pax_global_header 0000666 0000000 0000000 00000000064 13607351722 0014520 g ustar 00root root 0000000 0000000 52 comment=59c4dbd09821440df02b71fb963c4bae8e0fb6d0
avogadroapp-1.93.0/ 0000775 0000000 0000000 00000000000 13607351722 0014115 5 ustar 00root root 0000000 0000000 avogadroapp-1.93.0/.clang-format 0000664 0000000 0000000 00000000402 13607351722 0016464 0 ustar 00root root 0000000 0000000 ---
# This configuration requires clang-format 3.8 or higher.
BasedOnStyle: Mozilla
AlwaysBreakAfterReturnType: None
AlwaysBreakAfterDefinitionReturnType: None
BinPackArguments: true
BinPackParameters: true
BreakConstructorInitializersBeforeComma: false
...
avogadroapp-1.93.0/.github/ 0000775 0000000 0000000 00000000000 13607351722 0015455 5 ustar 00root root 0000000 0000000 avogadroapp-1.93.0/.github/FUNDING.yml 0000664 0000000 0000000 00000000172 13607351722 0017272 0 ustar 00root root 0000000 0000000 # These are supported funding model platforms
open_collective: avogadro # Replace with a single Open Collective username
avogadroapp-1.93.0/.github/ISSUE_TEMPLATE/ 0000775 0000000 0000000 00000000000 13607351722 0017640 5 ustar 00root root 0000000 0000000 avogadroapp-1.93.0/.github/ISSUE_TEMPLATE/bug_report.md 0000664 0000000 0000000 00000001531 13607351722 0022332 0 ustar 00root root 0000000 0000000 ---
name: Bug report
about: Create a report to help us improve
---
**Avogadro version: (please complete the following information from the About box):**
- Avogadrolibs: (e.g. 1.90.0-316-g6d14770)
- Qt: (e.g., 5.9.5)
**Desktop version: (please complete the following information):**
- OS: [e.g. MacOS]
- Version [e.g. 10.12.4]
- Compiler (if you built from source)
**Describe the bug**
A clear and concise description of what the bug is.
**To Reproduce**
Steps to reproduce the behavior:
1. Go to '...'
2. Click on '....'
3. Scroll down to '....'
4. See error
**Expected behavior**
A clear and concise description of what you expected to happen.
**Screenshots**
If applicable, add screenshots to help explain your problem.
**Additional context**
Add any other context about the problem here. **Please consider uploading or linking test files.**
avogadroapp-1.93.0/.github/ISSUE_TEMPLATE/feature_request.md 0000664 0000000 0000000 00000001425 13607351722 0023367 0 ustar 00root root 0000000 0000000 ---
name: Feature request
about: Suggest an idea for this project
---
**Is your feature request related to a problem? Please describe.**
A clear and concise description of what the problem is. Ex. I wish Avogadro calculated XYQ moments to render with ..
**Describe the solution you'd like**
A clear and concise description of what you want to happen. Please be detailed. How might this feature work (e.g., first a window would open and you'd click to …)
**Describe alternatives you've considered**
A clear and concise description of any alternative solutions or features you've considered.
**Additional context**
Add any other context or screenshots about the feature request here.
Please consider opening a topic on https://discuss.avogadro.cc/ to allow further public discussion
avogadroapp-1.93.0/.github/PULL_REQUEST_TEMPLATE 0000664 0000000 0000000 00000002615 13607351722 0020663 0 ustar 00root root 0000000 0000000 Developer Certificate of Origin
Version 1.1
Copyright (C) 2004, 2006 The Linux Foundation and its contributors.
1 Letterman Drive
Suite D4700
San Francisco, CA, 94129
Everyone is permitted to copy and distribute verbatim copies of this
license document, but changing it is not allowed.
Developer's Certificate of Origin 1.1
By making a contribution to this project, I certify that:
(a) The contribution was created in whole or in part by me and I
have the right to submit it under the open source license
indicated in the file; or
(b) The contribution is based upon previous work that, to the best
of my knowledge, is covered under an appropriate open source
license and I have the right under that license to submit that
work with modifications, whether created in whole or in part
by me, under the same open source license (unless I am
permitted to submit under a different license), as indicated
in the file; or
(c) The contribution was provided directly to me by some other
person who certified (a), (b) or (c) and I have not modified
it.
(d) I understand and agree that this project and the contribution
are public and that a record of the contribution (including all
personal information I submit with it, including my sign-off) is
maintained indefinitely and may be redistributed consistent with
this project or the open source license(s) involved.
avogadroapp-1.93.0/.github/config.yml 0000664 0000000 0000000 00000001770 13607351722 0017452 0 ustar 00root root 0000000 0000000 # Configuration for welcome - https://github.com/behaviorbot/welcome
# Configuration for new-issue-welcome - https://github.com/behaviorbot/new-issue-welcome
# Comment to be posted to on first time issues
newIssueWelcomeComment: >
Thanks for opening your first issue here! Please try to include example files and screenshots if possible.
If you're looking for support, please post on our forum: https://discuss.avogadro.cc/
# Configuration for new-pr-welcome - https://github.com/behaviorbot/new-pr-welcome
# Comment to be posted to on PRs from first time contributors in your repository
newPRWelcomeComment: >
Thanks for opening this pull request! Please check out our contributing guidelines and check for the automated tests.
# Configuration for first-pr-merge - https://github.com/behaviorbot/first-pr-merge
# Comment to be posted to on pull requests merged by a first time user
firstPRMergeComment: >
Congrats on merging your first pull request! 🎉 Thanks for making Avogadro better for everyone!
avogadroapp-1.93.0/.github/move.yml 0000664 0000000 0000000 00000001032 13607351722 0017142 0 ustar 00root root 0000000 0000000 # Configuration for move-issues - https://github.com/dessant/move-issues
# Delete the command comment when it contains no other content
deleteCommand: true
# Close the source issue after moving
closeSourceIssue: true
# Lock the source issue after moving
lockSourceIssue: false
# Mention issue and comment authors
mentionAuthors: true
# Preserve mentions in the issue content
keepContentMentions: false
# Set custom aliases for targets
# aliases:
# r: repo
# or: owner/repo
# Repository to extend settings from
# _extends: repo
avogadroapp-1.93.0/.travis.yml 0000664 0000000 0000000 00000000502 13607351722 0016223 0 ustar 00root root 0000000 0000000 sudo: false
branches:
only:
- master
language: python
python:
- "2.7"
dist: trusty
addons:
apt:
sources:
- ubuntu-toolchain-r-test
- llvm-toolchain-trusty-6.0
packages:
- clang-format-6.0
script:
- cd $TRAVIS_BUILD_DIR
- ./scripts/travis/run_clang_format_diff.sh master $TRAVIS_COMMIT
avogadroapp-1.93.0/CMakeLists.txt 0000664 0000000 0000000 00000004147 13607351722 0016663 0 ustar 00root root 0000000 0000000 cmake_minimum_required(VERSION 3.3 FATAL_ERROR)
# Use the new policy for linking to qtmain
if(POLICY CMP0020)
# cmake_policy(SET CMP0020 NEW)
endif()
project(AvogadroApp)
set(CMAKE_MODULE_PATH ${AvogadroApp_SOURCE_DIR}/cmake)
# Request C++11 standard, using new CMake variables.
set(CMAKE_CXX_STANDARD 11)
set(CMAKE_CXX_STANDARD_REQUIRED True)
set(CMAKE_CXX_EXTENSIONS False)
# Set symbol visibility defaults for all targets.
set(CMAKE_CXX_VISIBILITY_PRESET "hidden")
set(CMAKE_VISIBILITY_INLINES_HIDDEN True)
include(BuildType)
include(BuildLocation)
include(CompilerFlags)
include(InstallLocation)
include(DetermineVersion)
# Set up our version.
set(AvogadroApp_VERSION_MAJOR "1")
set(AvogadroApp_VERSION_MINOR "93")
set(AvogadroApp_VERSION_PATCH "0")
set(AvogadroApp_VERSION
"${AvogadroApp_VERSION_MAJOR}.${AvogadroApp_VERSION_MINOR}.${AvogadroApp_VERSION_PATCH}")
find_package(Git)
determine_version(${AvogadroApp_SOURCE_DIR} ${GIT_EXECUTABLE} "AvogadroApp")
if(APPLE)
set(MACOSX_BUNDLE_NAME "Avogadro2")
set(prefix "${MACOSX_BUNDLE_NAME}.app/Contents")
set(INSTALL_INCLUDE_DIR "${prefix}/${INSTALL_INCLUDE_DIR}")
set(INSTALL_RUNTIME_DIR "${prefix}/MacOS")
set(INSTALL_LIBRARY_DIR "${prefix}/${INSTALL_LIBRARY_DIR}")
set(INSTALL_ARCHIVE_DIR "${prefix}/${INSTALL_ARCHIVE_DIR}")
set(INSTALL_DATA_DIR "${prefix}/${INSTALL_DATA_DIR}")
set(INSTALL_DOC_DIR "${prefix}/${INSTALL_DOC_DIR}")
set(INSTALL_CMAKE_DIR "${prefix}/Resources")
endif()
include_directories(${CMAKE_CURRENT_SOURCE_DIR})
option(ENABLE_TESTING "Enable testing and building the tests." OFF)
if(ENABLE_TESTING)
include(CTest)
enable_testing()
endif()
option(Avogadro_ENABLE_RPC "Enable RPC server" ON)
add_subdirectory(avogadro)
option(BUILD_DOCUMENTATION "Build project documentation" OFF)
if(BUILD_DOCUMENTATION)
add_subdirectory(docs)
endif()
install(
FILES
README.md
CONTRIBUTING.md
LICENSE
DESTINATION "${INSTALL_DOC_DIR}/avogadro2")
include(AvogadroCPack)
if(ENABLE_TESTING)
include(BuildPackageTest)
BuildPackageTest_Add("AvogadroApp" "${CMAKE_CURRENT_BINARY_DIR}")
add_subdirectory(tests)
endif()
avogadroapp-1.93.0/CONTRIBUTING.md 0000664 0000000 0000000 00000001563 13607351722 0016353 0 ustar 00root root 0000000 0000000 Contributing
------------
Our project uses the standard GitHub pull request process for code review
and integration. Please check our [development][Development] guide for more
details on developing and contributing to the project. The GitHub issue
tracker can be used to report bugs, make feature requests, etc.
Our [wiki][Wiki] is used to document features, flesh out designs and host other
documentation. Our API is documented using Doxygen with updated
documentation generated nightly. We have several [mailing lists][MailingLists]
to coordinate development and to provide support.
[Development]: http://wiki.openchemistry.org/Development "Development guide"
[Wiki]: http://wiki.openchemistry.org/ "Open Chemistry wiki"
[Doxygen]: http://doc.openchemistry.org/avogadrolibs/api/ "API documentation"
[MailingLists]: http://openchemistry.org/mailing-lists "Mailing Lists"
avogadroapp-1.93.0/CTestConfig.cmake 0000664 0000000 0000000 00000000374 13607351722 0017273 0 ustar 00root root 0000000 0000000 set(CTEST_PROJECT_NAME "AvogadroApp")
set(CTEST_NIGHTLY_START_TIME "01:00:00 UTC")
set(CTEST_DROP_METHOD "http")
set(CTEST_DROP_SITE "cdash.openchemistry.org")
set(CTEST_DROP_LOCATION "/submit.php?project=AvogadroApp")
set(CTEST_DROP_SITE_CDASH TRUE)
avogadroapp-1.93.0/LICENSE 0000664 0000000 0000000 00000002745 13607351722 0015132 0 ustar 00root root 0000000 0000000 Copyright (c) 2011-2020, Kitware, Inc.
All rights reserved.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
1. Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer.
2. Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.
3. Neither the name of the copyright holder nor the names of its contributors
may be used to endorse or promote products derived from this software
without specific prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR
TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF
THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
avogadroapp-1.93.0/README.md 0000664 0000000 0000000 00000006052 13607351722 0015377 0 ustar 00root root 0000000 0000000 Avogadro 2
==========
![Avogadro 2][Avogadro2Logo]
Introduction
------------
Avogadro is an advanced molecular editor designed for cross-platform use in
computational chemistry, molecular modeling, bioinformatics, materials science,
and related areas. It offers flexible rendering and a powerful plugin
architecture. The code in this repository is a rewrite of Avogadro with source
code split across a libraries repository and an application repository. Core
features and goals of the Avogadro project:
* Open source distributed under the liberal 3-clause BSD license
* Cross platform with nightly builds on Linux, Mac OS X and Windows
* Intuitive interface designed to be useful to whole community
* Fast and efficient embracing the latest technologies
* Extensible, making extensive use of a plugin architecture
* Flexible supporting a range of chemical data formats and packages
![Open Chemistry project][OpenChemistryLogo]
![Kitware, Inc.][KitwareLogo]
Avogadro 2 is being developed as part of the [Open Chemistry][OpenChemistry]
project at [Kitware][Kitware], along with companion tools and libraries to
support the work. The Avogadro 1.x series currently has more features, and can
be found [here][Avogadro1]. We will be porting more features to the Avogadro 2
code base, and making regular releases to get feedback from the community.
Installing
----------
We provide nightly binaries built by our [dashboards][Dashboard] for Mac OS
X and Windows. If you would like to build from source we recommend that you
follow our [building Open Chemistry][Build] guide that will take care of
building most dependencies.
Contributing
------------
Our project uses the standard GitHub pull request process for code review
and integration. Please check our [development][Development] guide for more
details on developing and contributing to the project. The GitHub issue
tracker can be used to report bugs, make feature requests, etc.
Our [wiki][Wiki] is used to document features, flesh out designs and host other
documentation. Our API is [documented using Doxygen][Doxygen] with updated
documentation generated nightly. We have several [mailing lists][MailingLists]
to coordinate development and to provide support.
[Avogadro2Logo]: http://openchemistry.org/files/logos/avogadro2.png "Avogadro2"
[OpenChemistry]: http://openchemistry.org/ "Open Chemistry Project"
[OpenChemistryLogo]: http://openchemistry.org/files/logos/openchem128.png "Open Chemistry"
[Kitware]: http://kitware.com/ "Kitware, Inc."
[KitwareLogo]: http://www.kitware.com/img/small_logo_over.png "Kitware"
[Avogadro1]: http://avogadro.openmolecules.net/ "Avogadro 1"
[Dashboard]: http://cdash.openchemistry.org/index.php?project=AvogadroApp "Avogadro Dashboard"
[Build]: http://wiki.openchemistry.org/Build "Building Avogadro"
[Development]: http://wiki.openchemistry.org/Development "Development guide"
[Wiki]: http://wiki.openchemistry.org/ "Open Chemistry wiki"
[Doxygen]: http://doc.openchemistry.org/avogadrolibs/api/ "API documentation"
[MailingLists]: http://openchemistry.org/mailing-lists "Mailing Lists"
avogadroapp-1.93.0/avogadro/ 0000775 0000000 0000000 00000000000 13607351722 0015717 5 ustar 00root root 0000000 0000000 avogadroapp-1.93.0/avogadro/CMakeLists.txt 0000664 0000000 0000000 00000010113 13607351722 0020453 0 ustar 00root root 0000000 0000000 find_package(AvogadroLibs REQUIRED NO_MODULE)
include_directories(${AvogadroLibs_INCLUDE_DIRS})
list(APPEND CMAKE_MODULE_PATH ${AvogadroLibs_CMAKE_DIR})
find_package(Eigen3 REQUIRED)
include_directories(SYSTEM ${EIGEN3_INCLUDE_DIR})
option(USE_VTK "Build with VTK support" OFF)
if(USE_VTK)
find_package(VTK COMPONENTS vtkGUISupportQt vtkRenderingOpenGL2 REQUIRED)
include(${VTK_USE_FILE})
add_definitions(-DAVO_USE_VTK)
endif()
if(MSVC)
add_definitions("-D_CRT_SECURE_NO_WARNINGS")
endif()
# Find the Qt components we need.
find_package(Qt5 REQUIRED COMPONENTS Concurrent Widgets Network CONFIG)
configure_file(avogadroappconfig.h.in avogadroappconfig.h)
set(avogadro_srcs
aboutdialog.cpp
application.cpp
avogadro.cpp
backgroundfileformat.cpp
mainwindow.cpp
menubuilder.cpp
viewfactory.cpp
)
qt5_wrap_ui(ui_srcs
aboutdialog.ui
mainwindow.ui
)
qt5_add_resources(rcc_srcs avogadro.qrc)
if(Avogadro_ENABLE_RPC)
list(APPEND avogadro_srcs rpclistener.cpp)
# MoleQueue is required for its RPC functions.
find_package(MoleQueue REQUIRED)
include_directories(${MoleQueue_INCLUDE_DIRS})
add_definitions("-DAvogadro_ENABLE_RPC")
endif()
if(ENABLE_TESTING)
find_package(Qt5 COMPONENTS Test REQUIRED)
find_package(QtTesting REQUIRED NO_MODULE)
include_directories(${QtTesting_INCLUDE_DIRS})
link_directories(${QtTesting_LIBRARY_DIR})
add_definitions(-DQTTESTING)
endif()
# Need to add current binary dir to include path for UI file headers
include_directories(${CMAKE_CURRENT_BINARY_DIR})
# if we are building statically then we need HDF5 targets
if(NOT BUILD_SHARED_LIBS)
find_package(HDF5 REQUIRED COMPONENTS C)
endif()
# Handle Mac OS X specific icons etc.
if(APPLE)
# add some Objective-C++ code
list(APPEND avogadro_srcs mac.mm)
set(CMAKE_EXE_LINKER_FLAGS "-framework Foundation -framework Cocoa")
list(APPEND avogadro_srcs icons/avogadro.icns)
list(APPEND avogadro_srcs icons/doc.icns)
list(APPEND avogadro_srcs icons/cml.icns)
list(APPEND avogadro_srcs icons/cjson.icns)
set(MACOSX_BUNDLE_ICON_FILE avogadro.icns)
set(MACOSX_BUNDLE_BUNDLE_VERSION "${AvogadroApp_VERSION}")
set(MACOSX_BUNDLE_INFO_STRING "Avogadro - version ${AvogadroApp_VERSION}")
# Change following line to point to actual icns file in bundle.
set(MACOSX_BUNDLE_GUI_IDENTIFIER "cc.avogadro")
set(MACOSX_BUNDLE_BUNDLE_NAME "Avogadro")
set_source_files_properties(icons/avogadro.icns PROPERTIES
MACOSX_PACKAGE_LOCATION Resources)
set_source_files_properties(icons/doc.icns PROPERTIES
MACOSX_PACKAGE_LOCATION Resources)
set_source_files_properties(icons/cjson.icns PROPERTIES
MACOSX_PACKAGE_LOCATION Resources)
set_source_files_properties(icons/cml.icns PROPERTIES
MACOSX_PACKAGE_LOCATION Resources)
elseif(UNIX)
install(FILES "icons/avogadro2.desktop" DESTINATION "${INSTALL_XDG_APPS_DIR}")
install(FILES "icons/avogadro.png" DESTINATION "${INSTALL_XDG_ICON_DIR}"
RENAME "avogadro2.png")
elseif(WIN32)
list(APPEND avogadro_srcs icons/avogadro.rc)
endif()
add_executable(avogadro WIN32 MACOSX_BUNDLE
${avogadro_srcs} ${ui_srcs} ${rcc_srcs})
target_link_libraries(avogadro Qt5::Widgets Qt5::Network Qt5::Concurrent)
if(WIN32)
set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} /NODEFAULTLIB:MSVCRTD")
target_link_libraries(avogadro Qt5::WinMain)
endif()
set_target_properties(avogadro PROPERTIES AUTOMOC TRUE)
target_link_libraries(avogadro AvogadroQtOpenGL AvogadroQtGui AvogadroQtPlugins)
if(Avogadro_ENABLE_RPC)
target_link_libraries(avogadro MoleQueueServerCore MoleQueueClient)
endif()
if(USE_VTK)
target_link_libraries(avogadro ${VTK_LIBRARIES} AvogadroVtk)
endif()
if(APPLE)
set_target_properties(avogadro PROPERTIES OUTPUT_NAME ${MACOSX_BUNDLE_NAME})
else()
set_target_properties(avogadro PROPERTIES OUTPUT_NAME "avogadro2")
endif()
if(ENABLE_TESTING)
target_link_libraries(avogadro QtTesting)
endif()
install(TARGETS avogadro
RUNTIME DESTINATION ${INSTALL_RUNTIME_DIR}
BUNDLE DESTINATION .
)
# Keep "add_subdirectory(lastinstall)" last: fixup_bundle needs to be
# *after* all other install(TARGETS and install(FILES calls
add_subdirectory(lastinstall)
avogadroapp-1.93.0/avogadro/aboutdialog.cpp 0000664 0000000 0000000 00000003025 13607351722 0020715 0 ustar 00root root 0000000 0000000 /******************************************************************************
This source file is part of the Avogadro project.
Copyright 2013 Kitware, Inc.
This source code is released under the New BSD License, (the "License").
Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
******************************************************************************/
#include "aboutdialog.h"
#include "avogadroappconfig.h"
#include "ui_aboutdialog.h"
#include
" "%2" "
"); m_ui->version->setText(html.arg("20").arg(AvogadroApp_VERSION)); m_ui->libsVersion->setText(html.arg("10").arg(version())); m_ui->qtVersion->setText(html.arg("10").arg(qVersion())); // Add support for a 2x replacement (mainly Mac OS X retina at this point). if (window()->devicePixelRatio() == 2) { QPixmap pix(":/icons/Avogadro2_About@2x.png"); pix.setDevicePixelRatio(2); m_ui->Image->setPixmap(pix); } } AboutDialog::~AboutDialog() { delete m_ui; } } /* namespace Avogadro */ avogadroapp-1.93.0/avogadro/aboutdialog.h 0000664 0000000 0000000 00000001745 13607351722 0020371 0 ustar 00root root 0000000 0000000 /****************************************************************************** This source file is part of the Avogadro project. Copyright 2013-2014 Kitware, Inc. This source code is released under the New BSD License, (the "License"). Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. ******************************************************************************/ #ifndef AVOGADRO_ABOUTDIALOG_H #define AVOGADRO_ABOUTDIALOG_H #include