mirror of
https://github.com/arcan1s/moldyn.git
synced 2025-07-16 15:20:00 +00:00
Release 1.1.0
+ added help window + added help docs + small bug fixes
This commit is contained in:
arcan1s
@ -1,8 +1,8 @@
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cmake_minimum_required (VERSION 2.8)
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cmake_policy(SET CMP0003 OLD)
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cmake_policy(SET CMP0011 NEW)
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cmake_policy(SET CMP0015 NEW)
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cmake_policy (SET CMP0003 OLD)
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cmake_policy (SET CMP0011 NEW)
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cmake_policy (SET CMP0015 NEW)
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# set project name
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set (PROJECT mathmech)
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@ -1,6 +1,6 @@
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#############################################################################
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# Makefile for building: mathmech
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# Generated by qmake (2.01a) (Qt 4.8.5) on: ?? ??? 26 15:52:26 2013
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# Generated by qmake (2.01a) (Qt 4.8.5) on: ?? ??? 3 02:36:06 2013
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# Project: mathmech.pro
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# Template: app
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# Command: /usr/bin/qmake-qt4 -o Makefile mathmech.pro
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@ -54,7 +54,8 @@ SOURCES = main.cpp \
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aboutwindow.cpp \
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statgengraphwindow.cpp \
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settingswindow.cpp \
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aglallwindow.cpp moc_mainwindow.cpp \
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aglallwindow.cpp \
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helpwindow.cpp moc_mainwindow.cpp \
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moc_errorwindow.cpp \
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moc_clear_items.cpp \
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moc_start_events.cpp \
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@ -64,7 +65,8 @@ SOURCES = main.cpp \
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moc_aboutwindow.cpp \
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moc_statgengraphwindow.cpp \
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moc_settingswindow.cpp \
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moc_aglallwindow.cpp
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moc_aglallwindow.cpp \
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moc_helpwindow.cpp
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OBJECTS = main.o \
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mainwindow.o \
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errorwindow.o \
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@ -77,6 +79,7 @@ OBJECTS = main.o \
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statgengraphwindow.o \
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settingswindow.o \
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aglallwindow.o \
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helpwindow.o \
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moc_mainwindow.o \
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moc_errorwindow.o \
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moc_clear_items.o \
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@ -87,7 +90,8 @@ OBJECTS = main.o \
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moc_aboutwindow.o \
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moc_statgengraphwindow.o \
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moc_settingswindow.o \
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moc_aglallwindow.o
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moc_aglallwindow.o \
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moc_helpwindow.o
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DIST = /usr/share/qt4/mkspecs/common/unix.conf \
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/usr/share/qt4/mkspecs/common/linux.conf \
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/usr/share/qt4/mkspecs/common/gcc-base.conf \
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@ -146,7 +150,7 @@ first: all
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all: Makefile $(TARGET)
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$(TARGET): ui_mainwindow.h ui_errorwindow.h ui_atomtypeswindow.h ui_agglwindow.h ui_aboutwindow.h ui_statgengraphwindow.h ui_settingswindow.h ui_aglallwindow.h $(OBJECTS)
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$(TARGET): ui_mainwindow.h ui_errorwindow.h ui_atomtypeswindow.h ui_agglwindow.h ui_aboutwindow.h ui_statgengraphwindow.h ui_settingswindow.h ui_aglallwindow.h ui_helpwindow.h $(OBJECTS)
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$(LINK) $(LFLAGS) -o $(TARGET) $(OBJECTS) $(OBJCOMP) $(LIBS)
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Makefile: mathmech.pro /usr/share/qt4/mkspecs/linux-g++/qmake.conf /usr/share/qt4/mkspecs/common/unix.conf \
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@ -219,7 +223,7 @@ qmake: FORCE
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dist:
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@$(CHK_DIR_EXISTS) .tmp/mathmech1.0.0 || $(MKDIR) .tmp/mathmech1.0.0
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$(COPY_FILE) --parents $(SOURCES) $(DIST) .tmp/mathmech1.0.0/ && $(COPY_FILE) --parents mainwindow.h errorwindow.h clear_items.h start_events.h update_fields.h atomtypeswindow.h agglwindow.h aboutwindow.h statgengraphwindow.h settingswindow.h aglallwindow.h .tmp/mathmech1.0.0/ && $(COPY_FILE) --parents main.cpp mainwindow.cpp errorwindow.cpp clear_items.cpp start_events.cpp update_fields.cpp atomtypeswindow.cpp agglwindow.cpp aboutwindow.cpp statgengraphwindow.cpp settingswindow.cpp aglallwindow.cpp .tmp/mathmech1.0.0/ && $(COPY_FILE) --parents mainwindow.ui errorwindow.ui atomtypeswindow.ui agglwindow.ui aboutwindow.ui statgengraphwindow.ui settingswindow.ui aglallwindow.ui .tmp/mathmech1.0.0/ && $(COPY_FILE) --parents rus.ts eng.ts .tmp/mathmech1.0.0/ && (cd `dirname .tmp/mathmech1.0.0` && $(TAR) mathmech1.0.0.tar mathmech1.0.0 && $(COMPRESS) mathmech1.0.0.tar) && $(MOVE) `dirname .tmp/mathmech1.0.0`/mathmech1.0.0.tar.gz . && $(DEL_FILE) -r .tmp/mathmech1.0.0
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||||
$(COPY_FILE) --parents $(SOURCES) $(DIST) .tmp/mathmech1.0.0/ && $(COPY_FILE) --parents mainwindow.h errorwindow.h clear_items.h start_events.h update_fields.h atomtypeswindow.h agglwindow.h aboutwindow.h statgengraphwindow.h settingswindow.h aglallwindow.h helpwindow.h .tmp/mathmech1.0.0/ && $(COPY_FILE) --parents main.cpp mainwindow.cpp errorwindow.cpp clear_items.cpp start_events.cpp update_fields.cpp atomtypeswindow.cpp agglwindow.cpp aboutwindow.cpp statgengraphwindow.cpp settingswindow.cpp aglallwindow.cpp helpwindow.cpp .tmp/mathmech1.0.0/ && $(COPY_FILE) --parents mainwindow.ui errorwindow.ui atomtypeswindow.ui agglwindow.ui aboutwindow.ui statgengraphwindow.ui settingswindow.ui aglallwindow.ui helpwindow.ui .tmp/mathmech1.0.0/ && $(COPY_FILE) --parents rus.ts eng.ts .tmp/mathmech1.0.0/ && (cd `dirname .tmp/mathmech1.0.0` && $(TAR) mathmech1.0.0.tar mathmech1.0.0 && $(COMPRESS) mathmech1.0.0.tar) && $(MOVE) `dirname .tmp/mathmech1.0.0`/mathmech1.0.0.tar.gz . && $(DEL_FILE) -r .tmp/mathmech1.0.0
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||||
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||||
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clean:compiler_clean
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||||
@ -240,9 +244,9 @@ mocclean: compiler_moc_header_clean compiler_moc_source_clean
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||||
mocables: compiler_moc_header_make_all compiler_moc_source_make_all
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||||
|
||||
compiler_moc_header_make_all: moc_mainwindow.cpp moc_errorwindow.cpp moc_clear_items.cpp moc_start_events.cpp moc_update_fields.cpp moc_atomtypeswindow.cpp moc_agglwindow.cpp moc_aboutwindow.cpp moc_statgengraphwindow.cpp moc_settingswindow.cpp moc_aglallwindow.cpp
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||||
compiler_moc_header_make_all: moc_mainwindow.cpp moc_errorwindow.cpp moc_clear_items.cpp moc_start_events.cpp moc_update_fields.cpp moc_atomtypeswindow.cpp moc_agglwindow.cpp moc_aboutwindow.cpp moc_statgengraphwindow.cpp moc_settingswindow.cpp moc_aglallwindow.cpp moc_helpwindow.cpp
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compiler_moc_header_clean:
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-$(DEL_FILE) moc_mainwindow.cpp moc_errorwindow.cpp moc_clear_items.cpp moc_start_events.cpp moc_update_fields.cpp moc_atomtypeswindow.cpp moc_agglwindow.cpp moc_aboutwindow.cpp moc_statgengraphwindow.cpp moc_settingswindow.cpp moc_aglallwindow.cpp
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||||
-$(DEL_FILE) moc_mainwindow.cpp moc_errorwindow.cpp moc_clear_items.cpp moc_start_events.cpp moc_update_fields.cpp moc_atomtypeswindow.cpp moc_agglwindow.cpp moc_aboutwindow.cpp moc_statgengraphwindow.cpp moc_settingswindow.cpp moc_aglallwindow.cpp moc_helpwindow.cpp
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||||
moc_mainwindow.cpp: mainwindow.h
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/usr/lib/qt4/bin/moc $(DEFINES) $(INCPATH) mainwindow.h -o moc_mainwindow.cpp
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@ -276,6 +280,9 @@ moc_settingswindow.cpp: settingswindow.h
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moc_aglallwindow.cpp: aglallwindow.h
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/usr/lib/qt4/bin/moc $(DEFINES) $(INCPATH) aglallwindow.h -o moc_aglallwindow.cpp
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moc_helpwindow.cpp: helpwindow.h
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/usr/lib/qt4/bin/moc $(DEFINES) $(INCPATH) helpwindow.h -o moc_helpwindow.cpp
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||||
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||||
compiler_rcc_make_all:
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||||
compiler_rcc_clean:
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||||
compiler_image_collection_make_all: qmake_image_collection.cpp
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||||
@ -283,9 +290,9 @@ compiler_image_collection_clean:
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||||
-$(DEL_FILE) qmake_image_collection.cpp
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||||
compiler_moc_source_make_all:
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||||
compiler_moc_source_clean:
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||||
compiler_uic_make_all: ui_mainwindow.h ui_errorwindow.h ui_atomtypeswindow.h ui_agglwindow.h ui_aboutwindow.h ui_statgengraphwindow.h ui_settingswindow.h ui_aglallwindow.h
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compiler_uic_make_all: ui_mainwindow.h ui_errorwindow.h ui_atomtypeswindow.h ui_agglwindow.h ui_aboutwindow.h ui_statgengraphwindow.h ui_settingswindow.h ui_aglallwindow.h ui_helpwindow.h
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compiler_uic_clean:
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-$(DEL_FILE) ui_mainwindow.h ui_errorwindow.h ui_atomtypeswindow.h ui_agglwindow.h ui_aboutwindow.h ui_statgengraphwindow.h ui_settingswindow.h ui_aglallwindow.h
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||||
-$(DEL_FILE) ui_mainwindow.h ui_errorwindow.h ui_atomtypeswindow.h ui_agglwindow.h ui_aboutwindow.h ui_statgengraphwindow.h ui_settingswindow.h ui_aglallwindow.h ui_helpwindow.h
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||||
ui_mainwindow.h: mainwindow.ui
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/usr/lib/qt4/bin/uic mainwindow.ui -o ui_mainwindow.h
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@ -310,6 +317,9 @@ ui_settingswindow.h: settingswindow.ui
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ui_aglallwindow.h: aglallwindow.ui
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/usr/lib/qt4/bin/uic aglallwindow.ui -o ui_aglallwindow.h
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ui_helpwindow.h: helpwindow.ui
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/usr/lib/qt4/bin/uic helpwindow.ui -o ui_helpwindow.h
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compiler_yacc_decl_make_all:
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compiler_yacc_decl_clean:
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compiler_yacc_impl_make_all:
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@ -327,10 +337,11 @@ mainwindow.o: mainwindow.cpp aboutwindow.h \
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agglwindow.h \
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aglallwindow.h \
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atomtypeswindow.h \
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helpwindow.h \
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settingswindow.h \
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statgengraphwindow.h \
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clear_items.h \
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start_events.h \
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||||
statgengraphwindow.h \
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update_fields.h \
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mainwindow.h \
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ui_mainwindow.h
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@ -386,6 +397,10 @@ aglallwindow.o: aglallwindow.cpp errorwindow.h \
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ui_aglallwindow.h
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$(CXX) -c $(CXXFLAGS) $(INCPATH) -o aglallwindow.o aglallwindow.cpp
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helpwindow.o: helpwindow.cpp helpwindow.h \
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ui_helpwindow.h
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$(CXX) -c $(CXXFLAGS) $(INCPATH) -o helpwindow.o helpwindow.cpp
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moc_mainwindow.o: moc_mainwindow.cpp
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$(CXX) -c $(CXXFLAGS) $(INCPATH) -o moc_mainwindow.o moc_mainwindow.cpp
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@ -419,6 +434,9 @@ moc_settingswindow.o: moc_settingswindow.cpp
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||||
moc_aglallwindow.o: moc_aglallwindow.cpp
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$(CXX) -c $(CXXFLAGS) $(INCPATH) -o moc_aglallwindow.o moc_aglallwindow.cpp
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moc_helpwindow.o: moc_helpwindow.cpp
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$(CXX) -c $(CXXFLAGS) $(INCPATH) -o moc_helpwindow.o moc_helpwindow.cpp
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####### Install
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install: FORCE
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@ -1,3 +1,10 @@
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#include <QDir>
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#include <QFileDialog>
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#include <QKeyEvent>
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#include <QTextStream>
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#include "errorwindow.h"
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#include "helpwindow.h"
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#include "ui_helpwindow.h"
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@ -19,3 +26,43 @@ void HelpWindow::keyPressEvent(QKeyEvent *pressedKey)
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if (pressedKey->key() == Qt::Key_Escape)
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close();
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}
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void HelpWindow::on_pushButton_save_clicked()
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{
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errorwin = new ErrorWindow(this);
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QString filename = QFileDialog::getSaveFileName(
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||||
this,
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tr("Save file as"),
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QDir::currentPath(),
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tr("html files (*.html);;All files (*.*)"));
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if (filename.isEmpty())
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return;
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filename = QFileInfo(filename).absoluteFilePath();
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||||
QFile f_out(filename);
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if (!f_out.open(QIODevice::WriteOnly | QIODevice::Text))
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{
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errorwin->set_message(9);
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||||
errorwin->show();
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||||
return;
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||||
}
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QTextStream out(&f_out);
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||||
QString text = QString("");
|
||||
int page = ui->toolBox->currentIndex();
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||||
if (page == 0)
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||||
text = ui->textBrowser_trj->toHtml();
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else if (page == 1)
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||||
text = ui->textBrowser_statgen->toHtml();
|
||||
else if (page == 2)
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||||
text = ui->textBrowser_envir->toHtml();
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else if (page == 3)
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text = ui->textBrowser_radf->toHtml();
|
||||
else if (page == 4)
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||||
text = ui->textBrowser_agl->toHtml();
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||||
else if (page == 5)
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text = ui->textBrowser_trj2pdb->toHtml();
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||||
out << text;
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||||
f_out.close();
|
||||
|
||||
delete errorwin;
|
||||
}
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||||
|
||||
@ -3,6 +3,8 @@
|
||||
|
||||
#include <QMainWindow>
|
||||
|
||||
class ErrorWindow;
|
||||
|
||||
namespace Ui {
|
||||
class HelpWindow;
|
||||
}
|
||||
@ -15,8 +17,12 @@ public:
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||||
explicit HelpWindow(QWidget *parent = 0);
|
||||
~HelpWindow();
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||||
|
||||
private slots:
|
||||
void on_pushButton_save_clicked();
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||||
|
||||
private:
|
||||
Ui::HelpWindow *ui;
|
||||
ErrorWindow *errorwin;
|
||||
|
||||
// ESC pressed event
|
||||
void keyPressEvent(QKeyEvent *pressedKey);
|
||||
|
||||
@ -20,27 +20,6 @@
|
||||
<property name="currentIndex">
|
||||
<number>0</number>
|
||||
</property>
|
||||
<widget class="QWidget" name="page_general">
|
||||
<property name="geometry">
|
||||
<rect>
|
||||
<x>0</x>
|
||||
<y>0</y>
|
||||
<width>580</width>
|
||||
<height>233</height>
|
||||
</rect>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>General help</string>
|
||||
</property>
|
||||
<attribute name="label">
|
||||
<string>General</string>
|
||||
</attribute>
|
||||
<layout class="QGridLayout" name="gridLayout_2">
|
||||
<item row="0" column="0">
|
||||
<widget class="QTextBrowser" name="textBrowser_general"/>
|
||||
</item>
|
||||
</layout>
|
||||
</widget>
|
||||
<widget class="QWidget" name="page_trj">
|
||||
<property name="geometry">
|
||||
<rect>
|
||||
@ -58,7 +37,39 @@
|
||||
</attribute>
|
||||
<layout class="QGridLayout" name="gridLayout_3">
|
||||
<item row="0" column="0">
|
||||
<widget class="QTextBrowser" name="textBrowser_trj"/>
|
||||
<widget class="QTextBrowser" name="textBrowser_trj">
|
||||
<property name="html">
|
||||
<string><!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd">
|
||||
<html><head><meta name="qrichtext" content="1" /><style type="text/css">
|
||||
p, li { white-space: pre-wrap; }
|
||||
</style></head><body style=" font-family:'Liberation Serif'; font-size:10pt; font-weight:400; font-style:normal;">
|
||||
<p align="center" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600;">trj</span></p>
|
||||
<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />Program that generates trajectory files in special format from input trajectory.</p>
|
||||
<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Usage</span><br />mm_trj -i FILE -t TYPE -s NUMBER -a FILE -o MASK [ -tt NUMBER ] [ -l FILE ] [ -q ] [ -h ]<br /> <span style=" text-decoration: underline;">Parametrs</span><br />-i FILE – input trajectory file<br />-t TYPE – trajectory type. Supported formats: gmx, puma<br />-s NUMBER – number of trajectory steps<br />-a FILE – file with atom types<br />-o MASK – mask of output trajectory files<br />-tt NUMBER – maximum number of different atom types. Default is 1024<br />-l FILE – print log to specified file<br />-q – do not print messages to STDOUT<br />-h – show this help and exit</p>
|
||||
<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">File formats</span></p>
|
||||
<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"> <span style=" font-style:italic;">Trajectory files (*.[0-9])</span></p>
|
||||
<ul style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Number of atoms is shown in the title.</li>
|
||||
<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Trajectory snapshot (enumeration of all atoms in system). Format<br />00001 СА 1234.000000 1234.000000 1234.000000 01 0001<br />The sequence number of an atom (5 characters), space, character atom type (2 characters), 2 spaces, X coordinate (11 characters, 6 decimal part), Y coordinate (11 characters, 6 decimal part), Z coordinate (11 characters, 6 decimal part), 4 spaces, numerical atom type (2 characters), space, number of molecule (4 characters).</li></ul>
|
||||
<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"> <span style=" font-style:italic;">Atom types file (*.types)</span></p>
|
||||
<ul style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The number of different molecules (NUMTYPES=1) is shown in the title.</li>
|
||||
<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The molecules enumeration block. Variables are the number of molecules (NUMMOL=1), the number of atoms (NUMAT=1).<br />The atoms enumeration block. Format<br />CA=1<br />Character atom type (2 characters), equal sign, numerical atom type.</li></ul>
|
||||
<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Operation of the application</span></p>
|
||||
<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Reading titles of source files, setting values of initial variables.</li>
|
||||
<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Step by step reading of source files, print results to the specified output file.</li></ol>
|
||||
<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Working with GUI</span></p>
|
||||
<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Select Menu -&gt; File creator -&gt; Atom types file.</li>
|
||||
<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the output file.</li>
|
||||
<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set atom types. To add a new molecule you need select &quot;Add new molecule&quot; from the drop down list. To change the number of molecules you need change the corresponding numeric value. To add a new atom you need enter 2 character to the special field, set numerical atom type and press &quot;Add&quot;. After this the atom will appear in the special window. To remove an atom you need select the desired atom in the special window and press &quot;Remove&quot;.</li>
|
||||
<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Create the atom types file.</li>
|
||||
<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Go to the tab &quot;Generate trajectory&quot;. Set the work directory.</li>
|
||||
<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the input trajectory file.</li>
|
||||
<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Select the trajectory type from the drop down list, set the number of trajectory steps.</li>
|
||||
<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the atom types file.</li>
|
||||
<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the mask of output files.</li>
|
||||
<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the maximum number of different atom types and the log file if this needed.</li>
|
||||
<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Run application.</li></ol></body></html></string>
|
||||
</property>
|
||||
</widget>
|
||||
</item>
|
||||
</layout>
|
||||
</widget>
|
||||
@ -67,8 +78,8 @@
|
||||
<rect>
|
||||
<x>0</x>
|
||||
<y>0</y>
|
||||
<width>580</width>
|
||||
<height>233</height>
|
||||
<width>98</width>
|
||||
<height>88</height>
|
||||
</rect>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
@ -79,7 +90,39 @@
|
||||
</attribute>
|
||||
<layout class="QGridLayout" name="gridLayout_4">
|
||||
<item row="0" column="0">
|
||||
<widget class="QTextBrowser" name="textBrowser_statgen"/>
|
||||
<widget class="QTextBrowser" name="textBrowser_statgen">
|
||||
<property name="html">
|
||||
<string><!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd">
|
||||
<html><head><meta name="qrichtext" content="1" /><style type="text/css">
|
||||
p, li { white-space: pre-wrap; }
|
||||
</style></head><body style=" font-family:'Liberation Serif'; font-size:10pt; font-weight:400; font-style:normal;">
|
||||
<p align="center" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600;">statgen</span></p>
|
||||
<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />Program that analyzes molecular dynamics trajectories using topological analysis.</p>
|
||||
<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Usage</span><br />mm_statgen -i MASK -s NUMBER,NUMBER -c X,Y,Z -a FORMAT -r FORMAT -o FILE [ -g NUMBER ] [ -l FILE ] [ -q ] [ -h ]<br /> <span style=" text-decoration: underline;">Parametrs</span><br />-i MASK – mask of trajectory files<br />-s NUMBER,NUMBER – first and last trajectory steps<br />-c X,Y,Z – cell size, A<br />-a FORMAT – numerical atom types. Maximum number of different atom types is 4. Types are comma separated<br />-r FORMAT – criteria, A. This flag can be used multiple times. Different interactions are comma separated. Type interaction, colon character, criterion. For example &quot;0-0:2.4,0-1:3.0&quot; means set 0-0 interaction as &lt;2.4 А and 0-1 interaction as &lt;3.0 A<br />-o FILE – output file<br />-g NUMBER – chech graph isomorphism. NUMBER is a maximum depth for search cycles (&gt;= 3)<br />-l FILE – print log to specified file<br />-q – do not print messages to STDOUT<br />-h – show this help and exit</p>
|
||||
<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">File formats</span></p>
|
||||
<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"> <span style=" font-style:italic;">Output file (*.dat)</span></p>
|
||||
<ul style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Program name and version are shown in the title. For example, &quot;statgen ::: V.1.1.0&quot;. Blank line.</li>
|
||||
<li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The configuration block &quot;CONFIGURATION ... END&quot;. Print log (LOG=1), do not print messages to STDOUT (QUIET=1), mask of trajectory files (MASK=mask), first (FIRST=1) and last (LAST=1) trajectory steps, sell size (CELL=1.0000,2.0000,3.0000), atom types (ATOMS=1,2,3,4), interactions (INTERACTION=format), maximum depth for check cycle number (DEPTH=0, 0 - do not check graph isomorphism). Blank line.</li>
|
||||
<li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The enumeration of statistics on individual files.<br />File name (FILE=mask.001), the statistic block for file &quot;STATISTIC ... -----------------&quot;. Table layout (2 rows) follows after specifying the block. The table format<br /> 0000001 0000001 <br />Space, agglomerate size (7 characters), space, number of agglomerates of this size in the file (7 characters).<br />The enumeration of agglomerates in the file. Agglomerate title (AGL=2=1.3.4.) (1 – number of molecules in the agglomerate, 1.3.4. – agglomerate class, if verification of isomorphism is specified). The enumeration of molecules in the agglomerate. (0000001=2,3,4,5,) (1 – number of molecule (7 characters), equal sign, the enumeration of connected molecules separated by commas).</li>
|
||||
<li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The summary statistic block &quot;SUMMARY STATISTIC … ------------------------------------------------&quot;. Table layout (2 rows) follows after specifying the block. The table format<br /> 0000001 0000002 000003.00 004.00000 0005.00000<br />Space, agglomerate size (7 characters), space, total number of agglomerates of this size (7 characters), space, average concentration of agglomerates of this size (9 characters, 2 decimal part), space, probability of finding molecules in agglomerates of this size (9 characters, 5 decimal part), space, probability of finding molecules in agglomerates of this size multiplied by the size (10 characters, 5 decimal part).</li>
|
||||
<li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Summary statistic of agglomerates on classes (if verification of isomorphism is specified). The proportion of linear (LINEAR=0.10000) and cyclic (CYCLE=0.10000) agglomerates, blank line, the proportion of not branched (NOT BRANCHED=0.10000) and branched (BRANCHED=0.10000) agglomerates, blank line, the proportion of found cycles of the specified size (CYCLE_03=0.10000).</li></ul>
|
||||
<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Operation of the application</span></p>
|
||||
<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Reading titles of source files, setting values of initial variables.</li>
|
||||
<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Step by step reading of source files, settings values of variables.<br />Search for interactions that satisfy the specified criteria.<br />The analysis of all connections and specifying to the two molecules that connected, if the conditions are satisfied at least one of these criteria.<br />Adding molecules to agglomerates according to the obtained connectivity matrix.<br />Print agglomerates to the file, adding the summary statistics.</li>
|
||||
<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Print the summary statistic to the file.</li></ol>
|
||||
<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Working with GUI</span></p>
|
||||
<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Go to the tab &quot;Agglomeration&quot;. Set the work directory.</li>
|
||||
<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the mask of trajectory files.</li>
|
||||
<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the first and the last trajectory steps.</li>
|
||||
<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the cell size, A.</li>
|
||||
<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set needed atoms.</li>
|
||||
<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set interactions. Select type of interaction from the drop down list, change its criterion and press &quot;Save&quot;. Press &quot;Add&quot; after ending of edition. After this the interaction will appear in the special window. To remove an interaction you need select the desired interaction in the special window and press &quot;Remove&quot;.</li>
|
||||
<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the output file.</li>
|
||||
<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the maximum depth for search cycles, the log file and the graph generate if this needed.</li>
|
||||
<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">For the variation of geometric criteria you need specify the criteria step changes and the number of steps.</li>
|
||||
<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Run application.</li></ol></body></html></string>
|
||||
</property>
|
||||
</widget>
|
||||
</item>
|
||||
</layout>
|
||||
</widget>
|
||||
@ -88,8 +131,8 @@
|
||||
<rect>
|
||||
<x>0</x>
|
||||
<y>0</y>
|
||||
<width>580</width>
|
||||
<height>233</height>
|
||||
<width>98</width>
|
||||
<height>88</height>
|
||||
</rect>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
@ -100,7 +143,33 @@
|
||||
</attribute>
|
||||
<layout class="QGridLayout" name="gridLayout_5">
|
||||
<item row="0" column="0">
|
||||
<widget class="QTextBrowser" name="textBrowser_envir"/>
|
||||
<widget class="QTextBrowser" name="textBrowser_envir">
|
||||
<property name="html">
|
||||
<string><!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd">
|
||||
<html><head><meta name="qrichtext" content="1" /><style type="text/css">
|
||||
p, li { white-space: pre-wrap; }
|
||||
</style></head><body style=" font-family:'Liberation Serif'; font-size:10pt; font-weight:400; font-style:normal;">
|
||||
<p align="center" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600;">envir</span></p>
|
||||
<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />Program that searchs environment for chosen molecule by geometric criterion.</p>
|
||||
<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Usage</span><br />mm_envir -i FILE -c X,Y,Z -o FILE [ -n NUMBER ] [ -r NUMBER ] [ -l FILE ] [ -q ] [ -h ]<br /> <span style=" text-decoration: underline;">Parametrs</span><br />-i FILE – input trajectory file<br />-c X,Y,Z – cell size, A<br />-o FILE – output PDB file<br />-n NUMBER – number of molecule for search. Default is 1<br />-r NUMBER – radius of environment. Default is 6.0<br />-l FILE – print log to specified file<br />-q – do not print messages to STDOUT<br />-h – show this help and exit</p>
|
||||
<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">File formats</span></p>
|
||||
<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"> <span style=" font-style:italic;">Trajectory file (*.pdb)</span></p>
|
||||
<p align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><a href="http://www.wwpdb.org/documentation/format33/sect9.html"><span style=" text-decoration: underline; color:#0000ff;">http://www.wwpdb.org/documentation/format33/sect9.html</span></a></p>
|
||||
<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Operation of the application</span></p>
|
||||
<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Reading titles of source files, setting values of initial variables.</li>
|
||||
<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Reading of source file.</li>
|
||||
<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Search for the environment.</li>
|
||||
<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Print the environment to the file.</li></ol>
|
||||
<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Working with GUI</span></p>
|
||||
<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Go to the tab &quot;Environment&quot;. Set the work directory.</li>
|
||||
<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the input trajectory file.</li>
|
||||
<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the cell size, A.</li>
|
||||
<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the output PDB file.</li>
|
||||
<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the number of molecule for search and the radius of environment.</li>
|
||||
<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the log file if this needed.</li>
|
||||
<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Run application.</li></ol></body></html></string>
|
||||
</property>
|
||||
</widget>
|
||||
</item>
|
||||
</layout>
|
||||
</widget>
|
||||
@ -109,8 +178,8 @@
|
||||
<rect>
|
||||
<x>0</x>
|
||||
<y>0</y>
|
||||
<width>580</width>
|
||||
<height>233</height>
|
||||
<width>98</width>
|
||||
<height>88</height>
|
||||
</rect>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
@ -121,7 +190,92 @@
|
||||
</attribute>
|
||||
<layout class="QGridLayout" name="gridLayout_6">
|
||||
<item row="0" column="0">
|
||||
<widget class="QTextBrowser" name="textBrowser_radf"/>
|
||||
<widget class="QTextBrowser" name="textBrowser_radf">
|
||||
<property name="html">
|
||||
<string><!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd">
|
||||
<html><head><meta name="qrichtext" content="1" /><style type="text/css">
|
||||
p, li { white-space: pre-wrap; }
|
||||
</style></head><body style=" font-family:'Liberation Serif'; font-size:10pt; font-weight:400; font-style:normal;">
|
||||
<p align="center" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600;">radf</span></p>
|
||||
<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />Program that calculates radial distribution function (RDF) or radial-angles distribution function (RADF).</p>
|
||||
<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Usage</span><br />mm_radf -i MASK -s NUMBER,NUMBER -c X,Y,Z -at FORMAT -o FILE [ -r NUMBER,NUMBER ] [ -rs NUMBER ] [ -a NUMBER,NUMBER ] [ -as NUMBER ] [ -m ] [ -l FILE ] [ -q ] [ -h ]<br /> <span style=" text-decoration: underline;">Parametrs</span><br />-i MASK – mask of trajectory files<br />-s NUMBER,NUMBER – first and last trajectory steps<br />-c X,Y,Z – cell size, A<br />-at FORMAT – numerical atom types between which the function is calculated. Format is &quot;1-2&quot; or &quot;1,2,3-4,5,6&quot; (automatically enable calculation of radial distribution function between centers of mass)<br />-o FILE – output file<br />-r NUMBER,NUMBER – radial criteria, A. Default is 2.0 and 15.0<br />-rs NUMBER – radius change step, A. Default is 0.2<br />-a NUMBER,NUMBER – angular criteria, deg. Default is 0.0 and 90.0<br />-as NUMBER – angle change step, deg. This option will enable calculation of radial-angles distribution function<br />-as – enable matrix output<br />-l FILE – print log to specified file<br />-q – do not print messages to STDOUT<br />-h – show this help and exit</p>
|
||||
<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">File formats</span></p>
|
||||
<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"> <span style=" font-style:italic;">Output file (*.dat)</span></p>
|
||||
<ul style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Program name and version are shown in the title. For example, &quot;radf ::: V.1.1.0&quot;. Blank line.</li>
|
||||
<li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The configuration block &quot;CONFIGURATION ... END&quot;. Print log (LOG=1), do not print messages to STDOUT (QUIET=1), matrix output (MATRIX=1), mask of trajectory files (MASK=mask), first (FIRST=1) and last (LAST=1) trajectory steps, sell size (CELL=1.0000,2.0000,3.0000), mode (MODE=0) (0 – radial distribution function, 1 – radial distribution function between centers of mass, 2 – radial-angles distribution function), radial criteria (R_MIN=0.100) (R_MAX=0.100) (R_STEP=0.100), angular criteria for radial-angles distribution function (ANG_MIN=0.10) (ANG_MAX=0.10) (ANG_STEP=0.10), atom types (ATOM=1-2) or (ATOM=1,2,3-4,5,6). Blank line.</li>
|
||||
<li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The results block «SUMMARY STATISTIC … ------------------------------------------------». Table layout (2 rows) follows after specifying the block if matrix output disables.<br />The table format for radial distribution function (matrix output disables)<br /> 0001.0000 2.0000e-01 000000003 04.000000<br />Space, sphere radius (9 characters, 4 decimal part), space, segment volume (10 characters, 4 decimal part), space, number of molecules in this radius (9 characters), space, radial distribution function (9 characters, 6 decimal part).<br />The table format for radial distribution function (matrix output enables)<br /> 0001.0000 04.000000<br />Space, sphere radius (9 characters, 4 decimal part), space, radial distribution function (9 characters, 6 decimal part).<br />The table format for radial-angles distribution function (matrix output disables)<br /> 0001.0000 000005.00 2.0000e-01 000000003 04.000000<br />Space, sphere radius (9 characters, 4 decimal part), space, segment angle (9 characters, 2 decimal part), segment volume (10 characters, 4 decimal part), space, number of molecules in this segment (9 characters), space, radial-angles distribution function (9 characters, 6 decimal part).<br />The table format for radial-angles distribution function (matrix output enables). Segment angle (9 characters, 2 decimal part) is shown in the title<br /> 0001.0000 04.000000 ...<br />Space, sphere radius (9 characters, 4 decimal part), space, radial-angles distribution function (9 characters, 6 decimal part) separated by spaces.</li>
|
||||
<li style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">End of the table</li></ul>
|
||||
<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Operation of the application</span></p>
|
||||
<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Reading titles of source files, setting values of initial variables.</li>
|
||||
<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Step by step reading of source files, settings values of variables.<br />Calculating of the number of pairs of molecules in various relative configurations.</li>
|
||||
<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Print the result to the file.<br />Radial distribution function calculated by:<br />RDF(r) = (1 / norm) * sum(d(r_n-r), n),<br />norm(r) = (4*PI*r^2*dr) * ro * N * N_step,<br />where d(r_n-r) is the delta function, r is a shpere radius, n is a number of molecule, dr is the radius change step, ro is the number of molecules per volume unit, N is the number of molecules, N_step is a number of trajectory step.<br />Radial-angles distribution function calculated by:<br />RADF(r, fi) = (1 / norm) * sum(sum(d(r_n-r)*d(fi_n-fi), n), n),<br />norm(r, fi) = (4*PI*r^2*sin(fi)*dr*dfi) * ro * N * N_step,<br />where d(r_n-r) and d(fi_n-fi) are the delta functions, r is a shpere radius, fi is a segment angle, n is a number of molecule, dr is the radius change step, dfi is the angle change step, ro is the number of molecules per volume unit, N is the number of molecules, N_step is a number of trajectory step.</li></ol>
|
||||
<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Working with GUI</span></p>
|
||||
<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Go to the tab &quot;RADF&quot;. Set the work directory.</li>
|
||||
<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the mask of trajectory files.</li>
|
||||
<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the first and the last trajectory steps.</li>
|
||||
<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the cell size, A.</li>
|
||||
<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the output file.</li>
|
||||
<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set needed atoms.</li>
|
||||
<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set radial criteria. Set angular criteria if this needed.</li>
|
||||
<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the matrix output, the log file and the graph generate if this needed.</li>
|
||||
<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Run application.</li></ol></body></html></string>
|
||||
</property>
|
||||
</widget>
|
||||
</item>
|
||||
</layout>
|
||||
</widget>
|
||||
<widget class="QWidget" name="page_agl">
|
||||
<property name="geometry">
|
||||
<rect>
|
||||
<x>0</x>
|
||||
<y>0</y>
|
||||
<width>98</width>
|
||||
<height>88</height>
|
||||
</rect>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>Help about agl</string>
|
||||
</property>
|
||||
<attribute name="label">
|
||||
<string>agl</string>
|
||||
</attribute>
|
||||
<layout class="QGridLayout" name="gridLayout_2">
|
||||
<item row="0" column="0">
|
||||
<widget class="QTextBrowser" name="textBrowser_agl">
|
||||
<property name="html">
|
||||
<string><!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd">
|
||||
<html><head><meta name="qrichtext" content="1" /><style type="text/css">
|
||||
p, li { white-space: pre-wrap; }
|
||||
</style></head><body style=" font-family:'Liberation Serif'; font-size:10pt; font-weight:400; font-style:normal;">
|
||||
<p align="center" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600;">agl</span></p>
|
||||
<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />Program that creates PDB file with chosen agglomerate.</p>
|
||||
<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Usage</span><br />mm_agl -a FILE -i FILE -c X,Y,Z -o FILE [ -l FILE ] [ -q ] [ -h ]<br /> <span style=" text-decoration: underline;">Parametrs</span><br />-a FILE – input file with agglomerate<br />-i FILE – input trajectory file<br />-c X,Y,Z – cell size, A<br />-o FILE – output PDB file<br />-l FILE – print log to specified file<br />-q – do not print messages to STDOUT<br />-h – show this help and exit</p>
|
||||
<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">File formats</span></p>
|
||||
<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"> <span style=" font-style:italic;">Agglomerate file (*.agl)</span></p>
|
||||
<ul style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Agglomerate title (AGL=2=1.3.4.) (1 – number of molecules in the agglomerate, 1.3.4. – agglomerate class, if verification of isomorphism is specified).</li>
|
||||
<li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The enumeration of molecules in the agglomerate (0000001=2,3,4,5,) (1 – number of molecule (7 characters), equal sign, the enumeration of connected molecules separated by commas).</li></ul>
|
||||
<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"> <span style=" font-style:italic;">Trajectory file (*.pdb)</span></p>
|
||||
<p align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><a href="http://www.wwpdb.org/documentation/format33/sect9.html"><span style=" text-decoration: underline; color:#0000ff;">http://www.wwpdb.org/documentation/format33/sect9.html</span></a></p>
|
||||
<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Operation of the application</span></p>
|
||||
<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Reading titles of source files, setting values of initial variables.</li>
|
||||
<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Reading of source file.</li>
|
||||
<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Search for the best configuration.</li>
|
||||
<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Print the result to the file.</li></ol>
|
||||
<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Working with GUI</span></p>
|
||||
<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Select Menu -&gt; File creator -&gt; Agglomerate file.</li>
|
||||
<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the file generated by statgen. Push &quot;Select&quot;.</li>
|
||||
<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Select the trajectory file from the drop down list. Select the agglomerate.</li>
|
||||
<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the output file. Create file.</li>
|
||||
<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Go to the tab &quot;Generate PDB&quot;. Select &quot;From agglomerate&quot; from the drop down list.</li>
|
||||
<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the work directory.</li>
|
||||
<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the input trajectory file.</li>
|
||||
<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the agglomerate file.</li>
|
||||
<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the cell size, A.</li>
|
||||
<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the output PDB file.</li>
|
||||
<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the log file if this needed.</li>
|
||||
<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Run application.</li></ol></body></html></string>
|
||||
</property>
|
||||
</widget>
|
||||
</item>
|
||||
</layout>
|
||||
</widget>
|
||||
@ -130,8 +284,8 @@
|
||||
<rect>
|
||||
<x>0</x>
|
||||
<y>0</y>
|
||||
<width>580</width>
|
||||
<height>233</height>
|
||||
<width>98</width>
|
||||
<height>88</height>
|
||||
</rect>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
@ -142,7 +296,31 @@
|
||||
</attribute>
|
||||
<layout class="QGridLayout" name="gridLayout_7">
|
||||
<item row="0" column="0">
|
||||
<widget class="QTextBrowser" name="textBrowser_trj2pdb"/>
|
||||
<widget class="QTextBrowser" name="textBrowser_trj2pdb">
|
||||
<property name="html">
|
||||
<string><!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd">
|
||||
<html><head><meta name="qrichtext" content="1" /><style type="text/css">
|
||||
p, li { white-space: pre-wrap; }
|
||||
</style></head><body style=" font-family:'Liberation Serif'; font-size:10pt; font-weight:400; font-style:normal;">
|
||||
<p align="center" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600;">trj2pdb</span></p>
|
||||
<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />Program that creates PDB file from trajetory snapshot.</p>
|
||||
<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Usage</span><br />mm_trj2pdb -i FILE -o FILE [ -l FILE ] [ -q ] [ -h ]<br /> <span style=" text-decoration: underline;">Parametrs</span><br />-i FILE – input trajectory file<br />-o FILE – output PDB file<br />-l FILE – print log to specified file<br />-q – do not print messages to STDOUT<br />-h – show this help and exit</p>
|
||||
<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">File formats</span></p>
|
||||
<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"> <span style=" font-style:italic;">Trajectory file (*.pdb)</span></p>
|
||||
<p align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><a href="http://www.wwpdb.org/documentation/format33/sect9.html"><span style=" text-decoration: underline; color:#0000ff;">http://www.wwpdb.org/documentation/format33/sect9.html</span></a></p>
|
||||
<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Operation of the application</span></p>
|
||||
<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Reading titles of source files, setting values of initial variables.</li>
|
||||
<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Reading of source file.</li>
|
||||
<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Print the result to the file.</li></ol>
|
||||
<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Working with GUI</span></p>
|
||||
<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Go to the tab &quot;Generate PDB&quot;. Select &quot;From trajectory snapshot&quot; from the drop down list.</li>
|
||||
<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the work directory.</li>
|
||||
<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the input trajectory file.</li>
|
||||
<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the output PDB file.</li>
|
||||
<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the log file if this needed.</li>
|
||||
<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Run application.</li></ol></body></html></string>
|
||||
</property>
|
||||
</widget>
|
||||
</item>
|
||||
</layout>
|
||||
</widget>
|
||||
@ -164,7 +342,26 @@
|
||||
</spacer>
|
||||
</item>
|
||||
<item>
|
||||
<widget class="QPushButton" name="pushButton">
|
||||
<widget class="QPushButton" name="pushButton_save">
|
||||
<property name="minimumSize">
|
||||
<size>
|
||||
<width>80</width>
|
||||
<height>23</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>Save help to html</string>
|
||||
</property>
|
||||
<property name="text">
|
||||
<string>Save html</string>
|
||||
</property>
|
||||
<property name="autoDefault">
|
||||
<bool>true</bool>
|
||||
</property>
|
||||
</widget>
|
||||
</item>
|
||||
<item>
|
||||
<widget class="QPushButton" name="pushButton_close">
|
||||
<property name="minimumSize">
|
||||
<size>
|
||||
<width>80</width>
|
||||
@ -188,18 +385,19 @@
|
||||
</widget>
|
||||
</widget>
|
||||
<tabstops>
|
||||
<tabstop>textBrowser_general</tabstop>
|
||||
<tabstop>pushButton</tabstop>
|
||||
<tabstop>textBrowser_trj</tabstop>
|
||||
<tabstop>textBrowser_statgen</tabstop>
|
||||
<tabstop>textBrowser_envir</tabstop>
|
||||
<tabstop>textBrowser_radf</tabstop>
|
||||
<tabstop>textBrowser_agl</tabstop>
|
||||
<tabstop>textBrowser_trj2pdb</tabstop>
|
||||
<tabstop>pushButton_save</tabstop>
|
||||
<tabstop>pushButton_close</tabstop>
|
||||
</tabstops>
|
||||
<resources/>
|
||||
<connections>
|
||||
<connection>
|
||||
<sender>pushButton</sender>
|
||||
<sender>pushButton_close</sender>
|
||||
<signal>clicked()</signal>
|
||||
<receiver>HelpWindow</receiver>
|
||||
<slot>close()</slot>
|
||||
|
||||
@ -1,6 +1,6 @@
|
||||
<?xml version="1.0" encoding="UTF-8"?>
|
||||
<!DOCTYPE QtCreatorProject>
|
||||
<!-- Written by QtCreator 2.8.1, 2013-09-02T16:20:54. -->
|
||||
<!-- Written by QtCreator 2.8.1, 2013-09-03T05:28:10. -->
|
||||
<qtcreator>
|
||||
<data>
|
||||
<variable>ProjectExplorer.Project.ActiveTarget</variable>
|
||||
|
||||
Reference in New Issue
Block a user