Add openstructure

recipes/openstructure/LICENSE.txt

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+		   GNU LESSER GENERAL PUBLIC LICENSE
+                       Version 3, 29 June 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+
+  This version of the GNU Lesser General Public License incorporates
+the terms and conditions of version 3 of the GNU General Public
+License, supplemented by the additional permissions listed below.
+
+  0. Additional Definitions.
+
+  As used herein, "this License" refers to version 3 of the GNU Lesser
+General Public License, and the "GNU GPL" refers to version 3 of the GNU
+General Public License.
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+

recipes/openstructure/build.sh

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+#!/bin/bash
+
+# Use sed on code instead of patch, so we do not have to fix the library dir
+# for every OST version.
+sed -i.tmp 's/lib64/lib/g' cmake_support/OST.cmake
+# Use sed above patch as it should work for multiple OST versions.
+sed -i.tmp 's/"@Python_EXECUTABLE@"/`which python`/' scripts/ost_config.in
+
+if test "${target_platform}" = "osx-64"; then
+    ost_cmake_extra_args="-DCMAKE_OSX_SYSROOT=${CONDA_BUILD_SYSROOT}"
+else if test "${target_platform}" = "linux-64"; then
+         ost_cmake_extra_args="-DEIGEN3_INCLUDE_DIR=${BUILD_PREFIX}/include/eigen3 \
+                     -DSQLITE3_LIBRARY=${PREFIX}/lib/libsqlite3${SHLIB_EXT} \
+                     -DSQLITE3_INCLUDE_DIR=${PREFIX}/include \
+                     -DZLIB_LIBRARY=${PREFIX}/lib/libz${SHLIB_EXT} \
+                     -DZLIB_INCLUDE_DIR=${PREFIX}/include \
+                     -DPNG_LIBRARY=${PREFIX}/lib/libpng${SHLIB_EXT} \
+                     -DPNG_INCLUDE_DIR=${PREFIX}/include \
+                     -DFFTW_LIBRARY=${PREFIX}/lib/libfftw3${SHLIB_EXT} \
+                     -DFFTW_INCLUDE_DIR=${PREFIX}/include \
+                     -DTIFF_LIBRARY=${PREFIX}/lib/libtiff${SHLIB_EXT} \
+                     -DTIFF_INCLUDE_DIR=${PREFIX}/include"
+     else
+         echo "unsupported target platform: '${target_platform}'"
+         exit 1
+     fi
+fi
+
+cmake -Bbuild \
+      -G "${CMAKE_GENERATOR}" \
+      -DPREFIX="${PREFIX}" \
+      -DCMAKE_INSTALL_PREFIX="${PREFIX}" \
+      -DENABLE_MM=OFF \
+      -DCOMPILE_TMTOOLS=1 \
+      -DENABLE_GFX=OFF \
+      -DENABLE_GUI=OFF \
+      -DENABLE_INFO=OFF \
+      -DCMAKE_CXX_COMPILER_VERSION="${CMAKE_CXX_COMPILER_VERSION}" \
+      -DPython_EXECUTABLE="${PYTHON}" \
+      -DPYTHON_MODULE_PATH="${SP_DIR}" \
+      -DUSE_RPATH=1 \
+      ${ost_cmake_extra_args}
+
+cmake --build build --target all ${MAKEFLAGS}
+
+curl -OL https://files.wwpdb.org/pub/pdb/data/monomers/components.cif.gz
+${SRC_DIR}/build/stage/bin/chemdict_tool create ${SRC_DIR}/components.cif.gz compounds.chemlib pdb
+${SRC_DIR}/build/stage/bin/chemdict_tool update ${SRC_DIR}/modules/conop/data/charmm.cif compounds.chemlib charmm
+cmake -Bbuild -G "${CMAKE_GENERATOR}" -DCOMPOUND_LIB=${SRC_DIR}/compounds.chemlib
+cmake --build build --target install ${MAKEFLAGS}
+cmake --build build --target check ${MAKEFLAGS}

recipes/openstructure/meta.yaml

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+{% set checksum = "11e924ce74b9d1bab0d03aac74e01201d7672a32a672fe58854497296137e296" %}
+{% set cmake_cxx_compiler_version = "12.4.0" %} # [linux]
+{% set cmake_cxx_compiler_version = "19.1.4" %} # [osx-64]
+{% set name = "openstructure" %}
+{% set version = "2.9.0" %}
+# To avoid having the same YAML lists in `host` and `run`, lets define a Jinja
+# list and let the Jinja templating engine fill in the dependencies.
+{% set dependencies = [
+    "boost <1.84.0",
+    "fftw >=3.3.10,<4.0a0",
+    "libboost <1.84.0",
+    "libboost-python <1.84.0",
+    "libpng >=1.6.44,<1.7.0a0",
+    "libtiff >=4.7.0,<4.8.0a0",
+    "python >=3.7",
+    "sqlite >=3.47.0",
+    "zlib >=1.3.1",
+] %}
+
+package:
+  name: {{ name|lower }}
+  version: {{ version }}
+
+source:
+  sha256: {{ checksum }}
+  url: https://git.scicore.unibas.ch/schwede/{{ name|lower }}/-/archive/{{ version }}/{{ name|lower }}-{{ version }}.tar.gz
+
+cxx_compiler_version:
+  - {{ cmake_cxx_compiler_version }}
+
+build:
+  number: 0
+  run_exports:
+    - {{ pin_subpackage(name|lower, max_pin="x.x") }}
+  script_env:
+    - CMAKE_CXX_COMPILER_VERSION={{ cmake_cxx_compiler_version }}
+  ignore_run_exports:
+    - libzlib
+    - sqlite
+    - zlib
+
+requirements:
+  build:
+    - {{ compiler('cxx') }}
+    - {{ compiler('fortran') }}
+    - cmake >=3.23.1,<=3.29.0
+    # Eigen is header only, after compilation not needed any more
+    - eigen >=3.2
+    - make >=4.4.1
+  host:
+  {% for dep in dependencies %}
+    - {{ dep }}
+  {% endfor %}
+  run:
+  {% for dep in dependencies %}
+    - {{ dep }}
+  {% endfor %}
+    - networkx >=2.1
+    - scipy >=1.10.1
+
+test:
+  commands:
+    - lddt --help 2>&1 | grep usage
+    - molck --help
+    - ost --help | grep Usage
+    - ost compare-ligand-structures --help
+    - ost compare-structures --help
+    - ost compare-structures-legacy --help
+    - python -c "import sys; import ost; sys.exit(1) if ost.__version__ != '{{ version }}' else sys.exit(0)"
+
+about:
+  description: |
+    This project aims to provide an open-source, modular, flexible, molecular
+    modelling and visualization environment. It is targeted at interested
+    method developers in the field of structural bioinformatics.
+  dev_url: https://git.scicore.unibas.ch/schwede/openstructure
+  doc_url: https://openstructure.org/docs/{{ version }}/
+  home: https://openstructure.org/
+  license: LGPL-3.0
+  license_file: LICENSE.txt
+  license_url: https://git.scicore.unibas.ch/schwede/openstructure/-/raw/master/LICENSE.txt
+  summary: Open-Source Computational Structural Biology Framework
+
+# ToDo: Add DOIs for the publications on the various tools
+extra:
+  identifiers:
+    - biotools:openstructure
+    - doi:10.1107/S0907444913007051