#!/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-->
# < [Pose Basics](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/02.01-Pose-Basics.ipynb) | [Contents](toc.ipynb) | [Index](index.ipynb) | [Accessing PyRosetta Documentation](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/02.03-Accessing-PyRosetta-Documentation.ipynb) ><p><a href="https://colab.research.google.com/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/02.02-Working-with-Pose-Residues.ipynb"><img align="left" src="https://colab.research.google.com/assets/colab-badge.svg" alt="Open in Colab" title="Open in Google Colaboratory"></a>

# # Working with Pose residues
# Keywords: total_residue(), chain(), number(), pdb2pose(), pose2pdb()

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


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from pyrosetta import *
init()


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

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


#    We can use methods in `Pose` to count residues and pick out residues from the pose. Remember that `Pose` is a python class, and to access methods it implements, you need an instance of the class (here `pose` or `pose_clean`) and you then use a dot after the instance.

# In[9]:


print(pose.total_residue())
print(pose_clean.total_residue())
# Did you catch all the missing residues before?


#  Store the `Residue` information for residue 20 of the pose by using the `pose.residue(20)` function.

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# residue20 = type here
### BEGIN SOLUTION
residue20 =  pose.residue(20)
### END SOLUTION
print(residue20.name())


# ## Exercise 2: Residue objects
# 
# Use the `pose`'s `.residue()` object to get the 24th residue of the protein pose. What is the 24th residue in the PDB file (look in the PDB file)? Are they the same residue?

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# store the 24th residue in the pose into a variable (see residue20 example above)
### BEGIN SOLUTION
residue24 = pose.residue(24)
### END SOLUTION


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# what other methods are attached to that Residue object? (type "residue24." and hit Tab to see a list of commands)


# We can immediately see that the numbering PyRosetta internally uses for pose residues is different from the PDB file. The information corresponding to the PDB file can be accessed through the `pose.pdb_info()` object.

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print(pose.pdb_info().chain(24))
print(pose.pdb_info().number(24))


# By using the `pdb2pose` method in `pdb_info()`, we can turn PDB numbering (which requires a chain ID and a residue number) into Pose numbering

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# PDB numbering to Pose numbering
print(pose.pdb_info().pdb2pose('A', 24))


# Use the `pose2pdb` method in `pdb_info()` to see what is the corresponding PDB chain and residue ID for pose residue number 24

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# Pose numbering to PDB numbering


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### BEGIN SOLUTION
print(pose.pdb_info().pose2pdb(1))
### END SOLUTION


# Now we can see how to examine the identity of a residue by PDB chain and residue number.
# 
# Once we get a residue, there are various methods in the `Residue` class that might be for running analysis. We can get instances of the `Residue` class from `Pose`. For instance, we can do the following:

# In[17]:


res_24 = pose.residue(24)
print(res_24.name())
print(res_24.is_charged())


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# <!--NAVIGATION-->
# < [Pose Basics](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/02.01-Pose-Basics.ipynb) | [Contents](toc.ipynb) | [Index](index.ipynb) | [Accessing PyRosetta Documentation](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/02.03-Accessing-PyRosetta-Documentation.ipynb) ><p><a href="https://colab.research.google.com/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/02.02-Working-with-Pose-Residues.ipynb"><img align="left" src="https://colab.research.google.com/assets/colab-badge.svg" alt="Open in Colab" title="Open in Google Colaboratory"></a>