source: src/Actions/pyMoleCuilder.cpp@ 361805

Action_Thermostats Add_AtomRandomPerturbation Add_FitFragmentPartialChargesAction Add_RotateAroundBondAction Add_SelectAtomByNameAction Added_ParseSaveFragmentResults AddingActions_SaveParseParticleParameters Adding_Graph_to_ChangeBondActions Adding_MD_integration_tests Adding_ParticleName_to_Atom Adding_StructOpt_integration_tests AtomFragments Automaking_mpqc_open AutomationFragmentation_failures Candidate_v1.5.4 Candidate_v1.6.0 Candidate_v1.6.1 ChangeBugEmailaddress ChangingTestPorts ChemicalSpaceEvaluator CombiningParticlePotentialParsing Combining_Subpackages Debian_Package_split Debian_package_split_molecuildergui_only Disabling_MemDebug Docu_Python_wait EmpiricalPotential_contain_HomologyGraph EmpiricalPotential_contain_HomologyGraph_documentation Enable_parallel_make_install Enhance_userguide Enhanced_StructuralOptimization Enhanced_StructuralOptimization_continued Example_ManyWaysToTranslateAtom Exclude_Hydrogens_annealWithBondGraph FitPartialCharges_GlobalError Fix_BoundInBox_CenterInBox_MoleculeActions Fix_ChargeSampling_PBC Fix_ChronosMutex Fix_FitPartialCharges Fix_FitPotential_needs_atomicnumbers Fix_ForceAnnealing Fix_IndependentFragmentGrids Fix_ParseParticles Fix_ParseParticles_split_forward_backward_Actions Fix_PopActions Fix_QtFragmentList_sorted_selection Fix_Restrictedkeyset_FragmentMolecule Fix_StatusMsg Fix_StepWorldTime_single_argument Fix_Verbose_Codepatterns Fix_fitting_potentials Fixes ForceAnnealing_goodresults ForceAnnealing_oldresults ForceAnnealing_tocheck ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_continued ForceAnnealing_with_BondGraph_continued_betteresults ForceAnnealing_with_BondGraph_contraction-expansion FragmentAction_writes_AtomFragments FragmentMolecule_checks_bonddegrees GeometryObjects Gui_Fixes Gui_displays_atomic_force_velocity ImplicitCharges IndependentFragmentGrids IndependentFragmentGrids_IndividualZeroInstances IndependentFragmentGrids_IntegrationTest IndependentFragmentGrids_Sole_NN_Calculation JobMarket_RobustOnKillsSegFaults JobMarket_StableWorkerPool JobMarket_unresolvable_hostname_fix MoreRobust_FragmentAutomation ODR_violation_mpqc_open PartialCharges_OrthogonalSummation PdbParser_setsAtomName PythonUI_with_named_parameters QtGui_reactivate_TimeChanged_changes Recreated_GuiChecks Rewrite_FitPartialCharges RotateToPrincipalAxisSystem_UndoRedo SaturateAtoms_findBestMatching SaturateAtoms_singleDegree StoppableMakroAction Subpackage_CodePatterns Subpackage_JobMarket Subpackage_LinearAlgebra Subpackage_levmar Subpackage_mpqc_open Subpackage_vmg Switchable_LogView ThirdParty_MPQC_rebuilt_buildsystem TrajectoryDependenant_MaxOrder TremoloParser_IncreasedPrecision TremoloParser_MultipleTimesteps TremoloParser_setsAtomName Ubuntu_1604_changes stable
Last change on this file since 361805 was 0aa122, checked in by Frederik Heber <heber@…>, 13 years ago

Updated all source files's copyright note to current year 2012.

  • Property mode set to 100644
File size: 4.3 KB
Line 
1/*
2 * Project: MoleCuilder
3 * Description: creates and alters molecular systems
4 * Copyright (C) 2010-2012 University of Bonn. All rights reserved.
5 * Please see the LICENSE file or "Copyright notice" in builder.cpp for details.
6 */
7
8/*
9 * pyMoleCuilder.cpp
10 *
11 * Created on: Sep 21, 2011
12 * Author: heber
13 */
14
15// include config.h
16#ifdef HAVE_CONFIG_H
17#include <config.h>
18#endif
19
20#include <boost/python.hpp>
21#include <boost/python/module.hpp>
22#include <boost/python/args.hpp>
23
24#include "CodePatterns/MemDebug.hpp"
25
26//!> define all present actions
27#include "GlobalListOfActions.hpp"
28
29//!> python wrapping for all of these actions
30#include "AllActionPython.hpp"
31
32#include "cleanUp.hpp"
33#include "Actions/ActionHistory.hpp"
34#include "cleanUp.hpp"
35
36namespace MoleCuilder {
37
38namespace detail {
39
40void module_exit()
41{
42 // save everything
43 std::cout << "Saving." << std::endl;
44 saveAll();
45 // purge everything
46 std::cout << "Cleaning memory." << std::endl;
47 cleanUp();
48}
49
50void module_reinit()
51{
52 // save everything
53 std::cout << "Saving." << std::endl;
54 saveAll();
55 // purge everything
56 std::cout << "Cleaning static instances from memory." << std::endl;
57 purgeStaticInstances();
58 // need to init the history before any action is created
59 std::cout << "Reinitializing." << std::endl;
60 MoleCuilder::ActionHistory::init();
61}
62
63} /* namespace detail */
64
65namespace PythonTypes {
66
67inline void IndexError(){
68 PyErr_SetString(PyExc_IndexError, "Index out of range");
69 boost::python::throw_error_already_set();
70}
71
72template<class T>
73struct vec_item{
74 typedef typename T::value_type V;
75 static V& get(T& x, int i){
76 static V nothing;
77 if(i < 0) i += x.size();
78 if(i >= 0 && i < int(x.size())) return x[i];
79 IndexError();
80 return nothing;
81 }
82 static void set(T& x, int i, V const& v){
83 if(i < 0) i += x.size();
84 if(i >= 0 && i < int(x.size())) x[i] = v;
85 else IndexError();
86 }
87 static void del(T& x, int i){
88 if(i < 0) i += x.size();
89 if(i >= 0 && i < int(x.size())) x.erase(x.begin() + i);
90 else IndexError();
91 }
92 static void add(T& x, V const& v){
93 x.push_back(v);
94 }
95};
96
97
98} /* namespace PythonTypes */
99} /* namespace MoleCuilder */
100
101BOOST_PYTHON_MODULE(pyMoleCuilder)
102{
103 // need to init the history before any action is created
104 MoleCuilder::ActionHistory::init();
105
106 // from this moment on, we need to be sure to deeinitialize in the correct order
107 // this is handled by the cleanup function
108 atexit(MoleCuilder::detail::module_exit);
109
110 // set the docstring of the current module scope
111 boost::python::scope().attr("__doc__") = "pyMolecuilder are the python bindings to all Actions of the program suite MoleCuilder.\n\nMoleCuilder is a program to build molecular (dynamics) worlds, allowing you indefinite manipulation, control and analysis over the atoms and molecules within a simulation domain.";
112
113 boost::python::def("reinit", MoleCuilder::detail::module_reinit, "Reinitializes the internal state of the python module as if it had been freshly imported, saves all input files beforehand.");
114
115 // STL Vectors:
116 // doubleVec
117 boost::python::class_< std::vector< double > >("PythonType_doubleVec")
118 .def("__len__", &std::vector< double >::size)
119 .def("clear", &std::vector< double >::clear)
120 .def("append", &MoleCuilder::PythonTypes::vec_item< std::vector< double > >::add,
121 boost::python::with_custodian_and_ward<1, 2>()) // let container keep value
122 .def("__getitem__", &MoleCuilder::PythonTypes::vec_item< std::vector< double > >::get,
123 boost::python::return_value_policy<boost::python::copy_non_const_reference>())
124 .def("__setitem__", &MoleCuilder::PythonTypes::vec_item< std::vector< double > >::set,
125 boost::python::with_custodian_and_ward<1,2>()) // to let container keep value
126 .def("__delitem__", &MoleCuilder::PythonTypes::vec_item< std::vector< double > >::del)
127 .def("__iter__", boost::python::iterator< std::vector< double > >())
128 ;
129
130
131#define export_print(z,n,list) \
132 BOOST_PP_CAT(export_, BOOST_PP_SEQ_ELEM(n, list))();
133#define BOOST_PP_LOCAL_MACRO(n) export_print(~, n, GLOBALLISTOFACTIONS)
134#define BOOST_PP_LOCAL_LIMITS (0, BOOST_PP_DEC(BOOST_PP_SEQ_SIZE(GLOBALLISTOFACTIONS)))
135#include BOOST_PP_LOCAL_ITERATE()
136#undef instance_print
137}
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