salilab/rmf

The library to support reading and writing of RMF files.

RMF

The library provides support for the RMF file format for storing hierarchical molecular data (such as atomic or coarse grained representations of proteins), along with markup, including geometry and score data.

The main documentation is found on the web site.

Copyright 2007-2023 IMP Inventors.

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at

http://www.apache.org/licenses/LICENSE-2.0

rmf's Issues

Make it so examples make it into oxygen

Add support for saving derivatives of coordinates

Generate an RMF.h

Use a python script (which can later be used for IMP).

lots of unused parameters in hdf5 backend

Should clean them up.

RMF build fails on RHEL5

/usr/include/boost141/boost/exception_ptr.hpp:43: error: looser throw specifier for ‘virtual boost::exception_ptr::~exception_ptr()’
/usr/include/boost141/boost/exception/detail/exception_ptr_base.hpp:26: error: overriding ‘virtual boost::exception_detail::exception_ptr_base::~exception_ptr_base() throw ()’

Add backend using avro data files

Store the rmf as several avro data files, one (with only one bit of data) for the static data, and one that has the per frame data. Can add a frame hierarchy later. This should be more stable under interrupted consumer type situations than the hdf5 based one.

Embed json files in library

Can write a python script to escape them and produce .cpp code.

Add complicated RMF files in all three types and tests that they can be read

Use H5Pset_libver_bounds

To make sure we are using the latest (most efficient) storage scheme as there is no past to be compatible with yet.

Create repo for rmf file as samples

Add external reference decorator type

It would reference an external file with a relative path. We could be nice and always resolve to an absolute path just to make things easier.

Pull category out of key

and have it be a lookup and can use an array for the in disk indexes

Move rmf2 to a write and rename model for the file data

Fix compression and block sizes on Cache data sets

Add program to translate avro based rmfs to and from text files

Consider making current frame a per-file thing

Then we can have the concept of editing a frame, then moving to another. That would make supporting writing as an avro record easier. Have one record be the constant stuff and then a record for each per-frame data. Have to think about storing structure

Remove per-frame attribute of key

Keys are keys and the backends have to look first for per-frame and then for constant data. This requires adding a layer of indirection in HDF5 for going from key index to on-disk index.

Store number of frames in file

And update number after frame is written (how do I determine this?). That way a reader can tell how many frames to look for. Probably still have issues with cached index data, but at least one can open the file read only.

Perhaps add frame editor RAII object.

Bad RMF file, see if it is the lib, hdf5 or what

Crashes chimera and the attached script.

Document rmf2 format

.rmf files don't support frame types

Move functionality outbid Decorator and Factory

Warnings produced on miguelito

/Bis/home/yannick/imp/rmf_debug/swig/RMFPYTHON_wrap.cxx: In function �void init_RMF()�:
/Bis/home/yannick/imp/rmf_debug/swig/RMFPYTHON_wrap.cxx:52113:1: warning: no previous declaration for �void init_RMF()� [-Wmissing-declarations]
In file included from /Bis/home/yannick/imp/rmf_debug/swig/RMFPYTHON_wrap.cxx:3304:0:
/Bis/home/yannick/imp/src/modules/rmf/dependency/RMF/include/RMF/internal/swig_helpers.h: In static member function �static bool ConvertSequenceHelper<T, VT, ConvertVT>::get_is_cpp_object(PyObject_, SwigData) [with SwigData = swig_type_info_, T = std::vectorRMF::Key<RMF::IntTraits >, VT = RMF::KeyRMF::IntTraits, ConvertVT = ConvertRMF::Key<RMF::IntTraits >, PyObject = object]�:
/Bis/home/yannick/imp/src/modules/rmf/dependency/RMF/include/RMF/internal/swig_helpers.h:326:44: instantiated from �static bool ConvertVectorBase<T, ConvertT>::get_is_cpp_object(PyObject, SwigData) [with SwigData = swig_type_info_, T = std::vectorRMF::Key<RMF::IntTraits >, ConvertT = ConvertRMF::Key<RMF::IntTraits >, PyObject = object]�
/Bis/home/yannick/imp/rmf_debug/swig/RMFPYTHON_wrap.cxx:18371:135: instantiated from here
/Bis/home/yannick/imp/src/modules/rmf/dependency/RMF/include/RMF/internal/swig_helpers.h:212:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
/Bis/home/yannick/imp/src/modules/rmf/dependency/RMF/include/RMF/internal/swig_helpers.h: In static member function �static bool ConvertSequenceHelper<T, VT, ConvertVT>::get_is_cpp_object(PyObject, SwigData) [with SwigData = swig_type_info_, T = std::vectorRMF::Key<RMF::FloatTraits >, VT = RMF::KeyRMF::FloatTraits, ConvertVT = ConvertRMF::Key<RMF::FloatTraits >, PyObject = object]�:
/Bis/home/yannick/imp/src/modules/rmf/dependency/RMF/include/RMF/internal/swig_helpers.h:326:44: instantiated from �static bool ConvertVectorBase<T, ConvertT>::get_is_cpp_object(PyObject, SwigData) [with SwigData = swig_type_info_, T = std::vectorRMF::Key<RMF::FloatTraits >, ConvertT = ConvertRMF::Key<RMF::FloatTraits >, PyObject = object]�
/Bis/home/yannick/imp/rmf_debug/swig/RMFPYTHON_wrap.cxx:18401:141: instantiated from here
/Bis/home/yannick/imp/src/modules/rmf/dependency/RMF/include/RMF/internal/swig_helpers.h:212:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
/Bis/home/yannick/imp/src/modules/rmf/dependency/RMF/include/RMF/internal/swig_helpers.h: In static member function �static bool ConvertSequenceHelper<T, VT, ConvertVT>::get_is_cpp_object(PyObject, SwigData) [with SwigData = swig_type_info_, T = std::vectorRMF::Key<RMF::IndexTraits >, VT = RMF::KeyRMF::IndexTraits, ConvertVT = ConvertRMF::Key<RMF::IndexTraits >, PyObject = object]�:
/Bis/home/yannick/imp/src/modules/rmf/dependency/RMF/include/RMF/internal/swig_helpers.h:326:44: instantiated from �static bool ConvertVectorBase<T, ConvertT>::get_is_cpp_object(PyObject, SwigData) [with SwigData = swig_type_info_, T = std::vectorRMF::Key<RMF::IndexTraits >, ConvertT = ConvertRMF::Key<RMF::IndexTraits >, PyObject = object]�
/Bis/home/yannick/imp/rmf_debug/swig/RMFPYTHON_wrap.cxx:18431:141: instantiated from here
/Bis/home/yannick/imp/src/modules/rmf/dependency/RMF/include/RMF/internal/swig_helpers.h:212:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
/Bis/home/yannick/imp/src/modules/rmf/dependency/RMF/include/RMF/internal/swig_helpers.h: In static member function �static bool ConvertSequenceHelper<T, VT, ConvertVT>::get_is_cpp_object(PyObject, SwigData) [with SwigData = swig_type_info_, T = std::vectorRMF::Key<RMF::StringTraits >, VT = RMF::KeyRMF::StringTraits, ConvertVT = ConvertRMF::Key<RMF::StringTraits >, PyObject = object]�:
/Bis/home/yannick/imp/src/modules/rmf/dependency/RMF/include/RMF/internal/swig_helpers.h:326:44: instantiated from �static bool ConvertVectorBase<T, ConvertT>::get_is_cpp_object(PyObject, SwigData) [with SwigData = swig_type_info_, T = std::vectorRMF::Key<RMF::StringTraits >, ConvertT = ConvertRMF::Key<RMF::StringTraits >, PyObject = object]�
/Bis/home/yannick/imp/rmf_debug/swig/RMFPYTHON_wrap.cxx:18461:144: instantiated from here
/Bis/home/yannick/imp/src/modules/rmf/dependency/RMF/include/RMF/internal/swig_helpers.h:212:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
/Bis/home/yannick/imp/src/modules/rmf/dependency/RMF/include/RMF/internal/swig_helpers.h: In static member function �static bool ConvertSequenceHelper<T, VT, ConvertVT>::get_is_cpp_object(PyObject, SwigData) [with SwigData = swig_type_info_, T = std::vectorRMF::Key<RMF::StringsTraits >, VT = RMF::KeyRMF::StringsTraits, ConvertVT = ConvertRMF::Key<RMF::StringsTraits >, PyObject = object]�:
/Bis/home/yannick/imp/src/modules/rmf/dependency/RMF/include/RMF/internal/swig_helpers.h:326:44: instantiated from �static bool ConvertVectorBase<T, ConvertT>::get_is_cpp_object(PyObject, SwigData) [with SwigData = swig_type_info_, T = std::vectorRMF::Key<RMF::StringsTraits >, ConvertT = ConvertRMF::Key<RMF::StringsTraits >, PyObject = object]�
/Bis/home/yannick/imp/rmf_debug/swig/RMFPYTHON_wrap.cxx:18491:147: instantiated from here
/Bis/home/yannick/imp/src/modules/rmf/dependency/RMF/include/RMF/internal/swig_helpers.h:212:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
/Bis/home/yannick/imp/src/modules/rmf/dependency/RMF/include/RMF/internal/swig_helpers.h: In static member function �static bool ConvertSequenceHelper<T, VT, ConvertVT>::get_is_cpp_object(PyObject, SwigData) [with SwigData = swig_type_info_, T = std::vectorRMF::Key<RMF::NodeIDTraits >, VT = RMF::KeyRMF::NodeIDTraits, ConvertVT = ConvertRMF::Key<RMF::NodeIDTraits >, PyObject = object]�:
/Bis/home/yannick/imp/src/modules/rmf/dependency/RMF/include/RMF/internal/swig_helpers.h:326:44: instantiated from �static bool ConvertVectorBase<T, ConvertT>::get_is_cpp_object(PyObject, SwigData) [with SwigData = swig_type_info_, T = std::vectorRMF::Key<RMF::NodeIDTraits >, ConvertT = ConvertRMF::Key<RMF::NodeIDTraits >, PyObject = object]�
/Bis/home/yannick/imp/rmf_debug/swig/RMFPYTHON_wrap.cxx:18521:144: instantiated from here
/Bis/home/yannick/imp/src/modules/rmf/dependency/RMF/include/RMF/internal/swig_helpers.h:212:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
/Bis/home/yannick/imp/src/modules/rmf/dependency/RMF/include/RMF/internal/swig_helpers.h: In static member function �static bool ConvertSequenceHelper<T, VT, ConvertVT>::get_is_cpp_object(PyObject, SwigData) [with SwigData = swig_type_info_, T = std::vectorRMF::Key<RMF::NodeIDsTraits >, VT = RMF::KeyRMF::NodeIDsTraits, ConvertVT = ConvertRMF::Key<RMF::NodeIDsTraits >, PyObject = object]�:
/Bis/home/yannick/imp/src/modules/rmf/dependency/RMF/include/RMF/internal/swig_helpers.h:326:44: instantiated from �static bool ConvertVectorBase<T, ConvertT>::get_is_cpp_object(PyObject, SwigData) [with SwigData = swig_type_info_, T = std::vectorRMF::Key<RMF::NodeIDsTraits >, ConvertT = ConvertRMF::Key<RMF::NodeIDsTraits >, PyObject = object]�
/Bis/home/yannick/imp/rmf_debug/swig/RMFPYTHON_wrap.cxx:18551:147: instantiated from here
/Bis/home/yannick/imp/src/modules/rmf/dependency/RMF/include/RMF/internal/swig_helpers.h:212:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
/Bis/home/yannick/imp/src/modules/rmf/dependency/RMF/include/RMF/internal/swig_helpers.h: In static member function �static bool ConvertSequenceHelper<T, VT, ConvertVT>::get_is_cpp_object(PyObject, SwigData) [with SwigData = swig_type_info_, T = std::vectorRMF::Key<RMF::FloatsTraits >, VT = RMF::KeyRMF::FloatsTraits, ConvertVT = ConvertRMF::Key<RMF::FloatsTraits >, PyObject = object]�:
/Bis/home/yannick/imp/src/modules/rmf/dependency/RMF/include/RMF/internal/swig_helpers.h:326:44: instantiated from �static bool ConvertVectorBase<T, ConvertT>::get_is_cpp_object(PyObject, SwigData) [with SwigData = swig_type_info_, T = std::vectorRMF::Key<RMF::FloatsTraits >, ConvertT = ConvertRMF::Key<RMF::FloatsTraits >, PyObject = object]�
/Bis/home/yannick/imp/rmf_debug/swig/RMFPYTHON_wrap.cxx:18581:144: instantiated from here
/Bis/home/yannick/imp/src/modules/rmf/dependency/RMF/include/RMF/internal/swig_helpers.h:212:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
/Bis/home/yannick/imp/src/modules/rmf/dependency/RMF/include/RMF/internal/swig_helpers.h: In static member function �static bool ConvertSequenceHelper<T, VT, ConvertVT>::get_is_cpp_object(PyObject, SwigData) [with SwigData = swig_type_info_, T = std::vectorRMF::Key<RMF::IntsTraits >, VT = RMF::KeyRMF::IntsTraits, ConvertVT = ConvertRMF::Key<RMF::IntsTraits >, PyObject = object]�:
/Bis/home/yannick/imp/src/modules/rmf/dependency/RMF/include/RMF/internal/swig_helpers.h:326:44: instantiated from �static bool ConvertVectorBase<T, ConvertT>::get_is_cpp_object(PyObject, SwigData) [with SwigData = swig_type_info_, T = std::vectorRMF::Key<RMF::IntsTraits >, ConvertT = ConvertRMF::Key<RMF::IntsTraits >, PyObject = object]�
/Bis/home/yannick/imp/rmf_debug/swig/RMFPYTHON_wrap.cxx:18611:138: instantiated from here
/Bis/home/yannick/imp/src/modules/rmf/dependency/RMF/include/RMF/internal/swig_helpers.h:212:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
/Bis/home/yannick/imp/src/modules/rmf/dependency/RMF/include/RMF/internal/swig_helpers.h: In static member function �static bool ConvertSequenceHelper<T, VT, ConvertVT>::get_is_cpp_object(PyObject, SwigData) [with SwigData = swig_type_info_, T = std::vectorRMF::Key<RMF::IndexesTraits >, VT = RMF::KeyRMF::IndexesTraits, ConvertVT = ConvertRMF::Key<RMF::IndexesTraits >, PyObject = object]�:
/Bis/home/yannick/imp/src/modules/rmf/dependency/RMF/include/RMF/internal/swig_helpers.h:326:44: instantiated from �static bool ConvertVectorBase<T, ConvertT>::get_is_cpp_object(PyObject, SwigData) [with SwigData = swig_type_info_, T = std::vectorRMF::Key<RMF::IndexesTraits >, ConvertT = ConvertRMF::Key<RMF::IndexesTraits >, PyObject = object]�
/Bis/home/yannick/imp/rmf_debug/swig/RMFPYTHON_wrap.cxx:18641:147: instantiated from here
/Bis/home/yannick/imp/src/modules/rmf/dependency/RMF/include/RMF/internal/swig_helpers.h:212:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
/Bis/home/yannick/imp/src/modules/rmf/dependency/RMF/include/RMF/internal/swig_helpers.h: In static member function �static bool ConvertSequenceHelper<T, VT, ConvertVT>::get_is_cpp_object(PyObject, SwigData) [with SwigData = swig_type_info_, T = std::vectorstd::basic_string, VT = std::basic_string, ConvertVT = Convertstd::basic_string, PyObject = object]�:
/Bis/home/yannick/imp/src/modules/rmf/dependency/RMF/include/RMF/internal/swig_helpers.h:326:44: instantiated from �static bool ConvertVectorBase<T, ConvertT>::get_is_cpp_object(PyObject, SwigData) [with SwigData = swig_type_info_, T = std::vectorstd::basic_string, ConvertT = Convertstd::basic_string, PyObject = object]�
/Bis/home/yannick/imp/rmf_debug/swig/RMFPYTHON_wrap.cxx:25166:120: instantiated from here
/Bis/home/yannick/imp/src/modules/rmf/dependency/RMF/include/RMF/internal/swig_helpers.h:212:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
/Bis/home/yannick/imp/src/modules/rmf/dependency/RMF/include/RMF/internal/swig_helpers.h: In static member function �static bool ConvertSequenceHelper<T, VT, ConvertVT>::get_is_cpp_object(PyObject, SwigData) [with SwigData = swig_type_info_, T = std::vectorRMF::NodeID, VT = RMF::NodeID, ConvertVT = ConvertRMF::NodeID, PyObject = object]�:
/Bis/home/yannick/imp/src/modules/rmf/dependency/RMF/include/RMF/internal/swig_helpers.h:326:44: instantiated from �static bool ConvertVectorBase<T, ConvertT>::get_is_cpp_object(PyObject, SwigData) [with SwigData = swig_type_info_, T = std::vectorRMF::NodeID, ConvertT = ConvertRMF::NodeID, PyObject = object]�
/Bis/home/yannick/imp/rmf_debug/swig/RMFPYTHON_wrap.cxx:25241:120: instantiated from here
/Bis/home/yannick/imp/src/modules/rmf/dependency/RMF/include/RMF/internal/swig_helpers.h:212:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
/Bis/home/yannick/imp/src/modules/rmf/dependency/RMF/include/RMF/internal/swig_helpers.h: In static member function �static bool ConvertSequenceHelper<T, VT, ConvertVT>::get_is_cpp_object(PyObject, SwigData) [with SwigData = swig_type_info_, T = std::vector, VT = double, ConvertVT = Convert, PyObject = object]�:
/Bis/home/yannick/imp/src/modules/rmf/dependency/RMF/include/RMF/internal/swig_helpers.h:326:44: instantiated from �static bool ConvertVectorBase<T, ConvertT>::get_is_cpp_object(PyObject, SwigData) [with SwigData = swig_type_info_, T = std::vector, ConvertT = Convert, PyObject = object]�
/Bis/home/yannick/imp/rmf_debug/swig/RMFPYTHON_wrap.cxx:25279:113: instantiated from here
/Bis/home/yannick/imp/src/modules/rmf/dependency/RMF/include/RMF/internal/swig_helpers.h:212:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
/Bis/home/yannick/imp/src/modules/rmf/dependency/RMF/include/RMF/internal/swig_helpers.h: In static member function �static bool ConvertSequenceHelper<T, VT, ConvertVT>::get_is_cpp_object(PyObject, SwigData) [with SwigData = swig_type_info_, T = std::vector, VT = int, ConvertVT = Convert, PyObject = object]�:
/Bis/home/yannick/imp/src/modules/rmf/dependency/RMF/include/RMF/internal/swig_helpers.h:326:44: instantiated from �static bool ConvertVectorBase<T, ConvertT>::get_is_cpp_object(PyObject, SwigData) [with SwigData = swig_type_info_, T = std::vector, ConvertT = Convert, PyObject = object]�
/Bis/home/yannick/imp/rmf_debug/swig/RMFPYTHON_wrap.cxx:25317:106: instantiated from here
/Bis/home/yannick/imp/src/modules/rmf/dependency/RMF/include/RMF/internal/swig_helpers.h:212:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
/Bis/home/yannick/imp/src/modules/rmf/dependency/RMF/include/RMF/internal/swig_helpers.h: In static member function �static bool ConvertSequenceHelper<T, VT, ConvertVT>::get_is_cpp_object(PyObject, SwigData) [with SwigData = swig_type_info_, T = std::vectorstd::vector<std::basic_string >, VT = std::vectorstd::basic_string, ConvertVT = ConvertSequencestd::vector<std::basic_string, Convertstd::basic_string >, PyObject = object]�:
/Bis/home/yannick/imp/src/modules/rmf/dependency/RMF/include/RMF/internal/swig_helpers.h:326:44: instantiated from �static bool ConvertVectorBase<T, ConvertT>::get_is_cpp_object(PyObject, SwigData) [with SwigData = swig_type_info_, T = std::vectorstd::vector<std::basic_string >, ConvertT = ConvertSequencestd::vector<std::basic_string, Convertstd::basic_string >, PyObject = object]�
/Bis/home/yannick/imp/rmf_debug/swig/RMFPYTHON_wrap.cxx:25667:157: instantiated from here
/Bis/home/yannick/imp/src/modules/rmf/dependency/RMF/include/RMF/internal/swig_helpers.h:212:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
/Bis/home/yannick/imp/src/modules/rmf/dependency/RMF/include/RMF/internal/swig_helpers.h: In static member function �static bool ConvertSequenceHelper<T, VT, ConvertVT>::get_is_cpp_object(PyObject, SwigData) [with SwigData = swig_type_info_, T = std::vectorstd::vector, VT = std::vector, ConvertVT = ConvertSequencestd::vector<double, Convert >, PyObject = object]�:
/Bis/home/yannick/imp/src/modules/rmf/dependency/RMF/include/RMF/internal/swig_helpers.h:326:44: instantiated from �static bool ConvertVectorBase<T, ConvertT>::get_is_cpp_object(PyObject, SwigData) [with SwigData = swig_type_info_, T = std::vectorstd::vector, ConvertT = ConvertSequencestd::vector<double, Convert >, PyObject = object]�
/Bis/home/yannick/imp/rmf_debug/swig/RMFPYTHON_wrap.cxx:25783:145: instantiated from here
/Bis/home/yannick/imp/src/modules/rmf/dependency/RMF/include/RMF/internal/swig_helpers.h:212:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
/Bis/home/yannick/imp/src/modules/rmf/dependency/RMF/include/RMF/internal/swig_helpers.h: In static member function �static bool ConvertSequenceHelper<T, VT, ConvertVT>::get_is_cpp_object(PyObject, SwigData) [with SwigData = swig_type_info_, T = std::vectorstd::vector, VT = std::vector, ConvertVT = ConvertSequencestd::vector<int, Convert >, PyObject = object]�:
/Bis/home/yannick/imp/src/modules/rmf/dependency/RMF/include/RMF/internal/swig_helpers.h:326:44: instantiated from �static bool ConvertVectorBase<T, ConvertT>::get_is_cpp_object(PyObject, SwigData) [with SwigData = swig_type_info_, T = std::vectorstd::vector, ConvertT = ConvertSequencestd::vector<int, Convert >, PyObject = object]�
/Bis/home/yannick/imp/rmf_debug/swig/RMFPYTHON_wrap.cxx:25822:135: instantiated from here
/Bis/home/yannick/imp/src/modules/rmf/dependency/RMF/include/RMF/internal/swig_helpers.h:212:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
/Bis/home/yannick/imp/src/modules/rmf/dependency/RMF/include/RMF/internal/swig_helpers.h: In static member function �static bool ConvertSequenceHelper<T, VT, ConvertVT>::get_is_cpp_object(PyObject, SwigData) [with SwigData = swig_type_info_, T = std::vectorRMF::NodeConstHandle, VT = RMF::NodeConstHandle, ConvertVT = ConvertRMF::NodeConstHandle, PyObject = object]�:
/Bis/home/yannick/imp/src/modules/rmf/dependency/RMF/include/RMF/internal/swig_helpers.h:326:44: instantiated from �static bool ConvertVectorBase<T, ConvertT>::get_is_cpp_object(PyObject, SwigData) [with SwigData = swig_type_info_, T = std::vectorRMF::NodeConstHandle, ConvertT = ConvertRMF::NodeConstHandle, PyObject = object]�
/Bis/home/yannick/imp/rmf_debug/swig/RMFPYTHON_wrap.cxx:31890:147: instantiated from here
/Bis/home/yannick/imp/src/modules/rmf/dependency/RMF/include/RMF/internal/swig_helpers.h:212:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
/Bis/home/yannick/imp/src/modules/rmf/dependency/RMF/include/RMF/internal/swig_helpers.h: In static member function �static bool ConvertSequenceHelper<T, VT, ConvertVT>::get_is_cpp_object(PyObject, SwigData) [with SwigData = swig_type_info_, T = std::vectorRMF::NodeHandle, VT = RMF::NodeHandle, ConvertVT = ConvertRMF::NodeHandle, PyObject = object]�:
/Bis/home/yannick/imp/src/modules/rmf/dependency/RMF/include/RMF/internal/swig_helpers.h:326:44: instantiated from �static bool ConvertVectorBase<T, ConvertT>::get_is_cpp_object(PyObject, SwigData) [with SwigData = swig_type_info_, T = std::vectorRMF::NodeHandle, ConvertT = ConvertRMF::NodeHandle, PyObject = object]�
/Bis/home/yannick/imp/rmf_debug/swig/RMFPYTHON_wrap.cxx:46461:132: instantiated from here
/Bis/home/yannick/imp/src/modules/rmf/dependency/RMF/include/RMF/internal/swig_helpers.h:212:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
/Bis/home/yannick/imp/rmf_debug/swig/RMF_HDF5PYTHON_wrap.cxx: In function �void init_RMF_HDF5()�:
/Bis/home/yannick/imp/rmf_debug/swig/RMF_HDF5PYTHON_wrap.cxx:58489:1: warning: no previous declaration for �void init_RMF_HDF5()� [-Wmissing-declarations]
In file included from /Bis/home/yannick/imp/rmf_debug/swig/RMF_HDF5PYTHON_wrap.cxx:3325:0:
/Bis/home/yannick/imp/src/modules/rmf/dependency/RMF/include/RMF/internal/swig_helpers.h: In static member function �static bool ConvertSequenceHelper<T, VT, ConvertVT>::get_is_cpp_object(PyObject, SwigData) [with SwigData = swig_type_info_, T = std::vector, VT = int, ConvertVT = Convert, PyObject = object]�:
/Bis/home/yannick/imp/src/modules/rmf/dependency/RMF/include/RMF/internal/swig_helpers.h:326:44: instantiated from �static bool ConvertVectorBase<T, ConvertT>::get_is_cpp_object(PyObject, SwigData) [with SwigData = swig_type_info_, T = std::vector, ConvertT = Convert, PyObject = object]�
/Bis/home/yannick/imp/rmf_debug/swig/RMF_HDF5PYTHON_wrap.cxx:7181:118: instantiated from here
/Bis/home/yannick/imp/src/modules/rmf/dependency/RMF/include/RMF/internal/swig_helpers.h:212:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
/Bis/home/yannick/imp/src/modules/rmf/dependency/RMF/include/RMF/internal/swig_helpers.h: In static member function �static bool ConvertSequenceHelper<T, VT, ConvertVT>::get_is_cpp_object(PyObject, SwigData) [with SwigData = swig_type_info_, T = std::vector, VT = double, ConvertVT = Convert, PyObject = object]�:
/Bis/home/yannick/imp/src/modules/rmf/dependency/RMF/include/RMF/internal/swig_helpers.h:326:44: instantiated from �static bool ConvertVectorBase<T, ConvertT>::get_is_cpp_object(PyObject, SwigData) [with SwigData = swig_type_info_, T = std::vector, ConvertT = Convert, PyObject = object]�
/Bis/home/yannick/imp/src/modules/rmf/dependency/RMF/include/RMF/internal/swig_helpers.h:317:5: instantiated from �static T ConvertVectorBase<T, ConvertT>::get_cpp_object(PyObject, SwigData) [with SwigData = swig_type_info_, T = std::vector, ConvertT = Convert, PyObject = object]�
/Bis/home/yannick/imp/rmf_debug/swig/RMF_HDF5PYTHON_wrap.cxx:10987:124: instantiated from here
/Bis/home/yannick/imp/src/modules/rmf/dependency/RMF/include/RMF/internal/swig_helpers.h:212:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
/Bis/home/yannick/imp/src/modules/rmf/dependency/RMF/include/RMF/internal/swig_helpers.h: In static member function �static bool ConvertSequenceHelper<T, VT, ConvertVT>::get_is_cpp_object(PyObject, SwigData) [with SwigData = swig_type_info_, T = std::vectorstd::basic_string, VT = std::basic_string, ConvertVT = Convertstd::basic_string, PyObject = object]�:
/Bis/home/yannick/imp/src/modules/rmf/dependency/RMF/include/RMF/internal/swig_helpers.h:326:44: instantiated from �static bool ConvertVectorBase<T, ConvertT>::get_is_cpp_object(PyObject, SwigData) [with SwigData = swig_type_info_, T = std::vectorstd::basic_string, ConvertT = Convertstd::basic_string, PyObject = object]�
/Bis/home/yannick/imp/src/modules/rmf/dependency/RMF/include/RMF/internal/swig_helpers.h:317:5: instantiated from �static T ConvertVectorBase<T, ConvertT>::get_cpp_object(PyObject, SwigData) [with SwigData = swig_type_info_, T = std::vectorstd::basic_string, ConvertT = Convertstd::basic_string, PyObject = _object]�
/Bis/home/yannick/imp/rmf_debug/swig/RMF_HDF5PYTHON_wrap.cxx:36487:131: instantiated from here
/Bis/home/yannick/imp/src/modules/rmf/dependency/RMF/include/RMF/internal/swig_helpers.h:212:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]

Make sure there is an imp less rmf to pdb

Make frames hierarchical

Chimera and RMF

Very slow to display lots of restraints on lots of frames.

Would be very nice to do color mapping with restraint scores and the drawn edges

fix the make all header script to take the paths or glob strings

Windows XP doesn't like long command line argument lists.

Revisit rewriting of frames data file in rmf2

Put each backend in own namespace

Both in C++ and in CMake. That way I can clone/fork them more easily.

Move introspection functionality to the nodes

We could also just drop it for now. Might make sense.... but it is nice to be able to spit out all the data.

Check if avro exists first before building it

We probably need to ship avro as part of rmf. Can use something like this to test if it is there, and then subdir it if it is not already there.

• Try to find ImageMagick++
  Once done, this will define

Magick++_FOUND - system has Magick++
Magick++_INCLUDE_DIRS - the Magick++ include directories
Magick++_LIBRARIES - link these to use Magick++
include(LibFindMacros)

Dependencies
libfind_package(Magick++ Magick)

Use pkg-config to get hints about paths
libfind_pkg_check_modules(Magick++_PKGCONF ImageMagick++)

Include dir
find_path(Magick++_INCLUDE_DIR
NAMES Magick++.h
PATHS ${Magick++_PKGCONF_INCLUDE_DIRS}
)

Finally the library itself
find_library(Magick++_LIBRARY
NAMES Magick++
PATHS ${Magick++_PKGCONF_LIBRARY_DIRS}
)

Set the include dir variables and the libraries and let libfind_process do the rest.
NOTE: Singular variables for this library, plural for libraries this this lib depends on.
set(Magick++_PROCESS_INCLUDES Magick++_INCLUDE_DIR Magick_INCLUDE_DIRS)
set(Magick++_PROCESS_LIBS Magick++_LIBRARY Magick_LIBRARIES)
libfind_process(Magick++)

Make sure that boost::fileystem is used to get paths everywhere and to extract the right name

e:/home/conrad/chimera/rmf/cyl.rmf2\physics.frames

Check type of imp particles

Make sure nor rep if no coords.

Print out "locked" when file is locked and we are waiting

Preferably with file name. Put "." for later stalls.

Slowness opening large rmf file

• Open Miriam's rmf_for_conrad-MS.rmf in the latest Chimera daily build. This takes a few seconds, but not too bad.
• In the Hierarchy panel, open P0 and select P1. This is instantaneous.
• Double-click on P1 or click the Select button (they do the same thing). Chimera takes about one minute to respond.

Here's what's happening:

• Selecting in the Hierarchy panel updates the graphical selection.
• The Features panel is notified of the selected atom and highlights the features (in this case only one feature) in which the atom is used.
• The really slow step is when the Features panel updates the plot. I've attached the profiling output. Nearly all of the time is spent in RMF.get_all_scores (tottime column). In this case, there is only a single call to get_all_scores (ncalls column) so there's not much I can do on the Python side.

Can you please take a look? I'll try a few more things on my side as well. Thanks.

Take advantage of patch to Avro to perform seeks in rmf2 files.

Figure out something more elegant to tuple data

Perhaps put it into the hierarchy too as just another node type.

write PyMol plugin for RMF

http://www.pymolwiki.org/index.php/Plugins_Tutorial

Add Bond decorator

Establish convention for whether reference frames apply to the node itself

It probably should.

Make it so that examples are tested

Building on windows requires disabling the avro tests.

Probably might as well just disable them entirely.

The swig wrapper files are not updated when a header changes

Look into this.

Add overview of how different types of data would be mapped to RMF

Clean up windows build warnings

https://gist.github.com/drussel/5138395

Write VMD plugin to read rmf files

http://www.ks.uiuc.edu/Research/vmd/plugins/doxygen/molfileplugins.html#molfileplugins

Add rigid body support to RMF

So that we store local coordinates once and many rigid orientations.

Handling of exceptions on Windows doesn't work well

Current theory: if there are multiple c++ runtimes involved, then there can be multiple definitions of std::exception. Python may bring in its own C++ runtime.

Need a get_has_frame_name()

To check before asking for a frame name.

Set up doxygen

And make sure it gets uploaded to pages.