make PyRosetta and Rosetta import work and still be documented.

apps/pilot/jadolfbr/glycan_basic_LCM_protocol.py

@@ -3,13 +3,10 @@
 import os,sys
 from argparse import ArgumentParser
 
-from rosetta import *
-from pyrosetta import *
-from rosetta.protocols.carbohydrates import LinkageConformerMover
-from rosetta.protocols.carbohydrates import SimpleGlycosylateMover
-from rosetta.core.pose import parse_resnum
+import rosetta
+import pyrosetta
 
-init("-include_sugars -write_pdb_link_records")
+pyrosetta.init("-include_sugars -write_pdb_link_records")
 
 
 def get_parser():
@@ -47,24 +44,24 @@ def get_parser():
 
 
 
-    p = pose_from_file(options.infile)
-    scorefxn = get_score_function()
+    p = pyrosetta.pose_from_pdb(options.infile)
+    scorefxn = pyrosetta.get_score_function()
     KT = 1.0
 
 
 
 
-    LCM = LinkageConformerMover()
+    LCM = rosetta.protocols.carbohydrates.LinkageConformerMover()
     LCM.set_x_standard_deviations(2)
-    SGM = SimpleGlycosylateMover()
+    SGM = rosetta.protocols.carbohydrates.SimpleGlycosylateMover()
 
-    resnum = parse_resnum(options.glycosylation_position, p)
+    resnum = rosetta.core.pose.parse_resnum(options.glycosylation_position, p)
     SGM.set_position(resnum)
     SGM.set_glycosylation(options.glycosylation_name)
     SGM.apply(p)
 
     ### This will be unnessessary very soon!
-    mm = MoveMap()
+    mm = pyrosetta.MoveMap()
     for i in range(1, p.total_residue() + 1):
         if (p.residue_type(i).is_carbohydrate()):
             mm.set_bb(i, True)
@@ -73,9 +70,9 @@ def get_parser():
 
 
     for i in range(1, int(options.nstruct) + 1 ):
-        p_copy = Pose(p)
+        p_copy = pyrosetta.Pose(p)
 
-        MC = MonteCarlo(p_copy, scorefxn, KT)
+        MC = pyrosetta.MonteCarlo(p_copy, scorefxn, KT)
         outname = os.path.basename(options.infile).replace(".pdb", "")+"_out_"+repr(i)+".pdb"
         for x in range(1, int(options.cycles)+1):
             print "LCM Round "+repr(x)

apps/public/pyrosetta/build_loop_pyrosetta.py

@@ -7,10 +7,10 @@
 from jade.rosetta_jade.flag_util import get_common_flags_string_for_init
 from jade.basic.path import get_decoy_name
 
-from rosetta import *
-from pyrosetta import *
+import pyrosetta
+import rosetta
 
-init( get_common_flags_string_for_init() )
+pyrosetta.init( get_common_flags_string_for_init() )
 
 
 def get_parser():
@@ -62,7 +62,7 @@ def get_parser():
     options = parser.parse_args()
 
     print(options)
-    pose = pose_from_pdb(options.pdb)
+    pose = pyrosetta.pose_from_pdb(options.pdb)
 
     refpose_name = "starting_model_refpose"
     pose.reference_pose_from_current(refpose_name, True)

apps/public/pyrosetta/find_my_glycans.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 
-from rosetta import *
-from pyrosetta import *
+import pyrosetta
+import rosetta
 
 import sys
 import os
@@ -20,7 +20,7 @@ def get_parser():
 
 if __name__ == "__main__":
 
-    init("-include_sugars -write_pdb_link_records")
+    pyrosetta.init("-include_sugars -write_pdb_link_records")
     if len(sys.argv) == 1:
         sys.exit("Please specify a PDB on the command line as the only argument")
 
@@ -29,7 +29,7 @@ def get_parser():
         print "Please specifiy a PDB as the only argument to this script.\n"
         sys.exit()
 
-    pose = pose_from_pdb(sys.argv[1])
+    pose = pyrosetta.pose_from_pdb(sys.argv[1])
 
     for resnum in range(1, pose.total_residue() +1 ):
         if pose.residue( resnum ).is_carbohydrate():

apps/public/pyrosetta/find_my_residues.py

@@ -4,9 +4,10 @@
 import sys
 from argparse import ArgumentParser
 
-from rosetta import *
-from pyrosetta import *
-init("-include_sugars -ignore_unrecognized_res -ignore_zero_occupancy false")
+import rosetta
+import pyrosetta
+
+pyrosetta.init("-include_sugars -ignore_unrecognized_res -ignore_zero_occupancy false")
 
 
 def get_parser():
@@ -32,7 +33,7 @@ def get_parser():
     options = parser.parse_args()
 
 
-    pose = pose_from_pdb(options.pdb_file)
+    pose = pyrosetta.pose_from_pdb(options.pdb_file)
 
     print "#resnum chain_num pdb_num chain "
     for i in range(1, pose.total_residue() +1 ):

apps/public/pyrosetta/get_mutation_energy.py

@@ -8,8 +8,9 @@
 
 #Instructions: Look at the input options.  Set at least --pdb and --region. (python get_mutation_energy.py --pdb mypdbfile.pdb --region 1:10:B)
 
-from rosetta import *
-from pyrosetta import *
+import pyrosetta
+import rosetta
+
 from argparse import ArgumentParser
 import os
 import sys
@@ -21,7 +22,7 @@
 
 opts = [ '-ex1' , '-ex2', '-ignore_unrecognized_res', '-use_input_sc']
 
-init(" ".join(opts))
+pyrosetta.init(" ".join(opts))
 
 
 ##Setup Options and Script Inputs:
@@ -67,7 +68,7 @@ def get_parser():
 
     ##Check that options are set.
     parser = get_parser()
-    (options, args) = parser.parse_args()
+    options = parser.parse_args()
 
     if not options.pdb:
         sys.exit("Input PDB Required")
@@ -93,16 +94,16 @@ def get_parser():
     OUTFILE = open(options.outpath+"/"+options.filename, 'w')
 
     #Load the PDB
-    pose = Pose()
-    pose_from_pdb(pose, options.pdb)
+    pose = pyrosetta.Pose()
+    pyrosetta.pose_from_pdb(pose, options.pdb)
 
     #Create the Scorefunction
-    scorefxn = create_score_function("talaris2014")
-    scorefxn.set_weight(chainbreak, 100)
+    scorefxn = pyrosetta.get_fa_scorefxn()
+    scorefxn.set_weight(rosetta.core.scoring.chainbreak, 100)
 
 
     #Create the objects we need
-    rel = FastRelax(scorefxn)
+    rel = rosetta.protocols.relax.FastRelax(scorefxn)
     codes = RestypeDefinitions()
 
     if options.alanine_scan:
@@ -114,7 +115,7 @@ def get_parser():
     #Set movemap if nessessary
     if not options.relax_whole_structure:
         print "\nSetting backbone movement for chain "+chain+" only.\n"
-        mm = MoveMap()
+        mm = pyrosetta.MoveMap()
         for i in range(1, pose.total_residue()+1):
             if pose.pdb_info().chain(i) == chain:
                 mm.set_bb(i, True)
@@ -134,7 +135,7 @@ def get_parser():
         rosetta_end = pose.total_residue();
 
 
-    pose_copy = Pose()
+    pose_copy = pyrosetta.Pose()
     pose_copy.assign(pose)
 
 
@@ -170,7 +171,7 @@ def get_parser():
             print "\n Starting mutant "+pdbSP[0]+"_"+pdbSP[1]+"_"+residue+".pdb\n"
             #Start at the same structure.
             pose.assign(pose_copy)
-            mutate_residue(pose, i, residue)
+            pyrosetta.toolbox.mutate_residue(pose, i, residue)
 
 
 

docs/conf.py

@@ -52,7 +52,7 @@
 # Skip non-pip-installable dependencies
 #Python3.3 only:
 
-autodoc_mock_imports = ["rosetta", 'pyrosetta']
+autodoc_mock_imports = ["rosetta", 'pyrosetta'] #This did not work.
 
 """
 from unittest.mock import MagicMock
@@ -73,6 +73,26 @@ def __init__(self):
 sys.modules.update((mod_name, Mock()) for mod_name in MOCK_MODULES)
 """
 
+import mock
+
+MOCK_MODULES = ['rosetta', 
+                'pyrosetta', 
+                'pyrosetta.toolbox',
+                'rosetta.protocols.carbohydrates', 
+                'rosetta.core.pose',
+                'rosetta.core.conformation',
+                'rosetta.protocols.loops',
+                'rosetta.protocols.antibody',
+                'rosetta.protocols.carbohydrates',
+                'rosetta.core.kinematics',
+                'rosetta.protocols.loops.loop_closure.ccd',
+                'rosetta.core.chemical',
+                'rosetta.protocols.relax']
+
+for mod_name in MOCK_MODULES:
+    sys.modules[mod_name] = mock.Mock()
+
+
 
 # Get the project root dir, which is the parent dir of this
 cwd = os.getcwd()

requirements.txt

@@ -15,3 +15,4 @@ sphinxcontrib-websupport==1.0.1
 statsmodels==0.8.0
 weblogo>=3.4
 xmltodict>=0.10.2
+mock>=2.0.0