pax_global_header 0000666 0000000 0000000 00000000064 14112012603 0014500 g ustar 00root root 0000000 0000000 52 comment=b7dc60030cfae313f74edd1c2ea4f142630fe631
avogadroapp-1.95.1/ 0000775 0000000 0000000 00000000000 14112012603 0014100 5 ustar 00root root 0000000 0000000 avogadroapp-1.95.1/.clang-format 0000664 0000000 0000000 00000000402 14112012603 0016447 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-1.95.1/.github/ 0000775 0000000 0000000 00000000000 14112012603 0015440 5 ustar 00root root 0000000 0000000 avogadroapp-1.95.1/.github/FUNDING.yml 0000664 0000000 0000000 00000000172 14112012603 0017255 0 ustar 00root root 0000000 0000000 # These are supported funding model platforms
open_collective: avogadro # Replace with a single Open Collective username
avogadroapp-1.95.1/.github/ISSUE_TEMPLATE/ 0000775 0000000 0000000 00000000000 14112012603 0017623 5 ustar 00root root 0000000 0000000 avogadroapp-1.95.1/.github/ISSUE_TEMPLATE/bug_report.md 0000664 0000000 0000000 00000001531 14112012603 0022315 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-1.95.1/.github/ISSUE_TEMPLATE/feature_request.md 0000664 0000000 0000000 00000001425 14112012603 0023352 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-1.95.1/.github/PULL_REQUEST_TEMPLATE 0000664 0000000 0000000 00000002615 14112012603 0020646 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-1.95.1/.github/config.yml 0000664 0000000 0000000 00000001770 14112012603 0017435 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-1.95.1/.github/move.yml 0000664 0000000 0000000 00000001032 14112012603 0017125 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-1.95.1/.github/release-drafter.yml 0000664 0000000 0000000 00000001335 14112012603 0021232 0 ustar 00root root 0000000 0000000 name-template: 'Avogadro $RESOLVED_VERSION'
tag-template: '$RESOLVED_VERSION'
categories:
- title: 'Features'
labels:
- 'feature'
- 'enhancement'
- title: '🐛 Bug Fixes'
labels:
- 'fix'
- 'bugfix'
- 'bug'
- title: '🧰 Maintenance'
labels:
- 'chore'
- 'build'
change-template: '- $TITLE @$AUTHOR (#$NUMBER)'
change-title-escapes: '\<*_&' # You can add # and @ to disable mentions, and add ` to disable code blocks.
version-resolver:
major:
labels:
- 'major'
minor:
labels:
- 'minor'
patch:
labels:
- 'patch'
default: minor
template: |
## Changes
$CHANGES
## Credits
Thanks to many contributors, including: $CONTRIBUTORS
avogadroapp-1.95.1/.github/workflows/ 0000775 0000000 0000000 00000000000 14112012603 0017475 5 ustar 00root root 0000000 0000000 avogadroapp-1.95.1/.github/workflows/build_cmake.yml 0000664 0000000 0000000 00000014523 14112012603 0022464 0 ustar 00root root 0000000 0000000 name: CMake Build Matrix
# Many thanks to Cristian Adam for examples
# e.g. https://github.com/cristianadam/HelloWorld/blob/master/.github/workflows/build_cmake.yml
# https://cristianadam.eu/20191222/using-github-actions-with-c-plus-plus-and-cmake/
on: [push, pull_request]
env:
BUILD_TYPE: Release
QT_VERSION: 5.12.10
# this is different from MACOSX_DEPLOYMENT_TARGET to prevent build problems
# we set MACOSX_DEPLOYMENT_TARGET later
MACOS_TARGET: 10.12
FEATURES: -DUSE_VTK=ON -DBUILD_GPL_PLUGINS=ON
jobs:
build:
name: ${{ matrix.config.name }}
runs-on: ${{ matrix.config.os }}
strategy:
fail-fast: false
matrix:
config:
- {
name: "Ubuntu 20.04 GCC", artifact: "Ubuntu-2004.tar.gz",
os: ubuntu-20.04,
cc: "gcc", cxx: "g++",
cmake_flags: "-G Ninja -DENABLE_TESTING=ON ",
cpack: "",
}
- {
name: "Ubuntu 18.04 GCC", artifact: "",
os: ubuntu-18.04,
cc: "gcc", cxx: "g++",
cmake_flags: "-G Ninja -DENABLE_TESTING=ON ",
cpack: "",
}
- {
name: "macOS Latest Clang", artifact: "macOS.dmg",
os: macos-latest,
cc: "clang", cxx: "clang++",
cmake_flags: "-G Ninja -DENABLE_TESTING=ON ",
cpack_flags: "-G DragNDrop",
}
- {
name: "Windows Latest MSVC", artifact: "Win64.exe",
os: windows-latest,
cc: "cl", cxx: "cl",
cmake_flags: "",
cpack_flags: "-G NSIS",
}
steps:
- name: Install Dependencies (Linux)
if: runner.os == 'Linux'
run: |
sudo apt-get -qq update
sudo apt-get -qq install ninja-build libeigen3-dev libboost-all-dev libglew-dev libxml2-dev qt5-default libqt5x11extras5-dev
- name: Install Dependencies (macOS)
if: runner.os == 'macOS'
run: |
brew install ninja boost eigen glew open-babel
- name: Install Dependencies (Windows)
if: runner.os == 'Windows'
run: choco install ninja
- name: Checkout openchemistry
uses: actions/checkout@v2
with:
repository: openchemistry/openchemistry
submodules: recursive
- name: Checkout avogadroapp
uses: actions/checkout@v2
with:
path: avogadroapp
- name: Checkout avogadrolibs
uses: actions/checkout@v2
with:
repository: openchemistry/avogadrolibs
path: avogadrolibs
- name: Cache Qt
id: cache-qt
uses: actions/cache@v1
with:
path: ../Qt
key: ${{ runner.os }}-QtCache
- name: Install Qt
uses: jurplel/install-qt-action@v2
with:
cached: ${{ steps.cache-qt.outputs.cache-hit }}
version: ${{ env.QT_VERSION }}
- name: Configure MSVC Command Prompt
if: runner.os == 'Windows'
uses: ilammy/msvc-dev-cmd@v1
with:
arch: x64
- name: Configure
run: |
mkdir "${{ runner.workspace }}/build"
cd "${{ runner.workspace }}/build"
# won't have any effect except on Mac
echo "MACOSX_DEPLOYMENT_TARGET=${{ env.MACOS_TARGET }}" >> $GITHUB_ENV
CC=${{matrix.config.cc}} CXX=${{matrix.config.cxx}} cmake $GITHUB_WORKSPACE ${{env.FEATURES}} -DCMAKE_BUILD_TYPE=${{env.BUILD_TYPE}} ${{matrix.config.cmake_flags}}
shell: bash
- name: Build
run: |
CC=${{matrix.config.cc}} CXX=${{matrix.config.cxx}} cmake --build . --config ${{env.BUILD_TYPE}}
shell: bash
working-directory: ${{ runner.workspace }}/build
- name: Run tests
if: runner.os != 'Windows'
shell: cmake -P {0}
run: |
include(ProcessorCount)
ProcessorCount(N)
set(ENV{CTEST_OUTPUT_ON_FAILURE} "ON")
execute_process(
COMMAND ctest -j ${N}
WORKING_DIRECTORY ${{ runner.workspace }}/build
RESULT_VARIABLE result
)
if (NOT result EQUAL 0)
message(FATAL_ERROR "Running tests failed!")
endif()
- name: Pack
if: matrix.config.artifact != 0
run: cpack ${{ matrix.config.cpack_flags }}
working-directory: ${{ runner.workspace }}/build/avogadroapp
- name: Upload
if: matrix.config.artifact != 0
uses: actions/upload-artifact@v2
with:
path: ${{ runner.workspace }}/build/avogadroapp/Avogadro2*.*
name: ${{ matrix.config.artifact }}
release:
if: contains(github.ref, 'tags/')
runs-on: ubuntu-latest
needs: build
steps:
- name: Create Release
id: create_release
uses: actions/create-release@v1
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
with:
tag_name: ${{ github.ref }}
release_name: Avogadro ${{ github.ref }}
draft: true
prerelease: true
- name: Store Release url
run: |
echo "${{ steps.create_release.outputs.upload_url }}" > ./upload_url
- uses: actions/upload-artifact@v2
with:
path: ./upload_url
name: upload_url
publish:
if: contains(github.ref, 'tags/')
name: ${{ matrix.config.name }}
runs-on: ${{ matrix.config.os }}
strategy:
fail-fast: false
matrix:
config:
- {
name: "Ubuntu Latest GCC", artifact: "Ubuntu-2004.tar.gz",
os: ubuntu-latest
}
- {
name: "Windows Latest MSVC", artifact: "Win64.exe",
os: ubuntu-latest
}
- {
name: "macOS Latest Clang", artifact: "macOS.dmg",
os: ubuntu-latest
}
needs: release
steps:
- name: Download artifact
uses: actions/download-artifact@v1
with:
name: ${{ matrix.config.artifact }}
path: ./
- name: Download URL
uses: actions/download-artifact@v1
with:
name: upload_url
path: ./
- id: set_upload_url
run: |
upload_url=`cat ./upload_url`
echo ::set-output name=upload_url::$upload_url
- name: Upload to Release
id: upload_to_release
uses: actions/upload-release-asset@v1
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
with:
upload_url: ${{ steps.set_upload_url.outputs.upload_url }}
asset_path: ./${{ matrix.config.artifact }}
asset_name: ${{ matrix.config.artifact }}
asset_content_type: application/x-gtar avogadroapp-1.95.1/.github/workflows/release-drafter.yml 0000664 0000000 0000000 00000001515 14112012603 0023267 0 ustar 00root root 0000000 0000000 name: Release Drafter
# https://github.com/release-drafter/release-drafter
on:
push:
# branches to consider in the event; optional, defaults to all
branches:
- master
# pull_request event is required only for autolabeler
pull_request:
# Only following types are handled by the action, but one can default to all as well
types: [opened, reopened, synchronize]
jobs:
update_release_draft:
runs-on: ubuntu-latest
steps:
# Drafts your next Release notes as Pull Requests are merged into "master"
- uses: release-drafter/release-drafter@v5
# (Optional) specify config name to use, relative to .github/. Default: release-drafter.yml
# with:
# config-name: my-config.yml
# disable-autolabeler: true
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
avogadroapp-1.95.1/.gitmodules 0000664 0000000 0000000 00000000167 14112012603 0016261 0 ustar 00root root 0000000 0000000 [submodule "flatpak/shared-modules"]
path = flatpak/shared-modules
url = git://github.com/flathub/shared-modules.git
avogadroapp-1.95.1/CMakeLists.txt 0000664 0000000 0000000 00000004147 14112012603 0016646 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 ${AvogadroApp_SOURCE_DIR}/cmake)
# Request C++11 standard, using new CMake variables.
set(CMAKE_CXX_STANDARD 11)
set(CMAKE_CXX_STANDARD_REQUIRED True)
set(CMAKE_CXX_EXTENSIONS False)
# Set symbol visibility defaults for all targets.
set(CMAKE_CXX_VISIBILITY_PRESET "hidden")
set(CMAKE_VISIBILITY_INLINES_HIDDEN True)
include(BuildType)
include(BuildLocation)
include(CompilerFlags)
include(InstallLocation)
include(DetermineVersion)
# Set up our version.
set(AvogadroApp_VERSION_MAJOR "1")
set(AvogadroApp_VERSION_MINOR "95")
set(AvogadroApp_VERSION_PATCH "1")
set(AvogadroApp_VERSION
"${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-1.95.1/CONTRIBUTING.md 0000664 0000000 0000000 00000001563 14112012603 0016336 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-1.95.1/CTestConfig.cmake 0000664 0000000 0000000 00000000374 14112012603 0017256 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-1.95.1/LICENSE 0000664 0000000 0000000 00000002745 14112012603 0015115 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-1.95.1/README.md 0000664 0000000 0000000 00000013077 14112012603 0015367 0 ustar 00root root 0000000 0000000 ![Avogadro 2][Avogadro2Logo] Avogadro 2
==========
[](https://github.com/OpenChemistry/avogadroapp/releases) [](https://github.com/OpenChemistry/avogadroapp/blob/master/LICENSE)  [](http://makeapullrequest.com) []() [](https://opencollective.com/open-chemistry)
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.
Core features and goals of the Avogadro project include:
* Open source distributed under the liberal 3-clause BSD license
* Cross platform with 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
The code in this repository is a rewrite of Avogadro with source
code split across
a [libraries repository](https://github.com/openchemistry/avogadrolibs)
and an [application repository](https://github.com/openchemistry/avogadroapp).
The new code architecture provides a high-performance rendering engine, modern
code development, and significantly improved speed and stability.
Avogadro 2 is being developed as part of the [Open Chemistry][OpenChemistry]
project by an open community, and was started at [Kitware][Kitware] as
an open source community project. 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.
We are actively working to finish Avogadro 2.0 in 2021.
Installing
----------
We provide nightly binaries built by GitHub actions for:
* [MacOS](https://nightly.link/OpenChemistry/avogadrolibs/workflows/build_cmake/master/macOS.dmg.zip)
* [Windows 64-bit](https://nightly.link/OpenChemistry/avogadrolibs/workflows/build_cmake/master/Win64.exe.zip)
* [Ubuntu LTS](https://nightly.link/OpenChemistry/avogadrolibs/workflows/build_cmake/master/Ubuntu2004.tar.gz.zip)
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.
Contributors Hall of Fame:
[](https://sourcerer.io/fame/ghutchis/openchemistry/avogadrolibs/links/0)[](https://sourcerer.io/fame/ghutchis/openchemistry/avogadrolibs/links/1)[](https://sourcerer.io/fame/ghutchis/openchemistry/avogadrolibs/links/2)[](https://sourcerer.io/fame/ghutchis/openchemistry/avogadrolibs/links/3)[](https://sourcerer.io/fame/ghutchis/openchemistry/avogadrolibs/links/4)[](https://sourcerer.io/fame/ghutchis/openchemistry/avogadrolibs/links/5)[](https://sourcerer.io/fame/ghutchis/openchemistry/avogadrolibs/links/6)[](https://sourcerer.io/fame/ghutchis/openchemistry/avogadrolibs/links/7)
[Avogadro2Logo]: https://raw.githubusercontent.com/OpenChemistry/avogadrolibs/master/docs/avogadro2_64.png "Avogadro2"
[OpenChemistry]: http://openchemistry.org/ "Open Chemistry Project"
[OpenChemistryLogo]: https://raw.githubusercontent.com/OpenChemistry/avogadrolibs/master/docs/OpenChemistry128.png "Open Chemistry"
[Kitware]: http://kitware.com/ "Kitware, Inc."
[KitwareLogo]: http://www.kitware.com/img/small_logo_over.png "Kitware"
[Avogadro1]: http://avogadro.cc/ "Avogadro 1"
[Dashboard]: http://cdash.openchemistry.org/index.php?project=AvogadroLibs "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-1.95.1/avogadro/ 0000775 0000000 0000000 00000000000 14112012603 0015702 5 ustar 00root root 0000000 0000000 avogadroapp-1.95.1/avogadro/CMakeLists.txt 0000664 0000000 0000000 00000012464 14112012603 0020451 0 ustar 00root root 0000000 0000000 include(ExternalProject)
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)
# download and install QM translation files
# Look in parallel directory for the i18n repository
set(_i18n "${AvogadroApp_SOURCE_DIR}/../avogadro-i18n")
if(NOT EXISTS "${_i18n}")
# download molecules...
ExternalProject_Add(i18n
GIT_REPOSITORY https://github.com/openchemistry/avogadro-i18n
SOURCE_DIR "${AvogadroApp_SOURCE_DIR}/../avogadro-i18n"
CONFIGURE_COMMAND ""
BUILD_COMMAND ""
INSTALL_COMMAND ""
)
endif()
install(DIRECTORY "${AvogadroApp_SOURCE_DIR}/../avogadro-i18n/avogadroapp/"
"${AvogadroApp_SOURCE_DIR}/../avogadro-i18n/avogadrolibs/"
DESTINATION "${INSTALL_DATA_DIR}/avogadro2/i18n"
FILES_MATCHING PATTERN "*.qm"
)
if(INSTALL_BUNDLE_FILES)
# copy the qt translation files
get_filename_component(_qttranslationdir "${Qt5_DIR}/../../../translations" ABSOLUTE)
message(STATUS "Trying to install Qt translations ${_qttranslationdir}")
install(DIRECTORY "${_qttranslationdir}/"
DESTINATION "${INSTALL_DATA_DIR}/avogadro2/i18n"
FILES_MATCHING PATTERN "qt_*.qm" PATTERN "qtbase*.qm"
# technically, this also copies qt_help.* but that's not a big deal
)
endif()
if(Avogadro_ENABLE_RPC)
list(APPEND avogadro_srcs rpclistener.cpp)
# MoleQueue is required for its RPC functions.
find_package(MoleQueue REQUIRED)
include_directories(${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(${CMAKE_CURRENT_BINARY_DIR})
# if we are building statically then we need HDF5 targets
if(NOT BUILD_SHARED_LIBS)
find_package(HDF5 REQUIRED COMPONENTS C)
endif()
# Handle Mac OS X specific icons etc.
if(APPLE)
# add some Objective-C++ code
list(APPEND avogadro_srcs mac.mm ../thirdparty/qcocoacontrols/qcocoamessagebox.mm)
include_directories(SYSTEM "${AvogadroApp_SOURCE_DIR}/thirdparty/qcocoacontrols")
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-1.95.1/avogadro/aboutdialog.cpp 0000664 0000000 0000000 00000003025 14112012603 0020700 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-1.95.1/avogadro/aboutdialog.h 0000664 0000000 0000000 00000001745 14112012603 0020354 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