode 100644 index 0000000..ddc7504 --- /dev/null +++ b/mm_trj2pdb/README @@ -0,0 +1,13 @@ +mm_trj2pdb - program that creates PDB file from trajetory snapshot +Version: 1.0.1 +License: GPL + +Usage: + mm_trj2pdb -i FILENAME -o FILEMANE [ -l LOGFILE ] [ -q ] [ -h ] + +Parametrs: + -i - input file name + -o - output file name + -l - log enable + -q - quiet enable + -h - show this help and exit diff --git a/mm_trj2pdb/logo.png b/mm_trj2pdb/logo.png new file mode 100755 index 0000000000000000000000000000000000000000..41adc0cb46ab8b2f327c0851eae786631b4ba85a GIT binary patch literal 3478 zcmeAS@N?(olHy`uVBq!ia0y~yU`PRB4mJh`hJr^^Ll_tsSc;uILpV4%IBGajIv5xj zI14-?iy0XB4ude`@%$Aj3=F&$o-U3d6?5LstuC4JbnbEc{pD#wN^GZ&E?D%a^@iAb z1rDZ@DMCuDE=Q+!?~00bjM{ZgdG+yEH}!Vy*4sU8+l^g$Z{J<4(#$=axG=6sG3}m@ zkOIewoSjpwqjoE4>M)*ZJ!7-~Z*q@%OH0bS{1a!M@2^~Ue{%l4=e6(jmv~;jED;=M z_u|&3P5b;_Gi;b6_Q2$@x3}^6!kyRZ&pw{{ev6og^r6<;Up9>=W-EQlUB1CaUCNlWXP^;*rPyn_AD*G{-yd-~bM#nBB>r#F3?du__5wu;%cKzBV9AC3>k?ERMJAUvV;9Q^EUmOsXCDmlOpQFvG ze*4dB(bBirR;Nx~`6^|3iX)d)QEp^pykI70WLWWU3tqNtmy|OfE?x3b-{Qz6Wu%~- z+~aij*P=!Jw~vSV&-%h>kdP5}EtSuMIq1TKbplsowThMoe_hU-*&Z0Hx$uIl-_`kM 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diff --git a/mm_trj2pdb/mm_trj2pdb.cmake b/mm_trj2pdb/mm_trj2pdb.cmake new file mode 100644 index 0000000..2b4603e --- /dev/null +++ b/mm_trj2pdb/mm_trj2pdb.cmake @@ -0,0 +1,32 @@ +# set directories +set (${PROJECT}_BINARY_DIR bin) +set (${PROJECT}_SOURCE_DIR src) +set (${PROJECT}_INCLUDE_DIR include) +set (${PROJECT}_LIB_DIR lib) + +# include_path +include_directories (${${PROJECT}_INCLUDE_DIR}/${PROJECT} + ${${PROJECT}_SOURCE_DIR}) +# library path +link_directories (${${PROJECT}_LIB_DIR}) +# executable path +set (EXECUTABLE_OUTPUT_PATH ${${PROJECT}_BINARY_DIR}) + +# verbose +set (CMAKE_VERBOSE_MAKEFILE ON) + +# flags +if ( WITH_DEBUG_MODE ) + add_definitions ( -DDEBUG_MODE=1 ) +endif () +if ( CMAKE_COMPILER_IS_GNUCXX ) + set (ADD_CXX_FLAGS "-Wall") + set (CMAKE_CXX_FLAGS "-O0 ${ADD_CXX_FLAGS}") + set (CMAKE_CXX_FLAGS_DEBUG "-g -O0") + set (CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG") +elseif ( MSVC ) + set (ADD_CXX_FLAGS "/W4") + set (CMAKE_CXX_FLAGS "${ADD_CXX_FLAGS}") +else () + message ("Unknown compiler") +endif () \ No newline at end of file diff --git a/mm_trj2pdb/mm_trj2pdb.doxygen b/mm_trj2pdb/mm_trj2pdb.doxygen new file mode 100644 index 0000000..4c95052 --- /dev/null +++ b/mm_trj2pdb/mm_trj2pdb.doxygen @@ -0,0 +1,1889 @@ +# Doxyfile 1.8.4 + +# This file describes the settings to be used by the documentation system +# doxygen (www.doxygen.org) for a project +# +# All text after a hash (#) is considered a comment and will be ignored +# The format is: +# TAG = value [value, ...] +# For lists items can also be appended using: +# TAG += value [value, ...] +# Values that contain spaces should be placed between quotes (" ") + +#--------------------------------------------------------------------------- +# Project related configuration options +#--------------------------------------------------------------------------- + +# This tag specifies the encoding used for all characters in the config file +# that follow. The default is UTF-8 which is also the encoding used for all +# text before the first occurrence of this tag. Doxygen uses libiconv (or the +# iconv built into libc) for the transcoding. See +# http://www.gnu.org/software/libiconv for the list of possible encodings. + +DOXYFILE_ENCODING = UTF-8 + +# The PROJECT_NAME tag is a single word (or sequence of words) that should +# identify the project. Note that if you do not use Doxywizard you need +# to put quotes around the project name if it contains spaces. + +PROJECT_NAME = mm_trj2pdb + +# The PROJECT_NUMBER tag can be used to enter a project or revision number. +# This could be handy for archiving the generated documentation or +# if some version control system is used. + +PROJECT_NUMBER = V.1.0.1 + +# Using the PROJECT_BRIEF tag one can provide an optional one line description +# for a project that appears at the top of each page and should give viewer +# a quick idea about the purpose of the project. Keep the description short. + +PROJECT_BRIEF = "Program that creates PDB file from trajectory snapshot" + +# With the PROJECT_LOGO tag one can specify an logo or icon that is +# included in the documentation. The maximum height of the logo should not +# exceed 55 pixels and the maximum width should not exceed 200 pixels. +# Doxygen will copy the logo to the output directory. + +PROJECT_LOGO = ./logo.png + +# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute) +# base path where the generated documentation will be put. +# If a relative path is entered, it will be relative to the location +# where doxygen was started. If left blank the current directory will be used. + +OUTPUT_DIRECTORY = ./docs + +# If the CREATE_SUBDIRS tag is set to YES, then doxygen will create +# 4096 sub-directories (in 2 levels) under the output directory of each output +# format and will distribute the generated files over these directories. +# Enabling this option can be useful when feeding doxygen a huge amount of +# source files, where putting all generated files in the same directory would +# otherwise cause performance problems for the file system. + +CREATE_SUBDIRS = NO + +# The OUTPUT_LANGUAGE tag is used to specify the language in which all +# documentation generated by doxygen is written. Doxygen will use this +# information to generate all constant output in the proper language. +# The default language is English, other supported languages are: +# Afrikaans, Arabic, Brazilian, Catalan, Chinese, Chinese-Traditional, +# Croatian, Czech, Danish, Dutch, Esperanto, Farsi, Finnish, French, German, +# Greek, Hungarian, Italian, Japanese, Japanese-en (Japanese with English +# messages), Korean, Korean-en, Latvian, Lithuanian, Norwegian, Macedonian, +# Persian, Polish, Portuguese, Romanian, Russian, Serbian, Serbian-Cyrillic, +# Slovak, Slovene, Spanish, Swedish, Ukrainian, and Vietnamese. + +OUTPUT_LANGUAGE = English + +# If the BRIEF_MEMBER_DESC tag is set to YES (the default) Doxygen will +# include brief member descriptions after the members that are listed in +# the file and class documentation (similar to JavaDoc). +# Set to NO to disable this. + +BRIEF_MEMBER_DESC = YES + +# If the REPEAT_BRIEF tag is set to YES (the default) Doxygen will prepend +# the brief description of a member or function before the detailed description. +# Note: if both HIDE_UNDOC_MEMBERS and BRIEF_MEMBER_DESC are set to NO, the +# brief descriptions will be completely suppressed. + +REPEAT_BRIEF = YES + +# This tag implements a quasi-intelligent brief description abbreviator +# that is used to form the text in various listings. Each string +# in this list, if found as the leading text of the brief description, will be +# stripped from the text and the result after processing the whole list, is +# used as the annotated text. Otherwise, the brief description is used as-is. +# If left blank, the following values are used ("$name" is automatically +# replaced with the name of the entity): "The $name class" "The $name widget" +# "The $name file" "is" "provides" "specifies" "contains" +# "represents" "a" "an" "the" + +ABBREVIATE_BRIEF = "The $name class" \ + "The $name widget" \ + "The $name file" \ + is \ + provides \ + specifies \ + contains \ + represents \ + a \ + an \ + the + +# If the ALWAYS_DETAILED_SEC and REPEAT_BRIEF tags are both set to YES then +# Doxygen will generate a detailed section even if there is only a brief +# description. + +ALWAYS_DETAILED_SEC = NO + +# If the INLINE_INHERITED_MEMB tag is set to YES, doxygen will show all +# inherited members of a class in the documentation of that class as if those +# members were ordinary class members. Constructors, destructors and assignment +# operators of the base classes will not be shown. + +INLINE_INHERITED_MEMB = NO + +# If the FULL_PATH_NAMES tag is set to YES then Doxygen will prepend the full +# path before files name in the file list and in the header files. If set +# to NO the shortest path that makes the file name unique will be used. + +FULL_PATH_NAMES = YES + +# If the FULL_PATH_NAMES tag is set to YES then the STRIP_FROM_PATH tag +# can be used to strip a user-defined part of the path. Stripping is +# only done if one of the specified strings matches the left-hand part of +# the path. The tag can be used to show relative paths in the file list. +# If left blank the directory from which doxygen is run is used as the +# path to strip. Note that you specify absolute paths here, but also +# relative paths, which will be relative from the directory where doxygen is +# started. + +STRIP_FROM_PATH = + +# The STRIP_FROM_INC_PATH tag can be used to strip a user-defined part of +# the path mentioned in the documentation of a class, which tells +# the reader which header file to include in order to use a class. +# If left blank only the name of the header file containing the class +# definition is used. Otherwise one should specify the include paths that +# are normally passed to the compiler using the -I flag. + +STRIP_FROM_INC_PATH = + +# If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter +# (but less readable) file names. This can be useful if your file system +# doesn't support long names like on DOS, Mac, or CD-ROM. + +SHORT_NAMES = NO + +# If the JAVADOC_AUTOBRIEF tag is set to YES then Doxygen +# will interpret the first line (until the first dot) of a JavaDoc-style +# comment as the brief description. If set to NO, the JavaDoc +# comments will behave just like regular Qt-style comments +# (thus requiring an explicit @brief command for a brief description.) + +JAVADOC_AUTOBRIEF = NO + +# If the QT_AUTOBRIEF tag is set to YES then Doxygen will +# interpret the first line (until the first dot) of a Qt-style +# comment as the brief description. If set to NO, the comments +# will behave just like regular Qt-style comments (thus requiring +# an explicit \brief command for a brief description.) + +QT_AUTOBRIEF = NO + +# The MULTILINE_CPP_IS_BRIEF tag can be set to YES to make Doxygen +# treat a multi-line C++ special comment block (i.e. a block of //! or /// +# comments) as a brief description. This used to be the default behaviour. +# The new default is to treat a multi-line C++ comment block as a detailed +# description. Set this tag to YES if you prefer the old behaviour instead. + +MULTILINE_CPP_IS_BRIEF = NO + +# If the INHERIT_DOCS tag is set to YES (the default) then an undocumented +# member inherits the documentation from any documented member that it +# re-implements. + +INHERIT_DOCS = YES + +# If the SEPARATE_MEMBER_PAGES tag is set to YES, then doxygen will produce +# a new page for each member. If set to NO, the documentation of a member will +# be part of the file/class/namespace that contains it. + +SEPARATE_MEMBER_PAGES = NO + +# The TAB_SIZE tag can be used to set the number of spaces in a tab. +# Doxygen uses this value to replace tabs by spaces in code fragments. + +TAB_SIZE = 4 + +# This tag can be used to specify a number of aliases that acts +# as commands in the documentation. An alias has the form "name=value". +# For example adding "sideeffect=\par Side Effects:\n" will allow you to +# put the command \sideeffect (or @sideeffect) in the documentation, which +# will result in a user-defined paragraph with heading "Side Effects:". +# You can put \n's in the value part of an alias to insert newlines. + +ALIASES = + +# This tag can be used to specify a number of word-keyword mappings (TCL only). +# A mapping has the form "name=value". For example adding +# "class=itcl::class" will allow you to use the command class in the +# itcl::class meaning. + +TCL_SUBST = + +# Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C +# sources only. Doxygen will then generate output that is more tailored for C. +# For instance, some of the names that are used will be different. The list +# of all members will be omitted, etc. + +OPTIMIZE_OUTPUT_FOR_C = YES + +# Set the OPTIMIZE_OUTPUT_JAVA tag to YES if your project consists of Java +# sources only. Doxygen will then generate output that is more tailored for +# Java. For instance, namespaces will be presented as packages, qualified +# scopes will look different, etc. + +OPTIMIZE_OUTPUT_JAVA = NO + +# Set the OPTIMIZE_FOR_FORTRAN tag to YES if your project consists of Fortran +# sources only. Doxygen will then generate output that is more tailored for +# Fortran. + +OPTIMIZE_FOR_FORTRAN = NO + +# Set the OPTIMIZE_OUTPUT_VHDL tag to YES if your project consists of VHDL +# sources. Doxygen will then generate output that is tailored for +# VHDL. + +OPTIMIZE_OUTPUT_VHDL = NO + +# Doxygen selects the parser to use depending on the extension of the files it +# parses. With this tag you can assign which parser to use for a given +# extension. Doxygen has a built-in mapping, but you can override or extend it +# using this tag. The format is ext=language, where ext is a file extension, +# and language is one of the parsers supported by doxygen: IDL, Java, +# Javascript, CSharp, C, C++, D, PHP, Objective-C, Python, Fortran, VHDL, C, +# C++. For instance to make doxygen treat .inc files as Fortran files (default +# is PHP), and .f files as C (default is Fortran), use: inc=Fortran f=C. Note +# that for custom extensions you also need to set FILE_PATTERNS otherwise the +# files are not read by doxygen. + +EXTENSION_MAPPING = + +# If MARKDOWN_SUPPORT is enabled (the default) then doxygen pre-processes all +# comments according to the Markdown format, which allows for more readable +# documentation. See http://daringfireball.net/projects/markdown/ for details. +# The output of markdown processing is further processed by doxygen, so you +# can mix doxygen, HTML, and XML commands with Markdown formatting. +# Disable only in case of backward compatibilities issues. + +MARKDOWN_SUPPORT = YES + +# When enabled doxygen tries to link words that correspond to documented +# classes, or namespaces to their corresponding documentation. Such a link can +# be prevented in individual cases by by putting a % sign in front of the word +# or globally by setting AUTOLINK_SUPPORT to NO. + +AUTOLINK_SUPPORT = YES + +# If you use STL classes (i.e. std::string, std::vector, etc.) but do not want +# to include (a tag file for) the STL sources as input, then you should +# set this tag to YES in order to let doxygen match functions declarations and +# definitions whose arguments contain STL classes (e.g. func(std::string); v.s. +# func(std::string) {}). This also makes the inheritance and collaboration +# diagrams that involve STL classes more complete and accurate. + +BUILTIN_STL_SUPPORT = NO + +# If you use Microsoft's C++/CLI language, you should set this option to YES to +# enable parsing support. + +CPP_CLI_SUPPORT = NO + +# Set the SIP_SUPPORT tag to YES if your project consists of sip sources only. +# Doxygen will parse them like normal C++ but will assume all classes use public +# instead of private inheritance when no explicit protection keyword is present. + +SIP_SUPPORT = NO + +# For Microsoft's IDL there are propget and propput attributes to indicate +# getter and setter methods for a property. Setting this option to YES (the +# default) will make doxygen replace the get and set methods by a property in +# the documentation. This will only work if the methods are indeed getting or +# setting a simple type. If this is not the case, or you want to show the +# methods anyway, you should set this option to NO. + +IDL_PROPERTY_SUPPORT = YES + +# If member grouping is used in the documentation and the DISTRIBUTE_GROUP_DOC +# tag is set to YES, then doxygen will reuse the documentation of the first +# member in the group (if any) for the other members of the group. By default +# all members of a group must be documented explicitly. + +DISTRIBUTE_GROUP_DOC = NO + +# Set the SUBGROUPING tag to YES (the default) to allow class member groups of +# the same type (for instance a group of public functions) to be put as a +# subgroup of that type (e.g. under the Public Functions section). Set it to +# NO to prevent subgrouping. Alternatively, this can be done per class using +# the \nosubgrouping command. + +SUBGROUPING = YES + +# When the INLINE_GROUPED_CLASSES tag is set to YES, classes, structs and +# unions are shown inside the group in which they are included (e.g. using +# @ingroup) instead of on a separate page (for HTML and Man pages) or +# section (for LaTeX and RTF). + +INLINE_GROUPED_CLASSES = NO + +# When the INLINE_SIMPLE_STRUCTS tag is set to YES, structs, classes, and +# unions with only public data fields or simple typedef fields will be shown +# inline in the documentation of the scope in which they are defined (i.e. file, +# namespace, or group documentation), provided this scope is documented. If set +# to NO (the default), structs, classes, and unions are shown on a separate +# page (for HTML and Man pages) or section (for LaTeX and RTF). + +INLINE_SIMPLE_STRUCTS = NO + +# When TYPEDEF_HIDES_STRUCT is enabled, a typedef of a struct, union, or enum +# is documented as struct, union, or enum with the name of the typedef. So +# typedef struct TypeS {} TypeT, will appear in the documentation as a struct +# with name TypeT. When disabled the typedef will appear as a member of a file, +# namespace, or class. And the struct will be named TypeS. This can typically +# be useful for C code in case the coding convention dictates that all compound +# types are typedef'ed and only the typedef is referenced, never the tag name. + +TYPEDEF_HIDES_STRUCT = NO + +# The size of the symbol lookup cache can be set using LOOKUP_CACHE_SIZE. This +# cache is used to resolve symbols given their name and scope. Since this can +# be an expensive process and often the same symbol appear multiple times in +# the code, doxygen keeps a cache of pre-resolved symbols. If the cache is too +# small doxygen will become slower. If the cache is too large, memory is wasted. +# The cache size is given by this formula: 2^(16+LOOKUP_CACHE_SIZE). The valid +# range is 0..9, the default is 0, corresponding to a cache size of 2^16 = 65536 +# symbols. + +LOOKUP_CACHE_SIZE = 0 + +#--------------------------------------------------------------------------- +# Build related configuration options +#--------------------------------------------------------------------------- + +# If the EXTRACT_ALL tag is set to YES doxygen will assume all entities in +# documentation are documented, even if no documentation was available. +# Private class members and static file members will be hidden unless +# the EXTRACT_PRIVATE respectively EXTRACT_STATIC tags are set to YES + +EXTRACT_ALL = YES + +# If the EXTRACT_PRIVATE tag is set to YES all private members of a class +# will be included in the documentation. + +EXTRACT_PRIVATE = NO + +# If the EXTRACT_PACKAGE tag is set to YES all members with package or internal +# scope will be included in the documentation. + +EXTRACT_PACKAGE = NO + +# If the EXTRACT_STATIC tag is set to YES all static members of a file +# will be included in the documentation. + +EXTRACT_STATIC = NO + +# If the EXTRACT_LOCAL_CLASSES tag is set to YES classes (and structs) +# defined locally in source files will be included in the documentation. +# If set to NO only classes defined in header files are included. + +EXTRACT_LOCAL_CLASSES = YES + +# This flag is only useful for Objective-C code. When set to YES local +# methods, which are defined in the implementation section but not in +# the interface are included in the documentation. +# If set to NO (the default) only methods in the interface are included. + +EXTRACT_LOCAL_METHODS = NO + +# If this flag is set to YES, the members of anonymous namespaces will be +# extracted and appear in the documentation as a namespace called +# 'anonymous_namespace{file}', where file will be replaced with the base +# name of the file that contains the anonymous namespace. By default +# anonymous namespaces are hidden. + +EXTRACT_ANON_NSPACES = NO + +# If the HIDE_UNDOC_MEMBERS tag is set to YES, Doxygen will hide all +# undocumented members of documented classes, files or namespaces. +# If set to NO (the default) these members will be included in the +# various overviews, but no documentation section is generated. +# This option has no effect if EXTRACT_ALL is enabled. + +HIDE_UNDOC_MEMBERS = NO + +# If the HIDE_UNDOC_CLASSES tag is set to YES, Doxygen will hide all +# undocumented classes that are normally visible in the class hierarchy. +# If set to NO (the default) these classes will be included in the various +# overviews. This option has no effect if EXTRACT_ALL is enabled. + +HIDE_UNDOC_CLASSES = NO + +# If the HIDE_FRIEND_COMPOUNDS tag is set to YES, Doxygen will hide all +# friend (class|struct|union) declarations. +# If set to NO (the default) these declarations will be included in the +# documentation. + +HIDE_FRIEND_COMPOUNDS = NO + +# If the HIDE_IN_BODY_DOCS tag is set to YES, Doxygen will hide any +# documentation blocks found inside the body of a function. +# If set to NO (the default) these blocks will be appended to the +# function's detailed documentation block. + +HIDE_IN_BODY_DOCS = NO + +# The INTERNAL_DOCS tag determines if documentation +# that is typed after a \internal command is included. If the tag is set +# to NO (the default) then the documentation will be excluded. +# Set it to YES to include the internal documentation. + +INTERNAL_DOCS = NO + +# If the CASE_SENSE_NAMES tag is set to NO then Doxygen will only generate +# file names in lower-case letters. If set to YES upper-case letters are also +# allowed. This is useful if you have classes or files whose names only differ +# in case and if your file system supports case sensitive file names. Windows +# and Mac users are advised to set this option to NO. + +CASE_SENSE_NAMES = NO + +# If the HIDE_SCOPE_NAMES tag is set to NO (the default) then Doxygen +# will show members with their full class and namespace scopes in the +# documentation. If set to YES the scope will be hidden. + +HIDE_SCOPE_NAMES = YES + +# If the SHOW_INCLUDE_FILES tag is set to YES (the default) then Doxygen +# will put a list of the files that are included by a file in the documentation +# of that file. + +SHOW_INCLUDE_FILES = YES + +# If the FORCE_LOCAL_INCLUDES tag is set to YES then Doxygen +# will list include files with double quotes in the documentation +# rather than with sharp brackets. + +FORCE_LOCAL_INCLUDES = NO + +# If the INLINE_INFO tag is set to YES (the default) then a tag [inline] +# is inserted in the documentation for inline members. + +INLINE_INFO = YES + +# If the SORT_MEMBER_DOCS tag is set to YES (the default) then doxygen +# will sort the (detailed) documentation of file and class members +# alphabetically by member name. If set to NO the members will appear in +# declaration order. + +SORT_MEMBER_DOCS = YES + +# If the SORT_BRIEF_DOCS tag is set to YES then doxygen will sort the +# brief documentation of file, namespace and class members alphabetically +# by member name. If set to NO (the default) the members will appear in +# declaration order. + +SORT_BRIEF_DOCS = NO + +# If the SORT_MEMBERS_CTORS_1ST tag is set to YES then doxygen +# will sort the (brief and detailed) documentation of class members so that +# constructors and destructors are listed first. If set to NO (the default) +# the constructors will appear in the respective orders defined by +# SORT_MEMBER_DOCS and SORT_BRIEF_DOCS. +# This tag will be ignored for brief docs if SORT_BRIEF_DOCS is set to NO +# and ignored for detailed docs if SORT_MEMBER_DOCS is set to NO. + +SORT_MEMBERS_CTORS_1ST = NO + +# If the SORT_GROUP_NAMES tag is set to YES then doxygen will sort the +# hierarchy of group names into alphabetical order. If set to NO (the default) +# the group names will appear in their defined order. + +SORT_GROUP_NAMES = NO + +# If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be +# sorted by fully-qualified names, including namespaces. If set to +# NO (the default), the class list will be sorted only by class name, +# not including the namespace part. +# Note: This option is not very useful if HIDE_SCOPE_NAMES is set to YES. +# Note: This option applies only to the class list, not to the +# alphabetical list. + +SORT_BY_SCOPE_NAME = NO + +# If the STRICT_PROTO_MATCHING option is enabled and doxygen fails to +# do proper type resolution of all parameters of a function it will reject a +# match between the prototype and the implementation of a member function even +# if there is only one candidate or it is obvious which candidate to choose +# by doing a simple string match. By disabling STRICT_PROTO_MATCHING doxygen +# will still accept a match between prototype and implementation in such cases. + +STRICT_PROTO_MATCHING = NO + +# The GENERATE_TODOLIST tag can be used to enable (YES) or +# disable (NO) the todo list. This list is created by putting \todo +# commands in the documentation. + +GENERATE_TODOLIST = YES + +# The GENERATE_TESTLIST tag can be used to enable (YES) or +# disable (NO) the test list. This list is created by putting \test +# commands in the documentation. + +GENERATE_TESTLIST = YES + +# The GENERATE_BUGLIST tag can be used to enable (YES) or +# disable (NO) the bug list. This list is created by putting \bug +# commands in the documentation. + +GENERATE_BUGLIST = YES + +# The GENERATE_DEPRECATEDLIST tag can be used to enable (YES) or +# disable (NO) the deprecated list. This list is created by putting +# \deprecated commands in the documentation. + +GENERATE_DEPRECATEDLIST= YES + +# The ENABLED_SECTIONS tag can be used to enable conditional +# documentation sections, marked by \if section-label ... \endif +# and \cond section-label ... \endcond blocks. + +ENABLED_SECTIONS = + +# The MAX_INITIALIZER_LINES tag determines the maximum number of lines +# the initial value of a variable or macro consists of for it to appear in +# the documentation. If the initializer consists of more lines than specified +# here it will be hidden. Use a value of 0 to hide initializers completely. +# The appearance of the initializer of individual variables and macros in the +# documentation can be controlled using \showinitializer or \hideinitializer +# command in the documentation regardless of this setting. + +MAX_INITIALIZER_LINES = 30 + +# Set the SHOW_USED_FILES tag to NO to disable the list of files generated +# at the bottom of the documentation of classes and structs. If set to YES the +# list will mention the files that were used to generate the documentation. + +SHOW_USED_FILES = YES + +# Set the SHOW_FILES tag to NO to disable the generation of the Files page. +# This will remove the Files entry from the Quick Index and from the +# Folder Tree View (if specified). The default is YES. + +SHOW_FILES = YES + +# Set the SHOW_NAMESPACES tag to NO to disable the generation of the +# Namespaces page. This will remove the Namespaces entry from the Quick Index +# and from the Folder Tree View (if specified). The default is YES. + +SHOW_NAMESPACES = YES + +# The FILE_VERSION_FILTER tag can be used to specify a program or script that +# doxygen should invoke to get the current version for each file (typically from +# the version control system). Doxygen will invoke the program by executing (via +# popen()) the command , where is the value of +# the FILE_VERSION_FILTER tag, and is the name of an input file +# provided by doxygen. Whatever the program writes to standard output +# is used as the file version. See the manual for examples. + +FILE_VERSION_FILTER = + +# The LAYOUT_FILE tag can be used to specify a layout file which will be parsed +# by doxygen. The layout file controls the global structure of the generated +# output files in an output format independent way. To create the layout file +# that represents doxygen's defaults, run doxygen with the -l option. +# You can optionally specify a file name after the option, if omitted +# DoxygenLayout.xml will be used as the name of the layout file. + +LAYOUT_FILE = + +# The CITE_BIB_FILES tag can be used to specify one or more bib files +# containing the references data. This must be a list of .bib files. The +# .bib extension is automatically appended if omitted. Using this command +# requires the bibtex tool to be installed. See also +# http://en.wikipedia.org/wiki/BibTeX for more info. For LaTeX the style +# of the bibliography can be controlled using LATEX_BIB_STYLE. To use this +# feature you need bibtex and perl available in the search path. Do not use +# file names with spaces, bibtex cannot handle them. + +CITE_BIB_FILES = + +#--------------------------------------------------------------------------- +# configuration options related to warning and progress messages +#--------------------------------------------------------------------------- + +# The QUIET tag can be used to turn on/off the messages that are generated +# by doxygen. Possible values are YES and NO. If left blank NO is used. + +QUIET = NO + +# The WARNINGS tag can be used to turn on/off the warning messages that are +# generated by doxygen. Possible values are YES and NO. If left blank +# NO is used. + +WARNINGS = YES + +# If WARN_IF_UNDOCUMENTED is set to YES, then doxygen will generate warnings +# for undocumented members. If EXTRACT_ALL is set to YES then this flag will +# automatically be disabled. + +WARN_IF_UNDOCUMENTED = YES + +# If WARN_IF_DOC_ERROR is set to YES, doxygen will generate warnings for +# potential errors in the documentation, such as not documenting some +# parameters in a documented function, or documenting parameters that +# don't exist or using markup commands wrongly. + +WARN_IF_DOC_ERROR = YES + +# The WARN_NO_PARAMDOC option can be enabled to get warnings for +# functions that are documented, but have no documentation for their parameters +# or return value. If set to NO (the default) doxygen will only warn about +# wrong or incomplete parameter documentation, but not about the absence of +# documentation. + +WARN_NO_PARAMDOC = NO + +# The WARN_FORMAT tag determines the format of the warning messages that +# doxygen can produce. The string should contain the $file, $line, and $text +# tags, which will be replaced by the file and line number from which the +# warning originated and the warning text. Optionally the format may contain +# $version, which will be replaced by the version of the file (if it could +# be obtained via FILE_VERSION_FILTER) + +WARN_FORMAT = "$file:$line: $text" + +# The WARN_LOGFILE tag can be used to specify a file to which warning +# and error messages should be written. If left blank the output is written +# to stderr. + +WARN_LOGFILE = + +#--------------------------------------------------------------------------- +# configuration options related to the input files +#--------------------------------------------------------------------------- + +# The INPUT tag can be used to specify the files and/or directories that contain +# documented source files. You may enter file names like "myfile.cpp" or +# directories like "/usr/src/myproject". Separate the files or directories +# with spaces. + +INPUT = . + +# This tag can be used to specify the character encoding of the source files +# that doxygen parses. Internally doxygen uses the UTF-8 encoding, which is +# also the default input encoding. Doxygen uses libiconv (or the iconv built +# into libc) for the transcoding. See http://www.gnu.org/software/libiconv for +# the list of possible encodings. + +INPUT_ENCODING = UTF-8 + +# If the value of the INPUT tag contains directories, you can use the +# FILE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp +# and *.h) to filter out the source-files in the directories. If left +# blank the following patterns are tested: +# *.c *.cc *.cxx *.cpp *.c++ *.d *.java *.ii *.ixx *.ipp *.i++ *.inl *.h *.hh +# *.hxx *.hpp *.h++ *.idl *.odl *.cs *.php *.php3 *.inc *.m *.mm *.dox *.py +# *.f90 *.f *.for *.vhd *.vhdl + +FILE_PATTERNS = *.c \ + *.dox + +# The RECURSIVE tag can be used to turn specify whether or not subdirectories +# should be searched for input files as well. Possible values are YES and NO. +# If left blank NO is used. + +RECURSIVE = YES + +# The EXCLUDE tag can be used to specify files and/or directories that should be +# excluded from the INPUT source files. This way you can easily exclude a +# subdirectory from a directory tree whose root is specified with the INPUT tag. +# Note that relative paths are relative to the directory from which doxygen is +# run. + +EXCLUDE = + +# The EXCLUDE_SYMLINKS tag can be used to select whether or not files or +# directories that are symbolic links (a Unix file system feature) are excluded +# from the input. + +EXCLUDE_SYMLINKS = NO + +# If the value of the INPUT tag contains directories, you can use the +# EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude +# certain files from those directories. Note that the wildcards are matched +# against the file with absolute path, so to exclude all test directories +# for example use the pattern */test/* + +EXCLUDE_PATTERNS = + +# The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names +# (namespaces, classes, functions, etc.) that should be excluded from the +# output. The symbol name can be a fully qualified name, a word, or if the +# wildcard * is used, a substring. Examples: ANamespace, AClass, +# AClass::ANamespace, ANamespace::*Test + +EXCLUDE_SYMBOLS = + +# The EXAMPLE_PATH tag can be used to specify one or more files or +# directories that contain example code fragments that are included (see +# the \include command). + +EXAMPLE_PATH = + +# If the value of the EXAMPLE_PATH tag contains directories, you can use the +# EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp +# and *.h) to filter out the source-files in the directories. If left +# blank all files are included. + +EXAMPLE_PATTERNS = * + +# If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be +# searched for input files to be used with the \include or \dontinclude +# commands irrespective of the value of the RECURSIVE tag. +# Possible values are YES and NO. If left blank NO is used. + +EXAMPLE_RECURSIVE = NO + +# The IMAGE_PATH tag can be used to specify one or more files or +# directories that contain image that are included in the documentation (see +# the \image command). + +IMAGE_PATH = + +# The INPUT_FILTER tag can be used to specify a program that doxygen should +# invoke to filter for each input file. Doxygen will invoke the filter program +# by executing (via popen()) the command , where +# is the value of the INPUT_FILTER tag, and is the name of an +# input file. Doxygen will then use the output that the filter program writes +# to standard output. If FILTER_PATTERNS is specified, this tag will be ignored. +# Note that the filter must not add or remove lines; it is applied before the +# code is scanned, but not when the output code is generated. If lines are added +# or removed, the anchors will not be placed correctly. + +INPUT_FILTER = + +# The FILTER_PATTERNS tag can be used to specify filters on a per file pattern +# basis. Doxygen will compare the file name with each pattern and apply the +# filter if there is a match. The filters are a list of the form: +# pattern=filter (like *.cpp=my_cpp_filter). See INPUT_FILTER for further +# info on how filters are used. If FILTER_PATTERNS is empty or if +# non of the patterns match the file name, INPUT_FILTER is applied. + +FILTER_PATTERNS = + +# If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using +# INPUT_FILTER) will be used to filter the input files when producing source +# files to browse (i.e. when SOURCE_BROWSER is set to YES). + +FILTER_SOURCE_FILES = NO + +# The FILTER_SOURCE_PATTERNS tag can be used to specify source filters per file +# pattern. A pattern will override the setting for FILTER_PATTERN (if any) +# and it is also possible to disable source filtering for a specific pattern +# using *.ext= (so without naming a filter). This option only has effect when +# FILTER_SOURCE_FILES is enabled. + +FILTER_SOURCE_PATTERNS = + +# If the USE_MD_FILE_AS_MAINPAGE tag refers to the name of a markdown file that +# is part of the input, its contents will be placed on the main page +# (index.html). This can be useful if you have a project on for instance GitHub +# and want reuse the introduction page also for the doxygen output. + +USE_MDFILE_AS_MAINPAGE = + +#--------------------------------------------------------------------------- +# configuration options related to source browsing +#--------------------------------------------------------------------------- + +# If the SOURCE_BROWSER tag is set to YES then a list of source files will +# be generated. Documented entities will be cross-referenced with these sources. +# Note: To get rid of all source code in the generated output, make sure also +# VERBATIM_HEADERS is set to NO. + +SOURCE_BROWSER = NO + +# Setting the INLINE_SOURCES tag to YES will include the body +# of functions and classes directly in the documentation. + +INLINE_SOURCES = NO + +# Setting the STRIP_CODE_COMMENTS tag to YES (the default) will instruct +# doxygen to hide any special comment blocks from generated source code +# fragments. Normal C, C++ and Fortran comments will always remain visible. + +STRIP_CODE_COMMENTS = YES + +# If the REFERENCED_BY_RELATION tag is set to YES +# then for each documented function all documented +# functions referencing it will be listed. + +REFERENCED_BY_RELATION = NO + +# If the REFERENCES_RELATION tag is set to YES +# then for each documented function all documented entities +# called/used by that function will be listed. + +REFERENCES_RELATION = NO + +# If the REFERENCES_LINK_SOURCE tag is set to YES (the default) +# and SOURCE_BROWSER tag is set to YES, then the hyperlinks from +# functions in REFERENCES_RELATION and REFERENCED_BY_RELATION lists will +# link to the source code. Otherwise they will link to the documentation. + +REFERENCES_LINK_SOURCE = YES + +# If the USE_HTAGS tag is set to YES then the references to source code +# will point to the HTML generated by the htags(1) tool instead of doxygen +# built-in source browser. The htags tool is part of GNU's global source +# tagging system (see http://www.gnu.org/software/global/global.html). You +# will need version 4.8.6 or higher. + +USE_HTAGS = NO + +# If the VERBATIM_HEADERS tag is set to YES (the default) then Doxygen +# will generate a verbatim copy of the header file for each class for +# which an include is specified. Set to NO to disable this. + +VERBATIM_HEADERS = YES + +#--------------------------------------------------------------------------- +# configuration options related to the alphabetical class index +#--------------------------------------------------------------------------- + +# If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index +# of all compounds will be generated. Enable this if the project +# contains a lot of classes, structs, unions or interfaces. + +ALPHABETICAL_INDEX = YES + +# If the alphabetical index is enabled (see ALPHABETICAL_INDEX) then +# the COLS_IN_ALPHA_INDEX tag can be used to specify the number of columns +# in which this list will be split (can be a number in the range [1..20]) + +COLS_IN_ALPHA_INDEX = 5 + +# In case all classes in a project start with a common prefix, all +# classes will be put under the same header in the alphabetical index. +# The IGNORE_PREFIX tag can be used to specify one or more prefixes that +# should be ignored while generating the index headers. + +IGNORE_PREFIX = + +#--------------------------------------------------------------------------- +# configuration options related to the HTML output +#--------------------------------------------------------------------------- + +# If the GENERATE_HTML tag is set to YES (the default) Doxygen will +# generate HTML output. + +GENERATE_HTML = YES + +# The HTML_OUTPUT tag is used to specify where the HTML docs will be put. +# If a relative path is entered the value of OUTPUT_DIRECTORY will be +# put in front of it. If left blank `html' will be used as the default path. + +HTML_OUTPUT = html + +# The HTML_FILE_EXTENSION tag can be used to specify the file extension for +# each generated HTML page (for example: .htm,.php,.asp). If it is left blank +# doxygen will generate files with .html extension. + +HTML_FILE_EXTENSION = .html + +# The HTML_HEADER tag can be used to specify a personal HTML header for +# each generated HTML page. If it is left blank doxygen will generate a +# standard header. Note that when using a custom header you are responsible +# for the proper inclusion of any scripts and style sheets that doxygen +# needs, which is dependent on the configuration options used. +# It is advised to generate a default header using "doxygen -w html +# header.html footer.html stylesheet.css YourConfigFile" and then modify +# that header. Note that the header is subject to change so you typically +# have to redo this when upgrading to a newer version of doxygen or when +# changing the value of configuration settings such as GENERATE_TREEVIEW! + +HTML_HEADER = + +# The HTML_FOOTER tag can be used to specify a personal HTML footer for +# each generated HTML page. If it is left blank doxygen will generate a +# standard footer. + +HTML_FOOTER = + +# The HTML_STYLESHEET tag can be used to specify a user-defined cascading +# style sheet that is used by each HTML page. It can be used to +# fine-tune the look of the HTML output. If left blank doxygen will +# generate a default style sheet. Note that it is recommended to use +# HTML_EXTRA_STYLESHEET instead of this one, as it is more robust and this +# tag will in the future become obsolete. + +HTML_STYLESHEET = + +# The HTML_EXTRA_STYLESHEET tag can be used to specify an additional +# user-defined cascading style sheet that is included after the standard +# style sheets created by doxygen. Using this option one can overrule +# certain style aspects. This is preferred over using HTML_STYLESHEET +# since it does not replace the standard style sheet and is therefor more +# robust against future updates. Doxygen will copy the style sheet file to +# the output directory. + +HTML_EXTRA_STYLESHEET = + +# The HTML_EXTRA_FILES tag can be used to specify one or more extra images or +# other source files which should be copied to the HTML output directory. Note +# that these files will be copied to the base HTML output directory. Use the +# $relpath^ marker in the HTML_HEADER and/or HTML_FOOTER files to load these +# files. In the HTML_STYLESHEET file, use the file name only. Also note that +# the files will be copied as-is; there are no commands or markers available. + +HTML_EXTRA_FILES = + +# The HTML_COLORSTYLE_HUE tag controls the color of the HTML output. +# Doxygen will adjust the colors in the style sheet and background images +# according to this color. Hue is specified as an angle on a colorwheel, +# see http://en.wikipedia.org/wiki/Hue for more information. +# For instance the value 0 represents red, 60 is yellow, 120 is green, +# 180 is cyan, 240 is blue, 300 purple, and 360 is red again. +# The allowed range is 0 to 359. + +HTML_COLORSTYLE_HUE = 220 + +# The HTML_COLORSTYLE_SAT tag controls the purity (or saturation) of +# the colors in the HTML output. For a value of 0 the output will use +# grayscales only. A value of 255 will produce the most vivid colors. + +HTML_COLORSTYLE_SAT = 100 + +# The HTML_COLORSTYLE_GAMMA tag controls the gamma correction applied to +# the luminance component of the colors in the HTML output. Values below +# 100 gradually make the output lighter, whereas values above 100 make +# the output darker. The value divided by 100 is the actual gamma applied, +# so 80 represents a gamma of 0.8, The value 220 represents a gamma of 2.2, +# and 100 does not change the gamma. + +HTML_COLORSTYLE_GAMMA = 80 + +# If the HTML_TIMESTAMP tag is set to YES then the footer of each generated HTML +# page will contain the date and time when the page was generated. Setting +# this to NO can help when comparing the output of multiple runs. + +HTML_TIMESTAMP = YES + +# If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML +# documentation will contain sections that can be hidden and shown after the +# page has loaded. + +HTML_DYNAMIC_SECTIONS = NO + +# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of +# entries shown in the various tree structured indices initially; the user +# can expand and collapse entries dynamically later on. Doxygen will expand +# the tree to such a level that at most the specified number of entries are +# visible (unless a fully collapsed tree already exceeds this amount). +# So setting the number of entries 1 will produce a full collapsed tree by +# default. 0 is a special value representing an infinite number of entries +# and will result in a full expanded tree by default. + +HTML_INDEX_NUM_ENTRIES = 100 + +# If the GENERATE_DOCSET tag is set to YES, additional index files +# will be generated that can be used as input for Apple's Xcode 3 +# integrated development environment, introduced with OSX 10.5 (Leopard). +# To create a documentation set, doxygen will generate a Makefile in the +# HTML output directory. Running make will produce the docset in that +# directory and running "make install" will install the docset in +# ~/Library/Developer/Shared/Documentation/DocSets so that Xcode will find +# it at startup. +# See http://developer.apple.com/tools/creatingdocsetswithdoxygen.html +# for more information. + +GENERATE_DOCSET = NO + +# When GENERATE_DOCSET tag is set to YES, this tag determines the name of the +# feed. A documentation feed provides an umbrella under which multiple +# documentation sets from a single provider (such as a company or product suite) +# can be grouped. + +DOCSET_FEEDNAME = "Doxygen generated docs" + +# When GENERATE_DOCSET tag is set to YES, this tag specifies a string that +# should uniquely identify the documentation set bundle. This should be a +# reverse domain-name style string, e.g. com.mycompany.MyDocSet. Doxygen +# will append .docset to the name. + +DOCSET_BUNDLE_ID = org.doxygen.Project + +# When GENERATE_PUBLISHER_ID tag specifies a string that should uniquely +# identify the documentation publisher. This should be a reverse domain-name +# style string, e.g. com.mycompany.MyDocSet.documentation. + +DOCSET_PUBLISHER_ID = org.doxygen.Publisher + +# The GENERATE_PUBLISHER_NAME tag identifies the documentation publisher. + +DOCSET_PUBLISHER_NAME = Publisher + +# If the GENERATE_HTMLHELP tag is set to YES, additional index files +# will be generated that can be used as input for tools like the +# Microsoft HTML help workshop to generate a compiled HTML help file (.chm) +# of the generated HTML documentation. + +GENERATE_HTMLHELP = NO + +# If the GENERATE_HTMLHELP tag is set to YES, the CHM_FILE tag can +# be used to specify the file name of the resulting .chm file. You +# can add a path in front of the file if the result should not be +# written to the html output directory. + +CHM_FILE = + +# If the GENERATE_HTMLHELP tag is set to YES, the HHC_LOCATION tag can +# be used to specify the location (absolute path including file name) of +# the HTML help compiler (hhc.exe). If non-empty doxygen will try to run +# the HTML help compiler on the generated index.hhp. + +HHC_LOCATION = + +# If the GENERATE_HTMLHELP tag is set to YES, the GENERATE_CHI flag +# controls if a separate .chi index file is generated (YES) or that +# it should be included in the master .chm file (NO). + +GENERATE_CHI = NO + +# If the GENERATE_HTMLHELP tag is set to YES, the CHM_INDEX_ENCODING +# is used to encode HtmlHelp index (hhk), content (hhc) and project file +# content. + +CHM_INDEX_ENCODING = + +# If the GENERATE_HTMLHELP tag is set to YES, the BINARY_TOC flag +# controls whether a binary table of contents is generated (YES) or a +# normal table of contents (NO) in the .chm file. + +BINARY_TOC = NO + +# The TOC_EXPAND flag can be set to YES to add extra items for group members +# to the contents of the HTML help documentation and to the tree view. + +TOC_EXPAND = NO + +# If the GENERATE_QHP tag is set to YES and both QHP_NAMESPACE and +# QHP_VIRTUAL_FOLDER are set, an additional index file will be generated +# that can be used as input for Qt's qhelpgenerator to generate a +# Qt Compressed Help (.qch) of the generated HTML documentation. + +GENERATE_QHP = NO + +# If the QHG_LOCATION tag is specified, the QCH_FILE tag can +# be used to specify the file name of the resulting .qch file. +# The path specified is relative to the HTML output folder. + +QCH_FILE = + +# The QHP_NAMESPACE tag specifies the namespace to use when generating +# Qt Help Project output. For more information please see +# http://doc.trolltech.com/qthelpproject.html#namespace + +QHP_NAMESPACE = org.doxygen.Project + +# The QHP_VIRTUAL_FOLDER tag specifies the namespace to use when generating +# Qt Help Project output. For more information please see +# http://doc.trolltech.com/qthelpproject.html#virtual-folders + +QHP_VIRTUAL_FOLDER = doc + +# If QHP_CUST_FILTER_NAME is set, it specifies the name of a custom filter to +# add. For more information please see +# http://doc.trolltech.com/qthelpproject.html#custom-filters + +QHP_CUST_FILTER_NAME = + +# The QHP_CUST_FILT_ATTRS tag specifies the list of the attributes of the +# custom filter to add. For more information please see +# +# Qt Help Project / Custom Filters. + +QHP_CUST_FILTER_ATTRS = + +# The QHP_SECT_FILTER_ATTRS tag specifies the list of the attributes this +# project's +# filter section matches. +# +# Qt Help Project / Filter Attributes. + +QHP_SECT_FILTER_ATTRS = + +# If the GENERATE_QHP tag is set to YES, the QHG_LOCATION tag can +# be used to specify the location of Qt's qhelpgenerator. +# If non-empty doxygen will try to run qhelpgenerator on the generated +# .qhp file. + +QHG_LOCATION = + +# If the GENERATE_ECLIPSEHELP tag is set to YES, additional index files +# will be generated, which together with the HTML files, form an Eclipse help +# plugin. To install this plugin and make it available under the help contents +# menu in Eclipse, the contents of the directory containing the HTML and XML +# files needs to be copied into the plugins directory of eclipse. The name of +# the directory within the plugins directory should be the same as +# the ECLIPSE_DOC_ID value. After copying Eclipse needs to be restarted before +# the help appears. + +GENERATE_ECLIPSEHELP = NO + +# A unique identifier for the eclipse help plugin. When installing the plugin +# the directory name containing the HTML and XML files should also have +# this name. + +ECLIPSE_DOC_ID = org.doxygen.Project + +# The DISABLE_INDEX tag can be used to turn on/off the condensed index (tabs) +# at top of each HTML page. The value NO (the default) enables the index and +# the value YES disables it. Since the tabs have the same information as the +# navigation tree you can set this option to NO if you already set +# GENERATE_TREEVIEW to YES. + +DISABLE_INDEX = NO + +# The GENERATE_TREEVIEW tag is used to specify whether a tree-like index +# structure should be generated to display hierarchical information. +# If the tag value is set to YES, a side panel will be generated +# containing a tree-like index structure (just like the one that +# is generated for HTML Help). For this to work a browser that supports +# JavaScript, DHTML, CSS and frames is required (i.e. any modern browser). +# Windows users are probably better off using the HTML help feature. +# Since the tree basically has the same information as the tab index you +# could consider to set DISABLE_INDEX to NO when enabling this option. + +GENERATE_TREEVIEW = NO + +# The ENUM_VALUES_PER_LINE tag can be used to set the number of enum values +# (range [0,1..20]) that doxygen will group on one line in the generated HTML +# documentation. Note that a value of 0 will completely suppress the enum +# values from appearing in the overview section. + +ENUM_VALUES_PER_LINE = 4 + +# If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be +# used to set the initial width (in pixels) of the frame in which the tree +# is shown. + +TREEVIEW_WIDTH = 250 + +# When the EXT_LINKS_IN_WINDOW option is set to YES doxygen will open +# links to external symbols imported via tag files in a separate window. + +EXT_LINKS_IN_WINDOW = NO + +# Use this tag to change the font size of Latex formulas included +# as images in the HTML documentation. The default is 10. Note that +# when you change the font size after a successful doxygen run you need +# to manually remove any form_*.png images from the HTML output directory +# to force them to be regenerated. + +FORMULA_FONTSIZE = 10 + +# Use the FORMULA_TRANPARENT tag to determine whether or not the images +# generated for formulas are transparent PNGs. Transparent PNGs are +# not supported properly for IE 6.0, but are supported on all modern browsers. +# Note that when changing this option you need to delete any form_*.png files +# in the HTML output before the changes have effect. + +FORMULA_TRANSPARENT = YES + +# Enable the USE_MATHJAX option to render LaTeX formulas using MathJax +# (see http://www.mathjax.org) which uses client side Javascript for the +# rendering instead of using prerendered bitmaps. Use this if you do not +# have LaTeX installed or if you want to formulas look prettier in the HTML +# output. When enabled you may also need to install MathJax separately and +# configure the path to it using the MATHJAX_RELPATH option. + +USE_MATHJAX = NO + +# When MathJax is enabled you can set the default output format to be used for +# the MathJax output. Supported types are HTML-CSS, NativeMML (i.e. MathML) and +# SVG. The default value is HTML-CSS, which is slower, but has the best +# compatibility. + +MATHJAX_FORMAT = HTML-CSS + +# When MathJax is enabled you need to specify the location relative to the +# HTML output directory using the MATHJAX_RELPATH option. The destination +# directory should contain the MathJax.js script. For instance, if the mathjax +# directory is located at the same level as the HTML output directory, then +# MATHJAX_RELPATH should be ../mathjax. The default value points to +# the MathJax Content Delivery Network so you can quickly see the result without +# installing MathJax. However, it is strongly recommended to install a local +# copy of MathJax from http://www.mathjax.org before deployment. + +MATHJAX_RELPATH = http://cdn.mathjax.org/mathjax/latest + +# The MATHJAX_EXTENSIONS tag can be used to specify one or MathJax extension +# names that should be enabled during MathJax rendering. + +MATHJAX_EXTENSIONS = + +# The MATHJAX_CODEFILE tag can be used to specify a file with javascript +# pieces of code that will be used on startup of the MathJax code. + +MATHJAX_CODEFILE = + +# When the SEARCHENGINE tag is enabled doxygen will generate a search box +# for the HTML output. The underlying search engine uses javascript +# and DHTML and should work on any modern browser. Note that when using +# HTML help (GENERATE_HTMLHELP), Qt help (GENERATE_QHP), or docsets +# (GENERATE_DOCSET) there is already a search function so this one should +# typically be disabled. For large projects the javascript based search engine +# can be slow, then enabling SERVER_BASED_SEARCH may provide a better solution. + +SEARCHENGINE = YES + +# When the SERVER_BASED_SEARCH tag is enabled the search engine will be +# implemented using a web server instead of a web client using Javascript. +# There are two flavours of web server based search depending on the +# EXTERNAL_SEARCH setting. When disabled, doxygen will generate a PHP script for +# searching and an index file used by the script. When EXTERNAL_SEARCH is +# enabled the indexing and searching needs to be provided by external tools. +# See the manual for details. + +SERVER_BASED_SEARCH = NO + +# When EXTERNAL_SEARCH is enabled doxygen will no longer generate the PHP +# script for searching. Instead the search results are written to an XML file +# which needs to be processed by an external indexer. Doxygen will invoke an +# external search engine pointed to by the SEARCHENGINE_URL option to obtain +# the search results. Doxygen ships with an example indexer (doxyindexer) and +# search engine (doxysearch.cgi) which are based on the open source search +# engine library Xapian. See the manual for configuration details. + +EXTERNAL_SEARCH = NO + +# The SEARCHENGINE_URL should point to a search engine hosted by a web server +# which will returned the search results when EXTERNAL_SEARCH is enabled. +# Doxygen ships with an example search engine (doxysearch) which is based on +# the open source search engine library Xapian. See the manual for configuration +# details. + +SEARCHENGINE_URL = + +# When SERVER_BASED_SEARCH and EXTERNAL_SEARCH are both enabled the unindexed +# search data is written to a file for indexing by an external tool. With the +# SEARCHDATA_FILE tag the name of this file can be specified. + +SEARCHDATA_FILE = searchdata.xml + +# When SERVER_BASED_SEARCH AND EXTERNAL_SEARCH are both enabled the +# EXTERNAL_SEARCH_ID tag can be used as an identifier for the project. This is +# useful in combination with EXTRA_SEARCH_MAPPINGS to search through multiple +# projects and redirect the results back to the right project. + +EXTERNAL_SEARCH_ID = + +# The EXTRA_SEARCH_MAPPINGS tag can be used to enable searching through doxygen +# projects other than the one defined by this configuration file, but that are +# all added to the same external search index. Each project needs to have a +# unique id set via EXTERNAL_SEARCH_ID. The search mapping then maps the id +# of to a relative location where the documentation can be found. +# The format is: EXTRA_SEARCH_MAPPINGS = id1=loc1 id2=loc2 ... + +EXTRA_SEARCH_MAPPINGS = + +#--------------------------------------------------------------------------- +# configuration options related to the LaTeX output +#--------------------------------------------------------------------------- + +# If the GENERATE_LATEX tag is set to YES (the default) Doxygen will +# generate Latex output. + +GENERATE_LATEX = YES + +# The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put. +# If a relative path is entered the value of OUTPUT_DIRECTORY will be +# put in front of it. If left blank `latex' will be used as the default path. + +LATEX_OUTPUT = latex + +# The LATEX_CMD_NAME tag can be used to specify the LaTeX command name to be +# invoked. If left blank `latex' will be used as the default command name. +# Note that when enabling USE_PDFLATEX this option is only used for +# generating bitmaps for formulas in the HTML output, but not in the +# Makefile that is written to the output directory. + +LATEX_CMD_NAME = latex + +# The MAKEINDEX_CMD_NAME tag can be used to specify the command name to +# generate index for LaTeX. If left blank `makeindex' will be used as the +# default command name. + +MAKEINDEX_CMD_NAME = makeindex + +# If the COMPACT_LATEX tag is set to YES Doxygen generates more compact +# LaTeX documents. This may be useful for small projects and may help to +# save some trees in general. + +COMPACT_LATEX = NO + +# The PAPER_TYPE tag can be used to set the paper type that is used +# by the printer. Possible values are: a4, letter, legal and +# executive. If left blank a4 will be used. + +PAPER_TYPE = a4 + +# The EXTRA_PACKAGES tag can be to specify one or more names of LaTeX +# packages that should be included in the LaTeX output. + +EXTRA_PACKAGES = + +# The LATEX_HEADER tag can be used to specify a personal LaTeX header for +# the generated latex document. The header should contain everything until +# the first chapter. If it is left blank doxygen will generate a +# standard header. Notice: only use this tag if you know what you are doing! + +LATEX_HEADER = + +# The LATEX_FOOTER tag can be used to specify a personal LaTeX footer for +# the generated latex document. The footer should contain everything after +# the last chapter. If it is left blank doxygen will generate a +# standard footer. Notice: only use this tag if you know what you are doing! + +LATEX_FOOTER = + +# The LATEX_EXTRA_FILES tag can be used to specify one or more extra images +# or other source files which should be copied to the LaTeX output directory. +# Note that the files will be copied as-is; there are no commands or markers +# available. + +LATEX_EXTRA_FILES = + +# If the PDF_HYPERLINKS tag is set to YES, the LaTeX that is generated +# is prepared for conversion to pdf (using ps2pdf). The pdf file will +# contain links (just like the HTML output) instead of page references +# This makes the output suitable for online browsing using a pdf viewer. + +PDF_HYPERLINKS = YES + +# If the USE_PDFLATEX tag is set to YES, pdflatex will be used instead of +# plain latex in the generated Makefile. Set this option to YES to get a +# higher quality PDF documentation. + +USE_PDFLATEX = YES + +# If the LATEX_BATCHMODE tag is set to YES, doxygen will add the \\batchmode. +# command to the generated LaTeX files. This will instruct LaTeX to keep +# running if errors occur, instead of asking the user for help. +# This option is also used when generating formulas in HTML. + +LATEX_BATCHMODE = NO + +# If LATEX_HIDE_INDICES is set to YES then doxygen will not +# include the index chapters (such as File Index, Compound Index, etc.) +# in the output. + +LATEX_HIDE_INDICES = NO + +# If LATEX_SOURCE_CODE is set to YES then doxygen will include +# source code with syntax highlighting in the LaTeX output. +# Note that which sources are shown also depends on other settings +# such as SOURCE_BROWSER. + +LATEX_SOURCE_CODE = NO + +# The LATEX_BIB_STYLE tag can be used to specify the style to use for the +# bibliography, e.g. plainnat, or ieeetr. The default style is "plain". See +# http://en.wikipedia.org/wiki/BibTeX for more info. + +LATEX_BIB_STYLE = plain + +#--------------------------------------------------------------------------- +# configuration options related to the RTF output +#--------------------------------------------------------------------------- + +# If the GENERATE_RTF tag is set to YES Doxygen will generate RTF output +# The RTF output is optimized for Word 97 and may not look very pretty with +# other RTF readers or editors. + +GENERATE_RTF = NO + +# The RTF_OUTPUT tag is used to specify where the RTF docs will be put. +# If a relative path is entered the value of OUTPUT_DIRECTORY will be +# put in front of it. If left blank `rtf' will be used as the default path. + +RTF_OUTPUT = rtf + +# If the COMPACT_RTF tag is set to YES Doxygen generates more compact +# RTF documents. This may be useful for small projects and may help to +# save some trees in general. + +COMPACT_RTF = NO + +# If the RTF_HYPERLINKS tag is set to YES, the RTF that is generated +# will contain hyperlink fields. The RTF file will +# contain links (just like the HTML output) instead of page references. +# This makes the output suitable for online browsing using WORD or other +# programs which support those fields. +# Note: wordpad (write) and others do not support links. + +RTF_HYPERLINKS = NO + +# Load style sheet definitions from file. Syntax is similar to doxygen's +# config file, i.e. a series of assignments. You only have to provide +# replacements, missing definitions are set to their default value. + +RTF_STYLESHEET_FILE = + +# Set optional variables used in the generation of an rtf document. +# Syntax is similar to doxygen's config file. + +RTF_EXTENSIONS_FILE = + +#--------------------------------------------------------------------------- +# configuration options related to the man page output +#--------------------------------------------------------------------------- + +# If the GENERATE_MAN tag is set to YES (the default) Doxygen will +# generate man pages + +GENERATE_MAN = YES + +# The MAN_OUTPUT tag is used to specify where the man pages will be put. +# If a relative path is entered the value of OUTPUT_DIRECTORY will be +# put in front of it. If left blank `man' will be used as the default path. + +MAN_OUTPUT = man + +# The MAN_EXTENSION tag determines the extension that is added to +# the generated man pages (default is the subroutine's section .3) + +MAN_EXTENSION = .1 + +# If the MAN_LINKS tag is set to YES and Doxygen generates man output, +# then it will generate one additional man file for each entity +# documented in the real man page(s). These additional files +# only source the real man page, but without them the man command +# would be unable to find the correct page. The default is NO. + +MAN_LINKS = NO + +#--------------------------------------------------------------------------- +# configuration options related to the XML output +#--------------------------------------------------------------------------- + +# If the GENERATE_XML tag is set to YES Doxygen will +# generate an XML file that captures the structure of +# the code including all documentation. + +GENERATE_XML = NO + +# The XML_OUTPUT tag is used to specify where the XML pages will be put. +# If a relative path is entered the value of OUTPUT_DIRECTORY will be +# put in front of it. If left blank `xml' will be used as the default path. + +XML_OUTPUT = xml + +# The XML_SCHEMA tag can be used to specify an XML schema, +# which can be used by a validating XML parser to check the +# syntax of the XML files. + +XML_SCHEMA = + +# The XML_DTD tag can be used to specify an XML DTD, +# which can be used by a validating XML parser to check the +# syntax of the XML files. + +XML_DTD = + +# If the XML_PROGRAMLISTING tag is set to YES Doxygen will +# dump the program listings (including syntax highlighting +# and cross-referencing information) to the XML output. Note that +# enabling this will significantly increase the size of the XML output. + +XML_PROGRAMLISTING = YES + +#--------------------------------------------------------------------------- +# configuration options related to the DOCBOOK output +#--------------------------------------------------------------------------- + +# If the GENERATE_DOCBOOK tag is set to YES Doxygen will generate DOCBOOK files +# that can be used to generate PDF. + +GENERATE_DOCBOOK = NO + +# The DOCBOOK_OUTPUT tag is used to specify where the DOCBOOK pages will be put. +# If a relative path is entered the value of OUTPUT_DIRECTORY will be put in +# front of it. If left blank docbook will be used as the default path. + +DOCBOOK_OUTPUT = docbook + +#--------------------------------------------------------------------------- +# configuration options for the AutoGen Definitions output +#--------------------------------------------------------------------------- + +# If the GENERATE_AUTOGEN_DEF tag is set to YES Doxygen will +# generate an AutoGen Definitions (see autogen.sf.net) file +# that captures the structure of the code including all +# documentation. Note that this feature is still experimental +# and incomplete at the moment. + +GENERATE_AUTOGEN_DEF = NO + +#--------------------------------------------------------------------------- +# configuration options related to the Perl module output +#--------------------------------------------------------------------------- + +# If the GENERATE_PERLMOD tag is set to YES Doxygen will +# generate a Perl module file that captures the structure of +# the code including all documentation. Note that this +# feature is still experimental and incomplete at the +# moment. + +GENERATE_PERLMOD = NO + +# If the PERLMOD_LATEX tag is set to YES Doxygen will generate +# the necessary Makefile rules, Perl scripts and LaTeX code to be able +# to generate PDF and DVI output from the Perl module output. + +PERLMOD_LATEX = NO + +# If the PERLMOD_PRETTY tag is set to YES the Perl module output will be +# nicely formatted so it can be parsed by a human reader. This is useful +# if you want to understand what is going on. On the other hand, if this +# tag is set to NO the size of the Perl module output will be much smaller +# and Perl will parse it just the same. + +PERLMOD_PRETTY = YES + +# The names of the make variables in the generated doxyrules.make file +# are prefixed with the string contained in PERLMOD_MAKEVAR_PREFIX. +# This is useful so different doxyrules.make files included by the same +# Makefile don't overwrite each other's variables. + +PERLMOD_MAKEVAR_PREFIX = + +#--------------------------------------------------------------------------- +# Configuration options related to the preprocessor +#--------------------------------------------------------------------------- + +# If the ENABLE_PREPROCESSING tag is set to YES (the default) Doxygen will +# evaluate all C-preprocessor directives found in the sources and include +# files. + +ENABLE_PREPROCESSING = YES + +# If the MACRO_EXPANSION tag is set to YES Doxygen will expand all macro +# names in the source code. If set to NO (the default) only conditional +# compilation will be performed. Macro expansion can be done in a controlled +# way by setting EXPAND_ONLY_PREDEF to YES. + +MACRO_EXPANSION = NO + +# If the EXPAND_ONLY_PREDEF and MACRO_EXPANSION tags are both set to YES +# then the macro expansion is limited to the macros specified with the +# PREDEFINED and EXPAND_AS_DEFINED tags. + +EXPAND_ONLY_PREDEF = NO + +# If the SEARCH_INCLUDES tag is set to YES (the default) the includes files +# pointed to by INCLUDE_PATH will be searched when a #include is found. + +SEARCH_INCLUDES = YES + +# The INCLUDE_PATH tag can be used to specify one or more directories that +# contain include files that are not input files but should be processed by +# the preprocessor. + +INCLUDE_PATH = + +# You can use the INCLUDE_FILE_PATTERNS tag to specify one or more wildcard +# patterns (like *.h and *.hpp) to filter out the header-files in the +# directories. If left blank, the patterns specified with FILE_PATTERNS will +# be used. + +INCLUDE_FILE_PATTERNS = + +# The PREDEFINED tag can be used to specify one or more macro names that +# are defined before the preprocessor is started (similar to the -D option of +# gcc). The argument of the tag is a list of macros of the form: name +# or name=definition (no spaces). If the definition and the = are +# omitted =1 is assumed. To prevent a macro definition from being +# undefined via #undef or recursively expanded use the := operator +# instead of the = operator. + +PREDEFINED = + +# If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then +# this tag can be used to specify a list of macro names that should be expanded. +# The macro definition that is found in the sources will be used. +# Use the PREDEFINED tag if you want to use a different macro definition that +# overrules the definition found in the source code. + +EXPAND_AS_DEFINED = + +# If the SKIP_FUNCTION_MACROS tag is set to YES (the default) then +# doxygen's preprocessor will remove all references to function-like macros +# that are alone on a line, have an all uppercase name, and do not end with a +# semicolon, because these will confuse the parser if not removed. + +SKIP_FUNCTION_MACROS = YES + +#--------------------------------------------------------------------------- +# Configuration::additions related to external references +#--------------------------------------------------------------------------- + +# The TAGFILES option can be used to specify one or more tagfiles. For each +# tag file the location of the external documentation should be added. The +# format of a tag file without this location is as follows: +# TAGFILES = file1 file2 ... +# Adding location for the tag files is done as follows: +# TAGFILES = file1=loc1 "file2 = loc2" ... +# where "loc1" and "loc2" can be relative or absolute paths +# or URLs. Note that each tag file must have a unique name (where the name does +# NOT include the path). If a tag file is not located in the directory in which +# doxygen is run, you must also specify the path to the tagfile here. + +TAGFILES = + +# When a file name is specified after GENERATE_TAGFILE, doxygen will create +# a tag file that is based on the input files it reads. + +GENERATE_TAGFILE = + +# If the ALLEXTERNALS tag is set to YES all external classes will be listed +# in the class index. If set to NO only the inherited external classes +# will be listed. + +ALLEXTERNALS = NO + +# If the EXTERNAL_GROUPS tag is set to YES all external groups will be listed +# in the modules index. If set to NO, only the current project's groups will +# be listed. + +EXTERNAL_GROUPS = YES + +# If the EXTERNAL_PAGES tag is set to YES all external pages will be listed +# in the related pages index. If set to NO, only the current project's +# pages will be listed. + +EXTERNAL_PAGES = YES + +# The PERL_PATH should be the absolute path and name of the perl script +# interpreter (i.e. the result of `which perl'). + +PERL_PATH = /usr/bin/perl + +#--------------------------------------------------------------------------- +# Configuration options related to the dot tool +#--------------------------------------------------------------------------- + +# If the CLASS_DIAGRAMS tag is set to YES (the default) Doxygen will +# generate a inheritance diagram (in HTML, RTF and LaTeX) for classes with base +# or super classes. Setting the tag to NO turns the diagrams off. Note that +# this option also works with HAVE_DOT disabled, but it is recommended to +# install and use dot, since it yields more powerful graphs. + +CLASS_DIAGRAMS = NO + +# You can define message sequence charts within doxygen comments using the \msc +# command. Doxygen will then run the mscgen tool (see +# http://www.mcternan.me.uk/mscgen/) to produce the chart and insert it in the +# documentation. The MSCGEN_PATH tag allows you to specify the directory where +# the mscgen tool resides. If left empty the tool is assumed to be found in the +# default search path. + +MSCGEN_PATH = + +# If set to YES, the inheritance and collaboration graphs will hide +# inheritance and usage relations if the target is undocumented +# or is not a class. + +HIDE_UNDOC_RELATIONS = YES + +# If you set the HAVE_DOT tag to YES then doxygen will assume the dot tool is +# available from the path. This tool is part of Graphviz, a graph visualization +# toolkit from AT&T and Lucent Bell Labs. The other options in this section +# have no effect if this option is set to NO (the default) + +HAVE_DOT = NO + +# The DOT_NUM_THREADS specifies the number of dot invocations doxygen is +# allowed to run in parallel. When set to 0 (the default) doxygen will +# base this on the number of processors available in the system. You can set it +# explicitly to a value larger than 0 to get control over the balance +# between CPU load and processing speed. + +DOT_NUM_THREADS = 0 + +# By default doxygen will use the Helvetica font for all dot files that +# doxygen generates. When you want a differently looking font you can specify +# the font name using DOT_FONTNAME. You need to make sure dot is able to find +# the font, which can be done by putting it in a standard location or by setting +# the DOTFONTPATH environment variable or by setting DOT_FONTPATH to the +# directory containing the font. + +DOT_FONTNAME = Helvetica + +# The DOT_FONTSIZE tag can be used to set the size of the font of dot graphs. +# The default size is 10pt. + +DOT_FONTSIZE = 10 + +# By default doxygen will tell dot to use the Helvetica font. +# If you specify a different font using DOT_FONTNAME you can use DOT_FONTPATH to +# set the path where dot can find it. + +DOT_FONTPATH = + +# If the CLASS_GRAPH and HAVE_DOT tags are set to YES then doxygen +# will generate a graph for each documented class showing the direct and +# indirect inheritance relations. Setting this tag to YES will force the +# CLASS_DIAGRAMS tag to NO. + +CLASS_GRAPH = YES + +# If the COLLABORATION_GRAPH and HAVE_DOT tags are set to YES then doxygen +# will generate a graph for each documented class showing the direct and +# indirect implementation dependencies (inheritance, containment, and +# class references variables) of the class with other documented classes. + +COLLABORATION_GRAPH = YES + +# If the GROUP_GRAPHS and HAVE_DOT tags are set to YES then doxygen +# will generate a graph for groups, showing the direct groups dependencies + +GROUP_GRAPHS = YES + +# If the UML_LOOK tag is set to YES doxygen will generate inheritance and +# collaboration diagrams in a style similar to the OMG's Unified Modeling +# Language. + +UML_LOOK = NO + +# If the UML_LOOK tag is enabled, the fields and methods are shown inside +# the class node. If there are many fields or methods and many nodes the +# graph may become too big to be useful. The UML_LIMIT_NUM_FIELDS +# threshold limits the number of items for each type to make the size more +# manageable. Set this to 0 for no limit. Note that the threshold may be +# exceeded by 50% before the limit is enforced. + +UML_LIMIT_NUM_FIELDS = 10 + +# If set to YES, the inheritance and collaboration graphs will show the +# relations between templates and their instances. + +TEMPLATE_RELATIONS = NO + +# If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDE_GRAPH, and HAVE_DOT +# tags are set to YES then doxygen will generate a graph for each documented +# file showing the direct and indirect include dependencies of the file with +# other documented files. + +INCLUDE_GRAPH = YES + +# If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDED_BY_GRAPH, and +# HAVE_DOT tags are set to YES then doxygen will generate a graph for each +# documented header file showing the documented files that directly or +# indirectly include this file. + +INCLUDED_BY_GRAPH = YES + +# If the CALL_GRAPH and HAVE_DOT options are set to YES then +# doxygen will generate a call dependency graph for every global function +# or class method. Note that enabling this option will significantly increase +# the time of a run. So in most cases it will be better to enable call graphs +# for selected functions only using the \callgraph command. + +CALL_GRAPH = NO + +# If the CALLER_GRAPH and HAVE_DOT tags are set to YES then +# doxygen will generate a caller dependency graph for every global function +# or class method. Note that enabling this option will significantly increase +# the time of a run. So in most cases it will be better to enable caller +# graphs for selected functions only using the \callergraph command. + +CALLER_GRAPH = NO + +# If the GRAPHICAL_HIERARCHY and HAVE_DOT tags are set to YES then doxygen +# will generate a graphical hierarchy of all classes instead of a textual one. + +GRAPHICAL_HIERARCHY = YES + +# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES +# then doxygen will show the dependencies a directory has on other directories +# in a graphical way. The dependency relations are determined by the #include +# relations between the files in the directories. + +DIRECTORY_GRAPH = YES + +# The DOT_IMAGE_FORMAT tag can be used to set the image format of the images +# generated by dot. Possible values are svg, png, jpg, or gif. +# If left blank png will be used. If you choose svg you need to set +# HTML_FILE_EXTENSION to xhtml in order to make the SVG files +# visible in IE 9+ (other browsers do not have this requirement). + +DOT_IMAGE_FORMAT = png + +# If DOT_IMAGE_FORMAT is set to svg, then this option can be set to YES to +# enable generation of interactive SVG images that allow zooming and panning. +# Note that this requires a modern browser other than Internet Explorer. +# Tested and working are Firefox, Chrome, Safari, and Opera. For IE 9+ you +# need to set HTML_FILE_EXTENSION to xhtml in order to make the SVG files +# visible. Older versions of IE do not have SVG support. + +INTERACTIVE_SVG = NO + +# The tag DOT_PATH can be used to specify the path where the dot tool can be +# found. If left blank, it is assumed the dot tool can be found in the path. + +DOT_PATH = + +# The DOTFILE_DIRS tag can be used to specify one or more directories that +# contain dot files that are included in the documentation (see the +# \dotfile command). + +DOTFILE_DIRS = + +# The MSCFILE_DIRS tag can be used to specify one or more directories that +# contain msc files that are included in the documentation (see the +# \mscfile command). + +MSCFILE_DIRS = + +# The DOT_GRAPH_MAX_NODES tag can be used to set the maximum number of +# nodes that will be shown in the graph. If the number of nodes in a graph +# becomes larger than this value, doxygen will truncate the graph, which is +# visualized by representing a node as a red box. Note that doxygen if the +# number of direct children of the root node in a graph is already larger than +# DOT_GRAPH_MAX_NODES then the graph will not be shown at all. Also note +# that the size of a graph can be further restricted by MAX_DOT_GRAPH_DEPTH. + +DOT_GRAPH_MAX_NODES = 50 + +# The MAX_DOT_GRAPH_DEPTH tag can be used to set the maximum depth of the +# graphs generated by dot. A depth value of 3 means that only nodes reachable +# from the root by following a path via at most 3 edges will be shown. Nodes +# that lay further from the root node will be omitted. Note that setting this +# option to 1 or 2 may greatly reduce the computation time needed for large +# code bases. Also note that the size of a graph can be further restricted by +# DOT_GRAPH_MAX_NODES. Using a depth of 0 means no depth restriction. + +MAX_DOT_GRAPH_DEPTH = 0 + +# Set the DOT_TRANSPARENT tag to YES to generate images with a transparent +# background. This is disabled by default, because dot on Windows does not +# seem to support this out of the box. Warning: Depending on the platform used, +# enabling this option may lead to badly anti-aliased labels on the edges of +# a graph (i.e. they become hard to read). + +DOT_TRANSPARENT = NO + +# Set the DOT_MULTI_TARGETS tag to YES allow dot to generate multiple output +# files in one run (i.e. multiple -o and -T options on the command line). This +# makes dot run faster, but since only newer versions of dot (>1.8.10) +# support this, this feature is disabled by default. + +DOT_MULTI_TARGETS = NO + +# If the GENERATE_LEGEND tag is set to YES (the default) Doxygen will +# generate a legend page explaining the meaning of the various boxes and +# arrows in the dot generated graphs. + +GENERATE_LEGEND = YES + +# If the DOT_CLEANUP tag is set to YES (the default) Doxygen will +# remove the intermediate dot files that are used to generate +# the various graphs. + +DOT_CLEANUP = YES diff --git a/mm_trj2pdb/src/CMakeLists.txt b/mm_trj2pdb/src/CMakeLists.txt new file mode 100644 index 0000000..e3486ad --- /dev/null +++ b/mm_trj2pdb/src/CMakeLists.txt @@ -0,0 +1,29 @@ +set ("${PROJECT}_VERSION_MAJOR" 1) +set ("${PROJECT}_VERSION_MINOR" 0) +set ("${PROJECT}_VERSION_PATCH" 1) +set ("${PROJECT}_VERSION" ${${PROJECT}_VERSION_MAJOR}.${${PROJECT}_VERSION_MINOR}.${${PROJECT}_VERSION_PATCH}) + +message (STATUS "${PROJECT}: Version ${${PROJECT}_VERSION}") + +# set files +aux_source_directory (. SOURCES) + +# set library +if (CMAKE_COMPILER_IS_GNUCXX) + set (ADDITIONAL_LIB m) +else () + set (ADDITIONAL_LIB) +endif() + +# message +message (STATUS "SOURCES: ${SOURCES}") + +# link libraries and compile +add_executable (${PROJECT} ${SOURCES}) +target_link_libraries (${PROJECT} ${ADDITIONAL_LIB}) + +# install properties +INSTALL (TARGETS ${PROJECT} DESTINATION bin) +if (ADD_INCLUDE) + INSTALL (FILES ${PUBLIC_HEADERS} DESTINATION include/${PROJECT}) +endif () \ No newline at end of file diff --git a/mm_trj2pdb/src/Makefile b/mm_trj2pdb/src/Makefile new file mode 100644 index 0000000..df7b0dd --- /dev/null +++ b/mm_trj2pdb/src/Makefile @@ -0,0 +1,20 @@ +PROJECT=TRJ2PDB + +CC=gcc +CFLAGS=-c -Wall -fPIC +LDFLAGS=-lm +SOURCES_DIR=src +SOURCES=main.c add_main.c coords.c messages.c print_struct.c +OBJECTS=$(SOURCES:.c=.o) +EXECUTABLE=mm_trj2pdb + +$(PROJECT): $(SOURCES) $(EXECUTABLE) + +$(EXECUTABLE): $(OBJECTS) + $(CC) $(LDFLAGS) $(OBJECTS) -o $@ + +.c.o: + $(CC) $(CFLAGS) $< -o $@ + +clean: + rm -f *.o test* diff --git a/mm_trj2pdb/src/add_main.c b/mm_trj2pdb/src/add_main.c new file mode 100644 index 0000000..32abf70 --- /dev/null +++ b/mm_trj2pdb/src/add_main.c @@ -0,0 +1,93 @@ +/** + * @file + */ + +#include + +#include "messages.h" + + +/** + * @fn error_checking + */ +int error_checking (const const char *input, const char *output) +/** + * @brief function that checks errors in input variables + * @code + * error_checking (input, output); + * @endcode + * + * @param aglinp aglomerate file name + * @param cell massive of cell size + * @param input input file name + * @param output output file name + * + * @return 11 - error in 'input' + * @return 12 - error in 'output' + * @return 0 - exit without errors + */ +{ + if (input[0] == '#') + return 11; + if (output[0] == '#') + return 12; + + return 0; +} + + +/** + * @fn print_message + */ +int print_message (const int quiet, FILE *std_output, const int log, FILE *f_log, + const int mode, const char *str) +/** + * @brief function that prints message in log and stdout + * @code + * print_message (quiet, stdout, log, f_log, 0, str); + * @endcode + * + * @param quiet status of quiet-mode + * @param std_output stdout + * @param log status of log-mode + * @param f_log log file + * @param mode number of message in "messages.c" + * @param str additional text in message + * + * @return 0 - exit without errors + */ +{ + if ((quiet != 1) && (std_output != stderr)) + message (0, mode, str, std_output); + if (log == 1) + message (1, mode, str, f_log); + + return 0; +} + + +/** + * @fn set_defaults + */ +int set_defaults (char *input, int *log, char *output, int *quiet) +/** + * @brief function that sets default values of variables + * @code + * set_defaults (input, &log, output, &quiet); + * @endcode + * + * @param input mask of trajectory files + * @param log status of log-mode + * @param output output file name + * @param quiet status of quiet-mode + * + * @return 0 - exit without errors + */ +{ + input[0] = '#'; + *log = 0; + output[0] = '#'; + *quiet = 0; + + return 0; +} \ No newline at end of file diff --git a/mm_trj2pdb/src/add_main.h b/mm_trj2pdb/src/add_main.h new file mode 100644 index 0000000..c95aedd --- /dev/null +++ b/mm_trj2pdb/src/add_main.h @@ -0,0 +1,22 @@ +/** + * @file + */ + +#ifndef ADD_MAIN_H +#define ADD_MAIN_H + +/** + * @fn error_checking + */ +/** + * @fn print_message + */ +/** + * @fn set_defaults + */ + +int error_checking (const char *, const char *); +int print_message (const int, FILE *, const int, FILE *, const int, const char *); +int set_defaults (char *, int *, char *, int *); + +#endif /* ADD_MAIN_H */ \ No newline at end of file diff --git a/mm_trj2pdb/src/coords.c b/mm_trj2pdb/src/coords.c new file mode 100644 index 0000000..e7438cb --- /dev/null +++ b/mm_trj2pdb/src/coords.c @@ -0,0 +1,354 @@ +/** + * @file + */ + +#include +#include + +/** + * @fn reading_coords + */ +int reading_coords (const int mode, const char *filename, const int type_inter, + const int *label_atom, const float *cell, int *num_mol, + int *num_atoms, int *true_label_mol, int *label_mol, + int *type_atoms, float *coords, char *ch_type_atoms) +/** + * @brief function that reads coordinates from special file format + * @code + * reading_coords (0, filename, type_inter, label_atom, cell, &num_mol, &num_atoms, + * true_label_mol, label_mol, type_atoms, coords, ch_type_atoms); + * @endcode + * + * @param mode mode of reading; '1' is statgen, '2' is envir or + * frad, '3' is agl + * @param filename input file name + * @param type_inter number of needed atoms + * (number of needed molecules) + * @param label_atom massive of needed atom types + * (massive of needed molecules) + * @param cell massive of cell size + * @param num_mol number of molecules + * @param num_atoms number of atoms + * @param true_label_mol massive of true numbers of molecule for atoms + * @param label_mol massive of numbers of molecule for atoms + * @param type_atoms massive of atom types + * @param coords massive of coordinates + * @param ch_type_atoms massive of char atom types + * + * @return 1 - file $filename does not exist + * @return 2 - unknown mode + * @return 0 - exit without errors + */ +{ + char at_symb[32], file_string[256]; + int atoms, cur_at_num, cur_at_type, cur_mol, i, j, tr_num_atoms, ref_mol, x, y; + float cur_coords[3], *not_tr_coords, ref[3]; + FILE *inp; + +/* cur_* temp variables + * at_symb temp variable + * file_string temp string variable + * atoms total number of atoms in system + * tr_num_atoms number of translated atoms (must be 8*num_atoms) + * ref_mol number of molecule for reference in translation + * not_tr_coords massive of not translated coordinates + * ref massive of coordinates of reference molecule + * inp input file + */ + +/// Work blocks + + *num_atoms = 0; + *num_mol = 0; + +/// 
   reading file
+ inp = fopen (filename, "r"); + if (inp == NULL) + return 1; + + ref_mol = -1; + fscanf (inp, "%i", &atoms); + not_tr_coords = (float *) malloc (3 * atoms * sizeof (float)); + fgets (file_string, 256, inp); + for (i=0; i translation + tr_num_atoms = *num_atoms; + for (i=0; i<*num_atoms; i++) + for (j=0; j<3; j++) + coords[3*i+j] = not_tr_coords[3*i+j]; + +// assign initial value to reference coordinates + ref_mol = label_mol[0]; + for (i=0; i<3; i++) + ref[i] = coords[3*0+i]; + + for (i=0; i<*num_atoms; i++) + { + if (label_mol[i] != ref_mol) + { + ref_mol = label_mol[i]; + for (j=0; j<3; j++) + ref[j] = not_tr_coords[3*i+j]; + } + + for (x=0; x<3; x++) + { + if (ref[x] >= 0.0) +// if xyz >= 0.0 A + { + for (j=0; j<3; j++) + if (j == x) + coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j] - cell[j]; + else + coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j]; + + label_mol[tr_num_atoms] = label_mol[i]; + type_atoms[tr_num_atoms] = type_atoms[i]; + tr_num_atoms++; + } + else +// if xyz < 0.0 A + { + for (j=0; j<3; j++) + if (j == x) + coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j] + cell[j]; + else + coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j]; + + label_mol[tr_num_atoms] = label_mol[i]; + type_atoms[tr_num_atoms] = type_atoms[i]; + tr_num_atoms++; + } + } + + for (x=0; x<3; x++) + { + for (y=x+1; y<3; y++) + { + if ((ref[x] >= 0.0) && (ref[y] >= 0.0)) +// if xyz and xyz >= 0.0 A + { + for (j=0; j<3; j++) + if ((j == x) || (j == y)) + coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j] - cell[j]; + else + coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j]; + + label_mol[tr_num_atoms] = label_mol[i]; + type_atoms[tr_num_atoms] = type_atoms[i]; + tr_num_atoms++; + } + + if ((ref[x] < 0.0) && (ref[y] < 0.0)) +// if xyz and xyz < 0.0 A + { + for (j=0; j<3; j++) + if ((j == x) || (j == y)) + coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j] + cell[j]; + else + coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j]; + + label_mol[tr_num_atoms] = label_mol[i]; + type_atoms[tr_num_atoms] = type_atoms[i]; + tr_num_atoms++; + } + } + + for (y=0; y<3; y++) + if ((ref[x] < 0.0) && (ref[y] >= 0.0)) +// if xyz OR xyz >= 0.0 + { + for (j=0; j<3; j++) + { + if (j == x) + coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j] + cell[j]; + if (j == y) + coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j] - cell[j]; + if ((j != x) && (j != y)) + coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j]; + } + + label_mol[tr_num_atoms] = label_mol[i]; + type_atoms[tr_num_atoms] = type_atoms[i]; + tr_num_atoms++; + } + } + + if ((ref[0] >= 0.0) && (ref[1] >= 0.0) && (ref[2] >= 0.0)) +// if x and y and z >= 0.0 A + { + coords[3*tr_num_atoms+0] = not_tr_coords[3*i+0] - cell[0]; + coords[3*tr_num_atoms+1] = not_tr_coords[3*i+1] - cell[1]; + coords[3*tr_num_atoms+2] = not_tr_coords[3*i+2] - cell[2]; + + label_mol[tr_num_atoms] = label_mol[i]; + type_atoms[tr_num_atoms] = type_atoms[i]; + tr_num_atoms++; + } + + if ((ref[0] >= 0.0) && (ref[1] >= 0.0) && (ref[2] < 0.0)) +// if x and y >= 0.0 A and z < 0.0 A + { + coords[3*tr_num_atoms+0] = not_tr_coords[3*i+0] - cell[0]; + coords[3*tr_num_atoms+1] = not_tr_coords[3*i+1] - cell[1]; + coords[3*tr_num_atoms+2] = not_tr_coords[3*i+2] + cell[2]; + + label_mol[tr_num_atoms] = label_mol[i]; + type_atoms[tr_num_atoms] = type_atoms[i]; + tr_num_atoms++; + } + + if ((ref[0] >= 0.0) && (ref[1] < 0.0) && (ref[2] >= 0.0)) +// if x and z >= 0.0 A and y < 0.0 A + { + coords[3*tr_num_atoms+0] = not_tr_coords[3*i+0] - cell[0]; + coords[3*tr_num_atoms+1] = not_tr_coords[3*i+1] + cell[1]; + coords[3*tr_num_atoms+2] = not_tr_coords[3*i+2] - cell[2]; + + label_mol[tr_num_atoms] = label_mol[i]; + type_atoms[tr_num_atoms] = type_atoms[i]; + tr_num_atoms++; + } + + if ((ref[0] < 0.0) && (ref[1] >= 0.0) && (ref[2] >= 0.0)) +// if y and z >= 0.0 A and x < 0.0 A + { + coords[3*tr_num_atoms+0] = not_tr_coords[3*i+0] + cell[0]; + coords[3*tr_num_atoms+1] = not_tr_coords[3*i+1] - cell[1]; + coords[3*tr_num_atoms+2] = not_tr_coords[3*i+2] - cell[2]; + + label_mol[tr_num_atoms] = label_mol[i]; + type_atoms[tr_num_atoms] = type_atoms[i]; + tr_num_atoms++; + } + + if ((ref[0] < 0.0) && (ref[1] < 0.0) && (ref[2] >= 0.0)) +// if x and y < 0.0 A and z >= 0.0 A + { + coords[3*tr_num_atoms+0] = not_tr_coords[3*i+0] + cell[0]; + coords[3*tr_num_atoms+1] = not_tr_coords[3*i+1] + cell[1]; + coords[3*tr_num_atoms+2] = not_tr_coords[3*i+2] - cell[2]; + + label_mol[tr_num_atoms] = label_mol[i]; + type_atoms[tr_num_atoms] = type_atoms[i]; + tr_num_atoms++; + } + + if ((ref[0] < 0.0) && (ref[1] >= 0.0) && (ref[2] < 0.0)) +// if x and z < 0.0 A and y >= 0.0 A + { + coords[3*tr_num_atoms+0] = not_tr_coords[3*i+0] + cell[0]; + coords[3*tr_num_atoms+1] = not_tr_coords[3*i+1] - cell[1]; + coords[3*tr_num_atoms+2] = not_tr_coords[3*i+2] + cell[2]; + + label_mol[tr_num_atoms] = label_mol[i]; + type_atoms[tr_num_atoms] = type_atoms[i]; + tr_num_atoms++; + } + + if ((ref[0] >= 0.0) && (ref[1] < 0.0) && (ref[2] < 0.0)) +// if x >= 0.0 A and y and z < 0.0 A + { + coords[3*tr_num_atoms+0] = not_tr_coords[3*i+0] - cell[0]; + coords[3*tr_num_atoms+1] = not_tr_coords[3*i+1] + cell[1]; + coords[3*tr_num_atoms+2] = not_tr_coords[3*i+2] + cell[2]; + + label_mol[tr_num_atoms] = label_mol[i]; + type_atoms[tr_num_atoms] = type_atoms[i]; + tr_num_atoms++; + } + + if ((ref[0] < 0.0) && (ref[1] < 0.0) && (ref[2] < 0.0)) +// if x and y and z < 0.0 A + { + coords[3*tr_num_atoms+0] = not_tr_coords[3*i+0] + cell[0]; + coords[3*tr_num_atoms+1] = not_tr_coords[3*i+1] + cell[1]; + coords[3*tr_num_atoms+2] = not_tr_coords[3*i+2] + cell[2]; + + label_mol[tr_num_atoms] = label_mol[i]; + type_atoms[tr_num_atoms] = type_atoms[i]; + tr_num_atoms++; + } + } + +/// 
   free memory
+ free (not_tr_coords); + + return 0; +} \ No newline at end of file diff --git a/mm_trj2pdb/src/coords.h b/mm_trj2pdb/src/coords.h new file mode 100644 index 0000000..6bdf48e --- /dev/null +++ b/mm_trj2pdb/src/coords.h @@ -0,0 +1,16 @@ +/** + * @file + */ + +#ifndef COORDS_H +#define COORDS_H + +/** + * @fn reading_coords + */ + +int reading_coords (const int, const char *, const int, const int *, + const float *, int *, int *, int *, int *, int *, float *, + char *); + +#endif /* COORDS_H */ \ No newline at end of file diff --git a/mm_trj2pdb/src/main.c b/mm_trj2pdb/src/main.c new file mode 100644 index 0000000..d144661 --- /dev/null +++ b/mm_trj2pdb/src/main.c @@ -0,0 +1,255 @@ +/** + * @file + */ +/** + * @mainpage mm_trj2pdb + * @image latex ./logo.png + * + * @section intro_sec Introduction + * + * About this program: + *
    + *
  • Program that creates PDB file from trajectory snapshot + *
+ * + * Developer: + *
    + *
  • Evgeniy Alekseev aka arcanis
    + *
+ * License: + *
    + *
  • GPL + *
+ * + * @section How-To-Use How to use + * Usage: + * 
+ * mm_trj2pdb -i INPUT -o OUTPUT [ -l LOGFILE ] [ -q ] [ -h ]
+ *
+ * Parametrs:
+ *    -i          - input file name
+ *    -o          - output file name
+ *    -l          - log enable
+ *    -q          - quiet enable
+ *    -h          - show this help and exit
+ *
+ * + * @page Install + * + * @section Requirements Requirements + * The application mm_trj2pdb requires the following external stuff: + * - cmake >= 2.8 + * - gcc >= 4.8 + * + * @section How-To How to install + * + * @subsection Linux Linux + * @code + * mkdir build && cd build + * cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=Release ../ + * make + * make install + * @endcode + * + * @subsection Windows Windows + * @code + * create project file using 'cmake' + * compile project + * @endcode + * You may also download compiled executable file for Win_x86. + * + * @page Changelog + * V.1.0.1 (2013-07-27) + * * initial release + */ + +#include +#include +#include +#include + +#include "add_main.h" +#include "coords.h" +#include "messages.h" +#include "print_struct.h" + + +/** + * @fn main + */ +int main(int argc, char *argv[]) +/** + * @return 1 - error in error_checking + * @return 2 - input file does not exist + * @return 3 - memory error + * @return 4 - unknown flag + * @return 0 - exit without errors + */ +{ + char tmp_str[2048]; + int error, i, *tmp_int; + FILE *f_inp, *f_log; + + char *ch_type_atoms, input[256], logfile[256], output[256]; + float cell[3], *coords; + int *label_mol, log, *needed_mol, num_atoms, num_mol, quiet, *true_label_mol; + +/* ch_type_atoms massive of char atom types + * input input file name + * logfile log file name + * output output file name + * + * cell sell size + * coords massive of coordinates + * + * label_mol massive of numbers of molecule for atoms + * log status of log-mode + * needed_mol massive of numbers of needed molecule + * num_atoms number of atoms + * num_mol number of molecules + * quiet status of quiet-mode + * true_label_mol massive of true numbers of molecule for atoms + */ + + set_defaults (input, &log, output, &quiet); + + for (i=1; i +#include + + +/** + * @fn message + */ +int message (const int log, const int mode, const char *text, FILE *output) +/** + * @brief function that prints messages to output + * @code + * message (log, mode, text, output); + * @endcode + * + * @param log equal to 1 if print to logfile + * @param mode number of message + * @param text additional text + * @param output output file (may be stdout) + * + * @return 1 - unknown mode + * @return 0 - exit without errors + */ +{ + char out[4096]; + + if (log == 1) + { + char time_str[256]; + + time_t t = time (NULL); + struct tm* aTm = localtime (&t); + sprintf (time_str, "[%04d-%02d-%02d %02d:%02d:%02d] [%2i]: ", aTm->tm_year+1900, + aTm->tm_mon+1, aTm->tm_mday, aTm->tm_hour, aTm->tm_min, aTm->tm_sec, mode); + fputs (time_str, output); + } + + switch (mode) + { + case 0: + sprintf (out, "Start program: '%s'\n", text); + break; + case 1: + sprintf (out, "Checking errors\n"); + break; + case 2: + sprintf (out, "Errors are not detected\n"); + break; + case 3: + sprintf (out, "Initialization of variables from file '%s'\n", text); + break; + case 4: + sprintf (out, "%6cAglomerate was selected successfully\n", ' '); + break; + case 5: + sprintf (out, "Initial parametrs: \n%s", text); + break; + case 6: + sprintf (out, "Processing\n"); + break; + case 7: + sprintf (out, "Open file: '%s'\n", text); + break; + case 8: + sprintf (out, "%s", text); + break; + case 9: + sprintf (out, "%6cSize of variables was changed successfully\n", ' '); + break; + case 10: + sprintf (out, "%6cConnectivity matrix was created successfully\n", ' '); + break; + case 11: + sprintf (out, "%6cConnectivity matrix was processed successfully\n", ' '); + break; + case 12: + sprintf (out, "%6cResult was printed to file '%s' successfully\n", ' ', text); + break; + case 13: + sprintf (out, "End of processing\n"); + break; + case 14: + sprintf (out, "Print result to file '%s'\n", text); + break; + case 15: + sprintf (out, "Free memory\n"); + break; + case 16: + sprintf (out, "Exiting without errors\n"); + break; + case 17: + sprintf (out, "Something wrong!\nSee '%s -h' for more details\n", text); + break; + case 18: + sprintf (out, "File '%s' not found\nError\n", text); + break; + case 19: + sprintf (out, "Memory error\n"); + break; + case 20: + sprintf (out, "%6cCenter of molecules was set successfully\n", ' '); + break; + case 21: + sprintf (out, "%6cEnvironment was selected successfully\n", ' '); + break; + case 22: + sprintf (out, "%6cRADF was appended successfully\n", ' '); + break; + default: + return 1; + break; + } + + fputs (out, output); + return 0; +} \ No newline at end of file diff --git a/mm_trj2pdb/src/messages.h b/mm_trj2pdb/src/messages.h new file mode 100644 index 0000000..6e6ed21 --- /dev/null +++ b/mm_trj2pdb/src/messages.h @@ -0,0 +1,14 @@ +/** + * @file + */ + +#ifndef MESSAGES_H +#define MESSAGES_H + +/** + * @fn message + */ + +int message (const int, const int, const char *, FILE *); + +#endif /* MESSAGES_H */ \ No newline at end of file diff --git a/mm_trj2pdb/src/print_struct.c b/mm_trj2pdb/src/print_struct.c new file mode 100644 index 0000000..46d9b90 --- /dev/null +++ b/mm_trj2pdb/src/print_struct.c @@ -0,0 +1,69 @@ +/** + * @file + */ + +#include + + +/** + * @fn print_structure + */ +int print_structure (const char *output, const int num_needed_mol, const int *needed_mol, + const int num_atoms, const int *label_mol, const char *ch_type_atoms, + const float *coords) +/** + * @brief function that prints structure to pdb file + * @code + * print_structure (output, num_needed_mol, needed_mol, num_atoms, label_mol, + * char_type_atoms, coords); + * @endcode + * + * @param output output file name + * @param num_needed_mol number of needed molecules + * @param needed_mol massive of number of needed molecules + * @param num_atoms number of atoms + * @param label_mol massive of numbers of molecule for atoms + * @param ch_type_atoms massive of char atom types + * @param coords massive of coordinates + * + * @return 0 - exit without errors + */ +{ + int cur_atom, cur_atom_num, cur_mol, i, j; + FILE *f_out; + +/* cur_atom current atom + * cur_atom_num true atom number + * cur_mol current molecule + * f_out output file + */ + + cur_atom = 1; + f_out = fopen (output, "w"); + + for (i=0; i