add a few more xml scripts. Most are just examples.

SchiefLab · Sep 14, 2018 · 802ecaa · 802ecaa
1 parent 3bd3f7b
commit 802ecaa
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Showing 16 changed files with 484 additions and 40 deletions.
diff --git a/apps/public/pdb_utils/fix_space_chain.py b/apps/public/pdb_utils/fix_space_chain.py
@@ -0,0 +1,34 @@
+#!/usr/bin/env python
+import os,sys
+
+def insert (source_str, insert_str, pos):
+    return source_str[:pos]+insert_str+source_str[pos:]
+
+if __name__ == "__main__":
+
+    if len(sys.argv) == 1:
+        sys.exit("Fixes symmetry perl script issue with chains that are spaces.  First argument is the pdb file")
+    input_pdb_file = sys.argv[1]
+
+    lines = open(input_pdb_file, 'r').readlines()
+    new_lines = []
+    for line in lines:
+        #print line
+        new_line = line
+        if len(line) > 4:
+            print line[0:6]
+            if line[0:6] == "HETATM":
+                chain_column = 22-1
+                chain = line[chain_column]
+                print chain
+                if chain == ' ' or len(line.strip()) == 77:
+                    new_line = insert(new_line, " ", chain_column)
+
+
+        new_lines.append(new_line)
+
+
+    OUTFILE = open("test_pdb.pdb", 'w')
+    for line in new_lines:
+        OUTFILE.write(line)
+    OUTFILE.close()
diff --git a/apps/public/pyrosetta/get_phi_psi.py b/apps/public/pyrosetta/get_phi_psi.py
@@ -0,0 +1,43 @@
+#!/usr/bin/env python
+
+#Simple Script to get Phi/Psi using PyRosetta.
+from __future__ import print_function
+from argparse import ArgumentParser
+
+import rosetta
+from pyrosetta import *
+pyrosetta.init()
+
+
+
+
+
+
+
+if __name__ == "__main__":
+    parser = ArgumentParser("Get Phi/Psi of all residues in protein or a range of residues")
+
+
+    parser.add_argument('-s', help="Input Structure", required=True)
+    parser.add_argument('--start', help = "Starting resnum (pose/PDB - EX:24L)")
+    parser.add_argument('--span', help = "Number of residues to print from start")
+
+
+    options = parser.parse_args()
+
+
+    p = pose_from_pdb(options.s)
+
+    start = 1
+    if options.start:
+        start = rosetta.core.pose.parse_resnum(options.start, p)
+
+    end = p.total_residue()
+    if options.span:
+        end = start+int(options.span)
+
+    out = "res resPDB phi psi"
+    print(out)
+    for i in range(start, end+1):
+        out = str(i)+" "+p.pdb_info().pose2pdb(i)+" "+str(180+p.phi(i))+" "+str(180+p.psi(i))
+        print(out)
diff --git a/apps/public/rosetta/score_analysis.py b/apps/public/rosetta/score_analysis.py
@@ -15,7 +15,7 @@
 from jade.rosetta_jade.ScoreFiles import ScoreFile
 from jade.basic.plotting.MakeFigure import *
 
-import shutil
+import os
 
 ########################################################################
 
@@ -27,10 +27,15 @@ def get_parser():
     parser = ArgumentParser(
         description="This utility parses and extracts data from score files in JSON format")
 
-    parser.add_argument("scorefiles", nargs='*', help="A list of scorefiles")
+    #parser.add_argument("scorefiles", nargs='*', help="A list of scorefiles")
 
-    parser.add_argument("-s", "--scoretypes",
-                        default=["dSASA_int", "delta_unsatHbonds", "hbonds_int", "total_score", "dG_separated", "top_n_by_10"],
+    parser.add_argument("-s", "--scorefiles",
+                        help = "Scorefiles to use",
+                        nargs="*",
+                        required = True)
+
+    parser.add_argument("--scoretypes",
+                        default=["total_score"],
                         help="List of score terms to extract",
                         nargs='*')
 
@@ -376,14 +381,14 @@ def main():
 
                     for i in range(0, options.top_n):
                         print get_decoy_path(top_by_n_decoys[i][1])
-                        shutil.copy(get_decoy_path(top_by_n_decoys[i][1]), options.outdir)
+                        os.system("cp " +get_decoy_path(top_by_n_decoys[i][1]) +" "+options.outdir)
                 else:
                     ordered = sf.get_ordered_decoy_list(scoreterm, top_n=int(options.top_n), decoy_names=decoy_names)
                     top_decoys = [[o[0], pdb_dir + "/" + o[1]] for o in ordered]
 
                     for i in range(0, options.top_n):
                         print get_decoy_path(top_decoys[i][1])
-                        shutil.copy(get_decoy_path(top_decoys[i][1]), options.outdir)
+                        os.system("cp "+ get_decoy_path(top_decoys[i][1])+" "+ options.outdir)
 
 ########################################################################
 

diff --git a/database/rosetta/xml_scripts/GTR.xml b/database/rosetta/xml_scripts/GTR.xml
@@ -0,0 +1,14 @@
+<ROSETTASCRIPTS>
+    <RESIDUE_SELECTORS>
+        <Glycan name="all_glycans"/>
+    </RESIDUE_SELECTORS>
+    <SIMPLE_METRICS>
+        <TimingProfileMetric name="timing"/>
+    </SIMPLE_METRICS>
+    <MOVERS>
+        <GlycanTreeRelax name="model" layer_size="2" window_size="1" rounds="1" refine="false" />
+    </MOVERS>
+    <PROTOCOLS>
+        <Add mover="model" />
+    </PROTOCOLS>
+</ROSETTASCRIPTS>
diff --git a/database/rosetta/xml_scripts/analyze_interface_and_rmsd.xml b/database/rosetta/xml_scripts/analyze_interface_and_rmsd.xml
@@ -0,0 +1,24 @@
+<ROSETTASCRIPTS>
+	<SCOREFXNS>
+	</SCOREFXNS>
+	<RESIDUE_SELECTORS>
+	</RESIDUE_SELECTORS>
+	<TASKOPERATIONS>
+	</TASKOPERATIONS>
+	<MOVE_MAP_FACTORIES>
+	</MOVE_MAP_FACTORIES>
+	<SIMPLE_METRICS>
+		<RMSDMetric name="rmsd" use_native="1" rmsd_type="rmsd_all_heavy" />
+	</SIMPLE_METRICS>
+	<FILTERS>
+	</FILTERS>
+	<MOVERS>
+		<InterfaceAnalyzerMover name="iam" pack_separated="1" interface="LH_A" packstat="0" />
+		<RunSimpleMetrics name="metrics" metrics="rmsd" />
+	</MOVERS>
+	<PROTOCOLS>
+		<Add mover="iam" />
+		<Add mover="metrics" />
+	</PROTOCOLS>
+	<OUTPUT />
+</ROSETTASCRIPTS>
diff --git a/database/rosetta/xml_scripts/design_focus_basic.xml b/database/rosetta/xml_scripts/design_focus_basic.xml
@@ -0,0 +1,54 @@
+<ROSETTASCRIPTS>
+	<SCOREFXNS>
+	</SCOREFXNS>
+	<RESIDUE_SELECTORS>
+		<Index name="design_positions" resnums="%%positions%%"/>
+        	<Neighborhood name="nbrhood" selector="design_positions" include_focus_in_subset="0"/>
+        	<Neighborhood name="all_focus" selector="design_positions"/>
+        	<Not name="others" selector="all_focus" />
+
+	</RESIDUE_SELECTORS>
+	<TASKOPERATIONS>
+        	<OperateOnResidueSubset name="turn_off_others" selector="others"><PreventRepackingRLT/> </OperateOnResidueSubset>
+
+        	<OperateOnResidueSubset name="rtrp" selector="nbrhood" ><RestrictToRepackingRLT /></OperateOnResidueSubset>
+        	<OperateOnResidueSubset name="rtrp_all" selector="all_focus"><RestrictToRepackingRLT/> </OperateOnResidueSubset>
+	</TASKOPERATIONS>
+	<MOVE_MAP_FACTORIES>
+	</MOVE_MAP_FACTORIES>
+	<SIMPLE_METRICS>
+        	<TimingProfileMetric name="timing"/>
+        	<TotalEnergyMetric name="total_energy_delta" reference_name="pre_design_pose" custom_type="delta"/>
+        	<TotalEnergyMetric name="total_energy_delta_native" use_native="1" custom_type="delta-native"/>
+        	<SelectedResiduesMetric name="selection" residue_selector="design_positions"/>
+		<SelectedResiduesMetric name="rosetta_sele" residue_selector="design_positions" rosetta_numbering="1"/>
+		<SelectedResiduesPyMOLMetric name="pymol_selection" residue_selector="design_positions" />
+        	<SelectedResiduesPyMOLMetric name="region" residue_selector="all_focus" custom_type="region"/>
+        	<SequenceMetric name="sequence" residue_selector="design_positions" />
+        	<ProtocolSettingsMetric name="settings" limit_to_options="positions,protocol"/>
+	</SIMPLE_METRICS>
+	<FILTERS>
+	</FILTERS>
+	<MOVERS>
+		<PackRotamersMover name="pack_focus" task_operations="rtrp_all,turn_off_others" />
+		<PackRotamersMover name="pack_focus_design" task_operations="rtrp,turn_off_others" />
+        	<RunSimpleMetrics name="post_design_metrics" metrics="total_energy_delta,timing,selection,rosetta_sele,pymol_selection,region,sequence,total_energy_delta_native,settings" />
+        	<SavePoseMover name="store_pre_design_pose" restore_pose="0" reference_name="pre_design_pose" />
+        	<SavePoseMover name="store_current" restore_pose="0" reference_name="current"/>
+
+        	<SavePoseMover name="get_current" restore_pose="1" reference_name="current"/>
+	</MOVERS>
+	<PROTOCOLS>
+
+		Run Packer on input as a CONTROL for score comparisons
+		<Add mover="store_current"/>
+		<Add mover="pack_focus"/>
+		<Add mover="store_pre_design_pose"/>
+
+		Run Packer to do design
+		<Add mover="get_current"/>
+		<Add mover="pack_focus_design" />
+		<Add mover="post_design_metrics" />
+	</PROTOCOLS>
+	<OUTPUT />
+</ROSETTASCRIPTS>
diff --git a/database/rosetta/xml_scripts/design_focus_cart_rel.xml b/database/rosetta/xml_scripts/design_focus_cart_rel.xml
@@ -0,0 +1,71 @@
+<ROSETTASCRIPTS>
+	<SCOREFXNS>
+        	<ScoreFunction name="cart" weights="ref2015_cart" symmetric="0">
+            	<!--Reweight scoretype="dihedral_constraint" weight=".3" /!-->
+            	<Reweight scoretype="coordinate_constraint" weight="1.0"/>
+        	</ScoreFunction>
+	</SCOREFXNS>
+	<RESIDUE_SELECTORS>
+		<Index name="design_positions" resnums="%%positions%%"/>
+        	<Neighborhood name="nbrhood" selector="design_positions" include_focus_in_subset="0"/>
+        	<Neighborhood name="all_focus" selector="design_positions"/>
+        	<Not name="others" selector="all_focus" />
+
+	</RESIDUE_SELECTORS>
+	<TASKOPERATIONS>
+        	<OperateOnResidueSubset name="turn_off_others" selector="others"><PreventRepackingRLT/></OperateOnResidueSubset>
+
+        	<OperateOnResidueSubset name="rtrp" selector="nbrhood"><RestrictToRepackingRLT/></OperateOnResidueSubset>
+        	<OperateOnResidueSubset name="rtrp_all" selector="all_focus"><RestrictToRepackingRLT/></OperateOnResidueSubset>
+
+	</TASKOPERATIONS>
+	<MOVE_MAP_FACTORIES>
+        	<MoveMapFactory name="fr_mm_factory" bb="0" chi="0" cartesian="1">
+            		<Chi residue_selector="all_focus" enable="1"/>
+            		<Backbone residue_selector="all_focus" enable="1" />
+        	</MoveMapFactory>
+	</MOVE_MAP_FACTORIES>
+	<SIMPLE_METRICS>
+        	<TimingProfileMetric name="timing"/>
+        	<TotalEnergyMetric name="total_energy_delta" reference_name="pre_design_pose" custom_type="delta"/>
+        	<TotalEnergyMetric name="total_energy_delta_cart" reference_name="pre_design_pose" scorefxn="cart" custom_type="delta_cart"/>
+        	<TotalEnergyMetric name="total_energy_delta_native" use_native="1" custom_type="delta-native"/>
+        	<SelectedResiduesMetric name="selection" residue_selector="design_positions"/>
+		<SelectedResiduesMetric name="rosetta_sele" residue_selector="design_positions" rosetta_numbering="1"/>
+		<SelectedResiduesPyMOLMetric name="pymol_selection" residue_selector="design_positions" />
+        	<SelectedResiduesPyMOLMetric name="region" residue_selector="all_focus" custom_type="region"/>
+        	<SequenceMetric name="sequence" residue_selector="design_positions" />
+        	<RMSDMetric name="rmsd" use_native="1" rmsd_type="rmsd_protein_bb_heavy"/>
+        	<ProtocolSettingsMetric name="settings" limit_to_options="positions,protocol"/>
+	</SIMPLE_METRICS>
+	<FILTERS>
+	</FILTERS>
+	<MOVERS>
+		<FastRelax name="cart_focus" task_operations="rtrp_all,turn_off_others" movemap_factory="fr_mm_factory" cartesian="1" scorefxn="cart" ramp_down_constraints="1"/>
+		<FastRelax name="cart_focus_design" task_operations="rtrp,turn_off_others" movemap_factory="fr_mm_factory" cartesian="1" scorefxn="cart" ramp_down_constraints="1" disable_design="0"/>
+       		<AddConstraintsToCurrentConformationMover name="apply_coordinate_constraints" cst_weight="1.0" use_distance_cst="False" coord_dev="0.5" bound_width="0" CA_only="True" bb_only="False" />
+        	<ClearConstraintsMover name="remove_coordinate_constraints" />
+        	<RunSimpleMetrics name="post_design_metrics" metrics="total_energy_delta,timing,selection,rosetta_sele,pymol_selection,region,sequence,rmsd,total_energy_delta_native,settings" />
+        	<SavePoseMover name="store_pre_design_pose" restore_pose="0" reference_name="pre_design_pose" />
+        	<SavePoseMover name="store_current" restore_pose="0" reference_name="current"/>
+        	<SavePoseMover name="get_current" restore_pose="1" reference_name="current"/>
+	</MOVERS>
+	<PROTOCOLS>
+
+		Run Cartesian on input PDB as a SCORE CONTROL
+		<Add mover="apply_coordinate_constraints"/>
+		<Add mover="store_current"/>
+		<Add mover="cart_focus"/>
+
+		Make sure Coordinate Constraints are still there after ramp.
+		<Add mover="apply_coordinate_constraints" />
+		<Add mover="store_pre_design_pose"/>
+
+		Get original pose and run design.  
+		<Add mover="get_current"/>
+		<Add mover="cart_focus_design" />
+		<Add mover="remove_coordinate_constraints"/>
+		<Add mover="post_design_metrics" />
+	</PROTOCOLS>
+	<OUTPUT />
+</ROSETTASCRIPTS>
diff --git a/database/rosetta/xml_scripts/design_focus_rel_ab_scan.xml b/database/rosetta/xml_scripts/design_focus_rel_ab_scan.xml
@@ -0,0 +1,73 @@
+<ROSETTASCRIPTS>
+	<SCOREFXNS>
+        	<ScoreFunction name="cart" weights="ref2015_cart" symmetric="0">
+            	<!--Reweight scoretype="dihedral_constraint" weight=".3" /!-->
+            	<Reweight scoretype="dihedral_constraint" weight=".3"/>
+        	</ScoreFunction>
+	</SCOREFXNS>
+	<RESIDUE_SELECTORS>
+		<CDR name="cdr_rel" cdrs="%%cdrs%%" />
+		<Index name="design_positions" resnums="%%positions%%"/>
+        	<Neighborhood name="nbrhood" selector="cdr_rel" include_focus_in_subset="0"/>
+        	<Neighborhood name="all_cdrs_and_neighbors" selector="cdr_rel" include_focus_in_subset="1"/>
+
+        	<Not name="not_designing" selector="design_positions" />
+        	<Not name="not_packing" selector="all_cdrs_and_neighbors" />
+	</RESIDUE_SELECTORS>
+	<TASKOPERATIONS>
+        	<OperateOnResidueSubset name="turn_off_others" selector="not_packing"><PreventRepackingRLT/></OperateOnResidueSubset>
+
+        	<OperateOnResidueSubset name="rtrp" selector="not_designing"><RestrictToRepackingRLT/></OperateOnResidueSubset>
+
+        	<ResfileCommandOperation  name="cmd" command="%%cmd%%" residue_selector="design_positions"/> 
+	</TASKOPERATIONS>
+	<MOVE_MAP_FACTORIES>
+        	<MoveMapFactory name="fr_mm_factory" bb="0" chi="0" cartesian="1">
+            		<Chi residue_selector="cdr_rel" enable="1"/>
+            		<Backbone residue_selector="cdr_rel" enable="1" />
+        	</MoveMapFactory>
+	</MOVE_MAP_FACTORIES>
+	<SIMPLE_METRICS>
+        	<TimingProfileMetric name="timing"/>
+        	<TotalEnergyMetric name="total_energy_delta_native" use_native="1" custom_type="delta-native"/>
+        	<SelectedResiduesMetric name="selection" residue_selector="design_positions"/>
+		<SelectedResiduesMetric name="rosetta_sele" residue_selector="design_positions" rosetta_numbering="1"/>
+		<SelectedResiduesPyMOLMetric name="pymol_selection" residue_selector="design_positions" />
+        	<SelectedResiduesPyMOLMetric name="region" residue_selector="all_cdrs_and_neighbors" custom_type="region"/>
+        	<SequenceMetric name="sequence" residue_selector="design_positions" />
+        	<RMSDMetric name="rmsd" use_native="1" rmsd_type="rmsd_protein_bb_heavy"/>
+	</SIMPLE_METRICS>
+	<FILTERS>
+	</FILTERS>
+	<MOVERS>
+		<FastRelax name="cart_focus" task_operations="turn_off_others" movemap_factory="fr_mm_factory" cartesian="1" scorefxn="cart" ramp_down_constraints="0"/>
+		<FastRelax name="cart_focus_design" task_operations="rtrp,turn_off_others,cmd" movemap_factory="fr_mm_factory" cartesian="1" scorefxn="cart" ramp_down_constraints="1" disable_design="0"/>
+       		<AddConstraintsToCurrentConformationMover name="apply_coordinate_constraints" cst_weight="1.0" use_distance_cst="False" coord_dev="0.5" bound_width="0" CA_only="True" bb_only="False" />
+        	<ClearConstraintsMover name="remove_constraints" />
+        	<RunSimpleMetrics name="post_design_metrics" metrics="timing,selection,rosetta_sele,pymol_selection,region,sequence,rmsd,total_energy_delta_native" />
+		<AddConstraints name="apply_dih_csts">
+			<DihedralConstraintGenerator name="dih_cst_phi" dihedral="phi" residue_selector="cdr_rel" />
+			<DihedralConstraintGenerator name="dih_cst_psi" dihedral="psi" residue_selector="cdr_rel" />
+		</AddConstraints>
+		<RemoveConstraints name="rm_csts" constraint_generators="dih_cst_phi,dih_cst_psi" />
+
+		We are not going to do a general way here.  I need to refactor this to be able to set a specific set of CDRs
+		For now, we manually do it. 
+    		<CDRDihedralConstraintMover name="H1_cst" cdr="H1" use_cluster_csts="1" />
+    		<CDRDihedralConstraintMover name="H2_cst" cdr="H2" use_cluster_csts="1" />
+    		<CDRDihedralConstraintMover name="H3_cst" cdr="H3" use_cluster_csts="1" />
+	</MOVERS>
+	<PROTOCOLS>
+
+		<!--Add mover="apply_dih_csts"/-->
+		<Add mover="H1_cst"/>
+		<Add mover="H2_cst"/>
+		<Add mover="H3_cst"/>
+
+		Get original pose and run design.  
+		<Add mover="cart_focus_design" />
+		<Add mover="remove_constraints"/>
+		<Add mover="post_design_metrics" />
+	</PROTOCOLS>
+	<OUTPUT />
+</ROSETTASCRIPTS>
diff --git a/database/rosetta/xml_scripts/glycosylate_model.xml b/database/rosetta/xml_scripts/glycosylate_model.xml
@@ -0,0 +1,19 @@
+<ROSETTASCRIPTS>
+    <RESIDUE_SELECTORS>
+        <Glycan name="all_glycans"/>
+    </RESIDUE_SELECTORS>
+    <SIMPLE_METRICS>
+        <TimingProfileMetric name="timing"/>
+    </SIMPLE_METRICS>
+    <MOVERS>
+        <SimpleGlycosylateMover name="glycosylate" positions="88A,295A,362A,448A,625B,130C,160C,289C,295C,301C,362C,88E,130E,295E,356E,392E,448E,406C,411C,463C,611D,616D,637D,160E,186E,339E,396E,406E,411E,463E,611F,616F,637F" glycosylation="man5" />
+        <GlycanTreeRelax name="model" layer_size="2" window_size="1" rounds="1" refine="false" />
+        <RunSimpleMetrics name="post_modeling_metrics" metrics="timing" prefix="post-model_"/>
+    </MOVERS>
+    <PROTOCOLS>
+        <Add mover="glycosylate"/>
+        <Add mover="model_glycans" />
+        <Add mover="post_modeling_metrics" />
+    </PROTOCOLS>
+</ROSETTASCRIPTS>
+