Change log

v1.6:

• Added AtomSpan.mean() and AtomSelection.mean() to calculate mass/geom center of atom selections

v1.5:

• Added abstract base class for trajectory processors pipe.TrajectoryProcessor
• Trajectory pipe processors are required to be copyable to facilitate slices of pipe.ProcessedTrajectory
• Fix: check number of atoms in Trajectory.extend()

v1.4:

• Added nice __str__ representation for elements and selections
• New: read Frame.time from .xtc files
• Changed signature of TrajectoryInputFile.read_frame()
• Allow *args in .is_in() method of predicate generators (e.g. aName.is_in("CA", "CB"))
• Fixed x in {x} == False bug (Atom, Residue, Molecule, ResidueId were affected)

v1.3:

• Removed: Trajectory.Frame
• New: Added Frame.index, Frame.time (note: time is not read from trajectory files (yet))

v1.2:

• New: Support for .xtc trajectory format (see GromacsXtcFile, XtcWriter)
• New: Added Atom.vdw_radius property

v1.1:

• New: Trajectory reads Frame.cell from input formats (AmberNetCDF | PdbFile)
• Renamed AngleValue.{fabs -> abs}
• Renamed TorsionAngle.{set -> rotate_to}
• Fixed TrajectoryInputFile trampoline
• Added basic CRYST1 pdb record support

v1.0.0:

• Added pipe.AssembleQuaternaryStructure, pipe.ScaleUnitCell
• Changed internal representation of frame data to flat layout
• Introduced lightweight continuous "spans"
• Added coordinates selections
• 0.x submodules are flattened
• 0.x Chain renamed to Molecule
• Removed VectorXYZ in favor of numpy arrays
• Removed AtomName and others are replaced with bare strings
• XYZ become immutable
• LatticeVectors united with BestShiftFinder in UnitCell
• PdbRecords and others are removed from python API, replaced with PdbFile.Dialect
• Free functions distance, angle, dihedral_angle replaced with corresponding methods of XYZ
• asAtoms properties are renamed to atoms, same for residues and molecules
• PdbFile read files in AMBER compatible mode by default
• Introduced "pipe" trajectory processing, see overview
• Added weighted versions of alignment and rmsd calculation
• A number of minor improvements

v0.10.4:

• Fix doc generation
• Remove UB in remove_if() function

v0.10.3:

• License software under MIT license

v0.10.2:

• Fix typos in doc

v0.10.1:

• Fix cmake module path

v0.10.0:

• Add calc_autocorr_order_2_PRE()

v0.9.0:

• Add support for netcdf (.nc) Amber trajectory files

v0.8.2:

• Doc: improve doc generation, fix typos

v0.8.1:

• Fix: inertia tensor off diagonal elements opposite sign

v0.8.0:

• Allow python buffers as arguments of .to_pdb
• Add .to_pdb method to FRCA and selections
• Update dependencies
• CI: migrate to travis-ci.com, add missed gtests
• sanitize acos/asin inputs

v0.7.1:

• Fix Rotation3d.axis()

v0.7.0:

• Add Solvent Accessible Surface Area calculation procedure calc_sasa()
• Allow numpy-style array indexing for selections, see array_indexing

v0.6.1:

• Remove redundant quotes from str(AtomName)
• Explicitly set locale to avoid commas in float numbers
• Update docs

v0.6.0:

• Fix alignment shortcuts (AtomSelection.align_to, AtomSelection.alignment_to())
• Remove AtomSelection.alignment
• Add VectorXYZ.to_numpy, VectorXYZ.from_numpy
• Show detailed message or read error in PdbFile.get_frames
• Use live examples in docs (do avoid divergence with sources)

v0.5.0:

• Add convenient methods to AtomSelection, VectorXYZ
• Allow Rotation3d construction from numpy array
• Allow AtomSelection construction python lists of Atom
• Make Atom properties writable
• Move PyCharm stubs to a separate package (https://github.com/sizmailov/pyxmolpp2-stubs)
• Automate PyPI upload and github-pages generation

v0.4.0:

• Allow AtomSelection.transform to accept Transformation3d, UniformScale3d , Rotation3d and Translation3d
• Support .dat files created with charmm force field

v0.3.0:

• Add calc_autocorr_order_2()

v0.2.0:

• Change PdbFile interface
• Fix calc_alignment
• Support selection slicing
• Implement predicates on C++ side
• Implement convenient predicate generators (aName, rId, etc)
• Fix representation of XYZ
• Add conversion method XYZ -> numpy.ndarray
• Provide access to transformation matrices for Transformation3d and Rotation3d
• Add equality operations to Atom/Residue/Chain names
• Minor improvements
• Update docs

v0.1.1:

• Bug fix: name/index lookup in Frame and Chain

v0.1.0:

• Add set operations for selections
• Optimize selections construction
• Add torsion angles with definitions for protein chains
• Add basic operations on crystal/periodic lattice
• Wrap raw C++ references to avoid segfaults
• Support partial frame updates in trajectory traverse
• Drop compiler requirements from C++14 to C++11
• Test against python 2.7 and 3.5
• Version documentation on gh-pages
• Bug fix