diff --git a/prody/proteins/__init__.py b/prody/proteins/__init__.py index 93db9acb3..bfd0fec03 100644 --- a/prody/proteins/__init__.py +++ b/prody/proteins/__init__.py @@ -132,6 +132,20 @@ * :class:`.Interactions` - store inteactions for a single PDB structure * :class:`.InteractionsDCD` - store interactions for a trajectory +Detect channels, tunnels and pores with CaviFinder +==================== + +Use the following to analyze cavities within protein structures +in single PDB file or in trajectory: + + * :func:`.getVmdModel` - generates a 3D model of proten, using VMD, which is then use for visualization + * :func:`.calcChannels` - computes and identifies channels + * :func:`.calcChannelsMultipleFrames` - compute channels for each frame in a given trajectory or PDB ensemble + * :func:`.getChannelParameters` - extracts and returns the lengths, bottlenecks, and volumes of each channel + * :func:`.getChannelAtoms` - generates an AtomGroup object representing the atoms along the paths of the given channels + * :func:`.showChannels` - visualizes the channels using Open3D + * :func:`.showCavities` - visualizes the cavities using Open3D + Compare/align chains ====================