Add python bindings

.gitignore

@@ -39,3 +39,10 @@ build/*
 docs/html/*
 examples/out/*
 examples/out_json_ref/*
+
+# python eggs
+python_src/*.egg-info
+**/__pycache__
+**/*.pyc
+
+

.gitmodules

@@ -1,9 +1,12 @@
-[submodule "Catch2"]
-	path = submodules/Catch2
-	url = https://github.com/catchorg/Catch2
-[submodule "msgpack-c"]
+[submodule "submodules/pybind11"]
+	path = submodules/pybind11
+	url = https://github.com/pybind/pybind11.git
+[submodule "submodules/msgpack-c"]
 	path = submodules/msgpack-c
-	url = https://github.com/msgpack/msgpack-c
-[submodule "mmtf_spec"]
+	url = https://github.com/msgpack/msgpack-c.git
+[submodule "submodules/Catch2"]
+	path = submodules/Catch2
+	url = https://github.com/catchorg/Catch2.git
+[submodule "submodules/mmtf_spec"]
 	path = submodules/mmtf_spec
-	url = https://github.com/rcsb/mmtf
+	url = https://github.com/rcsb/mmtf.git

.travis.yml

@@ -1,3 +1,4 @@
+---
 language: cpp
 sudo: false
 dist: trusty
@@ -27,8 +28,25 @@ linux64_cpp17addons:
             sources:
                 - ubuntu-toolchain-r-test
 
+linux64_cpp17addons:
+    addons: &linux64cpp17
+        apt:
+            sources:
+                - ubuntu-toolchain-r-test
+
+
+linux64_cpp17addons_py:
+    addons: &linux64cpp17py
+        apt:
+            sources:
+                - ubuntu-toolchain-r-test
+                - gcc-7
+                - g++-7
+
+python_test_command_sub: &python_test_command TEST_COMMAND=$TRAVIS_BUILD_DIR/ci/build_and_run_python_tests.sh CC=gcc
 # Set empty values for allow_failures to work
 env: TEST_COMMAND=$TRAVIS_BUILD_DIR/ci/build_and_run_tests.sh
+python:
 
 matrix:
     fast_finish: true
@@ -54,7 +72,27 @@ matrix:
           compiler: gcc
           addons: *linux64cpp17
           dist: bionic
-
+        - os: linux
+          compiler: gcc
+          addons: *linux64cpp17py
+          dist: bionic
+          env: *python_test_command
+          python: 3.8
+          language: python
+        - os: linux
+          compiler: gcc
+          addons: *linux64cpp17py
+          dist: bionic
+          env: *python_test_command
+          python: 3.11
+          language: python
+        - os: linux
+          compiler: gcc
+          addons: *linux64cpp17py
+          dist: bionic
+          env: *python_test_command
+          python: 3.12
+          language: python
 
 before_install:
     # Setting environement

CMakeLists.txt

@@ -19,9 +19,7 @@ if (mmtf_build_local)
     add_library(msgpackc INTERFACE)
     target_include_directories(msgpackc INTERFACE ${MSGPACKC_INCLUDE_DIR})
     if (BUILD_TESTS)
-        set(CATCH_INCLUDE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/submodules/Catch2/single_include)
-        add_library(Catch INTERFACE)
-        target_include_directories(Catch INTERFACE ${CATCH_INCLUDE_DIR})
+        add_subdirectory(${CMAKE_CURRENT_SOURCE_DIR}/submodules/Catch2)
     endif()
 endif()
 
@@ -40,6 +38,34 @@ if (mmtf_build_examples)
     add_subdirectory(${CMAKE_CURRENT_SOURCE_DIR}/examples)
 endif()
 
+
+if (build_py)
+
+    if(NOT CMAKE_BUILD_TYPE)
+      set(CMAKE_BUILD_TYPE Release)
+    endif()
+    set(CMAKE_CXX_FLAGS "-Wall -Wextra")
+    set(CMAKE_CXX_FLAGS_DEBUG "-g")
+    set(CMAKE_CXX_FLAGS_RELEASE "-O3")
+    add_library(mmtf_bindings SHARED
+        ${CMAKE_CURRENT_SOURCE_DIR}/python_src/bindings.cpp
+    )
+
+    set(MSGPACKC_INCLUDE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/submodules/msgpack-c/include)
+    set(PYBIND_INCLUDE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/submodules/pybind11/include)
+
+    target_include_directories(mmtf_bindings PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}/include)
+    target_include_directories(mmtf_bindings PUBLIC ${MSGPACKC_INCLUDE_DIR})
+    target_include_directories(mmtf_bindings PUBLIC ${PYBIND_INCLUDE_DIR})
+    target_include_directories(mmtf_bindings PUBLIC ${python_include_A})
+    target_include_directories(mmtf_bindings PUBLIC ${python_include_B})
+
+    set_target_properties(mmtf_bindings PROPERTIES POSITION_INDEPENDENT_CODE ON)
+    set_target_properties(mmtf_bindings PROPERTIES PREFIX "")
+    set_target_properties(mmtf_bindings PROPERTIES SUFFIX ".so")
+    set_target_properties(mmtf_bindings PROPERTIES CXX_STANDARD 17)
+endif()
+
 install(
     DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/include/
     DESTINATION  "include"

README.md

@@ -45,6 +45,53 @@ Here, `<MSGPACK_INCLUDE_PATH>` and `<MMTF_INCLUDE_PATH>` are the paths to the
 
 For your more complicated projects, a `CMakeLists.txt` is included for you.
 
+
+### Python bindings
+
+The C++ MMTF library now can build python bindings using pybind11.  To use them
+you must have A) a c++11 compatible compiler and B) python >= 3.6
+
+to install, it is as simple as `pip install .`
+
+(in the future possible `pip install mmtf-cpp`)
+
+```python
+from mmtf_cppy import StructureData
+import numpy as np
+import math
+
+
+def rotation_matrix(axis, theta):
+    """
+    Return the rotation matrix associated with counterclockwise rotation about
+    the given axis by theta radians.
+    from https://stackoverflow.com/a/6802723
+    """
+    axis = np.asarray(axis)
+    axis = axis / math.sqrt(np.dot(axis, axis))
+    a = math.cos(theta / 2.0)
+    b, c, d = -axis * math.sin(theta / 2.0)
+    aa, bb, cc, dd = a * a, b * b, c * c, d * d
+    bc, ad, ac, ab, bd, cd = b * c, a * d, a * c, a * b, b * d, c * d
+    return np.array([[aa + bb - cc - dd, 2 * (bc + ad), 2 * (bd - ac)],
+                     [2 * (bc - ad), aa + cc - bb - dd, 2 * (cd + ab)],
+                     [2 * (bd + ac), 2 * (cd - ab), aa + dd - bb - cc]])
+
+
+theta = 1.2
+axis = [0, 0, 1]
+
+sd = StructureData("my_favorite_structure.mmtf")
+sd.atomProperties["pymol_colorList"] = [1 if x % 2 == 0 else 5 for x in sd.xCoordList]
+xyz = np.column_stack((sd.xCoordList, sd.yCoordList, sd.zCoordList))
+xyz_rot = rotation_matrix(axis, theta).dot(xyz.T).T
+sd.xCoordList, sd.yCoordList, sd.zCoordList = np.hsplit(xyz_rot, 3)
+sd.write_to_file("my_favorite_structure_rot.mmtf")
+
+```
+
+
+
 ## Installation
 You can also perform a system wide installation with `cmake` and `ninja` (or `make`).  
 To do so:

ci/build_and_run_python_tests.sh

@@ -0,0 +1,10 @@
+
+python3 --version
+pip3 --version
+pip3 install -r requirements.txt
+pip3 install -r requirements-dev.txt
+cd $TRAVIS_BUILD_DIR
+pip3 install .
+pytest python_src/tests/tests.py -s -vv
+
+

ci/build_and_run_tests.sh

@@ -1,5 +1,7 @@
+#!/usr/bin/env bash
+
 set -e
-cd $TRAVIS_BUILD_DIR
+cd "$TRAVIS_BUILD_DIR"
 mkdir build && cd build
 $CMAKE_CONFIGURE cmake $CMAKE_ARGS $CMAKE_EXTRA ..
 make -j2

include/mmtf/structure_data.hpp

@@ -163,7 +163,7 @@ struct StructureData {
   std::string                              title;
   std::string                              depositionDate;
   std::string                              releaseDate;
-  std::vector<std::vector<float> >         ncsOperatorList;
+  std::vector<std::vector<float>>          ncsOperatorList;
   std::vector<BioAssembly>                 bioAssemblyList;
   std::vector<Entity>                      entityList;
   std::vector<std::string>                 experimentalMethods;