Dtraj api

.gitignore

@@ -1,3 +1,4 @@
+# compilation / build files
 *.orig
 *.bak
 build*
@@ -15,17 +16,24 @@ __pycache__
 /pylint/pylint_*.txt
 /dist
 .externalToolBuilders
+
 # ignore untitled ipython notebooks
 Untitled*.ipynb
+
 # ignore c-files generated by cython
 /*/estimation/dense/mle_trev_given_pi.c
 /*/estimation/sparse/mle_trev.c
 /*/estimation/sparse/mle_trev_given_pi.c
 /*/estimation/dense/sampler_rev.c
 /*/estimation/dense/sampler_revpi.c
+
 # generated from MANIFEST.in
 MANIFEST
 doc/source/api/generated/
 .ipynb_checkpoints
 .project
 .pydevproject
+
+# project files
+.idea
+

msmtools/dtraj/__init__.py

@@ -46,6 +46,27 @@
    save_discrete_trajectory -  write microstate trajectory to binary file
    save_dtraj
 
+Simple statistics
+=================
+
+.. autosummary::
+   :toctree: generated/
+
+   count_states
+   visited_set
+   number_of_states
+   index_states
+
+Sampling trajectory indexes
+===========================
+
+.. autosummary::
+   :toctree: generated/
+
+   sample_indexes_by_distribution
+   sample_indexes_by_state
+   sample_indexes_by_sequence
+
 """
 from __future__ import absolute_import
 from .api import *