#!/usr/bin/env python
# coding: utf-8

# <!--NOTEBOOK_HEADER-->
# *This notebook contains material from [PyRosetta](https://RosettaCommons.github.io/PyRosetta.notebooks);
# content is available [on Github](https://github.com/RosettaCommons/PyRosetta.notebooks.git).*

# <!--NAVIGATION-->
# < [Working with Pose residues](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/02.02-Working-with-Pose-Residues.ipynb) | [Contents](toc.ipynb) | [Index](index.ipynb) | [Getting spatial features from a Pose](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/02.04-Getting-Spatial-Features-from-Pose.ipynb) ><p><a href="https://colab.research.google.com/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/02.03-Accessing-PyRosetta-Documentation.ipynb"><img align="left" src="https://colab.research.google.com/assets/colab-badge.svg" alt="Open in Colab" title="Open in Google Colaboratory"></a>

# # Accessing PyRosetta Documentation
# Keywords: help()

# In[ ]:


get_ipython().system('pip install pyrosettacolabsetup')
import pyrosettacolabsetup; pyrosettacolabsetup.install_pyrosetta()
import pyrosetta; pyrosetta.init()


# In[3]:


from pyrosetta import *
init()


# **From previous section:**
# Make sure you are in the directory with the pdb files:
# 
# `cd google_drive/MyDrive/student-notebooks/`

# In[5]:


pose = pose_from_pdb("inputs/5tj3.pdb")


# The full documentaton for PyRosetta can be found here: https://graylab.jhu.edu/PyRosetta.documentation/. You can use it to search for or learn more about any method in PyRosetta.
# 
# One benefit of working within Jupyter notebooks is that we can make use of its autocomplete features. To see an example, try typing `res_24.is_` and pressing `tab` to find other features of residues you can examine. Note that you can scroll down to see more features.

# In[ ]:





# Now that we've looked through those functions, we know how to confirm that PyRosetta has loaded in the zinc ions as metal ions. 

# In[6]:


zn_resid = pose.pdb_info().pdb2pose('A', 601)
res_zn = pose.residue(zn_resid) 
res_zn.is_metal() 


# ## Exercise 3: Python Object Help
# We can also explore documentation for objects and methods from Jupyter notebooks. Say you wanted to find out more about the Pose object. Try typing in `Pose?`, `?Pose` or `help(Pose)`.

# In[ ]:





# By the way, now if you ever go on to develop some PyRosetta functions, you can see the importance of docstrings!
# 
# This works for PyRosetta methods as well:

# In[8]:


res_24 = pose.residue(24)

# Uncomment this line:
# res_24.atom_index?


# ## Exercise 4: Some residue commands
# 
# Now use the `atom_index` method and the method below to find out whether the "CA" atom in res_24 is a backbone atom. 

# In[9]:


# Uncomment this line:
# res_24.atom_is_backbone?


# In[19]:


### BEGIN SOLUTION
res_24.atom_is_backbone(res_24.atom_index("CA"))
### END SOLUTION


# In[ ]:





# <!--NAVIGATION-->
# < [Working with Pose residues](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/02.02-Working-with-Pose-Residues.ipynb) | [Contents](toc.ipynb) | [Index](index.ipynb) | [Getting spatial features from a Pose](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/02.04-Getting-Spatial-Features-from-Pose.ipynb) ><p><a href="https://colab.research.google.com/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/02.03-Accessing-PyRosetta-Documentation.ipynb"><img align="left" src="https://colab.research.google.com/assets/colab-badge.svg" alt="Open in Colab" title="Open in Google Colaboratory"></a>