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6 Commits
| Author | SHA1 | Date | |
|---|---|---|---|
| cdbaa00d06 | |||
| 176918b005 | |||
| 4a86149349 | |||
| d642e083b9 | |||
| 7964d9a360 | |||
| d049cd091c |
3
mathmech/AUTHORS
Normal file
3
mathmech/AUTHORS
Normal file
@ -0,0 +1,3 @@
|
||||
Current developers:
|
||||
|
||||
Evgeniy Alekseev aka arcanis <esalexeev (at) gmail (dot) com>
|
||||
@ -1,3 +1,10 @@
|
||||
set ("PROJECT_VERSION_MAJOR" 1)
|
||||
set ("PROJECT_VERSION_MINOR" 0)
|
||||
set ("PROJECT_VERSION_PATCH" 3)
|
||||
set ("PROJECT_VERSION" ${PROJECT_VERSION_MAJOR}.${PROJECT_VERSION_MINOR}.${PROJECT_VERSION_PATCH})
|
||||
|
||||
message (STATUS "Version ${PROJECT_VERSION}")
|
||||
|
||||
set (COMPS mathmech
|
||||
mm_agl
|
||||
mm_envir
|
||||
@ -6,6 +13,19 @@ set (COMPS mathmech
|
||||
mm_trj
|
||||
mm_trj2pdb)
|
||||
|
||||
# install options
|
||||
set (MM_PREFIX "mm_" CACHE STRING "Prefix for mathmech tools")
|
||||
OPTION (WITH_DEBUG_MODE "Build with debug mode" OFF)
|
||||
OPTION (ADD_INCLUDE "Add include files" OFF)
|
||||
OPTION (ADD_DOCS "Add documentation" OFF)
|
||||
if (CMAKE_SYSTEM_NAME MATCHES Linux)
|
||||
set (QWT_INCLUDE_PATH "/usr/include" CACHE STRING "Path to qwt include")
|
||||
set (QWT_LIBRARY_PATH "/usr/lib" CACHE STRING "Path to qwt library")
|
||||
elseif (CMAKE_SYSTEM_NAME MATCHES Windows)
|
||||
set (QWT_INCLUDE_PATH "C:/Qwt-6.1.0/include" CACHE STRING "Path to qwt include")
|
||||
set (QWT_LIBRARY_PATH "C:/Qwt-6.1.0/lib" CACHE STRING "Path to qwt library")
|
||||
endif()
|
||||
|
||||
foreach (COMP ${COMPS})
|
||||
add_subdirectory (${COMP})
|
||||
endforeach()
|
||||
341
mathmech/COPYING
Normal file
341
mathmech/COPYING
Normal file
@ -0,0 +1,341 @@
|
||||
GNU GENERAL PUBLIC LICENSE
|
||||
Version 2, June 1991
|
||||
|
||||
Copyright (C) 1989, 1991 Free Software Foundation, Inc.
|
||||
59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
|
||||
|
||||
Everyone is permitted to copy and distribute verbatim copies
|
||||
of this license document, but changing it is not allowed.
|
||||
|
||||
Preamble
|
||||
|
||||
The licenses for most software are designed to take away your
|
||||
freedom to share and change it. By contrast, the GNU General Public
|
||||
License is intended to guarantee your freedom to share and change free
|
||||
software--to make sure the software is free for all its users. This
|
||||
General Public License applies to most of the Free Software
|
||||
Foundation's software and to any other program whose authors commit to
|
||||
using it. (Some other Free Software Foundation software is covered by
|
||||
the GNU Library General Public License instead.) You can apply it to
|
||||
your programs, too.
|
||||
|
||||
When we speak of free software, we are referring to freedom, not
|
||||
price. Our General Public Licenses are designed to make sure that you
|
||||
have the freedom to distribute copies of free software (and charge for
|
||||
this service if you wish), that you receive source code or can get it
|
||||
if you want it, that you can change the software or use pieces of it
|
||||
in new free programs; and that you know you can do these things.
|
||||
|
||||
To protect your rights, we need to make restrictions that forbid
|
||||
anyone to deny you these rights or to ask you to surrender the rights.
|
||||
These restrictions translate to certain responsibilities for you if you
|
||||
distribute copies of the software, or if you modify it.
|
||||
|
||||
For example, if you distribute copies of such a program, whether
|
||||
gratis or for a fee, you must give the recipients all the rights that
|
||||
you have. You must make sure that they, too, receive or can get the
|
||||
source code. And you must show them these terms so they know their
|
||||
rights.
|
||||
|
||||
We protect your rights with two steps: (1) copyright the software, and
|
||||
(2) offer you this license which gives you legal permission to copy,
|
||||
distribute and/or modify the software.
|
||||
|
||||
Also, for each author's protection and ours, we want to make certain
|
||||
that everyone understands that there is no warranty for this free
|
||||
software. If the software is modified by someone else and passed on, we
|
||||
want its recipients to know that what they have is not the original, so
|
||||
that any problems introduced by others will not reflect on the original
|
||||
authors' reputations.
|
||||
|
||||
Finally, any free program is threatened constantly by software
|
||||
patents. We wish to avoid the danger that redistributors of a free
|
||||
program will individually obtain patent licenses, in effect making the
|
||||
program proprietary. To prevent this, we have made it clear that any
|
||||
patent must be licensed for everyone's free use or not licensed at all.
|
||||
|
||||
The precise terms and conditions for copying, distribution and
|
||||
modification follow.
|
||||
|
||||
GNU GENERAL PUBLIC LICENSE
|
||||
TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
|
||||
|
||||
0. This License applies to any program or other work which contains
|
||||
a notice placed by the copyright holder saying it may be distributed
|
||||
under the terms of this General Public License. The "Program", below,
|
||||
refers to any such program or work, and a "work based on the Program"
|
||||
means either the Program or any derivative work under copyright law:
|
||||
that is to say, a work containing the Program or a portion of it,
|
||||
either verbatim or with modifications and/or translated into another
|
||||
language. (Hereinafter, translation is included without limitation in
|
||||
the term "modification".) Each licensee is addressed as "you".
|
||||
|
||||
Activities other than copying, distribution and modification are not
|
||||
covered by this License; they are outside its scope. The act of
|
||||
running the Program is not restricted, and the output from the Program
|
||||
is covered only if its contents constitute a work based on the
|
||||
Program (independent of having been made by running the Program).
|
||||
Whether that is true depends on what the Program does.
|
||||
|
||||
1. You may copy and distribute verbatim copies of the Program's
|
||||
source code as you receive it, in any medium, provided that you
|
||||
conspicuously and appropriately publish on each copy an appropriate
|
||||
copyright notice and disclaimer of warranty; keep intact all the
|
||||
notices that refer to this License and to the absence of any warranty;
|
||||
and give any other recipients of the Program a copy of this License
|
||||
along with the Program.
|
||||
|
||||
You may charge a fee for the physical act of transferring a copy, and
|
||||
you may at your option offer warranty protection in exchange for a fee.
|
||||
|
||||
2. You may modify your copy or copies of the Program or any portion
|
||||
of it, thus forming a work based on the Program, and copy and
|
||||
distribute such modifications or work under the terms of Section 1
|
||||
above, provided that you also meet all of these conditions:
|
||||
|
||||
a) You must cause the modified files to carry prominent notices
|
||||
stating that you changed the files and the date of any change.
|
||||
|
||||
b) You must cause any work that you distribute or publish, that in
|
||||
whole or in part contains or is derived from the Program or any
|
||||
part thereof, to be licensed as a whole at no charge to all third
|
||||
parties under the terms of this License.
|
||||
|
||||
c) If the modified program normally reads commands interactively
|
||||
when run, you must cause it, when started running for such
|
||||
interactive use in the most ordinary way, to print or display an
|
||||
announcement including an appropriate copyright notice and a
|
||||
notice that there is no warranty (or else, saying that you provide
|
||||
a warranty) and that users may redistribute the program under
|
||||
these conditions, and telling the user how to view a copy of this
|
||||
License. (Exception: if the Program itself is interactive but
|
||||
does not normally print such an announcement, your work based on
|
||||
the Program is not required to print an announcement.)
|
||||
|
||||
These requirements apply to the modified work as a whole. If
|
||||
identifiable sections of that work are not derived from the Program,
|
||||
and can be reasonably considered independent and separate works in
|
||||
themselves, then this License, and its terms, do not apply to those
|
||||
sections when you distribute them as separate works. But when you
|
||||
distribute the same sections as part of a whole which is a work based
|
||||
on the Program, the distribution of the whole must be on the terms of
|
||||
this License, whose permissions for other licensees extend to the
|
||||
entire whole, and thus to each and every part regardless of who wrote it.
|
||||
|
||||
Thus, it is not the intent of this section to claim rights or contest
|
||||
your rights to work written entirely by you; rather, the intent is to
|
||||
exercise the right to control the distribution of derivative or
|
||||
collective works based on the Program.
|
||||
|
||||
In addition, mere aggregation of another work not based on the Program
|
||||
with the Program (or with a work based on the Program) on a volume of
|
||||
a storage or distribution medium does not bring the other work under
|
||||
the scope of this License.
|
||||
|
||||
3. You may copy and distribute the Program (or a work based on it,
|
||||
under Section 2) in object code or executable form under the terms of
|
||||
Sections 1 and 2 above provided that you also do one of the following:
|
||||
|
||||
a) Accompany it with the complete corresponding machine-readable
|
||||
source code, which must be distributed under the terms of Sections
|
||||
1 and 2 above on a medium customarily used for software interchange; or,
|
||||
|
||||
b) Accompany it with a written offer, valid for at least three
|
||||
years, to give any third party, for a charge no more than your
|
||||
cost of physically performing source distribution, a complete
|
||||
machine-readable copy of the corresponding source code, to be
|
||||
distributed under the terms of Sections 1 and 2 above on a medium
|
||||
customarily used for software interchange; or,
|
||||
|
||||
c) Accompany it with the information you received as to the offer
|
||||
to distribute corresponding source code. (This alternative is
|
||||
allowed only for noncommercial distribution and only if you
|
||||
received the program in object code or executable form with such
|
||||
an offer, in accord with Subsection b above.)
|
||||
|
||||
The source code for a work means the preferred form of the work for
|
||||
making modifications to it. For an executable work, complete source
|
||||
code means all the source code for all modules it contains, plus any
|
||||
associated interface definition files, plus the scripts used to
|
||||
control compilation and installation of the executable. However, as a
|
||||
special exception, the source code distributed need not include
|
||||
anything that is normally distributed (in either source or binary
|
||||
form) with the major components (compiler, kernel, and so on) of the
|
||||
operating system on which the executable runs, unless that component
|
||||
itself accompanies the executable.
|
||||
|
||||
If distribution of executable or object code is made by offering
|
||||
access to copy from a designated place, then offering equivalent
|
||||
access to copy the source code from the same place counts as
|
||||
distribution of the source code, even though third parties are not
|
||||
compelled to copy the source along with the object code.
|
||||
|
||||
4. You may not copy, modify, sublicense, or distribute the Program
|
||||
except as expressly provided under this License. Any attempt
|
||||
otherwise to copy, modify, sublicense or distribute the Program is
|
||||
void, and will automatically terminate your rights under this License.
|
||||
However, parties who have received copies, or rights, from you under
|
||||
this License will not have their licenses terminated so long as such
|
||||
parties remain in full compliance.
|
||||
|
||||
5. You are not required to accept this License, since you have not
|
||||
signed it. However, nothing else grants you permission to modify or
|
||||
distribute the Program or its derivative works. These actions are
|
||||
prohibited by law if you do not accept this License. Therefore, by
|
||||
modifying or distributing the Program (or any work based on the
|
||||
Program), you indicate your acceptance of this License to do so, and
|
||||
all its terms and conditions for copying, distributing or modifying
|
||||
the Program or works based on it.
|
||||
|
||||
6. Each time you redistribute the Program (or any work based on the
|
||||
Program), the recipient automatically receives a license from the
|
||||
original licensor to copy, distribute or modify the Program subject to
|
||||
these terms and conditions. You may not impose any further
|
||||
restrictions on the recipients' exercise of the rights granted herein.
|
||||
You are not responsible for enforcing compliance by third parties to
|
||||
this License.
|
||||
|
||||
7. If, as a consequence of a court judgment or allegation of patent
|
||||
infringement or for any other reason (not limited to patent issues),
|
||||
conditions are imposed on you (whether by court order, agreement or
|
||||
otherwise) that contradict the conditions of this License, they do not
|
||||
excuse you from the conditions of this License. If you cannot
|
||||
distribute so as to satisfy simultaneously your obligations under this
|
||||
License and any other pertinent obligations, then as a consequence you
|
||||
may not distribute the Program at all. For example, if a patent
|
||||
license would not permit royalty-free redistribution of the Program by
|
||||
all those who receive copies directly or indirectly through you, then
|
||||
the only way you could satisfy both it and this License would be to
|
||||
refrain entirely from distribution of the Program.
|
||||
|
||||
If any portion of this section is held invalid or unenforceable under
|
||||
any particular circumstance, the balance of the section is intended to
|
||||
apply and the section as a whole is intended to apply in other
|
||||
circumstances.
|
||||
|
||||
It is not the purpose of this section to induce you to infringe any
|
||||
patents or other property right claims or to contest validity of any
|
||||
such claims; this section has the sole purpose of protecting the
|
||||
integrity of the free software distribution system, which is
|
||||
implemented by public license practices. Many people have made
|
||||
generous contributions to the wide range of software distributed
|
||||
through that system in reliance on consistent application of that
|
||||
system; it is up to the author/donor to decide if he or she is willing
|
||||
to distribute software through any other system and a licensee cannot
|
||||
impose that choice.
|
||||
|
||||
This section is intended to make thoroughly clear what is believed to
|
||||
be a consequence of the rest of this License.
|
||||
|
||||
8. If the distribution and/or use of the Program is restricted in
|
||||
certain countries either by patents or by copyrighted interfaces, the
|
||||
original copyright holder who places the Program under this License
|
||||
may add an explicit geographical distribution limitation excluding
|
||||
those countries, so that distribution is permitted only in or among
|
||||
countries not thus excluded. In such case, this License incorporates
|
||||
the limitation as if written in the body of this License.
|
||||
|
||||
9. The Free Software Foundation may publish revised and/or new versions
|
||||
of the General Public License from time to time. Such new versions will
|
||||
be similar in spirit to the present version, but may differ in detail to
|
||||
address new problems or concerns.
|
||||
|
||||
Each version is given a distinguishing version number. If the Program
|
||||
specifies a version number of this License which applies to it and "any
|
||||
later version", you have the option of following the terms and conditions
|
||||
either of that version or of any later version published by the Free
|
||||
Software Foundation. If the Program does not specify a version number of
|
||||
this License, you may choose any version ever published by the Free Software
|
||||
Foundation.
|
||||
|
||||
10. If you wish to incorporate parts of the Program into other free
|
||||
programs whose distribution conditions are different, write to the author
|
||||
to ask for permission. For software which is copyrighted by the Free
|
||||
Software Foundation, write to the Free Software Foundation; we sometimes
|
||||
make exceptions for this. Our decision will be guided by the two goals
|
||||
of preserving the free status of all derivatives of our free software and
|
||||
of promoting the sharing and reuse of software generally.
|
||||
|
||||
NO WARRANTY
|
||||
|
||||
11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY
|
||||
FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN
|
||||
OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES
|
||||
PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED
|
||||
OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
|
||||
MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS
|
||||
TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE
|
||||
PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING,
|
||||
REPAIR OR CORRECTION.
|
||||
|
||||
12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
|
||||
WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR
|
||||
REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES,
|
||||
INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING
|
||||
OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED
|
||||
TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY
|
||||
YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER
|
||||
PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE
|
||||
POSSIBILITY OF SUCH DAMAGES.
|
||||
|
||||
END OF TERMS AND CONDITIONS
|
||||
|
||||
How to Apply These Terms to Your New Programs
|
||||
|
||||
If you develop a new program, and you want it to be of the greatest
|
||||
possible use to the public, the best way to achieve this is to make it
|
||||
free software which everyone can redistribute and change under these terms.
|
||||
|
||||
To do so, attach the following notices to the program. It is safest
|
||||
to attach them to the start of each source file to most effectively
|
||||
convey the exclusion of warranty; and each file should have at least
|
||||
the "copyright" line and a pointer to where the full notice is found.
|
||||
|
||||
<one line to give the program's name and a brief idea of what it does.>
|
||||
Copyright (C) 19yy <name of author>
|
||||
|
||||
This program is free software; you can redistribute it and/or modify
|
||||
it under the terms of the GNU General Public License as published by
|
||||
the Free Software Foundation; either version 2 of the License, or
|
||||
(at your option) any later version.
|
||||
|
||||
This program is distributed in the hope that it will be useful,
|
||||
but WITHOUT ANY WARRANTY; without even the implied warranty of
|
||||
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
|
||||
GNU General Public License for more details.
|
||||
|
||||
You should have received a copy of the GNU General Public License
|
||||
along with this program; if not, write to the Free Software
|
||||
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
|
||||
|
||||
|
||||
Also add information on how to contact you by electronic and paper mail.
|
||||
|
||||
If the program is interactive, make it output a short notice like this
|
||||
when it starts in an interactive mode:
|
||||
|
||||
Gnomovision version 69, Copyright (C) 19yy name of author
|
||||
Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
|
||||
This is free software, and you are welcome to redistribute it
|
||||
under certain conditions; type `show c' for details.
|
||||
|
||||
The hypothetical commands `show w' and `show c' should show the appropriate
|
||||
parts of the General Public License. Of course, the commands you use may
|
||||
be called something other than `show w' and `show c'; they could even be
|
||||
mouse-clicks or menu items--whatever suits your program.
|
||||
|
||||
You should also get your employer (if you work as a programmer) or your
|
||||
school, if any, to sign a "copyright disclaimer" for the program, if
|
||||
necessary. Here is a sample; alter the names:
|
||||
|
||||
Yoyodyne, Inc., hereby disclaims all copyright interest in the program
|
||||
`Gnomovision' (which makes passes at compilers) written by James Hacker.
|
||||
|
||||
<signature of Ty Coon>, 1 April 1989
|
||||
Ty Coon, President of Vice
|
||||
|
||||
This General Public License does not permit incorporating your program into
|
||||
proprietary programs. If your program is a subroutine library, you may
|
||||
consider it more useful to permit linking proprietary applications with the
|
||||
library. If this is what you want to do, use the GNU Library General
|
||||
Public License instead of this License.
|
||||
19
mathmech/INSTALL
Normal file
19
mathmech/INSTALL
Normal file
@ -0,0 +1,19 @@
|
||||
CMakeFlags:
|
||||
-DCMAKE_INSTALL_PREFIX= - install prefix (default is '/usr/local')
|
||||
-DADD_INCLUDE=1 - install include files (default is disable)
|
||||
-DADD_DOCS=1 - install documentation (default is disable)
|
||||
-DWITH_DEBUG_MODE=1 - compile with flag '-g' (default is disable)
|
||||
-DMM_PREFIX - prefix for mm components
|
||||
-DQWT_INCLUDE_PATH - path to qwt includes
|
||||
-DQWT_LIBRARY_PATH - path to qwt library
|
||||
|
||||
Install for Linux:
|
||||
mkdir build && cd build
|
||||
cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=Release ../
|
||||
make
|
||||
make install
|
||||
Install for Windows:
|
||||
create project file using 'cmake'
|
||||
compile project
|
||||
copy QtCore4.dll, QtGui4.dll, QtOpenGL4.dll, QtSvg4.dll, qwt.dll to directory with mathmech
|
||||
You may also download compiled executable file for Win_x86.
|
||||
36
mathmech/PKGBUILD
Normal file
36
mathmech/PKGBUILD
Normal file
@ -0,0 +1,36 @@
|
||||
# Author: Evgeniy "arcanis" Alexeev <esalexeev@gmail.com>
|
||||
# Maintainer: Evgeniy "arcanis" Alexeev <esalexeev@gmail.com>
|
||||
|
||||
pkgname=mathmech
|
||||
pkgver=1.0.3
|
||||
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-${pkgver}/${pkgname}-${pkgver}-src.zip)
|
||||
md5sums=('4eccb72efd4a8a531d7fda1aabc04f62')
|
||||
_cmakekeys="-DCMAKE_INSTALL_PREFIX=/usr
|
||||
-DQWT_INCLUDE_PATH=/usr/include/qwt
|
||||
-DMM_PREFIX=mm_
|
||||
-DCMAKE_BUILD_TYPE=Release"
|
||||
|
||||
build ()
|
||||
{
|
||||
unzip -o -q ${srcdir}/${pkgname}-${pkgver}-src.zip -d ${srcdir}/${pkgname}
|
||||
if [ -d ${srcdir}/${pkgname}/build ]; then
|
||||
rm -rf ${srcdir}/${pkgname}/build
|
||||
fi
|
||||
mkdir ${srcdir}/${pkgname}/build && cd ${srcdir}/${pkgname}/build
|
||||
cmake ${_cmakekeys} ../
|
||||
make
|
||||
}
|
||||
|
||||
package()
|
||||
{
|
||||
cd ${srcdir}/${pkgname}/build
|
||||
make DESTDIR=${pkgdir} install
|
||||
}
|
||||
|
||||
BIN
mathmech/mathmech-1.0.3-src.zip
Normal file
BIN
mathmech/mathmech-1.0.3-src.zip
Normal file
Binary file not shown.
BIN
mathmech/mathmech-1.0.3-win32.zip
Executable file
BIN
mathmech/mathmech-1.0.3-win32.zip
Executable file
Binary file not shown.
@ -12,7 +12,6 @@ include (${PROJECT}.cmake)
|
||||
|
||||
# additional options
|
||||
OPTION (WITH_DEBUG_MODE "Build with debug mode" OFF)
|
||||
OPTION (ADD_INCLUDE "Add include files" OFF)
|
||||
|
||||
# set libraries
|
||||
set (LIBRARIES)
|
||||
|
||||
@ -1,7 +1,8 @@
|
||||
CMakeFlags:
|
||||
-DCMAKE_INSTALL_PREFIX= - install prefix (default is '/usr/local')
|
||||
-DADD_INCLUDE=1 - install include files (default is disable)
|
||||
-DWITH_DEBUG_MODE=1 - compile with flag '-g' (default is disable)
|
||||
-DQWT_INCLUDE_PATH - path to qwt includes
|
||||
-DQWT_LIBRARY_PATH - path to qwt library
|
||||
|
||||
Install for Linux:
|
||||
mkdir build && cd build
|
||||
@ -11,4 +12,5 @@ Install for Linux:
|
||||
Install for Windows:
|
||||
create project file using 'cmake'
|
||||
compile project
|
||||
copy QtCore4.dll, QtGui4.dll, QtOpenGL4.dll, QtSvg4.dll, qwt.dll to directory with mathmech
|
||||
You may also download compiled executable file for Win_x86.
|
||||
|
||||
@ -1 +1,3 @@
|
||||
Mathematical Molecular Mechanics is GUI for "mm" program pack
|
||||
Version: 1.0.3
|
||||
License: GPL
|
||||
|
||||
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
|
Before Width: | Height: | Size: 3.4 KiB After Width: | Height: | Size: 3.4 KiB |
9
mathmech/mathmech/mathmech.desktop
Normal file
9
mathmech/mathmech/mathmech.desktop
Normal file
@ -0,0 +1,9 @@
|
||||
[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;
|
||||
BIN
mathmech/mathmech/mathmech.png
Executable file
BIN
mathmech/mathmech/mathmech.png
Executable file
Binary file not shown.
|
After Width: | Height: | Size: 1.0 KiB |
BIN
mathmech/mathmech/resources/mathmech.ico
Normal file
BIN
mathmech/mathmech/resources/mathmech.ico
Normal file
Binary file not shown.
|
After Width: | Height: | Size: 4.2 KiB |
1
mathmech/mathmech/resources/res_icon.rc
Normal file
1
mathmech/mathmech/resources/res_icon.rc
Normal file
@ -0,0 +1 @@
|
||||
IDI_ICON1 ICON DISCARDABLE "mathmech.ico"
|
||||
Binary file not shown.
File diff suppressed because it is too large
Load Diff
Binary file not shown.
File diff suppressed because it is too large
Load Diff
@ -1,20 +1,16 @@
|
||||
set (PROJECT_VERSION_MAJOR 1)
|
||||
set (PROJECT_VERSION_MINOR 0)
|
||||
set (PROJECT_VERSION_PATCH 0)
|
||||
set (PROJECT_VERSION ${PROJECT_VERSION_MAJOR}.${PROJECT_VERSION_MINOR}.${PROJECT_VERSION_PATCH})
|
||||
|
||||
message (STATUS "${PROJECT}: Version ${PROJECT_VERSION}")
|
||||
|
||||
# set files
|
||||
file (GLOB SOURCES *.cpp)
|
||||
file (GLOB HEADERS *.h)
|
||||
file (GLOB FORMS *.ui)
|
||||
if (CMAKE_SYSTEM_NAME MATCHES Windows)
|
||||
set (SOURCES ${SOURCES} ${PROJECT_RESOURCE_DIR}/res_icon.rc)
|
||||
endif ()
|
||||
# set library
|
||||
if (CMAKE_COMPILER_IS_GNUCXX)
|
||||
set (LIBRARIES m qwt)
|
||||
else ()
|
||||
set (LIBRARIES qwt)
|
||||
endif()
|
||||
endif ()
|
||||
set (LANGUAGES
|
||||
eng
|
||||
rus)
|
||||
@ -28,9 +24,11 @@ message (STATUS "FORMS: ${FORMS}")
|
||||
# compile
|
||||
project (${PROJECT})
|
||||
# include_path
|
||||
link_directories (${QWT_LIBRARY_PATH})
|
||||
include_directories (${PROJECT_INCLUDE_DIR}/${PROJECT}
|
||||
${PROJECT_SOURCE_DIR}
|
||||
${CMAKE_CURRENT_BINARY_DIR})
|
||||
${CMAKE_CURRENT_BINARY_DIR}
|
||||
${QWT_INCLUDE_PATH})
|
||||
|
||||
find_package (Qt4 REQUIRED)
|
||||
include (${QT_USE_FILE})
|
||||
@ -46,7 +44,7 @@ foreach (LANGUAGE ${LANGUAGES})
|
||||
OUTPUT ${QM}
|
||||
COMMAND ${QT_LRELEASE_EXECUTABLE} ${TS}
|
||||
MAIN_DEPENDENCY ${TS})
|
||||
endforeach()
|
||||
endforeach ()
|
||||
add_custom_target (
|
||||
translations
|
||||
COMMAND ${QT_LUPDATE_EXECUTABLE} ${HEADERS} ${SOURCES} ${UI_HEADERS} -ts ${TRANSLATIONS})
|
||||
@ -65,4 +63,12 @@ add_executable (${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)
|
||||
if (CMAKE_SYSTEM_NAME MATCHES Linux)
|
||||
install (FILES ../mathmech.desktop
|
||||
DESTINATION share/applications/)
|
||||
install (FILES ../mathmech-logo.png
|
||||
DESTINATION share/pixmaps/)
|
||||
install (FILES ../mathmech.png
|
||||
DESTINATION share/icons/hicolor/32x32/apps/)
|
||||
endif ()
|
||||
|
||||
@ -57,6 +57,9 @@ p, li { white-space: pre-wrap; }
|
||||
<height>23</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>Close window</string>
|
||||
</property>
|
||||
<property name="text">
|
||||
<string>Close</string>
|
||||
</property>
|
||||
|
||||
@ -44,6 +44,9 @@
|
||||
<height>16777215</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>Path to input file</string>
|
||||
</property>
|
||||
</widget>
|
||||
</item>
|
||||
<item>
|
||||
@ -87,6 +90,9 @@
|
||||
<height>23</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>Read selected file</string>
|
||||
</property>
|
||||
<property name="text">
|
||||
<string>Select</string>
|
||||
</property>
|
||||
@ -98,17 +104,28 @@
|
||||
</layout>
|
||||
</item>
|
||||
<item>
|
||||
<widget class="QComboBox" name="agl_comboBox"/>
|
||||
<widget class="QComboBox" name="agl_comboBox">
|
||||
<property name="toolTip">
|
||||
<string>File name</string>
|
||||
</property>
|
||||
</widget>
|
||||
</item>
|
||||
<item>
|
||||
<widget class="QListWidget" name="agl_listWidget">
|
||||
<property name="toolTip">
|
||||
<string>List of agglomerates</string>
|
||||
</property>
|
||||
<property name="editTriggers">
|
||||
<set>QAbstractItemView::NoEditTriggers</set>
|
||||
</property>
|
||||
</widget>
|
||||
</item>
|
||||
<item>
|
||||
<widget class="QTextBrowser" name="agl_textBrowser"/>
|
||||
<widget class="QTextBrowser" name="agl_textBrowser">
|
||||
<property name="toolTip">
|
||||
<string>Agglomerate</string>
|
||||
</property>
|
||||
</widget>
|
||||
</item>
|
||||
<item>
|
||||
<layout class="QHBoxLayout" name="agl_layout_output">
|
||||
@ -139,6 +156,9 @@
|
||||
<height>16777215</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>Path to output file</string>
|
||||
</property>
|
||||
</widget>
|
||||
</item>
|
||||
<item>
|
||||
@ -169,6 +189,9 @@
|
||||
<height>23</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>Clear window</string>
|
||||
</property>
|
||||
<property name="text">
|
||||
<string>Clear</string>
|
||||
</property>
|
||||
@ -204,6 +227,9 @@
|
||||
<height>16777215</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>Create file</string>
|
||||
</property>
|
||||
<property name="text">
|
||||
<string>Create</string>
|
||||
</property>
|
||||
@ -220,6 +246,9 @@
|
||||
<height>23</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>Close window</string>
|
||||
</property>
|
||||
<property name="text">
|
||||
<string>Close</string>
|
||||
</property>
|
||||
|
||||
@ -38,6 +38,9 @@
|
||||
<height>23</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>Path to work directory</string>
|
||||
</property>
|
||||
</widget>
|
||||
</item>
|
||||
<item>
|
||||
@ -81,6 +84,9 @@
|
||||
<height>23</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>Path to input file</string>
|
||||
</property>
|
||||
</widget>
|
||||
</item>
|
||||
<item>
|
||||
@ -124,6 +130,9 @@
|
||||
<height>23</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>Mask of output files</string>
|
||||
</property>
|
||||
</widget>
|
||||
</item>
|
||||
<item>
|
||||
@ -167,6 +176,9 @@
|
||||
<height>23</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>Number of file. '0' is all files</string>
|
||||
</property>
|
||||
<property name="alignment">
|
||||
<set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
|
||||
</property>
|
||||
@ -209,6 +221,9 @@
|
||||
<height>23</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>Number of molecules in agglomerates. '0' is all agglomerates</string>
|
||||
</property>
|
||||
<property name="alignment">
|
||||
<set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
|
||||
</property>
|
||||
@ -252,6 +267,9 @@
|
||||
<height>23</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>Clear window</string>
|
||||
</property>
|
||||
<property name="text">
|
||||
<string>Clear</string>
|
||||
</property>
|
||||
@ -287,6 +305,9 @@
|
||||
<height>16777215</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>Start analysis</string>
|
||||
</property>
|
||||
<property name="text">
|
||||
<string>Start</string>
|
||||
</property>
|
||||
@ -303,6 +324,9 @@
|
||||
<height>23</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>Close window</string>
|
||||
</property>
|
||||
<property name="text">
|
||||
<string>Close</string>
|
||||
</property>
|
||||
|
||||
@ -44,6 +44,9 @@
|
||||
<height>16777215</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>Path to output file</string>
|
||||
</property>
|
||||
</widget>
|
||||
</item>
|
||||
<item>
|
||||
@ -93,6 +96,9 @@
|
||||
<height>23</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>Number of molecule</string>
|
||||
</property>
|
||||
<item>
|
||||
<property name="text">
|
||||
<string>1</string>
|
||||
@ -126,6 +132,9 @@
|
||||
<height>23</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>Number of selected molecules</string>
|
||||
</property>
|
||||
<property name="alignment">
|
||||
<set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
|
||||
</property>
|
||||
@ -162,6 +171,9 @@
|
||||
<height>23</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>Character atop type</string>
|
||||
</property>
|
||||
</widget>
|
||||
</item>
|
||||
<item>
|
||||
@ -185,6 +197,9 @@
|
||||
<height>23</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>Numerical atom type</string>
|
||||
</property>
|
||||
<property name="alignment">
|
||||
<set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
|
||||
</property>
|
||||
@ -201,6 +216,9 @@
|
||||
<height>23</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>Add atom</string>
|
||||
</property>
|
||||
<property name="text">
|
||||
<string>Add</string>
|
||||
</property>
|
||||
@ -213,6 +231,9 @@
|
||||
</item>
|
||||
<item>
|
||||
<widget class="QListWidget" name="atomTypes_listWidget">
|
||||
<property name="toolTip">
|
||||
<string>Added atoms</string>
|
||||
</property>
|
||||
<property name="editTriggers">
|
||||
<set>QAbstractItemView::NoEditTriggers</set>
|
||||
</property>
|
||||
@ -241,6 +262,9 @@
|
||||
<height>23</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>Remove selected atom</string>
|
||||
</property>
|
||||
<property name="text">
|
||||
<string>Remove</string>
|
||||
</property>
|
||||
@ -261,6 +285,9 @@
|
||||
<height>23</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>Clear window</string>
|
||||
</property>
|
||||
<property name="text">
|
||||
<string>Clear</string>
|
||||
</property>
|
||||
@ -296,6 +323,9 @@
|
||||
<height>16777215</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>Create file</string>
|
||||
</property>
|
||||
<property name="text">
|
||||
<string>Create</string>
|
||||
</property>
|
||||
@ -312,6 +342,9 @@
|
||||
<height>23</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>Close window</string>
|
||||
</property>
|
||||
<property name="text">
|
||||
<string>Close</string>
|
||||
</property>
|
||||
|
||||
@ -19,7 +19,7 @@ MainWindow::MainWindow(QWidget *parent) :
|
||||
ui(new Ui::MainWindow),
|
||||
clear_items(new Clear_items(this)),
|
||||
update_fields(new Update_fields(this))
|
||||
{
|
||||
{
|
||||
ui->setupUi(this);
|
||||
statgen_crit = new float[10];
|
||||
|
||||
@ -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))
|
||||
|
||||
@ -48,6 +48,9 @@
|
||||
<height>23</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>Path to work directory</string>
|
||||
</property>
|
||||
</widget>
|
||||
</item>
|
||||
<item>
|
||||
@ -91,6 +94,9 @@
|
||||
<height>23</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>Path to input file</string>
|
||||
</property>
|
||||
</widget>
|
||||
</item>
|
||||
<item>
|
||||
@ -134,6 +140,9 @@
|
||||
<height>23</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>Input trajectory type</string>
|
||||
</property>
|
||||
<item>
|
||||
<property name="text">
|
||||
<string>GROMACS text</string>
|
||||
@ -180,6 +189,9 @@
|
||||
<height>23</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>Number of steps in trajectory</string>
|
||||
</property>
|
||||
<property name="alignment">
|
||||
<set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
|
||||
</property>
|
||||
@ -229,6 +241,9 @@
|
||||
<height>23</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>Path to file with atom types</string>
|
||||
</property>
|
||||
</widget>
|
||||
</item>
|
||||
<item>
|
||||
@ -272,6 +287,9 @@
|
||||
<height>23</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>Mask of output files</string>
|
||||
</property>
|
||||
</widget>
|
||||
</item>
|
||||
<item>
|
||||
@ -315,6 +333,9 @@
|
||||
<height>23</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>Maximum number of atom types</string>
|
||||
</property>
|
||||
<property name="layoutDirection">
|
||||
<enum>Qt::LeftToRight</enum>
|
||||
</property>
|
||||
@ -353,6 +374,9 @@
|
||||
<height>23</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>Path to log file</string>
|
||||
</property>
|
||||
</widget>
|
||||
</item>
|
||||
<item>
|
||||
@ -396,6 +420,9 @@
|
||||
<height>23</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>Clear window</string>
|
||||
</property>
|
||||
<property name="text">
|
||||
<string>Clear</string>
|
||||
</property>
|
||||
@ -431,6 +458,9 @@
|
||||
<height>16777215</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>Start application</string>
|
||||
</property>
|
||||
<property name="text">
|
||||
<string>Start</string>
|
||||
</property>
|
||||
@ -471,6 +501,9 @@
|
||||
<height>23</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>Path to work directory</string>
|
||||
</property>
|
||||
</widget>
|
||||
</item>
|
||||
<item>
|
||||
@ -514,6 +547,9 @@
|
||||
<height>23</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>Mask of input files</string>
|
||||
</property>
|
||||
</widget>
|
||||
</item>
|
||||
<item>
|
||||
@ -570,6 +606,9 @@
|
||||
<height>23</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>First trajectory step</string>
|
||||
</property>
|
||||
<property name="alignment">
|
||||
<set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
|
||||
</property>
|
||||
@ -615,6 +654,9 @@
|
||||
<height>23</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>Last trajectory step</string>
|
||||
</property>
|
||||
<property name="alignment">
|
||||
<set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
|
||||
</property>
|
||||
@ -683,6 +725,9 @@
|
||||
<height>23</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>Cell size, X</string>
|
||||
</property>
|
||||
<property name="alignment">
|
||||
<set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
|
||||
</property>
|
||||
@ -724,6 +769,9 @@
|
||||
<height>23</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>Cell size, Y</string>
|
||||
</property>
|
||||
<property name="alignment">
|
||||
<set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
|
||||
</property>
|
||||
@ -765,6 +813,9 @@
|
||||
<height>23</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>Cell size, Z</string>
|
||||
</property>
|
||||
<property name="alignment">
|
||||
<set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
|
||||
</property>
|
||||
@ -816,6 +867,9 @@
|
||||
<height>23</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>atom0 type</string>
|
||||
</property>
|
||||
<property name="alignment">
|
||||
<set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
|
||||
</property>
|
||||
@ -851,6 +905,9 @@
|
||||
<height>23</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>atom1 type</string>
|
||||
</property>
|
||||
<property name="alignment">
|
||||
<set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
|
||||
</property>
|
||||
@ -889,6 +946,9 @@
|
||||
<height>23</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>atom2 type</string>
|
||||
</property>
|
||||
<property name="alignment">
|
||||
<set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
|
||||
</property>
|
||||
@ -927,6 +987,9 @@
|
||||
<height>23</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>atom3 type</string>
|
||||
</property>
|
||||
<property name="alignment">
|
||||
<set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
|
||||
</property>
|
||||
@ -963,6 +1026,9 @@
|
||||
<height>23</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>Type of interaction</string>
|
||||
</property>
|
||||
<item>
|
||||
<property name="text">
|
||||
<string>0-0</string>
|
||||
@ -984,6 +1050,9 @@
|
||||
<height>23</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>Criterion</string>
|
||||
</property>
|
||||
<property name="alignment">
|
||||
<set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
|
||||
</property>
|
||||
@ -1006,6 +1075,9 @@
|
||||
<height>23</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>Save this criterion</string>
|
||||
</property>
|
||||
<property name="text">
|
||||
<string>Save</string>
|
||||
</property>
|
||||
@ -1022,6 +1094,9 @@
|
||||
<height>23</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>Add this interaction</string>
|
||||
</property>
|
||||
<property name="text">
|
||||
<string>Add</string>
|
||||
</property>
|
||||
@ -1040,6 +1115,9 @@
|
||||
<height>85</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>Added interactions</string>
|
||||
</property>
|
||||
<property name="editTriggers">
|
||||
<set>QAbstractItemView::NoEditTriggers</set>
|
||||
</property>
|
||||
@ -1068,6 +1146,9 @@
|
||||
<height>23</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>Remove selected interaction</string>
|
||||
</property>
|
||||
<property name="text">
|
||||
<string>Remove</string>
|
||||
</property>
|
||||
@ -1101,6 +1182,9 @@
|
||||
<height>23</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>Path to output file</string>
|
||||
</property>
|
||||
</widget>
|
||||
</item>
|
||||
<item>
|
||||
@ -1147,6 +1231,9 @@
|
||||
<height>23</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>Search depth of related graphs</string>
|
||||
</property>
|
||||
<property name="alignment">
|
||||
<set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
|
||||
</property>
|
||||
@ -1185,6 +1272,9 @@
|
||||
<height>23</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>Path to log file</string>
|
||||
</property>
|
||||
</widget>
|
||||
</item>
|
||||
<item>
|
||||
@ -1231,6 +1321,9 @@
|
||||
<height>23</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>Step of analysis</string>
|
||||
</property>
|
||||
<property name="alignment">
|
||||
<set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
|
||||
</property>
|
||||
@ -1245,6 +1338,28 @@
|
||||
</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="toolTip">
|
||||
<string>Number of steps of analysis</string>
|
||||
</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">
|
||||
@ -1266,6 +1381,9 @@
|
||||
<height>23</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>Show graph</string>
|
||||
</property>
|
||||
<property name="text">
|
||||
<string>Graph</string>
|
||||
</property>
|
||||
@ -1299,6 +1417,9 @@
|
||||
<height>23</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>Clear window</string>
|
||||
</property>
|
||||
<property name="text">
|
||||
<string>Clear</string>
|
||||
</property>
|
||||
@ -1334,6 +1455,9 @@
|
||||
<height>16777215</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>Start application</string>
|
||||
</property>
|
||||
<property name="text">
|
||||
<string>Start</string>
|
||||
</property>
|
||||
@ -1374,6 +1498,9 @@
|
||||
<height>23</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>Path to work directory</string>
|
||||
</property>
|
||||
</widget>
|
||||
</item>
|
||||
<item>
|
||||
@ -1417,6 +1544,9 @@
|
||||
<height>23</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>Path to input file</string>
|
||||
</property>
|
||||
</widget>
|
||||
</item>
|
||||
<item>
|
||||
@ -1479,6 +1609,9 @@
|
||||
<height>23</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>Cell size, X</string>
|
||||
</property>
|
||||
<property name="alignment">
|
||||
<set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
|
||||
</property>
|
||||
@ -1520,6 +1653,9 @@
|
||||
<height>23</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>Cell size, Y</string>
|
||||
</property>
|
||||
<property name="alignment">
|
||||
<set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
|
||||
</property>
|
||||
@ -1561,6 +1697,9 @@
|
||||
<height>23</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>Cell size, Z</string>
|
||||
</property>
|
||||
<property name="alignment">
|
||||
<set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
|
||||
</property>
|
||||
@ -1600,6 +1739,9 @@
|
||||
<height>23</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>Path to output file</string>
|
||||
</property>
|
||||
</widget>
|
||||
</item>
|
||||
<item>
|
||||
@ -1643,6 +1785,9 @@
|
||||
<height>23</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>Number of selected molecule</string>
|
||||
</property>
|
||||
<property name="alignment">
|
||||
<set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
|
||||
</property>
|
||||
@ -1688,6 +1833,9 @@
|
||||
<height>23</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>Radius of environment</string>
|
||||
</property>
|
||||
<property name="alignment">
|
||||
<set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
|
||||
</property>
|
||||
@ -1737,6 +1885,9 @@
|
||||
<height>23</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>Path to log file</string>
|
||||
</property>
|
||||
</widget>
|
||||
</item>
|
||||
<item>
|
||||
@ -1780,6 +1931,9 @@
|
||||
<height>23</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>Clear window</string>
|
||||
</property>
|
||||
<property name="text">
|
||||
<string>Clear</string>
|
||||
</property>
|
||||
@ -1815,6 +1969,9 @@
|
||||
<height>16777215</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>Start application</string>
|
||||
</property>
|
||||
<property name="text">
|
||||
<string>Start</string>
|
||||
</property>
|
||||
@ -1855,6 +2012,9 @@
|
||||
<height>23</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>Path to work directory</string>
|
||||
</property>
|
||||
</widget>
|
||||
</item>
|
||||
<item>
|
||||
@ -1898,6 +2058,9 @@
|
||||
<height>23</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>Mask of input files</string>
|
||||
</property>
|
||||
</widget>
|
||||
</item>
|
||||
<item>
|
||||
@ -1954,6 +2117,9 @@
|
||||
<height>23</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>First trajectory step</string>
|
||||
</property>
|
||||
<property name="alignment">
|
||||
<set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
|
||||
</property>
|
||||
@ -1999,6 +2165,9 @@
|
||||
<height>23</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>Last trajectory step</string>
|
||||
</property>
|
||||
<property name="alignment">
|
||||
<set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
|
||||
</property>
|
||||
@ -2067,6 +2236,9 @@
|
||||
<height>23</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>Cell size, X</string>
|
||||
</property>
|
||||
<property name="alignment">
|
||||
<set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
|
||||
</property>
|
||||
@ -2108,6 +2280,9 @@
|
||||
<height>23</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>Cell size, Y</string>
|
||||
</property>
|
||||
<property name="alignment">
|
||||
<set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
|
||||
</property>
|
||||
@ -2149,6 +2324,9 @@
|
||||
<height>23</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>Cell size, Z</string>
|
||||
</property>
|
||||
<property name="alignment">
|
||||
<set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
|
||||
</property>
|
||||
@ -2188,6 +2366,9 @@
|
||||
<height>23</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>Path to output file</string>
|
||||
</property>
|
||||
</widget>
|
||||
</item>
|
||||
<item>
|
||||
@ -2218,6 +2399,9 @@
|
||||
<height>23</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>Type of function</string>
|
||||
</property>
|
||||
<item>
|
||||
<property name="text">
|
||||
<string>One atom function</string>
|
||||
@ -2263,6 +2447,9 @@
|
||||
<height>23</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>atom1 type</string>
|
||||
</property>
|
||||
<property name="alignment">
|
||||
<set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
|
||||
</property>
|
||||
@ -2282,6 +2469,9 @@
|
||||
<height>23</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>atom2 type</string>
|
||||
</property>
|
||||
<property name="text">
|
||||
<string>atom 2</string>
|
||||
</property>
|
||||
@ -2323,6 +2513,9 @@
|
||||
<height>23</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>atom3 type</string>
|
||||
</property>
|
||||
<property name="text">
|
||||
<string>atom 3</string>
|
||||
</property>
|
||||
@ -2384,6 +2577,9 @@
|
||||
<height>23</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>atom1 type</string>
|
||||
</property>
|
||||
<property name="text">
|
||||
<string>atom 1</string>
|
||||
</property>
|
||||
@ -2422,6 +2618,9 @@
|
||||
<height>23</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>atom2 type</string>
|
||||
</property>
|
||||
<property name="text">
|
||||
<string>atom 2</string>
|
||||
</property>
|
||||
@ -2463,6 +2662,9 @@
|
||||
<height>23</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>atom3 type</string>
|
||||
</property>
|
||||
<property name="text">
|
||||
<string>atom 3</string>
|
||||
</property>
|
||||
@ -2534,6 +2736,9 @@
|
||||
<height>23</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>Minimal radius</string>
|
||||
</property>
|
||||
<property name="alignment">
|
||||
<set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
|
||||
</property>
|
||||
@ -2578,6 +2783,9 @@
|
||||
<height>23</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>Maximal radius</string>
|
||||
</property>
|
||||
<property name="alignment">
|
||||
<set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
|
||||
</property>
|
||||
@ -2622,6 +2830,9 @@
|
||||
<height>23</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>Radius step</string>
|
||||
</property>
|
||||
<property name="alignment">
|
||||
<set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
|
||||
</property>
|
||||
@ -2689,6 +2900,9 @@
|
||||
<height>23</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>Minimal angle</string>
|
||||
</property>
|
||||
<property name="alignment">
|
||||
<set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
|
||||
</property>
|
||||
@ -2739,6 +2953,9 @@
|
||||
<height>23</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>Maximal angle</string>
|
||||
</property>
|
||||
<property name="alignment">
|
||||
<set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
|
||||
</property>
|
||||
@ -2789,6 +3006,9 @@
|
||||
<height>23</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>Angle step</string>
|
||||
</property>
|
||||
<property name="alignment">
|
||||
<set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
|
||||
</property>
|
||||
@ -2821,6 +3041,9 @@
|
||||
<height>23</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>Matrix output</string>
|
||||
</property>
|
||||
<property name="text">
|
||||
<string>Matrix</string>
|
||||
</property>
|
||||
@ -2850,6 +3073,9 @@
|
||||
<height>23</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>Path to log file</string>
|
||||
</property>
|
||||
</widget>
|
||||
</item>
|
||||
<item>
|
||||
@ -2893,6 +3119,9 @@
|
||||
<height>23</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>Clear window</string>
|
||||
</property>
|
||||
<property name="text">
|
||||
<string>Clear</string>
|
||||
</property>
|
||||
@ -2922,6 +3151,9 @@
|
||||
<height>23</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>Show graph</string>
|
||||
</property>
|
||||
<property name="text">
|
||||
<string>Graph</string>
|
||||
</property>
|
||||
@ -2944,6 +3176,9 @@
|
||||
<height>16777215</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>Start application</string>
|
||||
</property>
|
||||
<property name="text">
|
||||
<string>Start</string>
|
||||
</property>
|
||||
@ -2963,6 +3198,9 @@
|
||||
<layout class="QVBoxLayout" name="verticalLayout_5">
|
||||
<item>
|
||||
<widget class="QComboBox" name="pdb_comboBox_mode">
|
||||
<property name="toolTip">
|
||||
<string>Input file type</string>
|
||||
</property>
|
||||
<item>
|
||||
<property name="text">
|
||||
<string>From agglomerate</string>
|
||||
@ -2998,6 +3236,9 @@
|
||||
<height>23</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>Path to work directory</string>
|
||||
</property>
|
||||
</widget>
|
||||
</item>
|
||||
<item>
|
||||
@ -3041,6 +3282,9 @@
|
||||
<height>23</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>Path to input file</string>
|
||||
</property>
|
||||
</widget>
|
||||
</item>
|
||||
<item>
|
||||
@ -3084,6 +3328,9 @@
|
||||
<height>23</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>Path to file with agglomerate</string>
|
||||
</property>
|
||||
</widget>
|
||||
</item>
|
||||
<item>
|
||||
@ -3146,6 +3393,9 @@
|
||||
<height>23</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>Cell size, X</string>
|
||||
</property>
|
||||
<property name="alignment">
|
||||
<set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
|
||||
</property>
|
||||
@ -3187,6 +3437,9 @@
|
||||
<height>23</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>Cell size, Y</string>
|
||||
</property>
|
||||
<property name="alignment">
|
||||
<set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
|
||||
</property>
|
||||
@ -3228,6 +3481,9 @@
|
||||
<height>23</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>Cell size, Z</string>
|
||||
</property>
|
||||
<property name="alignment">
|
||||
<set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
|
||||
</property>
|
||||
@ -3267,6 +3523,9 @@
|
||||
<height>23</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>Path to output file</string>
|
||||
</property>
|
||||
</widget>
|
||||
</item>
|
||||
<item>
|
||||
@ -3313,6 +3572,9 @@
|
||||
<height>23</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>Path to log file</string>
|
||||
</property>
|
||||
</widget>
|
||||
</item>
|
||||
<item>
|
||||
@ -3356,6 +3618,9 @@
|
||||
<height>23</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>Clear window</string>
|
||||
</property>
|
||||
<property name="text">
|
||||
<string>Clear</string>
|
||||
</property>
|
||||
@ -3391,6 +3656,9 @@
|
||||
<height>16777215</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>Start application</string>
|
||||
</property>
|
||||
<property name="text">
|
||||
<string>Start</string>
|
||||
</property>
|
||||
@ -3447,14 +3715,6 @@
|
||||
<addaction name="menuMenu"/>
|
||||
<addaction name="menuHelp"/>
|
||||
</widget>
|
||||
<widget class="QToolBar" name="mainToolBar">
|
||||
<attribute name="toolBarArea">
|
||||
<enum>TopToolBarArea</enum>
|
||||
</attribute>
|
||||
<attribute name="toolBarBreak">
|
||||
<bool>false</bool>
|
||||
</attribute>
|
||||
</widget>
|
||||
<widget class="QStatusBar" name="statusBar"/>
|
||||
<action name="actionExit">
|
||||
<property name="text">
|
||||
@ -3467,14 +3727,6 @@
|
||||
<string>Ctrl+Q</string>
|
||||
</property>
|
||||
</action>
|
||||
<action name="actionHelp">
|
||||
<property name="text">
|
||||
<string>&Help</string>
|
||||
</property>
|
||||
<property name="shortcut">
|
||||
<string>F1</string>
|
||||
</property>
|
||||
</action>
|
||||
<action name="actionAbout">
|
||||
<property name="text">
|
||||
<string>About</string>
|
||||
@ -3494,17 +3746,15 @@
|
||||
<property name="text">
|
||||
<string>&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 +3806,7 @@
|
||||
<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>
|
||||
|
||||
@ -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 2.8.1, 2013-08-30T19:09:45. -->
|
||||
<qtcreator>
|
||||
<data>
|
||||
<variable>ProjectExplorer.Project.ActiveTarget</variable>
|
||||
|
||||
@ -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()
|
||||
|
||||
@ -31,7 +31,11 @@
|
||||
</widget>
|
||||
</item>
|
||||
<item>
|
||||
<widget class="QLineEdit" name="settings_lineEdit_trj"/>
|
||||
<widget class="QLineEdit" name="settings_lineEdit_trj">
|
||||
<property name="toolTip">
|
||||
<string>Path to component</string>
|
||||
</property>
|
||||
</widget>
|
||||
</item>
|
||||
<item>
|
||||
<widget class="QPushButton" name="settings_pushButton_trj">
|
||||
@ -67,7 +71,11 @@
|
||||
</widget>
|
||||
</item>
|
||||
<item>
|
||||
<widget class="QLineEdit" name="settings_lineEdit_statgen"/>
|
||||
<widget class="QLineEdit" name="settings_lineEdit_statgen">
|
||||
<property name="toolTip">
|
||||
<string>Path to component</string>
|
||||
</property>
|
||||
</widget>
|
||||
</item>
|
||||
<item>
|
||||
<widget class="QPushButton" name="settings_pushButton_statgen">
|
||||
@ -103,7 +111,11 @@
|
||||
</widget>
|
||||
</item>
|
||||
<item>
|
||||
<widget class="QLineEdit" name="settings_lineEdit_envir"/>
|
||||
<widget class="QLineEdit" name="settings_lineEdit_envir">
|
||||
<property name="toolTip">
|
||||
<string>Path to component</string>
|
||||
</property>
|
||||
</widget>
|
||||
</item>
|
||||
<item>
|
||||
<widget class="QPushButton" name="settings_pushButton_envir">
|
||||
@ -139,7 +151,11 @@
|
||||
</widget>
|
||||
</item>
|
||||
<item>
|
||||
<widget class="QLineEdit" name="settings_lineEdit_radf"/>
|
||||
<widget class="QLineEdit" name="settings_lineEdit_radf">
|
||||
<property name="toolTip">
|
||||
<string>Path to component</string>
|
||||
</property>
|
||||
</widget>
|
||||
</item>
|
||||
<item>
|
||||
<widget class="QPushButton" name="settings_pushButton_radf">
|
||||
@ -175,7 +191,11 @@
|
||||
</widget>
|
||||
</item>
|
||||
<item>
|
||||
<widget class="QLineEdit" name="settings_lineEdit_trj2pdb"/>
|
||||
<widget class="QLineEdit" name="settings_lineEdit_trj2pdb">
|
||||
<property name="toolTip">
|
||||
<string>Path to component</string>
|
||||
</property>
|
||||
</widget>
|
||||
</item>
|
||||
<item>
|
||||
<widget class="QPushButton" name="settings_pushButton_trj2pdb">
|
||||
@ -211,7 +231,11 @@
|
||||
</widget>
|
||||
</item>
|
||||
<item>
|
||||
<widget class="QLineEdit" name="settings_lineEdit_agl"/>
|
||||
<widget class="QLineEdit" name="settings_lineEdit_agl">
|
||||
<property name="toolTip">
|
||||
<string>Path to component</string>
|
||||
</property>
|
||||
</widget>
|
||||
</item>
|
||||
<item>
|
||||
<widget class="QPushButton" name="settings_pushButton_agl">
|
||||
@ -254,6 +278,9 @@
|
||||
<verstretch>0</verstretch>
|
||||
</sizepolicy>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>Application language</string>
|
||||
</property>
|
||||
<item>
|
||||
<property name="text">
|
||||
<string>English</string>
|
||||
@ -336,6 +363,9 @@
|
||||
<height>23</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>Save settings</string>
|
||||
</property>
|
||||
<property name="text">
|
||||
<string>Save</string>
|
||||
</property>
|
||||
@ -352,6 +382,9 @@
|
||||
<height>23</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>Close window</string>
|
||||
</property>
|
||||
<property name="text">
|
||||
<string>Close</string>
|
||||
</property>
|
||||
|
||||
@ -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((float)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;
|
||||
}
|
||||
|
||||
|
||||
@ -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,
|
||||
|
||||
@ -3,9 +3,9 @@
|
||||
#include <QKeyEvent>
|
||||
#include <QTextStream>
|
||||
|
||||
#include <qwt/qwt_plot.h>
|
||||
#include <qwt/qwt_plot_curve.h>
|
||||
#include <qwt/qwt_series_data.h>
|
||||
#include <qwt_plot.h>
|
||||
#include <qwt_plot_curve.h>
|
||||
#include <qwt_series_data.h>
|
||||
|
||||
#include "statgengraphwindow.h"
|
||||
#include "ui_statgengraphwindow.h"
|
||||
|
||||
@ -2,7 +2,7 @@
|
||||
#define STATGENGRAPHWINDOW_H
|
||||
|
||||
#include <QMainWindow>
|
||||
#include <qwt/qwt_plot.h>
|
||||
#include <qwt_plot.h>
|
||||
|
||||
namespace Ui {
|
||||
class StatgenGraphWindow;
|
||||
|
||||
@ -38,6 +38,9 @@
|
||||
<height>23</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>Save graph</string>
|
||||
</property>
|
||||
<property name="text">
|
||||
<string>Save</string>
|
||||
</property>
|
||||
@ -54,6 +57,9 @@
|
||||
<height>23</height>
|
||||
</size>
|
||||
</property>
|
||||
<property name="toolTip">
|
||||
<string>Close window</string>
|
||||
</property>
|
||||
<property name="text">
|
||||
<string>Close</string>
|
||||
</property>
|
||||
|
||||
@ -5,14 +5,10 @@ cmake_policy(SET CMP0011 NEW)
|
||||
cmake_policy(SET CMP0015 NEW)
|
||||
|
||||
# set project name
|
||||
set (PROJECT mm_agl)
|
||||
set (PROJECT ${MM_PREFIX}agl)
|
||||
set (_PROJECT mm_agl)
|
||||
# set additional cmake file
|
||||
include (${PROJECT}.cmake)
|
||||
|
||||
|
||||
# additional options
|
||||
OPTION (WITH_DEBUG_MODE "Build with debug mode" OFF)
|
||||
OPTION (ADD_INCLUDE "Add include files" OFF)
|
||||
include (${_PROJECT}.cmake)
|
||||
|
||||
# set libraries
|
||||
set (LIBRARIES)
|
||||
@ -29,4 +25,4 @@ set (LIBRARIES)
|
||||
set (TARGETS "")
|
||||
set (HEADERS "")
|
||||
|
||||
add_subdirectory (${${PROJECT}_SOURCE_DIR})
|
||||
add_subdirectory (${PROJECT_SOURCE_DIR})
|
||||
@ -1,7 +1,9 @@
|
||||
CMakeFlags:
|
||||
-DCMAKE_INSTALL_PREFIX= - install prefix (default is '/usr/local')
|
||||
-DADD_INCLUDE=1 - install include files (default is disable)
|
||||
-DADD_DOCS=1 - install documentation (default is disable)
|
||||
-DWITH_DEBUG_MODE=1 - compile with flag '-g' (default is disable)
|
||||
-DMM_PREFIX - prefix for mm components (test flag)
|
||||
|
||||
Install for Linux:
|
||||
mkdir build && cd build
|
||||
|
||||
@ -1,12 +1,12 @@
|
||||
mm_agl - program that creates PDB file with chosen aglomerate
|
||||
Version: 1.0.1
|
||||
mm_agl - program that creates PDB file with chosen agglomerate
|
||||
Version: 1.0.3
|
||||
License: GPL
|
||||
|
||||
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
|
||||
|
||||
@ -1,16 +1,16 @@
|
||||
# set directories
|
||||
set (${PROJECT}_BINARY_DIR bin)
|
||||
set (${PROJECT}_SOURCE_DIR src)
|
||||
set (${PROJECT}_INCLUDE_DIR include)
|
||||
set (${PROJECT}_LIB_DIR lib)
|
||||
set (PROJECT_BINARY_DIR bin)
|
||||
set (PROJECT_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/src)
|
||||
set (PROJECT_INCLUDE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/include)
|
||||
set (PROJECT_LIB_DIR ${CMAKE_CURRENT_SOURCE_DIR}/lib)
|
||||
|
||||
# include_path
|
||||
include_directories (${${PROJECT}_INCLUDE_DIR}/${PROJECT}
|
||||
${${PROJECT}_SOURCE_DIR})
|
||||
include_directories (${PROJECT_INCLUDE_DIR}/${PROJECT}
|
||||
${PROJECT_SOURCE_DIR})
|
||||
# library path
|
||||
link_directories (${${PROJECT}_LIB_DIR})
|
||||
link_directories (${PROJECT_LIB_DIR})
|
||||
# executable path
|
||||
set (EXECUTABLE_OUTPUT_PATH ${${PROJECT}_BINARY_DIR})
|
||||
set (EXECUTABLE_OUTPUT_PATH ${PROJECT_BINARY_DIR})
|
||||
|
||||
# verbose
|
||||
set (CMAKE_VERBOSE_MAKEFILE ON)
|
||||
|
||||
@ -32,13 +32,13 @@ PROJECT_NAME = mm_agl
|
||||
# This could be handy for archiving the generated documentation or
|
||||
# if some version control system is used.
|
||||
|
||||
PROJECT_NUMBER = V.1.0.1
|
||||
PROJECT_NUMBER = V.1.0.3
|
||||
|
||||
# Using the PROJECT_BRIEF tag one can provide an optional one line description
|
||||
# for a project that appears at the top of each page and should give viewer
|
||||
# a quick idea about the purpose of the project. Keep the description short.
|
||||
|
||||
PROJECT_BRIEF = "Program that creates PDB file with chosen aglomerate"
|
||||
PROJECT_BRIEF = "Program that creates PDB file with chosen agglomerate"
|
||||
|
||||
# With the PROJECT_LOGO tag one can specify an logo or icon that is
|
||||
# included in the documentation. The maximum height of the logo should not
|
||||
|
||||
Binary file not shown.
@ -1,10 +1,3 @@
|
||||
set ("${PROJECT}_VERSION_MAJOR" 1)
|
||||
set ("${PROJECT}_VERSION_MINOR" 0)
|
||||
set ("${PROJECT}_VERSION_PATCH" 1)
|
||||
set ("${PROJECT}_VERSION" ${${PROJECT}_VERSION_MAJOR}.${${PROJECT}_VERSION_MINOR}.${${PROJECT}_VERSION_PATCH})
|
||||
|
||||
message (STATUS "${PROJECT}: Version ${${PROJECT}_VERSION}")
|
||||
|
||||
# set files
|
||||
aux_source_directory (. SOURCES)
|
||||
|
||||
@ -26,4 +19,7 @@ target_link_libraries (${PROJECT} ${ADDITIONAL_LIB})
|
||||
INSTALL (TARGETS ${PROJECT} DESTINATION bin)
|
||||
if (ADD_INCLUDE)
|
||||
INSTALL (FILES ${PUBLIC_HEADERS} DESTINATION include/${PROJECT})
|
||||
endif ()
|
||||
endif ()
|
||||
if (ADD_DOCS)
|
||||
INSTALL (FILES ${PROJECT_SOURCE_DIR}/../${_PROJECT}.pdf DESTINATION share/doc/mathmech)
|
||||
endif ()
|
||||
|
||||
@ -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
|
||||
|
||||
@ -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
|
||||
@ -61,8 +61,14 @@
|
||||
* You may also download compiled executable file for Win_x86.
|
||||
*
|
||||
* @page Changelog
|
||||
* V.1.0.3 (2013-08-30)
|
||||
* <ul>
|
||||
* <li> Bug fixes
|
||||
* </ul>
|
||||
* V.1.0.1 (2013-07-27)
|
||||
* * initial release
|
||||
* <ul>
|
||||
* <li> initial release
|
||||
* </ul>
|
||||
*/
|
||||
|
||||
#include <math.h>
|
||||
@ -100,7 +106,7 @@ 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 +133,14 @@ 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, "%sVersion : 1.0.1 License : GPL\n", tmp_str);
|
||||
sprintf (tmp_str, "%sProgram for create PDB file with chosen agglomerate\n", tmp_str);
|
||||
sprintf (tmp_str, "%sVersion : 1.0.3 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 +244,13 @@ 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);
|
||||
|
||||
@ -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);
|
||||
|
||||
@ -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");
|
||||
|
||||
@ -5,14 +5,10 @@ cmake_policy(SET CMP0011 NEW)
|
||||
cmake_policy(SET CMP0015 NEW)
|
||||
|
||||
# set project name
|
||||
set (PROJECT mm_envir)
|
||||
set (PROJECT ${MM_PREFIX}envir)
|
||||
set (_PROJECT mm_envir)
|
||||
# set additional cmake file
|
||||
include (${PROJECT}.cmake)
|
||||
|
||||
|
||||
# additional options
|
||||
OPTION (WITH_DEBUG_MODE "Build with debug mode" OFF)
|
||||
OPTION (ADD_INCLUDE "Add include files" OFF)
|
||||
include (${_PROJECT}.cmake)
|
||||
|
||||
# set libraries
|
||||
set (LIBRARIES)
|
||||
@ -29,4 +25,4 @@ set (LIBRARIES)
|
||||
set (TARGETS "")
|
||||
set (HEADERS "")
|
||||
|
||||
add_subdirectory (${${PROJECT}_SOURCE_DIR})
|
||||
add_subdirectory (${PROJECT_SOURCE_DIR})
|
||||
@ -1,7 +1,9 @@
|
||||
CMakeFlags:
|
||||
-DCMAKE_INSTALL_PREFIX= - install prefix (default is '/usr/local')
|
||||
-DADD_INCLUDE=1 - install include files (default is disable)
|
||||
-DADD_DOCS=1 - install documentation (default is disable)
|
||||
-DWITH_DEBUG_MODE=1 - compile with flag '-g' (default is disable)
|
||||
-DMM_PREFIX - prefix for mm components (test flag)
|
||||
|
||||
Install for Linux:
|
||||
mkdir build && cd build
|
||||
|
||||
@ -1,5 +1,5 @@
|
||||
mm_envir - program that searchs environment for chosen molecule by geometric criterion
|
||||
Version: 1.0.1
|
||||
Version: 1.0.3
|
||||
License: GPL
|
||||
|
||||
Usage:
|
||||
|
||||
@ -1,16 +1,16 @@
|
||||
# set directories
|
||||
set (${PROJECT}_BINARY_DIR bin)
|
||||
set (${PROJECT}_SOURCE_DIR src)
|
||||
set (${PROJECT}_INCLUDE_DIR include)
|
||||
set (${PROJECT}_LIB_DIR lib)
|
||||
set (PROJECT_BINARY_DIR bin)
|
||||
set (PROJECT_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/src)
|
||||
set (PROJECT_INCLUDE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/include)
|
||||
set (PROJECT_LIB_DIR ${CMAKE_CURRENT_SOURCE_DIR}/lib)
|
||||
|
||||
# include_path
|
||||
include_directories (${${PROJECT}_INCLUDE_DIR}/${PROJECT}
|
||||
${${PROJECT}_SOURCE_DIR})
|
||||
include_directories (${PROJECT_INCLUDE_DIR}/${PROJECT}
|
||||
${PROJECT_SOURCE_DIR})
|
||||
# library path
|
||||
link_directories (${${PROJECT}_LIB_DIR})
|
||||
link_directories (${PROJECT_LIB_DIR})
|
||||
# executable path
|
||||
set (EXECUTABLE_OUTPUT_PATH ${${PROJECT}_BINARY_DIR})
|
||||
set (EXECUTABLE_OUTPUT_PATH ${PROJECT_BINARY_DIR})
|
||||
|
||||
# verbose
|
||||
set (CMAKE_VERBOSE_MAKEFILE ON)
|
||||
|
||||
@ -32,7 +32,7 @@ PROJECT_NAME = mm_envir
|
||||
# This could be handy for archiving the generated documentation or
|
||||
# if some version control system is used.
|
||||
|
||||
PROJECT_NUMBER = V.1.0.1
|
||||
PROJECT_NUMBER = V.1.0.3
|
||||
|
||||
# Using the PROJECT_BRIEF tag one can provide an optional one line description
|
||||
# for a project that appears at the top of each page and should give viewer
|
||||
|
||||
Binary file not shown.
@ -1,10 +1,3 @@
|
||||
set ("${PROJECT}_VERSION_MAJOR" 1)
|
||||
set ("${PROJECT}_VERSION_MINOR" 0)
|
||||
set ("${PROJECT}_VERSION_PATCH" 1)
|
||||
set ("${PROJECT}_VERSION" ${${PROJECT}_VERSION_MAJOR}.${${PROJECT}_VERSION_MINOR}.${${PROJECT}_VERSION_PATCH})
|
||||
|
||||
message (STATUS "${PROJECT}: Version ${${PROJECT}_VERSION}")
|
||||
|
||||
# set files
|
||||
aux_source_directory (. SOURCES)
|
||||
|
||||
@ -26,4 +19,7 @@ target_link_libraries (${PROJECT} ${ADDITIONAL_LIB})
|
||||
INSTALL (TARGETS ${PROJECT} DESTINATION bin)
|
||||
if (ADD_INCLUDE)
|
||||
INSTALL (FILES ${PUBLIC_HEADERS} DESTINATION include/${PROJECT})
|
||||
endif ()
|
||||
endif ()
|
||||
if (ADD_DOCS)
|
||||
INSTALL (FILES ${PROJECT_SOURCE_DIR}/../${_PROJECT}.pdf DESTINATION share/doc/mathmech)
|
||||
endif ()
|
||||
|
||||
@ -63,8 +63,14 @@
|
||||
* You may also download compiled executable file for Win_x86.
|
||||
*
|
||||
* @page Changelog
|
||||
* V.1.0.3 (2013-08-30)
|
||||
* <ul>
|
||||
* <li> Bug fixes
|
||||
* </ul>
|
||||
* V.1.0.1 (2013-07-27)
|
||||
* * initial release
|
||||
* <ul>
|
||||
* <li> initial release
|
||||
* </ul>
|
||||
*/
|
||||
|
||||
#include <math.h>
|
||||
@ -130,7 +136,7 @@ int main(int argc, char *argv[])
|
||||
{
|
||||
sprintf (tmp_str, " mm_envir\n");
|
||||
sprintf (tmp_str, "%sProgram for search environment for chosen molecule by geometric criterion\n", tmp_str);
|
||||
sprintf (tmp_str, "%sVersion : 1.0.1 License : GPL\n", tmp_str);
|
||||
sprintf (tmp_str, "%sVersion : 1.0.3 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);
|
||||
|
||||
@ -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);
|
||||
|
||||
@ -5,14 +5,10 @@ cmake_policy(SET CMP0011 NEW)
|
||||
cmake_policy(SET CMP0015 NEW)
|
||||
|
||||
# set project name
|
||||
set (PROJECT mm_radf)
|
||||
set (PROJECT ${MM_PREFIX}radf)
|
||||
set (_PROJECT mm_radf)
|
||||
# set additional cmake file
|
||||
include (${PROJECT}.cmake)
|
||||
|
||||
|
||||
# additional options
|
||||
OPTION (WITH_DEBUG_MODE "Build with debug mode" OFF)
|
||||
OPTION (ADD_INCLUDE "Add include files" OFF)
|
||||
include (${_PROJECT}.cmake)
|
||||
|
||||
# set libraries
|
||||
set (LIBRARIES)
|
||||
@ -29,4 +25,4 @@ set (LIBRARIES)
|
||||
set (TARGETS "")
|
||||
set (HEADERS "")
|
||||
|
||||
add_subdirectory (${${PROJECT}_SOURCE_DIR})
|
||||
add_subdirectory (${PROJECT_SOURCE_DIR})
|
||||
@ -1,7 +1,9 @@
|
||||
CMakeFlags:
|
||||
-DCMAKE_INSTALL_PREFIX= - install prefix (default is '/usr/local')
|
||||
-DADD_INCLUDE=1 - install include files (default is disable)
|
||||
-DADD_DOCS=1 - install documentation (default is disable)
|
||||
-DWITH_DEBUG_MODE=1 - compile with flag '-g' (default is disable)
|
||||
-DMM_PREFIX - prefix for mm components (test flag)
|
||||
|
||||
Install for Linux:
|
||||
mkdir build && cd build
|
||||
|
||||
@ -1,6 +1,6 @@
|
||||
mm_radf - program that calculates radial distribution function (RDF) or radial-angles
|
||||
distribution function
|
||||
Version : 1.0.1
|
||||
Version : 1.0.3
|
||||
License : GPL
|
||||
|
||||
Usage:
|
||||
|
||||
@ -1,16 +1,16 @@
|
||||
# set directories
|
||||
set (${PROJECT}_BINARY_DIR bin)
|
||||
set (${PROJECT}_SOURCE_DIR src)
|
||||
set (${PROJECT}_INCLUDE_DIR include)
|
||||
set (${PROJECT}_LIB_DIR lib)
|
||||
set (PROJECT_BINARY_DIR bin)
|
||||
set (PROJECT_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/src)
|
||||
set (PROJECT_INCLUDE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/include)
|
||||
set (PROJECT_LIB_DIR ${CMAKE_CURRENT_SOURCE_DIR}/lib)
|
||||
|
||||
# include_path
|
||||
include_directories (${${PROJECT}_INCLUDE_DIR}/${PROJECT}
|
||||
${${PROJECT}_SOURCE_DIR})
|
||||
include_directories (${PROJECT_INCLUDE_DIR}/${PROJECT}
|
||||
${PROJECT_SOURCE_DIR})
|
||||
# library path
|
||||
link_directories (${${PROJECT}_LIB_DIR})
|
||||
link_directories (${PROJECT_LIB_DIR})
|
||||
# executable path
|
||||
set (EXECUTABLE_OUTPUT_PATH ${${PROJECT}_BINARY_DIR})
|
||||
set (EXECUTABLE_OUTPUT_PATH ${PROJECT_BINARY_DIR})
|
||||
|
||||
# verbose
|
||||
set (CMAKE_VERBOSE_MAKEFILE ON)
|
||||
|
||||
@ -32,7 +32,7 @@ PROJECT_NAME = mm_radf
|
||||
# This could be handy for archiving the generated documentation or
|
||||
# if some version control system is used.
|
||||
|
||||
PROJECT_NUMBER = V.1.0.1
|
||||
PROJECT_NUMBER = V.1.0.3
|
||||
|
||||
# Using the PROJECT_BRIEF tag one can provide an optional one line description
|
||||
# for a project that appears at the top of each page and should give viewer
|
||||
|
||||
Binary file not shown.
@ -1,10 +1,3 @@
|
||||
set ("${PROJECT}_VERSION_MAJOR" 1)
|
||||
set ("${PROJECT}_VERSION_MINOR" 0)
|
||||
set ("${PROJECT}_VERSION_PATCH" 1)
|
||||
set ("${PROJECT}_VERSION" ${${PROJECT}_VERSION_MAJOR}.${${PROJECT}_VERSION_MINOR}.${${PROJECT}_VERSION_PATCH})
|
||||
|
||||
message (STATUS "${PROJECT}: Version ${${PROJECT}_VERSION}")
|
||||
|
||||
# set files
|
||||
aux_source_directory (. SOURCES)
|
||||
|
||||
@ -26,4 +19,7 @@ target_link_libraries (${PROJECT} ${ADDITIONAL_LIB})
|
||||
INSTALL (TARGETS ${PROJECT} DESTINATION bin)
|
||||
if (ADD_INCLUDE)
|
||||
INSTALL (FILES ${PUBLIC_HEADERS} DESTINATION include/${PROJECT})
|
||||
endif ()
|
||||
endif ()
|
||||
if (ADD_DOCS)
|
||||
INSTALL (FILES ${PROJECT_SOURCE_DIR}/../${_PROJECT}.pdf DESTINATION share/doc/mathmech)
|
||||
endif ()
|
||||
|
||||
@ -70,8 +70,14 @@
|
||||
* You may also download compiled executable file for Win_x86.
|
||||
*
|
||||
* @page Changelog
|
||||
* V.1.0.3 (2013-08-30)
|
||||
* <ul>
|
||||
* <li> Bug fixes
|
||||
* </ul>
|
||||
* V.1.0.1 (2013-07-27)
|
||||
* * initial release
|
||||
* <ul>
|
||||
* <li> initial release
|
||||
* </ul>
|
||||
*/
|
||||
|
||||
#include <math.h>
|
||||
@ -147,7 +153,7 @@ int main(int argc, char *argv[])
|
||||
sprintf (tmp_str, " mm_radf\n");
|
||||
sprintf (tmp_str, "%sProgram that calculates radial distribution function (RDF) or radial-angles\n", tmp_str);
|
||||
sprintf (tmp_str, "%sdistribution function\n", tmp_str);
|
||||
sprintf (tmp_str, "%sVersion : 1.0.1 License : GPL\n", tmp_str);
|
||||
sprintf (tmp_str, "%sVersion : 1.0.3 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);
|
||||
|
||||
@ -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);
|
||||
|
||||
@ -5,14 +5,10 @@ cmake_policy(SET CMP0011 NEW)
|
||||
cmake_policy(SET CMP0015 NEW)
|
||||
|
||||
# set project name
|
||||
set (PROJECT mm_statgen)
|
||||
set (PROJECT ${MM_PREFIX}statgen)
|
||||
set (_PROJECT mm_statgen)
|
||||
# set additional cmake file
|
||||
include (${PROJECT}.cmake)
|
||||
|
||||
|
||||
# additional options
|
||||
OPTION (WITH_DEBUG_MODE "Build with debug mode" OFF)
|
||||
OPTION (ADD_INCLUDE "Add include files" OFF)
|
||||
include (${_PROJECT}.cmake)
|
||||
|
||||
# set libraries
|
||||
set (LIBRARIES)
|
||||
@ -29,4 +25,4 @@ set (LIBRARIES)
|
||||
set (TARGETS "")
|
||||
set (HEADERS "")
|
||||
|
||||
add_subdirectory (${${PROJECT}_SOURCE_DIR})
|
||||
add_subdirectory (${PROJECT_SOURCE_DIR})
|
||||
@ -1,7 +1,9 @@
|
||||
CMakeFlags:
|
||||
-DCMAKE_INSTALL_PREFIX= - install prefix (default is '/usr/local')
|
||||
-DADD_INCLUDE=1 - install include files (default is disable)
|
||||
-DADD_DOCS=1 - install documentation (default is disable)
|
||||
-DWITH_DEBUG_MODE=1 - compile with flag '-g' (default is disable)
|
||||
-DMM_PREFIX - prefix for mm components (test flag)
|
||||
|
||||
Install for Linux:
|
||||
mkdir build && cd build
|
||||
|
||||
@ -1,5 +1,5 @@
|
||||
mm_statgen - program that analyzes molecular dynamic trajectories using topological analysis
|
||||
Version: 1.0.1
|
||||
Version: 1.0.3
|
||||
License: GPL
|
||||
|
||||
Usage:
|
||||
|
||||
@ -1,16 +1,16 @@
|
||||
# set directories
|
||||
set (${PROJECT}_BINARY_DIR bin)
|
||||
set (${PROJECT}_SOURCE_DIR src)
|
||||
set (${PROJECT}_INCLUDE_DIR include)
|
||||
set (${PROJECT}_LIB_DIR lib)
|
||||
set (PROJECT_BINARY_DIR bin)
|
||||
set (PROJECT_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/src)
|
||||
set (PROJECT_INCLUDE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/include)
|
||||
set (PROJECT_LIB_DIR ${CMAKE_CURRENT_SOURCE_DIR}/lib)
|
||||
|
||||
# include_path
|
||||
include_directories (${${PROJECT}_INCLUDE_DIR}/${PROJECT}
|
||||
${${PROJECT}_SOURCE_DIR})
|
||||
include_directories (${PROJECT_INCLUDE_DIR}/${PROJECT}
|
||||
${PROJECT_SOURCE_DIR})
|
||||
# library path
|
||||
link_directories (${${PROJECT}_LIB_DIR})
|
||||
link_directories (${PROJECT_LIB_DIR})
|
||||
# executable path
|
||||
set (EXECUTABLE_OUTPUT_PATH ${${PROJECT}_BINARY_DIR})
|
||||
set (EXECUTABLE_OUTPUT_PATH ${PROJECT_BINARY_DIR})
|
||||
|
||||
# verbose
|
||||
set (CMAKE_VERBOSE_MAKEFILE ON)
|
||||
|
||||
@ -32,7 +32,7 @@ PROJECT_NAME = mm_statgen
|
||||
# This could be handy for archiving the generated documentation or
|
||||
# if some version control system is used.
|
||||
|
||||
PROJECT_NUMBER = V.1.0.1
|
||||
PROJECT_NUMBER = V.1.0.3
|
||||
|
||||
# Using the PROJECT_BRIEF tag one can provide an optional one line description
|
||||
# for a project that appears at the top of each page and should give viewer
|
||||
|
||||
Binary file not shown.
@ -1,10 +1,3 @@
|
||||
set ("${PROJECT}_VERSION_MAJOR" 1)
|
||||
set ("${PROJECT}_VERSION_MINOR" 0)
|
||||
set ("${PROJECT}_VERSION_PATCH" 1)
|
||||
set ("${PROJECT}_VERSION" ${${PROJECT}_VERSION_MAJOR}.${${PROJECT}_VERSION_MINOR}.${${PROJECT}_VERSION_PATCH})
|
||||
|
||||
message (STATUS "${PROJECT}: Version ${${PROJECT}_VERSION}")
|
||||
|
||||
# set files
|
||||
aux_source_directory (. SOURCES)
|
||||
|
||||
@ -26,4 +19,7 @@ target_link_libraries (${PROJECT} ${ADDITIONAL_LIB})
|
||||
INSTALL (TARGETS ${PROJECT} DESTINATION bin)
|
||||
if (ADD_INCLUDE)
|
||||
INSTALL (FILES ${PUBLIC_HEADERS} DESTINATION include/${PROJECT})
|
||||
endif ()
|
||||
endif ()
|
||||
if (ADD_DOCS)
|
||||
INSTALL (FILES ${PROJECT_SOURCE_DIR}/../${_PROJECT}.pdf DESTINATION share/doc/mathmech)
|
||||
endif ()
|
||||
|
||||
@ -66,8 +66,14 @@
|
||||
* You may also download compiled executable file for Win_x86.
|
||||
*
|
||||
* @page Changelog
|
||||
* V.1.0.3 (2013-08-30)
|
||||
* <ul>
|
||||
* <li> Bug fixes
|
||||
* </ul>
|
||||
* V.1.0.1 (2013-07-27)
|
||||
* * initial release
|
||||
* <ul>
|
||||
* <li> initial release
|
||||
* </ul>
|
||||
*/
|
||||
|
||||
#include <math.h>
|
||||
@ -116,7 +122,7 @@ 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 +131,14 @@ 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
|
||||
@ -162,7 +168,7 @@ int main (int argc, char *argv[])
|
||||
{
|
||||
sprintf (tmp_str, " mm_statgen\n");
|
||||
sprintf (tmp_str, "%sProgram for analyze molecular dynamic trajectories\n", tmp_str);
|
||||
sprintf (tmp_str, "%sVersion : 1.0.1 License : GPL\n", tmp_str);
|
||||
sprintf (tmp_str, "%sVersion : 1.0.3 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);
|
||||
|
||||
@ -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);
|
||||
|
||||
@ -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++)
|
||||
{
|
||||
|
||||
@ -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
|
||||
*
|
||||
|
||||
@ -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];
|
||||
|
||||
@ -5,14 +5,10 @@ cmake_policy(SET CMP0011 NEW)
|
||||
cmake_policy(SET CMP0015 NEW)
|
||||
|
||||
# set project name
|
||||
set (PROJECT mm_trj)
|
||||
set (PROJECT ${MM_PREFIX}trj)
|
||||
set (_PROJECT mm_trj)
|
||||
# set additional cmake file
|
||||
include (${PROJECT}.cmake)
|
||||
|
||||
|
||||
# additional options
|
||||
OPTION (WITH_DEBUG_MODE "Build with debug mode" OFF)
|
||||
OPTION (ADD_INCLUDE "Add include files" OFF)
|
||||
include (${_PROJECT}.cmake)
|
||||
|
||||
# set libraries
|
||||
set (LIBRARIES)
|
||||
@ -29,4 +25,4 @@ set (LIBRARIES)
|
||||
set (TARGETS "")
|
||||
set (HEADERS "")
|
||||
|
||||
add_subdirectory (${${PROJECT}_SOURCE_DIR})
|
||||
add_subdirectory (${PROJECT_SOURCE_DIR})
|
||||
@ -1,7 +1,9 @@
|
||||
CMakeFlags:
|
||||
-DCMAKE_INSTALL_PREFIX= - install prefix (default is '/usr/local')
|
||||
-DADD_INCLUDE=1 - install include files (default is disable)
|
||||
-DADD_DOCS=1 - install documentation (default is disable)
|
||||
-DWITH_DEBUG_MODE=1 - compile with flag '-g' (default is disable)
|
||||
-DMM_PREFIX - prefix for mm components (test flag)
|
||||
|
||||
Install for Linux:
|
||||
mkdir build && cd build
|
||||
|
||||
@ -1,5 +1,5 @@
|
||||
mm_trj - program that generates trajectory files
|
||||
Version : 1.0.1
|
||||
Version : 1.0.3
|
||||
License : GPL
|
||||
|
||||
Usage:
|
||||
|
||||
@ -1,16 +1,16 @@
|
||||
# set directories
|
||||
set (${PROJECT}_BINARY_DIR bin)
|
||||
set (${PROJECT}_SOURCE_DIR src)
|
||||
set (${PROJECT}_INCLUDE_DIR include)
|
||||
set (${PROJECT}_LIB_DIR lib)
|
||||
set (PROJECT_BINARY_DIR bin)
|
||||
set (PROJECT_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/src)
|
||||
set (PROJECT_INCLUDE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/include)
|
||||
set (PROJECT_LIB_DIR ${CMAKE_CURRENT_SOURCE_DIR}/lib)
|
||||
|
||||
# include_path
|
||||
include_directories (${${PROJECT}_INCLUDE_DIR}/${PROJECT}
|
||||
${${PROJECT}_SOURCE_DIR})
|
||||
include_directories (${PROJECT_INCLUDE_DIR}/${PROJECT}
|
||||
${PROJECT_SOURCE_DIR})
|
||||
# library path
|
||||
link_directories (${${PROJECT}_LIB_DIR})
|
||||
link_directories (${PROJECT_LIB_DIR})
|
||||
# executable path
|
||||
set (EXECUTABLE_OUTPUT_PATH ${${PROJECT}_BINARY_DIR})
|
||||
set (EXECUTABLE_OUTPUT_PATH ${PROJECT_BINARY_DIR})
|
||||
|
||||
# verbose
|
||||
set (CMAKE_VERBOSE_MAKEFILE ON)
|
||||
|
||||
@ -32,7 +32,7 @@ PROJECT_NAME = mm_trj
|
||||
# This could be handy for archiving the generated documentation or
|
||||
# if some version control system is used.
|
||||
|
||||
PROJECT_NUMBER = V.1.0.1
|
||||
PROJECT_NUMBER = V.1.0.3
|
||||
|
||||
# Using the PROJECT_BRIEF tag one can provide an optional one line description
|
||||
# for a project that appears at the top of each page and should give viewer
|
||||
|
||||
Binary file not shown.
@ -1,10 +1,3 @@
|
||||
set ("${PROJECT}_VERSION_MAJOR" 1)
|
||||
set ("${PROJECT}_VERSION_MINOR" 0)
|
||||
set ("${PROJECT}_VERSION_PATCH" 1)
|
||||
set ("${PROJECT}_VERSION" ${${PROJECT}_VERSION_MAJOR}.${${PROJECT}_VERSION_MINOR}.${${PROJECT}_VERSION_PATCH})
|
||||
|
||||
message (STATUS "${PROJECT}: Version ${${PROJECT}_VERSION}")
|
||||
|
||||
# set files
|
||||
aux_source_directory (. SOURCES)
|
||||
|
||||
@ -26,4 +19,7 @@ target_link_libraries (${PROJECT} ${ADDITIONAL_LIB})
|
||||
INSTALL (TARGETS ${PROJECT} DESTINATION bin)
|
||||
if (ADD_INCLUDE)
|
||||
INSTALL (FILES ${PUBLIC_HEADERS} DESTINATION include/${PROJECT})
|
||||
endif ()
|
||||
endif ()
|
||||
if (ADD_DOCS)
|
||||
INSTALL (FILES ${PROJECT_SOURCE_DIR}/../${_PROJECT}.pdf DESTINATION share/doc/mathmech)
|
||||
endif ()
|
||||
|
||||
@ -63,8 +63,14 @@
|
||||
* You may also download compiled executable file for Win_x86.
|
||||
*
|
||||
* @page Changelog
|
||||
* V.1.0.3 (2013-08-30)
|
||||
* <ul>
|
||||
* <li> Bug fixes
|
||||
* </ul>
|
||||
* V.1.0.1 (2013-07-27)
|
||||
* * initial release
|
||||
* <ul>
|
||||
* <li> initial release
|
||||
* </ul>
|
||||
*/
|
||||
|
||||
#include <math.h>
|
||||
@ -127,7 +133,7 @@ int main(int argc, char *argv[])
|
||||
{
|
||||
sprintf (tmp_str, " mm_trj\n");
|
||||
sprintf (tmp_str, "%sProgram that generates trajectory files\n", tmp_str);
|
||||
sprintf (tmp_str, "%sVersion : 1.0.1 License : GPL\n", tmp_str);
|
||||
sprintf (tmp_str, "%sVersion : 1.0.3 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);
|
||||
|
||||
@ -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);
|
||||
|
||||
@ -5,14 +5,10 @@ cmake_policy(SET CMP0011 NEW)
|
||||
cmake_policy(SET CMP0015 NEW)
|
||||
|
||||
# set project name
|
||||
set (PROJECT mm_trj2pdb)
|
||||
set (PROJECT ${MM_PREFIX}trj2pdb)
|
||||
set (_PROJECT mm_trj2pdb)
|
||||
# set additional cmake file
|
||||
include (${PROJECT}.cmake)
|
||||
|
||||
|
||||
# additional options
|
||||
OPTION (WITH_DEBUG_MODE "Build with debug mode" OFF)
|
||||
OPTION (ADD_INCLUDE "Add include files" OFF)
|
||||
include (${_PROJECT}.cmake)
|
||||
|
||||
# set libraries
|
||||
set (LIBRARIES)
|
||||
@ -29,4 +25,4 @@ set (LIBRARIES)
|
||||
set (TARGETS "")
|
||||
set (HEADERS "")
|
||||
|
||||
add_subdirectory (${${PROJECT}_SOURCE_DIR})
|
||||
add_subdirectory (${PROJECT_SOURCE_DIR})
|
||||
@ -1,7 +1,9 @@
|
||||
CMakeFlags:
|
||||
-DCMAKE_INSTALL_PREFIX= - install prefix (default is '/usr/local')
|
||||
-DADD_INCLUDE=1 - install include files (default is disable)
|
||||
-DADD_DOCS=1 - install documentation (default is disable)
|
||||
-DWITH_DEBUG_MODE=1 - compile with flag '-g' (default is disable)
|
||||
-DMM_PREFIX - prefix for mm components (test flag)
|
||||
|
||||
Install for Linux:
|
||||
mkdir build && cd build
|
||||
|
||||
@ -1,5 +1,5 @@
|
||||
mm_trj2pdb - program that creates PDB file from trajetory snapshot
|
||||
Version: 1.0.1
|
||||
Version: 1.0.3
|
||||
License: GPL
|
||||
|
||||
Usage:
|
||||
|
||||
@ -1,16 +1,16 @@
|
||||
# set directories
|
||||
set (${PROJECT}_BINARY_DIR bin)
|
||||
set (${PROJECT}_SOURCE_DIR src)
|
||||
set (${PROJECT}_INCLUDE_DIR include)
|
||||
set (${PROJECT}_LIB_DIR lib)
|
||||
set (PROJECT_BINARY_DIR bin)
|
||||
set (PROJECT_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/src)
|
||||
set (PROJECT_INCLUDE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/include)
|
||||
set (PROJECT_LIB_DIR ${CMAKE_CURRENT_SOURCE_DIR}/lib)
|
||||
|
||||
# include_path
|
||||
include_directories (${${PROJECT}_INCLUDE_DIR}/${PROJECT}
|
||||
${${PROJECT}_SOURCE_DIR})
|
||||
include_directories (${PROJECT_INCLUDE_DIR}/${PROJECT}
|
||||
${PROJECT_SOURCE_DIR})
|
||||
# library path
|
||||
link_directories (${${PROJECT}_LIB_DIR})
|
||||
link_directories (${PROJECT_LIB_DIR})
|
||||
# executable path
|
||||
set (EXECUTABLE_OUTPUT_PATH ${${PROJECT}_BINARY_DIR})
|
||||
set (EXECUTABLE_OUTPUT_PATH ${PROJECT_BINARY_DIR})
|
||||
|
||||
# verbose
|
||||
set (CMAKE_VERBOSE_MAKEFILE ON)
|
||||
|
||||
@ -32,7 +32,7 @@ PROJECT_NAME = mm_trj2pdb
|
||||
# This could be handy for archiving the generated documentation or
|
||||
# if some version control system is used.
|
||||
|
||||
PROJECT_NUMBER = V.1.0.1
|
||||
PROJECT_NUMBER = V.1.0.3
|
||||
|
||||
# Using the PROJECT_BRIEF tag one can provide an optional one line description
|
||||
# for a project that appears at the top of each page and should give viewer
|
||||
|
||||
Binary file not shown.
@ -1,10 +1,3 @@
|
||||
set ("${PROJECT}_VERSION_MAJOR" 1)
|
||||
set ("${PROJECT}_VERSION_MINOR" 0)
|
||||
set ("${PROJECT}_VERSION_PATCH" 1)
|
||||
set ("${PROJECT}_VERSION" ${${PROJECT}_VERSION_MAJOR}.${${PROJECT}_VERSION_MINOR}.${${PROJECT}_VERSION_PATCH})
|
||||
|
||||
message (STATUS "${PROJECT}: Version ${${PROJECT}_VERSION}")
|
||||
|
||||
# set files
|
||||
aux_source_directory (. SOURCES)
|
||||
|
||||
@ -26,4 +19,7 @@ target_link_libraries (${PROJECT} ${ADDITIONAL_LIB})
|
||||
INSTALL (TARGETS ${PROJECT} DESTINATION bin)
|
||||
if (ADD_INCLUDE)
|
||||
INSTALL (FILES ${PUBLIC_HEADERS} DESTINATION include/${PROJECT})
|
||||
endif ()
|
||||
endif ()
|
||||
if (ADD_DOCS)
|
||||
INSTALL (FILES ${PROJECT_SOURCE_DIR}/../${_PROJECT}.pdf DESTINATION share/doc/mathmech)
|
||||
endif ()
|
||||
|
||||
@ -59,8 +59,14 @@
|
||||
* You may also download compiled executable file for Win_x86.
|
||||
*
|
||||
* @page Changelog
|
||||
* V.1.0.3 (2013-08-30)
|
||||
* <ul>
|
||||
* <li> Bug fixes
|
||||
* </ul>
|
||||
* V.1.0.1 (2013-07-27)
|
||||
* * initial release
|
||||
* <ul>
|
||||
* <li> initial release
|
||||
* </ul>
|
||||
*/
|
||||
|
||||
#include <math.h>
|
||||
@ -119,7 +125,7 @@ int main(int argc, char *argv[])
|
||||
{
|
||||
sprintf (tmp_str, " mm_trj2pdb\n");
|
||||
sprintf (tmp_str, "%sProgram for create PDB file from trajectory snapshot\n", tmp_str);
|
||||
sprintf (tmp_str, "%sVersion : 1.0.1 License : GPL\n", tmp_str);
|
||||
sprintf (tmp_str, "%sVersion : 1.0.3 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);
|
||||
|
||||
@ -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);
|
||||
|
||||
11
mathmech/update_docs.sh
Executable file
11
mathmech/update_docs.sh
Executable file
@ -0,0 +1,11 @@
|
||||
#!/bin/bash
|
||||
|
||||
COMPONENTS=( mm_agl mm_envir mm_radf mm_statgen mm_trj mm_trj2pdb )
|
||||
for COMPONENT in ${COMPONENTS[*]}; do
|
||||
cd $COMPONENT
|
||||
doxygen $COMPONENT.doxygen
|
||||
cp logo.png docs/latex
|
||||
cd docs/latex && make && cd ../../../
|
||||
mv $COMPONENT/docs/latex/refman.pdf $COMPONENT/$COMPONENT.pdf
|
||||
rm -rf $COMPONENT/docs
|
||||
done
|
||||
Some files were not shown because too many files have changed in this diff Show More
Reference in New Issue
Block a user