Accessing PyRosetta Documentation¶
Keywords: help()
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# Notebook setup
import sys
if 'google.colab' in sys.modules:
!pip install pyrosettacolabsetup
import pyrosettacolabsetup
pyrosettacolabsetup.setup()
print ("Notebook is set for PyRosetta use in Colab. Have fun!")
In [3]:
from pyrosetta import *
init()
core.init: Checking for fconfig files in pwd and ./rosetta/flags core.init: Rosetta version: PyRosetta4.Release.python36.mac r208 2019.04+release.fd666910a5e fd666910a5edac957383b32b3b4c9d10020f34c1 http://www.pyrosetta.org 2019-01-22T15:55:37 core.init: command: PyRosetta -ex1 -ex2aro -database /Users/kathyle/Computational Protein Prediction and Design/PyRosetta4.Release.python36.mac.release-208/pyrosetta/database core.init: 'RNG device' seed mode, using '/dev/urandom', seed=-261722691 seed_offset=0 real_seed=-261722691 core.init.random: RandomGenerator:init: Normal mode, seed=-261722691 RG_type=mt19937
From previous section: Make sure you are in the directory with the pdb files:
cd google_drive/My\ Drive/student-notebooks/
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pose = pose_from_pdb("inputs/5tj3.pdb")
core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 696 residue types core.chemical.GlobalResidueTypeSet: Total time to initialize 0.972394 seconds. core.import_pose.import_pose: File 'inputs/5tj3.pdb' automatically determined to be of type PDB core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 233 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 233 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 233 core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 233 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ASP 350 core.conformation.Conformation: [ WARNING ] missing heavyatom: OD1 on residue ASP 350 core.conformation.Conformation: [ WARNING ] missing heavyatom: OD2 on residue ASP 350 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 353 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 353 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 353 core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 353 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLU 354 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLU 354 core.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLU 354 core.conformation.Conformation: [ WARNING ] missing heavyatom: OE2 on residue GLU 354 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 382 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 382 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 382 core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 382 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue TYR 454 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD1 on residue TYR 454 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD2 on residue TYR 454 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE1 on residue TYR 454 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE2 on residue TYR 454 core.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue TYR 454 core.conformation.Conformation: [ WARNING ] missing heavyatom: OH on residue TYR 454 core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue GLY:CtermProteinFull 520 core.pack.pack_missing_sidechains: packing residue number 233 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 350 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 353 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 354 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 382 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 454 because of missing atom number 6 atom name CG core.pack.task: Packer task: initialize from command line() core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015 core.scoring.etable: Starting energy table calculation core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6) core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6) core.scoring.etable: Finished calculating energy tables. basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv basic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb basic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n core.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated. basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop basic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat core.scoring.elec.util: Read 40 countpair representative atoms core.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true. core.pack.dunbrack.RotamerLibrary: shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated. core.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /Users/kathyle/Computational Protein Prediction and Design/PyRosetta4.Release.python36.mac.release-208/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin core.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/Users/kathyle/Computational Protein Prediction and Design/PyRosetta4.Release.python36.mac.release-208/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'. core.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.325361 seconds to load from binary core.pack.pack_rotamers: built 90 rotamers at 6 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
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.
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Now that we've looked through those functions, we know how to confirm that PyRosetta has loaded in the zinc ions as metal ions.
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zn_resid = pose.pdb_info().pdb2pose('A', 601)
res_zn = pose.residue(zn_resid)
res_zn.is_metal()
Out[6]:
True
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).
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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:
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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.
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# Uncomment this line:
# res_24.atom_is_backbone?
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### BEGIN SOLUTION
res_24.atom_is_backbone(res_24.atom_index("CA"))
### END SOLUTION
Out[19]:
True
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