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Release mathmech 1.0.1

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arcan1s
2013-08-29 04:46:58 +04:00
parent 69fd9fd15e
commit d049cd091c
38 changed files with 623 additions and 516 deletions
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# Author: Evgeniy "arcanis" Alexeev <esalexeev@gmail.com>
# Maintainer: Evgeniy "arcanis" Alexeev <esalexeev@gmail.com>
pkgname=mathmech
pkgver=1.0.1
pkgrel=1
pkgdesc="Software package for analysis of molecular dynamics trajectories"
arch=(any)
url="https://github.com/arcan1s/moldyn/mathmech"
license=('GPL')
depends=('qt4' 'qwt')
makedepends=('unzip' 'cmake' 'automoc4')
source=(https://github.com/arcan1s/moldyn/releases/download/mm-1.0.1/${pkgname}-${pkgver}.zip)
md5sums=('5fab4bc7707d580ff41d384b1875b32c')
build ()
{
unzip -o -q ${srcdir}/${pkgname}-${pkgver}.zip -d ${srcdir}/${pkgname}
if [ -d ${srcdir}/${pkgname}/build ]; then
rm -rf build
fi
mkdir ${srcdir}/${pkgname}/build && cd ${srcdir}/${pkgname}/build
cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=Release ../
make
}
package()
{
cd ${srcdir}/${pkgname}/build
make DESTDIR=${pkgdir} install
}

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[Desktop Entry]
Name=Mathematical Molecular Mechanics
Comment=GUI for mathmech program pack
Exec=mathmech
Icon=mathmech-logo
Terminal=false
Encoding=UTF-8
Type=Application
Categories=Qt;Science;Chemistry;Physics;Education;

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@ -383,562 +383,564 @@ p, li { white-space: pre-wrap; }
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<location filename="../../build/src/ui_mainwindow.h" line="2257"/>
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<location filename="../../build/src/ui_mainwindow.h" line="2268"/>
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<location filename="../../build/src/ui_mainwindow.h" line="2269"/>
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<location filename="../../build/src/ui_mainwindow.h" line="2274"/>
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<location filename="../../build/src/ui_mainwindow.h" line="2290"/>
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<message>
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<location filename="../../build/src/ui_mainwindow.h" line="2291"/>
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<message>
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<location filename="../../build/src/ui_mainwindow.h" line="2299"/>
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<message>
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<location filename="../../build/src/ui_mainwindow.h" line="2301"/>
<location filename="../../build/src/ui_mainwindow.h" line="2300"/>
<location filename="../../build/src/ui_mainwindow.h" line="2304"/>
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<translation>min</translation>
</message>
<message>
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<location filename="../../build/src/ui_mainwindow.h" line="2302"/>
<location filename="../../build/src/ui_mainwindow.h" line="2301"/>
<location filename="../../build/src/ui_mainwindow.h" line="2305"/>
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<translation>max</translation>
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<message>
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<location filename="../../build/src/ui_mainwindow.h" line="2303"/>
<location filename="../../build/src/ui_mainwindow.h" line="2302"/>
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<message>
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<location filename="../../build/src/ui_mainwindow.h" line="2303"/>
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<translation>Angle, deg</translation>
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<message>
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<location filename="../../build/src/ui_mainwindow.h" line="2307"/>
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<translation>Matrix</translation>
</message>
<message>
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<location filename="../../build/src/ui_mainwindow.h" line="2313"/>
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<translation>RADF</translation>
</message>
<message>
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<location filename="../../build/src/ui_mainwindow.h" line="2316"/>
<source>From agglomerate</source>
<translation></translation>
</message>
<message>
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<location filename="../../build/src/ui_mainwindow.h" line="2317"/>
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<translation>From trajectory snapshot</translation>
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<message>
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<location filename="../../build/src/ui_mainwindow.h" line="2323"/>
<source>File with agglomerate</source>
<translation>File with agglomerate</translation>
</message>
<message>
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<location filename="../../build/src/ui_mainwindow.h" line="2335"/>
<source>Generate PDB</source>
<translation>Generate PDB</translation>
</message>
<message>
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<location filename="../../build/src/ui_mainwindow.h" line="2336"/>
<source>Menu</source>
<translation>Menu</translation>
</message>
<message>
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<location filename="../../build/src/ui_mainwindow.h" line="2337"/>
<source>File &amp;creator</source>
<translation>File &amp;creator</translation>
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<message>
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<location filename="../../build/src/ui_mainwindow.h" line="2338"/>
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<translation>&amp;Tools</translation>
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<message>
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<location filename="../../build/src/ui_mainwindow.h" line="2339"/>
<source>Help</source>
<translation>Help</translation>
</message>
@ -966,72 +968,72 @@ p, li { white-space: pre-wrap; }
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<message>
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<location filename="../../build/src/ui_settingswindow.h" line="315"/>
<source>Settings</source>
<translation>Settings</translation>
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<message>
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<location filename="../../build/src/ui_settingswindow.h" line="316"/>
<source>mm_trj</source>
<translation>mm_trj</translation>
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<message>
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<translation>Browse</translation>
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<message>
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<location filename="../../build/src/ui_settingswindow.h" line="318"/>
<source>mm_statgen</source>
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</message>
<message>
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<location filename="../../build/src/ui_settingswindow.h" line="320"/>
<source>mm_envir</source>
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</message>
<message>
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<location filename="../../build/src/ui_settingswindow.h" line="322"/>
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<message>
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<location filename="../../build/src/ui_settingswindow.h" line="324"/>
<source>mm_trj2pdb</source>
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<message>
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<location filename="../../build/src/ui_settingswindow.h" line="326"/>
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<message>
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<location filename="../../build/src/ui_settingswindow.h" line="330"/>
<source>English</source>
<translation>English</translation>
</message>
<message>
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<location filename="../../build/src/ui_settingswindow.h" line="331"/>
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<translation>Russian</translation>
</message>
<message>
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<location filename="../../build/src/ui_settingswindow.h" line="333"/>
<source>You need to restart application</source>
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<message>
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<location filename="../../build/src/ui_settingswindow.h" line="334"/>
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<message>
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<location filename="../../build/src/ui_settingswindow.h" line="335"/>
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mathmech/mathmech/resources/translations/rus.ts
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@ -383,564 +383,566 @@ p, li { white-space: pre-wrap; }
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<message>
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<location filename="../../src/mainwindow.cpp" line="290"/>
<location filename="../../src/mainwindow.cpp" line="333"/>
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<translation>Выбор рабочей директории</translation>
</message>
<message>
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<location filename="../../src/mainwindow.cpp" line="343"/>
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<location filename="../../src/mainwindow.cpp" line="439"/>
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<translation>Выбор файла траектории</translation>
</message>
<message>
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<location filename="../../src/mainwindow.cpp" line="258"/>
<source>All files (*.*)</source>
<translation>Все файлы (*.*)</translation>
</message>
<message>
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<location filename="../../src/mainwindow.cpp" line="267"/>
<source>Select atom types file</source>
<translation>Выбор файла типов атомов</translation>
</message>
<message>
<location filename="../../src/mainwindow.cpp" line="259"/>
<location filename="../../src/mainwindow.cpp" line="269"/>
<source>Atom types files (*.types);;All files (*.*)</source>
<translation>Файл типов атомов (*.types);;Все файлы (*.*)</translation>
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<message>
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<location filename="../../src/mainwindow.cpp" line="278"/>
<source>Save files as</source>
<translation>Сохранить файл как...</translation>
</message>
<message>
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<location filename="../../src/mainwindow.cpp" line="280"/>
<source>Mask of trajectory files</source>
<translation>Маска файлов траектории</translation>
</message>
<message>
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<location filename="../../src/mainwindow.cpp" line="322"/>
<location filename="../../src/mainwindow.cpp" line="365"/>
<location filename="../../src/mainwindow.cpp" line="408"/>
<location filename="../../src/mainwindow.cpp" line="462"/>
<location filename="../../src/mainwindow.cpp" line="289"/>
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<location filename="../../src/mainwindow.cpp" line="375"/>
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<source>Save log file as...</source>
<translation>Сохранить лог как...</translation>
</message>
<message>
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<location filename="../../src/mainwindow.cpp" line="324"/>
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<location filename="../../src/mainwindow.cpp" line="410"/>
<location filename="../../src/mainwindow.cpp" line="464"/>
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<location filename="../../src/mainwindow.cpp" line="377"/>
<location filename="../../src/mainwindow.cpp" line="420"/>
<location filename="../../src/mainwindow.cpp" line="474"/>
<source>Log files (*.log)</source>
<translation>Лог (*.log)</translation>
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<message>
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<location filename="../../src/mainwindow.cpp" line="386"/>
<location filename="../../src/mainwindow.cpp" line="310"/>
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<source>Select trajectory files</source>
<translation>Выбор файла траектории</translation>
</message>
<message>
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<location filename="../../src/mainwindow.cpp" line="345"/>
<location filename="../../src/mainwindow.cpp" line="388"/>
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<location filename="../../src/mainwindow.cpp" line="355"/>
<location filename="../../src/mainwindow.cpp" line="398"/>
<location filename="../../src/mainwindow.cpp" line="441"/>
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<translation>Файлы траектории (*.*[0-9])</translation>
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<message>
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<location filename="../../src/mainwindow.cpp" line="397"/>
<location filename="../../src/mainwindow.cpp" line="321"/>
<location filename="../../src/mainwindow.cpp" line="407"/>
<source>Save output file as...</source>
<translation>Сохранить файл как...</translation>
</message>
<message>
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<location filename="../../src/mainwindow.cpp" line="399"/>
<location filename="../../src/mainwindow.cpp" line="323"/>
<location filename="../../src/mainwindow.cpp" line="409"/>
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<translation>Выходной файл (*.dat)</translation>
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<message>
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<location filename="../../src/mainwindow.cpp" line="451"/>
<location filename="../../src/mainwindow.cpp" line="364"/>
<location filename="../../src/mainwindow.cpp" line="461"/>
<source>Save PDB file as...</source>
<translation>Сохранить PDB как...</translation>
</message>
<message>
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<location filename="../../src/mainwindow.cpp" line="453"/>
<location filename="../../src/mainwindow.cpp" line="366"/>
<location filename="../../src/mainwindow.cpp" line="463"/>
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<translation>PDB файл (*.pdb)</translation>
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<message>
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<location filename="../../src/mainwindow.cpp" line="450"/>
<source>Select agglomerate file</source>
<translation>Выбор файла с агломератом</translation>
</message>
<message>
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<location filename="../../src/mainwindow.cpp" line="452"/>
<source>Agglomerate files (*.agl);;All files (*.*)</source>
<translation>Файл с агломератом (*.agl);Все файлы (*.*)</translation>
</message>
<message>
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<location filename="../../src/mainwindow.cpp" line="612"/>
<location filename="../../src/mainwindow.cpp" line="621"/>
<location filename="../../src/mainwindow.cpp" line="622"/>
<source>Processing &apos;trj&apos;...</source>
<translation>Выполняется &apos;trj&apos;...</translation>
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<message>
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<location filename="../../src/mainwindow.cpp" line="703"/>
<location filename="../../src/mainwindow.cpp" line="751"/>
<location filename="../../src/mainwindow.cpp" line="821"/>
<location filename="../../src/mainwindow.cpp" line="889"/>
<location filename="../../src/mainwindow.cpp" line="632"/>
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<location filename="../../src/mainwindow.cpp" line="765"/>
<location filename="../../src/mainwindow.cpp" line="835"/>
<location filename="../../src/mainwindow.cpp" line="903"/>
<source>Done</source>
<translation>Готово</translation>
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<message>
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<location filename="../../src/mainwindow.cpp" line="676"/>
<location filename="../../src/mainwindow.cpp" line="689"/>
<location filename="../../src/mainwindow.cpp" line="690"/>
<source>Processing &apos;statgen&apos;...</source>
<translation>Выполняется &apos;statgen&apos;...</translation>
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<message>
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<location filename="../../src/mainwindow.cpp" line="742"/>
<location filename="../../src/mainwindow.cpp" line="755"/>
<location filename="../../src/mainwindow.cpp" line="756"/>
<source>Processing &apos;envir&apos;...</source>
<translation>Выполняется &apos;envir&apos;...</translation>
</message>
<message>
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<location filename="../../src/mainwindow.cpp" line="808"/>
<location filename="../../src/mainwindow.cpp" line="821"/>
<location filename="../../src/mainwindow.cpp" line="822"/>
<source>Processing &apos;radf&apos;...</source>
<translation>Выполняется &apos;radf&apos;...</translation>
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<message>
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<location filename="../../src/mainwindow.cpp" line="865"/>
<location filename="../../src/mainwindow.cpp" line="878"/>
<location filename="../../src/mainwindow.cpp" line="879"/>
<source>Processing &apos;agl&apos;...</source>
<translation>Выполняется &apos;agl&apos;...</translation>
</message>
<message>
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<location filename="../../src/mainwindow.cpp" line="870"/>
<location filename="../../src/mainwindow.cpp" line="883"/>
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<source>Processing &apos;trj2pdb&apos;...</source>
<translation>Выполняется &apos;trj2pdb&apos;...</translation>
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<message>
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<source>Mathematical Molecular Mechanics</source>
<translation>Mathematical Molecular Mechanics</translation>
</message>
<message>
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<location filename="../../build/src/ui_mainwindow.h" line="2224"/>
<source>Generate trajectory</source>
<translation>Создать траекторию</translation>
</message>
<message>
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<location filename="../../build/src/ui_mainwindow.h" line="2222"/>
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<source>Work directory</source>
<translation>Рабочая директория</translation>
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<message>
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<location filename="../../build/src/ui_mainwindow.h" line="2332"/>
<source>Browse</source>
<translation>Обзор</translation>
</message>
<message>
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<location filename="../../build/src/ui_mainwindow.h" line="2257"/>
<location filename="../../build/src/ui_mainwindow.h" line="2318"/>
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<location filename="../../build/src/ui_mainwindow.h" line="2260"/>
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<source>Input file</source>
<translation>Входной файл</translation>
</message>
<message>
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<location filename="../../build/src/ui_mainwindow.h" line="2208"/>
<source>Type of trajectory</source>
<translation>Тип траектории</translation>
</message>
<message>
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<location filename="../../build/src/ui_mainwindow.h" line="2211"/>
<source>GROMACS text</source>
<translation>GROMACS</translation>
</message>
<message>
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<location filename="../../build/src/ui_mainwindow.h" line="2212"/>
<source>PUMA</source>
<translation>PUMA</translation>
</message>
<message>
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<location filename="../../build/src/ui_mainwindow.h" line="2214"/>
<source>Number of steps</source>
<translation>Число шагов</translation>
</message>
<message>
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<location filename="../../build/src/ui_mainwindow.h" line="2215"/>
<source>Atom type file</source>
<translation>Файл типов атомов</translation>
</message>
<message>
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<location filename="../../build/src/ui_mainwindow.h" line="2217"/>
<source>Mask of output files</source>
<translation>Маска файлов</translation>
</message>
<message>
<location filename="../../build/src/ui_mainwindow.h" line="2216"/>
<location filename="../../build/src/ui_mainwindow.h" line="2219"/>
<source>Total atom types</source>
<translation>Всего типов атомов</translation>
</message>
<message>
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<location filename="../../build/src/ui_mainwindow.h" line="2248"/>
<location filename="../../build/src/ui_mainwindow.h" line="2267"/>
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<location filename="../../build/src/ui_mainwindow.h" line="2331"/>
<source>Log</source>
<translation>Лог</translation>
</message>
<message>
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<location filename="../../build/src/ui_mainwindow.h" line="2269"/>
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<location filename="../../build/src/ui_mainwindow.h" line="2310"/>
<location filename="../../build/src/ui_mainwindow.h" line="2333"/>
<source>Clear</source>
<translation>Очистить</translation>
</message>
<message>
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<location filename="../../build/src/ui_mainwindow.h" line="2253"/>
<location filename="../../build/src/ui_mainwindow.h" line="2270"/>
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<location filename="../../build/src/ui_mainwindow.h" line="2312"/>
<location filename="../../build/src/ui_mainwindow.h" line="2334"/>
<source>Start</source>
<translation>Старт</translation>
</message>
<message>
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<location filename="../../build/src/ui_mainwindow.h" line="2257"/>
<source>Agglomeration</source>
<translation>Агломерация</translation>
</message>
<message>
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<location filename="../../build/src/ui_mainwindow.h" line="2274"/>
<location filename="../../build/src/ui_mainwindow.h" line="2227"/>
<location filename="../../build/src/ui_mainwindow.h" line="2277"/>
<source>Mask of input files</source>
<translation>Маска файлов</translation>
</message>
<message>
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<location filename="../../build/src/ui_mainwindow.h" line="2276"/>
<location filename="../../build/src/ui_mainwindow.h" line="2202"/>
<source>Ctrl+P</source>
<translation>Ctrl+P</translation>
</message>
<message>
<location filename="../../build/src/ui_mainwindow.h" line="2229"/>
<location filename="../../build/src/ui_mainwindow.h" line="2279"/>
<source>Steps</source>
<translation>Шаги</translation>
</message>
<message>
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<location filename="../../build/src/ui_mainwindow.h" line="2277"/>
<location filename="../../build/src/ui_mainwindow.h" line="2230"/>
<location filename="../../build/src/ui_mainwindow.h" line="2280"/>
<source>first</source>
<translation>первый</translation>
</message>
<message>
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<location filename="../../build/src/ui_mainwindow.h" line="2231"/>
<location filename="../../build/src/ui_mainwindow.h" line="2281"/>
<source>last</source>
<translation>последний</translation>
</message>
<message>
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<location filename="../../build/src/ui_mainwindow.h" line="2279"/>
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<source>Cell, A</source>
<translation>Ячейка, А</translation>
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<message>
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<location filename="../../build/src/ui_mainwindow.h" line="2260"/>
<location filename="../../build/src/ui_mainwindow.h" line="2280"/>
<location filename="../../build/src/ui_mainwindow.h" line="2323"/>
<source>X</source>
<translation>X</translation>
</message>
<message>
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<location filename="../../build/src/ui_mainwindow.h" line="2261"/>
<location filename="../../build/src/ui_mainwindow.h" line="2281"/>
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<source>Y</source>
<translation>Y</translation>
</message>
<message>
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<location filename="../../build/src/ui_mainwindow.h" line="2262"/>
<location filename="../../build/src/ui_mainwindow.h" line="2282"/>
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<source>Cell, A</source>
<translation>Ячейка, А</translation>
</message>
<message>
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<location filename="../../build/src/ui_mainwindow.h" line="2263"/>
<location filename="../../build/src/ui_mainwindow.h" line="2283"/>
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<source>X</source>
<translation>X</translation>
</message>
<message>
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<location filename="../../build/src/ui_mainwindow.h" line="2264"/>
<location filename="../../build/src/ui_mainwindow.h" line="2284"/>
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<source>Y</source>
<translation>Y</translation>
</message>
<message>
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<location filename="../../build/src/ui_mainwindow.h" line="2265"/>
<location filename="../../build/src/ui_mainwindow.h" line="2285"/>
<location filename="../../build/src/ui_mainwindow.h" line="2328"/>
<source>Z</source>
<translation>Z</translation>
</message>
<message>
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<location filename="../../build/src/ui_mainwindow.h" line="2236"/>
<source>atom 0</source>
<translation>атом 0</translation>
</message>
<message>
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<location filename="../../build/src/ui_mainwindow.h" line="2290"/>
<location filename="../../build/src/ui_mainwindow.h" line="2237"/>
<location filename="../../build/src/ui_mainwindow.h" line="2293"/>
<location filename="../../build/src/ui_mainwindow.h" line="2296"/>
<source>atom 1</source>
<translation>атом 1</translation>
</message>
<message>
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<location filename="../../build/src/ui_mainwindow.h" line="2291"/>
<location filename="../../build/src/ui_mainwindow.h" line="2238"/>
<location filename="../../build/src/ui_mainwindow.h" line="2294"/>
<location filename="../../build/src/ui_mainwindow.h" line="2297"/>
<source>atom 2</source>
<translation>атом 2</translation>
</message>
<message>
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<location filename="../../build/src/ui_mainwindow.h" line="2292"/>
<location filename="../../build/src/ui_mainwindow.h" line="2239"/>
<location filename="../../build/src/ui_mainwindow.h" line="2295"/>
<location filename="../../build/src/ui_mainwindow.h" line="2298"/>
<source>atom 3</source>
<translation>атом 3</translation>
</message>
<message>
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<location filename="../../build/src/ui_mainwindow.h" line="2240"/>
<source>Interaction</source>
<translation>Взаимодействие</translation>
</message>
<message>
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<location filename="../../build/src/ui_mainwindow.h" line="2243"/>
<source>0-0</source>
<translation>0-0</translation>
</message>
<message>
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<location filename="../../build/src/ui_mainwindow.h" line="2245"/>
<source>Save</source>
<translation>Сохранить</translation>
</message>
<message>
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<location filename="../../build/src/ui_mainwindow.h" line="2246"/>
<source>Add</source>
<translation>Добавить</translation>
</message>
<message>
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<location filename="../../build/src/ui_mainwindow.h" line="2247"/>
<source>Remove</source>
<translation>Удалить</translation>
</message>
<message>
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<location filename="../../build/src/ui_mainwindow.h" line="2263"/>
<location filename="../../build/src/ui_mainwindow.h" line="2283"/>
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<location filename="../../build/src/ui_mainwindow.h" line="2266"/>
<location filename="../../build/src/ui_mainwindow.h" line="2286"/>
<location filename="../../build/src/ui_mainwindow.h" line="2329"/>
<source>Output file</source>
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</message>
<message>
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<location filename="../../build/src/ui_mainwindow.h" line="2250"/>
<source>Depth of search</source>
<translation>Глубина поиска</translation>
</message>
<message>
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<location filename="../../build/src/ui_mainwindow.h" line="2253"/>
<source>Analysis</source>
<translation>Анализ</translation>
</message>
<message>
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<location filename="../../build/src/ui_mainwindow.h" line="2308"/>
<location filename="../../build/src/ui_mainwindow.h" line="2254"/>
<location filename="../../build/src/ui_mainwindow.h" line="2311"/>
<source>Graph</source>
<translation>График</translation>
</message>
<message>
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<location filename="../../build/src/ui_mainwindow.h" line="2274"/>
<source>Environment</source>
<translation>Окружение</translation>
</message>
<message>
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<location filename="../../build/src/ui_mainwindow.h" line="2268"/>
<source>Molecule</source>
<translation>Молекула</translation>
</message>
<message>
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<location filename="../../build/src/ui_mainwindow.h" line="2269"/>
<source>Radius</source>
<translation>Радиус</translation>
</message>
<message>
<location filename="../../build/src/ui_mainwindow.h" line="2310"/>
<location filename="../../build/src/ui_mainwindow.h" line="2313"/>
<source>RADF</source>
<translation>ФРУР</translation>
</message>
<message>
<location filename="../../build/src/ui_mainwindow.h" line="2287"/>
<location filename="../../build/src/ui_mainwindow.h" line="2290"/>
<source>One atom function</source>
<translation>Одноатомная функция</translation>
</message>
<message>
<location filename="../../build/src/ui_mainwindow.h" line="2288"/>
<location filename="../../build/src/ui_mainwindow.h" line="2291"/>
<source>Three atom function</source>
<translation>Трехатомная функция</translation>
</message>
<message>
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<location filename="../../build/src/ui_mainwindow.h" line="2299"/>
<source>R, A</source>
<translation>R, A</translation>
</message>
<message>
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<location filename="../../build/src/ui_mainwindow.h" line="2301"/>
<location filename="../../build/src/ui_mainwindow.h" line="2300"/>
<location filename="../../build/src/ui_mainwindow.h" line="2304"/>
<source>min</source>
<translation>min</translation>
</message>
<message>
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<location filename="../../build/src/ui_mainwindow.h" line="2302"/>
<location filename="../../build/src/ui_mainwindow.h" line="2301"/>
<location filename="../../build/src/ui_mainwindow.h" line="2305"/>
<source>max</source>
<translation>max</translation>
</message>
<message>
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<location filename="../../build/src/ui_mainwindow.h" line="2303"/>
<location filename="../../build/src/ui_mainwindow.h" line="2302"/>
<location filename="../../build/src/ui_mainwindow.h" line="2306"/>
<source>step</source>
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</message>
<message>
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<location filename="../../build/src/ui_mainwindow.h" line="2303"/>
<source>Angle, deg</source>
<translation>Угол, град</translation>
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<message>
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<location filename="../../build/src/ui_mainwindow.h" line="2307"/>
<source>Matrix</source>
<translation>Матрица</translation>
</message>
<message>
<location filename="../../build/src/ui_mainwindow.h" line="2332"/>
<location filename="../../build/src/ui_mainwindow.h" line="2335"/>
<source>Generate PDB</source>
<translation>Создать PDB</translation>
</message>
<message>
<location filename="../../build/src/ui_mainwindow.h" line="2313"/>
<location filename="../../build/src/ui_mainwindow.h" line="2316"/>
<source>From agglomerate</source>
<translation>Из агломерата</translation>
</message>
<message>
<location filename="../../build/src/ui_mainwindow.h" line="2314"/>
<location filename="../../build/src/ui_mainwindow.h" line="2317"/>
<source>From trajectory snapshot</source>
<translation>Из снимка траектории</translation>
</message>
<message>
<location filename="../../build/src/ui_mainwindow.h" line="2320"/>
<location filename="../../build/src/ui_mainwindow.h" line="2323"/>
<source>File with agglomerate</source>
<translation>Файл с агломератом</translation>
</message>
<message>
<location filename="../../build/src/ui_mainwindow.h" line="2333"/>
<location filename="../../build/src/ui_mainwindow.h" line="2336"/>
<source>Menu</source>
<translation>Меню</translation>
</message>
<message>
<location filename="../../build/src/ui_mainwindow.h" line="2334"/>
<location filename="../../build/src/ui_mainwindow.h" line="2337"/>
<source>File &amp;creator</source>
<translation>&amp;Создание файлов</translation>
</message>
<message>
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<location filename="../../build/src/ui_mainwindow.h" line="2338"/>
<source>&amp;Tools</source>
<translation>&amp;Утилиты</translation>
</message>
<message>
<location filename="../../build/src/ui_mainwindow.h" line="2336"/>
<location filename="../../build/src/ui_mainwindow.h" line="2339"/>
<source>Help</source>
<translation>Помощь</translation>
</message>
<message>
<location filename="../../build/src/ui_mainwindow.h" line="2188"/>
<location filename="../../build/src/ui_mainwindow.h" line="2193"/>
<source>&amp;Quit</source>
<translation>&amp;Выход</translation>
</message>
<message>
<location filename="../../build/src/ui_mainwindow.h" line="2190"/>
<location filename="../../build/src/ui_mainwindow.h" line="2195"/>
<source>Quit</source>
<translation>Выход</translation>
</message>
<message>
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<location filename="../../build/src/ui_mainwindow.h" line="2197"/>
<source>Ctrl+Q</source>
<translation>Ctrl+Q</translation>
</message>
<message>
<location filename="../../build/src/ui_mainwindow.h" line="2193"/>
<source>&amp;Help</source>
<translation>&amp;Помощь</translation>
<translation type="obsolete">&amp;Помощь</translation>
</message>
<message>
<location filename="../../build/src/ui_mainwindow.h" line="2194"/>
<source>F1</source>
<translation>F1</translation>
<translation type="obsolete">F1</translation>
</message>
<message>
<location filename="../../build/src/ui_mainwindow.h" line="2195"/>
<location filename="../../build/src/ui_mainwindow.h" line="2198"/>
<source>About</source>
<translation>О программе</translation>
</message>
<message>
<location filename="../../build/src/ui_mainwindow.h" line="2196"/>
<location filename="../../build/src/ui_mainwindow.h" line="2199"/>
<source>Atom &amp;types file</source>
<translation>Файл типов &amp;атомов</translation>
</message>
<message>
<location filename="../../build/src/ui_mainwindow.h" line="2197"/>
<location filename="../../build/src/ui_mainwindow.h" line="2200"/>
<source>&amp;Agglomerate file</source>
<translation>Файл с &amp;агломератом</translation>
</message>
<message>
<location filename="../../build/src/ui_mainwindow.h" line="2198"/>
<location filename="../../build/src/ui_mainwindow.h" line="2201"/>
<source>&amp;Settings</source>
<translation>&amp;Настройки</translation>
</message>
<message>
<location filename="../../build/src/ui_mainwindow.h" line="2199"/>
<location filename="../../build/src/ui_mainwindow.h" line="2203"/>
<source>agl_all</source>
<translation>agl_all</translation>
</message>
<message>
<location filename="../../build/src/ui_mainwindow.h" line="2200"/>
<source>statgen_all</source>
<translation>statgen_all</translation>
<translation type="obsolete">statgen_all</translation>
</message>
</context>
<context>
@ -966,72 +968,72 @@ p, li { white-space: pre-wrap; }
<translation>Все файлы (*)</translation>
</message>
<message>
<location filename="../../build/src/ui_settingswindow.h" line="316"/>
<location filename="../../build/src/ui_settingswindow.h" line="315"/>
<source>Settings</source>
<translation>Настройки</translation>
</message>
<message>
<location filename="../../build/src/ui_settingswindow.h" line="317"/>
<location filename="../../build/src/ui_settingswindow.h" line="316"/>
<source>mm_trj</source>
<translation>mm_trj</translation>
</message>
<message>
<location filename="../../build/src/ui_settingswindow.h" line="318"/>
<location filename="../../build/src/ui_settingswindow.h" line="320"/>
<location filename="../../build/src/ui_settingswindow.h" line="322"/>
<location filename="../../build/src/ui_settingswindow.h" line="324"/>
<location filename="../../build/src/ui_settingswindow.h" line="326"/>
<location filename="../../build/src/ui_settingswindow.h" line="328"/>
<location filename="../../build/src/ui_settingswindow.h" line="317"/>
<location filename="../../build/src/ui_settingswindow.h" line="319"/>
<location filename="../../build/src/ui_settingswindow.h" line="321"/>
<location filename="../../build/src/ui_settingswindow.h" line="323"/>
<location filename="../../build/src/ui_settingswindow.h" line="325"/>
<location filename="../../build/src/ui_settingswindow.h" line="327"/>
<source>Browse</source>
<translation>Обзор</translation>
</message>
<message>
<location filename="../../build/src/ui_settingswindow.h" line="319"/>
<location filename="../../build/src/ui_settingswindow.h" line="318"/>
<source>mm_statgen</source>
<translation>mm_statgen</translation>
</message>
<message>
<location filename="../../build/src/ui_settingswindow.h" line="321"/>
<location filename="../../build/src/ui_settingswindow.h" line="320"/>
<source>mm_envir</source>
<translation>mm_envir</translation>
</message>
<message>
<location filename="../../build/src/ui_settingswindow.h" line="323"/>
<location filename="../../build/src/ui_settingswindow.h" line="322"/>
<source>mm_radf</source>
<translation>mm_radf</translation>
</message>
<message>
<location filename="../../build/src/ui_settingswindow.h" line="325"/>
<location filename="../../build/src/ui_settingswindow.h" line="324"/>
<source>mm_trj2pdb</source>
<translation>mm_trj2pdb</translation>
</message>
<message>
<location filename="../../build/src/ui_settingswindow.h" line="327"/>
<location filename="../../build/src/ui_settingswindow.h" line="326"/>
<source>mm_agl</source>
<translation>mm_agl</translation>
</message>
<message>
<location filename="../../build/src/ui_settingswindow.h" line="331"/>
<location filename="../../build/src/ui_settingswindow.h" line="330"/>
<source>English</source>
<translation>English</translation>
</message>
<message>
<location filename="../../build/src/ui_settingswindow.h" line="332"/>
<location filename="../../build/src/ui_settingswindow.h" line="331"/>
<source>Russian</source>
<translation>Russian</translation>
</message>
<message>
<location filename="../../build/src/ui_settingswindow.h" line="334"/>
<location filename="../../build/src/ui_settingswindow.h" line="333"/>
<source>You need to restart application</source>
<translation>You need to restart application</translation>
</message>
<message>
<location filename="../../build/src/ui_settingswindow.h" line="335"/>
<location filename="../../build/src/ui_settingswindow.h" line="334"/>
<source>Save</source>
<translation>Сохранить</translation>
</message>
<message>
<location filename="../../build/src/ui_settingswindow.h" line="336"/>
<location filename="../../build/src/ui_settingswindow.h" line="335"/>
<source>Close</source>
<translation>Закрыть</translation>
</message>

6
mathmech/mathmech/src/CMakeLists.txt
View File

@ -65,4 +65,8 @@ add_executable (${PROJECT} WIN32 ${UI_HEADERS} ${HEADERS} ${SOURCES} ${MOC_SOURC
target_link_libraries (${PROJECT} ${LIBRARIES} ${QT_LIBRARIES} ${QT_QTMAIN_LIBRARY})
# install properties
INSTALL (TARGETS ${PROJECT} DESTINATION bin)
install (TARGETS ${PROJECT} DESTINATION bin)
install (FILES ../mathmech.desktop
DESTINATION share/applications/)
install (FILES ../mathmech-logo.png
DESTINATION share/pixmaps/)

16
mathmech/mathmech/src/mainwindow.cpp
View File

@ -123,9 +123,19 @@ void MainWindow::on_statgen_checkBox_atoms3_stateChanged(int arg1)
void MainWindow::on_statgen_checkBox_anal_stateChanged(int arg1)
{
if (arg1 == 0)
{
ui->statgen_doubleSpinBox_anal->setDisabled(true);
ui->statgen_spinBox_anal->setDisabled(true);
ui->statgen_checkBox_graph->setCheckState(Qt::Checked);
ui->statgen_checkBox_graph->setEnabled(true);
}
else if (arg1 == 2)
{
ui->statgen_doubleSpinBox_anal->setEnabled(true);
ui->statgen_spinBox_anal->setEnabled(true);
ui->statgen_checkBox_graph->setCheckState(Qt::Unchecked);
ui->statgen_checkBox_graph->setDisabled(true);
}
}
void MainWindow::on_envir_checkBox_log_stateChanged(int arg1)
@ -664,8 +674,12 @@ void MainWindow::start_events_statgen()
else
depth = QString("#");
float int_step;
int imax;
if (ui->statgen_checkBox_anal->checkState() == 2)
{
int_step = ui->statgen_doubleSpinBox_anal->value();
imax = ui->statgen_spinBox_anal->value();
}
QString log;
if (ui->statgen_checkBox_log->checkState() == 2)
log = ui->statgen_lineEdit_log->text();
@ -699,7 +713,7 @@ void MainWindow::start_events_statgen()
output,
depth,
log,
int_step);
int_step, imax);
ui->statusBar->showMessage(QApplication::translate("MainWindow", "Done"));
if ((ui->statgen_checkBox_graph->checkState() == 2) && (check == true))

36
mathmech/mathmech/src/mainwindow.ui
View File

@ -1245,6 +1245,25 @@
</property>
</widget>
</item>
<item>
<widget class="QSpinBox" name="statgen_spinBox_anal">
<property name="enabled">
<bool>false</bool>
</property>
<property name="minimumSize">
<size>
<width>80</width>
<height>23</height>
</size>
</property>
<property name="minimum">
<number>1</number>
</property>
<property name="value">
<number>10</number>
</property>
</widget>
</item>
<item>
<spacer name="horizontalSpacer_16">
<property name="orientation">
@ -3467,14 +3486,6 @@
<string>Ctrl+Q</string>
</property>
</action>
<action name="actionHelp">
<property name="text">
<string>&amp;Help</string>
</property>
<property name="shortcut">
<string>F1</string>
</property>
</action>
<action name="actionAbout">
<property name="text">
<string>About</string>
@ -3494,17 +3505,15 @@
<property name="text">
<string>&amp;Settings</string>
</property>
<property name="shortcut">
<string>Ctrl+P</string>
</property>
</action>
<action name="actionAgl_all">
<property name="text">
<string>agl_all</string>
</property>
</action>
<action name="actionStatgen_all">
<property name="text">
<string>statgen_all</string>
</property>
</action>
</widget>
<layoutdefault spacing="6" margin="11"/>
<tabstops>
@ -3556,6 +3565,7 @@
<tabstop>statgen_pushButton_log</tabstop>
<tabstop>statgen_checkBox_anal</tabstop>
<tabstop>statgen_doubleSpinBox_anal</tabstop>
<tabstop>statgen_spinBox_anal</tabstop>
<tabstop>statgen_checkBox_graph</tabstop>
<tabstop>statgen_pushButton_clear</tabstop>
<tabstop>statgen_pushButton_start</tabstop>

2
mathmech/mathmech/src/mathmech.pro.user
View File

@ -1,6 +1,6 @@
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE QtCreatorProject>
<!-- Written by QtCreator 2.8.0, 2013-08-28T17:33:30. -->
<!-- Written by QtCreator 2.8.0, 2013-08-29T03:32:50. -->
<qtcreator>
<data>
<variable>ProjectExplorer.Project.ActiveTarget</variable>

14
mathmech/mathmech/src/settingswindow.cpp
View File

@ -30,7 +30,7 @@ SettingsWindow::SettingsWindow(MainWindow *parent) :
else
{
setDefaults();
applySettings();
printSettings();
}
showSettings();
ui->settings_layout_lang_2->setHidden(true);
@ -117,12 +117,12 @@ void SettingsWindow::setDefaults()
suffix = QString(".exe");
#endif
_parent->language = QString("eng");
_parent->mm_trj_path = QDir::currentPath() + QDir::separator() + "mm_trj" + suffix;
_parent->mm_statgen_path = QDir::currentPath() + QDir::separator() + "mm_statgen" + suffix;
_parent->mm_envir_path = QDir::currentPath() + QDir::separator() + "mm_envir" + suffix;
_parent->mm_radf_path = QDir::currentPath() + QDir::separator() + "mm_radf" + suffix;
_parent->mm_trj2pdb_path = QDir::currentPath() + QDir::separator() + "mm_trj2pdb" + suffix;
_parent->mm_agl_path = QDir::currentPath() + QDir::separator() + "mm_agl" + suffix;
_parent->mm_trj_path = qApp->applicationDirPath() + QDir::separator() + "mm_trj" + suffix;
_parent->mm_statgen_path = qApp->applicationDirPath() + QDir::separator() + "mm_statgen" + suffix;
_parent->mm_envir_path = qApp->applicationDirPath() + QDir::separator() + "mm_envir" + suffix;
_parent->mm_radf_path = qApp->applicationDirPath() + QDir::separator() + "mm_radf" + suffix;
_parent->mm_trj2pdb_path = qApp->applicationDirPath() + QDir::separator() + "mm_trj2pdb" + suffix;
_parent->mm_agl_path = qApp->applicationDirPath() + QDir::separator() + "mm_agl" + suffix;
}
void SettingsWindow::readSettings()

66
mathmech/mathmech/src/start_events.cpp
View File

@ -1,4 +1,5 @@
#include <QDir>
#include <math.h>
#include "mainwindow.h"
#include "ui_mainwindow.h"
@ -189,7 +190,7 @@ bool Start_events::start_statgen_analysis(QString mm_statgen_path,
QString output,
QString depth,
QString log,
float int_step)
float int_step, int imax)
{
// error check
errorwin = new ErrorWindow(parent);
@ -238,12 +239,11 @@ bool Start_events::start_statgen_analysis(QString mm_statgen_path,
delete errorwin;
// parsing criteria
int imax = 10;
QStringList inter_list = inter.split(QString(" -r "), QString::SkipEmptyParts);
float *inter_list_one;
inter_list_one = new float[16*inter_list.count()];
for (int i=0; i<16*inter_list.count(); i++)
inter_list_one[i] = -1.0;
inter_list_one[i] = 0.0;
float item;
int index;
for (int i=0; i<inter_list.count(); i++)
@ -259,15 +259,24 @@ bool Start_events::start_statgen_analysis(QString mm_statgen_path,
split(QString("-"), QString::SkipEmptyParts)[1].toInt() * 4;
inter_list_one[16*i+index] = item;
}
QList<int> inter_list_index;
for (int i=0; i<16*inter_list.count(); i++)
if (inter_list_one[i] > 0.0)
while (imax*int_step > inter_list_one[i])
imax--;
if (inter_list_one[i] != 0.0)
inter_list_index.append(i);
int files = pow(2*imax+1, inter_list_index.count());
// exec
for (int i=-imax; i<=imax; i++)
char file[32];
int first, second, step;
float *cur_inter;
cur_inter = new float[16*inter_list.count()];
QString one_inter;
for (int i=0; i<16*inter_list.count(); i++)
cur_inter[i] = 0.0;
for (int i=0; i<files; i++)
{
QString command;
inter = QString("");
command.append(mm_statgen_path);
if (mask.contains(QDir::separator()))
command.append(" -i " + QFileInfo(mask).absoluteFilePath());
@ -282,25 +291,50 @@ bool Start_events::start_statgen_analysis(QString mm_statgen_path,
command.append("," + atom2);
if (atom3 != QString("#"))
command.append("," + atom3);
command.append(inter);
if (output.contains(QDir::separator()))
command.append(" -o " + QFileInfo(output).absoluteFilePath());
else
command.append(" -o " + QFileInfo(QDir(workDir), output).absoluteFilePath());
if (depth != QString("#"))
command.append(" -g " + depth);
command.append(" -q");
step = i;
for (int j=0; j<inter_list_index.count(); j++)
{
index = step % (2 * imax + 1);
cur_inter[inter_list_index[j]] = inter_list_one[inter_list_index[j]] + int_step * (index - imax);
if (cur_inter[inter_list_index[j]] < 0.0)
cur_inter[inter_list_index[j]] = 0.1;
step = step / (2 * imax + 1);
}
for (int j=0; j<inter_list.count(); j++)
{
one_inter = " -r ";
for (int k=0; k<16; k++)
if (cur_inter[16*j+k] != 0.0)
{
first = k % 4;
second = k / 4;
one_inter.append(QString::number(first) + "-" + QString::number(second) +
":" + QString::number(cur_inter[16*j+k], 'f', 3) + ",");
}
one_inter.remove(one_inter.count()-1, 1);
inter.append(one_inter);
}
command.append(inter);
sprintf(file, "_%06i", i);
if (output.contains(QDir::separator()))
command.append(" -o " + QFileInfo(output).absoluteFilePath() + QString(file) + ".dat");
else
command.append(" -o " + QFileInfo(QDir(workDir), output).absoluteFilePath() + QString(file) + ".dat");
if (log != QString("#"))
{
if (log.contains(QDir::separator()))
command.append(" -l " + QFileInfo(log).absoluteFilePath());
command.append(" -l " + QFileInfo(log).absoluteFilePath() + QString(file) + ".log");
else
command.append(" -l " + QFileInfo(QDir(workDir), log).absoluteFilePath());
command.append(" -l " + QFileInfo(QDir(workDir), log).absoluteFilePath() + QString(file) + ".log");
}
command.append(" -q");
system(command.toStdString().c_str());
}
delete inter_list_one;
delete cur_inter;
return true;
}

2
mathmech/mathmech/src/start_events.h
View File

@ -42,7 +42,7 @@ public:
QString output,
QString depth,
QString log,
float int_step);
float int_step, int imax);
bool start_envir(QString mm_envir_path,
QString workDir,
QString input,

4
mathmech/mm_agl/README
View File

@ -1,4 +1,4 @@
mm_agl - program that creates PDB file with chosen aglomerate
mm_agl - program that creates PDB file with chosen agglomerate
Version: 1.0.1
License: GPL
@ -6,7 +6,7 @@ Usage:
mm_agl -a FILENAME -i FILENAME -c X,Y,Z -o FILEMANE [ -l LOGFILE ] [ -q ] [ -h ]
Parametrs:
-a - input file with aglomerates (in format statgen)
-a - input file with agglomerates (in format statgen)
-i - input file with coordinates
-c - cell size (float), A
-o - output file with coordinates

2
mathmech/mm_agl/mm_agl.doxygen
View File

@ -38,7 +38,7 @@ PROJECT_NUMBER = V.1.0.1
# 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 with chosen aglomerate"
PROJECT_BRIEF = "Program that creates PDB file with chosen agglomerate"
# 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

BIN
mathmech/mm_agl/mm_agl.pdf
View File

Binary file not shown.

4
mathmech/mm_agl/src/add_main.c
View File

@ -18,7 +18,7 @@ int error_checking (const char *aglinp, const float *cell, const char *input,
* error_checking (aglinp, cell, input, output);
* @endcode
*
* @param aglinp aglomerate file name
* @param aglinp agglomerate file name
* @param cell massive of cell size
* @param input input file name
* @param output output file name
@ -83,7 +83,7 @@ int set_defaults (char *aglinp, float *cell, char *input, int *log, char *output
* set_defaults (aglinp, cell, input, &log, output, &quiet);
* @endcode
*
* @param aglinp aglomerate file name
* @param aglinp agglomerate file name
* @param cell massive of cell size
* @param input mask of trajectory files
* @param log status of log-mode

14
mathmech/mm_agl/src/main.c
View File

@ -9,7 +9,7 @@
*
* <b>About this program</b>:
* <ul>
* <li>Program that creates PDB file with chosen aglomerate
* <li>Program that creates PDB file with chosen agglomerate
* </ul>
*
* <b>Developer</b>:
@ -27,7 +27,7 @@
* mm_agl -a AGL_INP -i INPUT -c X,Y,Z -o OUTPUT [ -l LOGFILE ] [ -q ] [ -h ]
*
* Parametrs:
* -a - input file with aglomerates (in format statgen)
* -a - input file with agglomerates (in format statgen)
* -i - input file with coordinates
* -c - cell size (float), A
* -o - output file name
@ -100,7 +100,7 @@ int main(int argc, char *argv[])
int *label_mol, log, num_atoms, num_mol, num_needed_mol, *needed_mol, quiet,
*true_label_mol;
/* aglinp aglomerate file name
/* aglinp agglomerate file name
* ch_type_atoms massive of char atom types
* input input file name
* logfile log file name
@ -127,14 +127,14 @@ int main(int argc, char *argv[])
if ((argv[i][0] == '-') && (argv[i][1] == 'h') && (argv[i][2] == '\0'))
{
sprintf (tmp_str, " mm_agl\n");
sprintf (tmp_str, "%sProgram for create PDB file with chosen aglomerate\n", tmp_str);
sprintf (tmp_str, "%sProgram for create PDB file with chosen agglomerate\n", tmp_str);
sprintf (tmp_str, "%sVersion : 1.0.1 License : GPL\n", tmp_str);
sprintf (tmp_str, "%s Evgeniy Alekseev aka arcanis\n", tmp_str);
sprintf (tmp_str, "%s E-mail : esalexeev@gmail.com\n\n", tmp_str);
sprintf (tmp_str, "%sUsage:\n", tmp_str);
sprintf (tmp_str, "%smm_agl -a AGL_INP -i INPUT -c X,Y,Z -o OUTPUT [ -l LOGFILE ] [ -q ] [ -h ]\n\n", tmp_str);
sprintf (tmp_str, "%sParametrs:\n", tmp_str);
sprintf (tmp_str, "%s -a - input file with aglomerates (in format statgen)\n", tmp_str);
sprintf (tmp_str, "%s -a - input file with agglomerates (in format statgen)\n", tmp_str);
sprintf (tmp_str, "%s -i - input file with coordinates\n", tmp_str);
sprintf (tmp_str, "%s -c - cell size (float), A\n", tmp_str);
sprintf (tmp_str, "%s -o - output file name\n", tmp_str);
@ -238,13 +238,13 @@ int main(int argc, char *argv[])
print_message (quiet, stdout, log, f_log, 6, argv[0]);
// reading aglomerate
// reading agglomerate
print_message (quiet, stdout, log, f_log, 7, aglinp);
error = reading_agl (aglinp, &num_needed_mol, tmp_str, needed_mol);
if (error == 0)
{
sprintf (tmp_str, "%6cNumber of molecules in aglomerate: %i\n", ' ', num_needed_mol);
sprintf (tmp_str, "%6cNumber of molecules in agglomerate: %i\n", ' ', num_needed_mol);
print_message (quiet, stdout, log, f_log, 8, tmp_str);
// reading coordinates
print_message (quiet, stdout, log, f_log, 7, input);

2
mathmech/mm_agl/src/messages.c
View File

@ -53,7 +53,7 @@ int message (const int log, const int mode, const char *text, FILE *output)
sprintf (out, "Initialization of variables from file '%s'\n", text);
break;
case 4:
sprintf (out, "%6cAglomerate was selected successfully\n", ' ');
sprintf (out, "%6cAgglomerate was selected successfully\n", ' ');
break;
case 5:
sprintf (out, "Initial parametrs: \n%s", text);

10
mathmech/mm_agl/src/read_agl.c
View File

@ -1,7 +1,7 @@
/**
* @file
*/
/* Library for reading aglomerate from statgen-file
/* Library for reading agglomerate from statgen-file
*
* Usage:
* reading_agl (aglinput, &num_needed_mol, agl_class, needed_mol)
@ -15,14 +15,14 @@
*/
int reading_agl (const char *aglinp, int *num_needed_mol, char *agl_class, int *needed_mol)
/**
* @brief function that reads aglomerate from statgen-formated file
* @brief function that reads agglomerate from statgen-formated file
* @code
* reading_agl (aglinput, &num_needed_mol, agl_class, needed_mol);
* @endcode
*
* @param aglinp aglomerate file name
* @param aglinp agglomerate file name
* @param num_needed_mol number of needed molecules
* @param agl_class aglomerate class
* @param agl_class agglomerate class
* @param needed_mol massive of numbed of needed molecules
*
* @return 0 - exit without errors
@ -33,7 +33,7 @@ int reading_agl (const char *aglinp, int *num_needed_mol, char *agl_class, int *
FILE *f_agl;
/* connect - connectivity matrix for molecule
* f_agl - aglomerate file
* f_agl - agglomerate file
*/
f_agl = fopen (aglinp, "r");

2
mathmech/mm_envir/src/messages.c
View File

@ -53,7 +53,7 @@ int message (const int log, const int mode, const char *text, FILE *output)
sprintf (out, "Initialization of variables from file '%s'\n", text);
break;
case 4:
sprintf (out, "%6cAglomerate was selected successfully\n", ' ');
sprintf (out, "%6cAgglomerate was selected successfully\n", ' ');
break;
case 5:
sprintf (out, "Initial parametrs: \n%s", text);

2
mathmech/mm_radf/src/messages.c
View File

@ -53,7 +53,7 @@ int message (const int log, const int mode, const char *text, FILE *output)
sprintf (out, "Initialization of variables from file '%s'\n", text);
break;
case 4:
sprintf (out, "%6cAglomerate was selected successfully\n", ' ');
sprintf (out, "%6cAgglomerate was selected successfully\n", ' ');
break;
case 5:
sprintf (out, "Initial parametrs: \n%s", text);

BIN
mathmech/mm_statgen/mm_statgen.pdf
View File

Binary file not shown.

6
mathmech/mm_statgen/src/main.c
View File

@ -116,7 +116,7 @@ int main (int argc, char *argv[])
* coords massive of coordinates
* crit massive of criteria
*
* agl massive of aglomerates
* agl massive of agglomerates
* connect connectivity graph for all molecules
* from first trajectory step
* label_atom massive of atom types for interactions
@ -125,14 +125,14 @@ int main (int argc, char *argv[])
* max_depth maximum depth for check cycles in graph analyze
* num_atoms number of atoms
* num_mol number of molecules
* num_mol_agl massive of number of molecules in aglomerates
* num_mol_agl massive of number of molecules in agglomerates
* num_of_inter number of different interactions
* stat massive of statistic
* stat_all massive of summary statistic
* step $(to - from + 1)
* to last trajectory step
* true_label_mol massive of true numbers of molecule for atoms
* type_agl massive of number of aglomerate types
* type_agl massive of number of agglomerate types
* type_atoms massive of atom types
* type_inter number of atoms for interactions
* quiet status of quiet-mode

2
mathmech/mm_statgen/src/messages.c
View File

@ -53,7 +53,7 @@ int message (const int log, const int mode, const char *text, FILE *output)
sprintf (out, "Initialization of variables from file '%s'\n", text);
break;
case 4:
sprintf (out, "%6cAglomerate was selected successfully\n", ' ');
sprintf (out, "%6cAgglomerate was selected successfully\n", ' ');
break;
case 5:
sprintf (out, "Initial parametrs: \n%s", text);

14
mathmech/mm_statgen/src/stat_print.c
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@ -15,11 +15,11 @@ int printing_agl (const char *input, const char *output, const int *connect,
const int num_mol, const int *true_label_mol, const int *num_mol_agl,
const int *agl, const int *stat, const int max_depth, int *type_agl)
/**
* @brief function that prints aglomerates to output file
* @brief function that prints agglomerates to output file
* @code
* printing_agl (input_file, output_file, number_of_molecules, true_label_molecules,
* num_of_molecules_in_aglomerates, aglomerates, statistic, max_depth,
* type_of_aglomerate);
* num_of_molecules_in_agglomerates, agglomerates, statistic, max_depth,
* type_of_agglomerate);
* @endcode
*
* @param input input file name
@ -27,11 +27,11 @@ int printing_agl (const char *input, const char *output, const int *connect,
* @param connect connectivity graph for all molecules
* @param num_mol number of molecules
* @param true_label_mol massive of true numbers of molecule for atoms
* @param num_mol_agl massive of number of molecules in aglomerates
* @param agl massive of aglomerates
* @param num_mol_agl massive of number of molecules in agglomerates
* @param agl massive of agglomerates
* @param stat massive of statistic
* @param max_depth maximum depth for check cycles in graph analyze
* @param type_agl massive of number of aglomerate types
* @param type_agl massive of number of agglomerate types
*
* @return 1 - memory error
* @return 0 - exit without errors
@ -90,7 +90,7 @@ int printing_agl (const char *input, const char *output, const int *connect,
if (error > 0)
return 1;
// print class of aglomerate
// print class of agglomerate
fprintf (f_out, "AGL=%i=", num_mol_agl[i]);
for (j=0; j<max_depth; j++)
{

8
mathmech/mm_statgen/src/stat_sort.c
View File

@ -13,14 +13,14 @@ int proc_matrix (const int num_mol, const int *connect, int *num_mol_agl, int *a
/**
* @brief function that processes connectivity matrix
* @code
* proc_matrix (number_of_molecules, connect_matrix, num_of_molecules_in_aglomerates,
* aglomerates, statistic, summary_statistic);
* proc_matrix (number_of_molecules, connect_matrix, num_of_molecules_in_agglomerates,
* agglomerates, statistic, summary_statistic);
* @endcode
*
* @param num_mol number of molecules
* @param connect connectivity graph for all molecules
* @param num_mol_agl massive of number of molecules in aglomerates
* @param agl massive of aglomerates
* @param num_mol_agl massive of number of molecules in agglomerates
* @param agl massive of agglomerates
* @param stat massive of statistic
* @param stat_all massive of summary statistic
*

12
mathmech/mm_statgen/src/summary_stat.c
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@ -14,14 +14,14 @@ int summary_statistic (const char *filename, const int step, const int num_mol,
* @brief function that prints summary statistic
* @code
* summary_statistic (filename, number_of_step, number_of_molecules, max_depth,
* type_of_aglomerate, summary_statistic);
* type_of_agglomerate, summary_statistic);
* @endcode
*
* @param filename output file name
* @param step number of steps
* @param num_mol number of molecules
* @param max_depth maximum depth for check cycles in graph analyze
* @param type_agl massive of number of aglomerate types
* @param type_agl massive of number of agglomerate types
* @param stat_all massive of summary statistic
*
* @return 0 - exit without errors
@ -31,9 +31,9 @@ int summary_statistic (const char *filename, const int step, const int num_mol,
int i, index;
FILE *f_out;
/* conc concentrate of aglomerates
* p probability of aglomerates
* pn weight probability of aglomerates
/* conc concentrate of agglomerates
* p probability of agglomerates
* pn weight probability of agglomerates
* f_out output file
*/
@ -66,7 +66,7 @@ int summary_statistic (const char *filename, const int step, const int num_mol,
if (max_depth > 0)
{
// types of aglomerates
// types of agglomerates
// linear and cycle
x = type_agl[0] + type_agl[1];
type[0] = type_agl[0];

2
mathmech/mm_trj/src/messages.c
View File

@ -53,7 +53,7 @@ int message (const int log, const int mode, const char *text, FILE *output)
sprintf (out, "Initialization of variables from file '%s'\n", text);
break;
case 4:
sprintf (out, "%6cAglomerate was selected successfully\n", ' ');
sprintf (out, "%6cAgglomerate was selected successfully\n", ' ');
break;
case 5:
sprintf (out, "Initial parametrs: \n%s", text);

2
mathmech/mm_trj2pdb/src/messages.c
View File

@ -53,7 +53,7 @@ int message (const int log, const int mode, const char *text, FILE *output)
sprintf (out, "Initialization of variables from file '%s'\n", text);
break;
case 4:
sprintf (out, "%6cAglomerate was selected successfully\n", ' ');
sprintf (out, "%6cAgglomerate was selected successfully\n", ' ');
break;
case 5:
sprintf (out, "Initial parametrs: \n%s", text);