From ba9c2b985b16f9f4523f420bb05bb0d41a5e1ba3 Mon Sep 17 00:00:00 2001 From: martinvoegele Date: Sun, 26 Nov 2023 23:37:13 -0500 Subject: [PATCH] update tutorial for water/single-atom features --- docs/tut-3-featurization.rst | 26 ++++++++++---------------- 1 file changed, 10 insertions(+), 16 deletions(-) diff --git a/docs/tut-3-featurization.rst b/docs/tut-3-featurization.rst index 401cbc0..2a09b48 100644 --- a/docs/tut-3-featurization.rst +++ b/docs/tut-3-featurization.rst @@ -156,8 +156,8 @@ water .. code:: python - struc = "traj/cond-a_water.gro" - xtc = "traj/cond-a_water.gro" + struc = "traj/condition-a_water.gro" + xtc = "traj/condition-a_water.gro" water_feat, water_data = read_water_features( structure_input = struc, xtc_input = xtc, @@ -165,19 +165,18 @@ water atomgroup = "OH2", write = True, write_grid_as="TIP3P", - out_name = "11426_dyn_151" + out_name = "features/11426_dyn_151_water" ) To featurize sites common to both ensembles, we obtain the density grid -following the preprocessing steps in the density tutorial. This is then input -and waters are featurized according to the combined ensemble density. Sites are -therefore conserved across both ensembles and can be compared. +following the steps in the density section of the preprocessing tutorial. +This way, sites are the same across both ensembles and can be compared. .. code:: python - struc = "traj/cond-a_water.gro" - xtc = "dens/cond-a_wateraligned.xtc" - grid = "dens/ab_grid_OH2_density.xtc" + struc = "traj/condition-a_water.gro" + xtc = "traj/condition-a_water_aligned.xtc" + grid = "traj/water_grid_ab_OH2_density.dx" water_feat, water_data = read_water_features( structure_input = struc, xtc_input = xtc, @@ -187,11 +186,9 @@ therefore conserved across both ensembles and can be compared. ) - Single-Atom Features ******************** - For single atoms we use a similar function which provides the same functionality but ignores orientations as atoms are considered spherically symmetric. @@ -213,9 +210,6 @@ written (write=True) using the default density conversion "Angstrom^{-3}" in MDA atomgroup = "SOD", element = "Na", write = True, - out_name = "11426_dyn_151" + out_name = "features/11426_dyn_151_sodium" ) - - - - \ No newline at end of file + \ No newline at end of file