owl/trunk/testGraph2Pml.java

import java.sql.*;
import java.io.*;
import tools.*;

/**
 * Package:             tools
 * Class:               testGraph2Pml
 * Author:              Ioannis Filippis, filippis@molgen.mpg.de
 * Date:                21/03/2006
 * 
 * Simple test class for visualizing contact graphs using Graph2Pml class plus
 * PyMol class. Run PyMol with the -R option to run the server.
 * 
 * Changelog:
 * 27/03/06 modified by IF (functional with comments - added cgo examples)
 * 21/03/06 first created by IF (non functional)
 */

public class testGraph2Pml {

        public static void main(String[] args) {
                
                String connFile = "/project/StruPPi/ioannis/cnfs/msdgraph.my.cnf", pdbFileName = "", molObjName = "";
                Graph2Pml graphPml = null;
                PyMol pml = null;
                
                mySQLConnect SQLC =  new mySQLConnect();
                SQLC.readConnectionFile(connFile);
                Connection conn = SQLC.openConnection();
        
                //Create a new output stream to the pymol server running at the localhost
                //all commands will be send there
                PrintWriter serverOutPw = new PrintWriter(new PymolServerOutputStream("http://"+Machine.getClient()+":9123"), true);
                pml = new PyMol(serverOutPw);
                
                //Edges as lines
                //export the pdb file directly from msdsd and load it in pymol
                pdbFileName = Msdsd2Pdb.export2File("1rx4", 20717, 52567, 9, "/project/StruPPi/ioannis/tmp");
                molObjName = pml.loadPDB(pdbFileName, "/project/StruPPi/ioannis/tmp");
                System.out.println(molObjName);
                
                //create a pymol contact graph object for the graph 33729
                //use only SC_SC edges with SC_SC edge weight and nodes that have SC_SC edges
                //no further filtering in the edges based on the contact range is applied
                //no user based graph filtering is applied
                //the graph comes from msdsd
                //normal edges will be utilised
                //the graph will not be visualised as "directed" 
                graphPml = new Graph2Pml(serverOutPw, molObjName, 33729, "SC_SC", "SC_SC_in+SC_SC_out", "SC_SC", "true", "true", true, false, false, conn);
                //draw nodes, edges, special residues but not surface
                //the node size will be calculated based on the SC_SC_out field on asc order
                //the node color will be calculated based on the BB_BB_out field not discretised
                //all ALA nodes will be transparent
                //all residues that do not have any SC interactions will be the special ones colored green
                //all edges will be lines of width determined by the SC_SC field in asc order
                //all edges lines will have color calculated based on the BB_BB_out field not discretised
                //all edges lines with adjacent ALA's will have gaps
                graphPml.draw(true, true, true, false);         
                graphPml.setNodeSizeMethod("SC_SC_out", false);
                graphPml.setNodeColorMethod("BB_BB_out", false);
                graphPml.setNodeTranspCondition("(res = \"ALA\")");
                graphPml.setSpecialRes("green", "SELECT cid, num FROM newmsdgraph.nodes WHERE (graph_id = 33729) AND (sc_sc_in+sc_sc_out = 0);");
                graphPml.setEdgeSizeMethod("SC_SC", false);
                graphPml.setEdgeColorMethod("BB_BB", false);
                graphPml.setEdgeGapCondition("(i_res = \"ALA\" OR j_res = \"ALA\")");
                //create the contact graph
                graphPml.outputGraph();
                //save the image not ray-traced
                pml.saveImage("test1","/home/filippis/Desktop", false);
                //if you want later to read the view from a log file
                //pml.openLog("test1_log","/home/filippis/Desktop");
                //get the view
                pml.getView("test1_view");
                //pml.closeLog();

                // delete all and reload the structure
                pml.delete("all", false);
                pml.loadPDB(pdbFileName, "/project/StruPPi/ioannis/tmp");
                
                //to check reversibility in setNodeSizeMethod, setEdgeSizeMethod 
                //and discretised coloring in setNodeColorMethod, setEdgeColorMethod
                graphPml.setNodeSizeMethod("SC_SC_out", true);
                graphPml.setNodeColorMethod("BB_BB_out", true);
                graphPml.setEdgeSizeMethod("SC_SC", true);
                graphPml.setEdgeColorMethod("BB_BB", true);
                graphPml.outputGraph();
                //set view by reading a log file
                //pml.getFileView("test2_view", "/home/filippis/Desktop/test1_log.pml");
                //pml.setView("test2_view");
                //set view based on the view of the first structure so that you can compare
                //different graphs for the same structure
                pml.setView("test1_view");
                pml.saveImage("test2","/home/filippis/Desktop", false);
                
                pml.delete("all", false);
                pml.loadPDB(pdbFileName, "/project/StruPPi/ioannis/tmp");
                
                //to check node method for edge coloring when nodeColor method not discretised
                graphPml.setUniformNodeSize(0.6);
                graphPml.setNodeColorMethod("BB_BB_out", false);
                graphPml.setUniformEdgeSize(4);
                graphPml.setEdgeColorMethod("node", true);
                graphPml.outputGraph();
                pml.setView("test1_view");
                pml.saveImage("test3","/home/filippis/Desktop", false);
                
                pml.delete("all", false);
                pml.loadPDB(pdbFileName, "/project/StruPPi/ioannis/tmp");
                                
                //to check node method for edge coloring when nodeColor method is discretised
                graphPml.setUniformNodeSize(0.6);
                graphPml.setNodeColorMethod("BB_BB_out", true);
                graphPml.setUniformEdgeSize(4);
                graphPml.setEdgeColorMethod("node", true);
                graphPml.outputGraph();
                pml.setView("test1_view");
                pml.saveImage("test4","/home/filippis/Desktop", false);
                
                pml.delete("all", false);
                pml.loadPDB(pdbFileName, "/project/StruPPi/ioannis/tmp");
                                
                //to check node method for edge coloring when nodeColor method is uniform
                graphPml.setUniformNodeSize(0.6);
                graphPml.setUniformNodeColor("blue");
                graphPml.setUniformEdgeSize(4);
                graphPml.setEdgeColorMethod("node", true);
                graphPml.outputGraph();
                pml.setView("test1_view");
                pml.saveImage("test5","/home/filippis/Desktop", false);         
                
                pml.delete("all", false);
                pml.loadPDB(pdbFileName, "/project/StruPPi/ioannis/tmp");
                
                //to check the trick of directionality with gapped lines for "half" edges
                //for this purpose a SC_BB graph model is used that doesn't ensure bidirectionality
                graphPml = new Graph2Pml(serverOutPw, molObjName, 33729, "SC_BB", "SC_BB_in+SC_BB_out", "SC_BB", "true", "true", true, false, true, conn);
                graphPml.outputGraph();
                pml.setView("test1_view");
                pml.saveImage("test6","/home/filippis/Desktop", false);         
                
                
                pml.delete("all", false);
                
                //test multi-chain macromolecule with RNA also
                pdbFileName = Msdsd2Pdb.export2File("1a0a", 1107, 2560, 1, "/project/StruPPi/ioannis/tmp");
                molObjName = pml.loadPDB(pdbFileName, "/project/StruPPi/ioannis/tmp");
                System.out.println(molObjName);
                
                graphPml = new Graph2Pml(serverOutPw, molObjName, 95, "SC_SC", "SC_SC_in+SC_SC_out", "SC_SC", "true", "true", true, false, false, conn);
                graphPml.draw(true, true, false, false);
                //color nodes based on the chains they belong to
                graphPml.setNodeColorMethod("chain", true);
                graphPml.setNodeTransp(0.2);            
                graphPml.setUniformEdgeColor("red");
                graphPml.setUniformEdgeSize(4.5);
                graphPml.setEdgeGap(0.5);
                graphPml.outputGraph();
                pml.saveImage("test7","/home/filippis/Desktop", false);
                pml.getView("test2_view");
                
                pml.delete("all", false);
                pml.loadPDB(pdbFileName, "/project/StruPPi/ioannis/tmp");
                
                //color edges based on the chains they belong to
                graphPml.draw(true, true, false, false);                
                graphPml.setUniformNodeColor("red");
                graphPml.setEdgeColorMethod("chain", true);
                graphPml.outputGraph();
                pml.setView("test2_view");
                pml.saveImage("test8","/home/filippis/Desktop", false);         
                
                pml.delete("all", false);
                pml.loadPDB(pdbFileName, "/project/StruPPi/ioannis/tmp");
                
                //to check node method for edge coloring when nodeColor method is based on chain coloring       
                graphPml.setNodeColorMethod("chain", true);
                graphPml.setEdgeColorMethod("node", true);
                graphPml.outputGraph();
                pml.setView("test2_view");
                pml.saveImage("test9","/home/filippis/Desktop", false);
                
                pml.delete("all", false);
                pml.loadPDB(pdbFileName, "/project/StruPPi/ioannis/tmp");
                
                //draw also surface - you can not see the graph anymore
                graphPml.draw(true, true, false, true);
                graphPml.setSurfTransp(0.7);
                graphPml.outputGraph();
                pml.setView("test2_view");
                pml.saveImage("test10","/home/filippis/Desktop", false);
                
                try { Thread.sleep(10000); } catch (Exception e) {}
                
                //hide the surface, show the RNA also
                //change the color of the nodes for each chain using the pymol defined list of nodes for each chain 
                pml.hideWhat("surface", "graphMol", false);
                pml.showWhat("lines", "restMol", false);
                graphPml.setNodesColorUniform("nodes_cidA","red");
                graphPml.setNodesColorUniform("nodes_cidA","yellow");
                
                try { Thread.sleep(10000); } catch (Exception e) {}
                
                //if you believe that the objects contained in the list won't exceed the pymol command length limit,
                //you can concatenate all objects as a single string selection and handle them all together 
                pml.concatList("nodes", "+", "nodesStr");
                pml.setNodeColor("blue", "nodesStr", true);
                pml.selPml("nodes", "nodesStr", true, true);
                                
                pml.delete("all", false);
                pml.loadPDB(pdbFileName, "/project/StruPPi/ioannis/tmp");
                
                //check a graph model with only inter-secondary-structure-elements SC_SC edges
                //remember that all the nodes with SC_SC will be selected
                //use default behaviour
                graphPml = new Graph2Pml(serverOutPw, molObjName, 95, "SC_SC", "SC_SC_in+SC_SC_out", "SC_SC", "(!((i_ssid = j_ssid) AND (i_sstype = j_sstype)))", "true", true, false, false, conn);
                graphPml.draw(true, true, false, false);
                graphPml.outputGraph();
                pml.setView("test2_view");
                pml.saveImage("test11","/home/filippis/Desktop", false);
                
                pml.delete("all", false);
                
                //CGO EDGES SECTION
                pdbFileName = Msdsd2Pdb.export2File("1kj0", 21698, 55132, 9, "/project/StruPPi/ioannis/tmp");
                molObjName = pml.loadPDB(pdbFileName, "/project/StruPPi/ioannis/tmp");
                
                //Cgo makes sense to be used with directed graph
                graphPml = new Graph2Pml(serverOutPw, molObjName, 35666, "SC_SC", "SC_SC_in+SC_SC_out", "SC_SC", "true", "true", true, true, true, conn);
                graphPml.draw(true, true, false, false);                
                graphPml.outputGraph();
                pml.saveImage("test12","/home/filippis/Desktop", false);
                pml.getView("test3_view");

                // delete all edges
                pml.iterateList("edges", "edge");
                pml.delete("edge", true);
                
                graphPml.draw(false, true, false, false);
                graphPml.setUniformCgoEdgeSize(0.2);
                graphPml.setEdgeColorMethod("node", true);
                graphPml.outputGraph();
                pml.setView("test3_view");
                pml.saveImage("test13","/home/filippis/Desktop", false);
                
                // delete all edges
                pml.iterateList("edges", "edge");
                pml.delete("edge", true);
                                
                graphPml.setEdgeSizeMethod("SC_SC", false);
                graphPml.setEdgeColorMethod("BB_BB", false);
                graphPml.outputGraph();
                pml.setView("test3_view");
                pml.saveImage("test14","/home/filippis/Desktop", false);
                
                pml.iterateList("edges", "edge");
                pml.delete("edge", true);
                
                graphPml.setEdgeSizeMethod("SC_SC", true);
                graphPml.setEdgeColorMethod("BB_BB", true);
                graphPml.outputGraph();
                pml.setView("test3_view");
                pml.saveImage("test15","/home/filippis/Desktop", false);
                                
                pml.delete("all", false);
                pml.loadPDB(pdbFileName, "/project/StruPPi/ioannis/tmp");
                                
                //to check node method for edge coloring when nodeColor method not discretised
                graphPml.draw(true, true, false, false);
                graphPml.setUniformNodeSize(0.6);
                graphPml.setNodeColorMethod("BB_BB_out", false);
                graphPml.setUniformEdgeSize(0.4);
                graphPml.setEdgeColorMethod("node", true);
                graphPml.outputGraph();
                pml.setView("test3_view");
                pml.saveImage("test16","/home/filippis/Desktop", false);
                
                pml.delete("all", false);
                pml.loadPDB(pdbFileName, "/project/StruPPi/ioannis/tmp");
                
                //to check node method for edge coloring when nodeColor method not discretised
                graphPml.setUniformNodeSize(0.6);
                graphPml.setNodeColorMethod("BB_BB_out", true);
                graphPml.setUniformEdgeSize(0.4);
                graphPml.setEdgeColorMethod("node", true);
                graphPml.outputGraph();
                pml.setView("test3_view");
                pml.saveImage("test17","/home/filippis/Desktop", false);
                
                pml.delete("all", false);
                pml.loadPDB(pdbFileName, "/project/StruPPi/ioannis/tmp");
                
                //see "real" half-edges
                graphPml = new Graph2Pml(serverOutPw, molObjName, 35666, "SC_BB", "SC_BB_in+SC_BB_out", "SC_BB", "true", "true", true, true, true, conn);
                graphPml.outputGraph();
                pml.setView("test3_view");
                pml.saveImage("test18","/home/filippis/Desktop", false);                
                
                pml.delete("all", false);
                
                //test multi-chain macromolecule with RNA also
                pdbFileName = "1a0a_1107_2560.pdb";
                molObjName = pml.loadPDB(pdbFileName, "/project/StruPPi/ioannis/tmp");
                System.out.println(molObjName);
                
                graphPml = new Graph2Pml(serverOutPw, molObjName, 95, "SC_SC", "SC_SC_in+SC_SC_out", "SC_SC", "true", "true", true, true, true, conn);
                graphPml.draw(true, true, false, false);
                graphPml.setNodeColorMethod("SC_SC_out", false);
                graphPml.setNodeTransp(0);              
                graphPml.setEdgeSizeMethod("SC_SC", false);
                graphPml.setEdgeColorMethod("chain", true);
                graphPml.outputGraph();
                pml.saveImage("test19","/home/filippis/Desktop", false);
                
                pml.delete("all", false);
                
                pdbFileName = "1rx4_20717_52567.pdb";
                pml.loadPDB(pdbFileName, "/project/StruPPi/ioannis/tmp");
                
                graphPml = new Graph2Pml(serverOutPw, molObjName, 33729, "SC_SC", "SC_SC_in+SC_SC_out", "SC_SC", "true", "true", true, true, true, conn);
                graphPml.draw(true, true, false, false);
                graphPml.setNodeSizeMethod("SC_SC_out", false);
                graphPml.setNodeColorMethod("SC_SC_out", false);
                graphPml.setNodeTransp(0.6);            
                graphPml.setEdgeSizeMethod("SC_SC", false);
                graphPml.setEdgeColorMethod("SC_SC", false);
                graphPml.outputGraph();
                pml.saveImage("test20","/home/filippis/Desktop", false);
                
                SQLC.closeConnection(conn);     

    }

} // end of class testGraph2Pml
Revision:	47
Committed:	Mon Mar 27 21:01:06 2006 UTC (18 years, 6 months ago) by filippis
File size:	13533 byte(s)
Log Message:	Added cgo functionality/examples in Graph2Pml and testGraph2Pml
Line	User	Rev	File contents
1	filippis	42	import java.sql.*;
2			import java.io.*;
3			import tools.*;
4
5	filippis	45	/**
6			* Package: tools
7			* Class: testGraph2Pml
8			* Author: Ioannis Filippis, filippis@molgen.mpg.de
9			* Date: 21/03/2006
10			*
11			* Simple test class for visualizing contact graphs using Graph2Pml class plus
12			* PyMol class. Run PyMol with the -R option to run the server.
13			*
14			* Changelog:
15	filippis	47	* 27/03/06 modified by IF (functional with comments - added cgo examples)
16	filippis	45	* 21/03/06 first created by IF (non functional)
17			*/
18
19	filippis	42	public class testGraph2Pml {
20
21			public static void main(String[] args) {
22	filippis	45
23			String connFile = "/project/StruPPi/ioannis/cnfs/msdgraph.my.cnf", pdbFileName = "", molObjName = "";
24			Graph2Pml graphPml = null;
25			PyMol pml = null;
26
27	filippis	42	mySQLConnect SQLC = new mySQLConnect();
28			SQLC.readConnectionFile(connFile);
29			Connection conn = SQLC.openConnection();
30
31	filippis	45	//Create a new output stream to the pymol server running at the localhost
32			//all commands will be send there
33			PrintWriter serverOutPw = new PrintWriter(new PymolServerOutputStream("http://"+Machine.getClient()+":9123"), true);
34			pml = new PyMol(serverOutPw);
35
36	filippis	47	//Edges as lines
37	filippis	45	//export the pdb file directly from msdsd and load it in pymol
38			pdbFileName = Msdsd2Pdb.export2File("1rx4", 20717, 52567, 9, "/project/StruPPi/ioannis/tmp");
39			molObjName = pml.loadPDB(pdbFileName, "/project/StruPPi/ioannis/tmp");
40	filippis	42	System.out.println(molObjName);
41	filippis	45
42			//create a pymol contact graph object for the graph 33729
43			//use only SC_SC edges with SC_SC edge weight and nodes that have SC_SC edges
44			//no further filtering in the edges based on the contact range is applied
45			//no user based graph filtering is applied
46			//the graph comes from msdsd
47			//normal edges will be utilised
48			//the graph will not be visualised as "directed"
49			graphPml = new Graph2Pml(serverOutPw, molObjName, 33729, "SC_SC", "SC_SC_in+SC_SC_out", "SC_SC", "true", "true", true, false, false, conn);
50			//draw nodes, edges, special residues but not surface
51			//the node size will be calculated based on the SC_SC_out field on asc order
52			//the node color will be calculated based on the BB_BB_out field not discretised
53			//all ALA nodes will be transparent
54			//all residues that do not have any SC interactions will be the special ones colored green
55			//all edges will be lines of width determined by the SC_SC field in asc order
56			//all edges lines will have color calculated based on the BB_BB_out field not discretised
57			//all edges lines with adjacent ALA's will have gaps
58			graphPml.draw(true, true, true, false);
59			graphPml.setNodeSizeMethod("SC_SC_out", false);
60			graphPml.setNodeColorMethod("BB_BB_out", false);
61			graphPml.setNodeTranspCondition("(res = \"ALA\")");
62			graphPml.setSpecialRes("green", "SELECT cid, num FROM newmsdgraph.nodes WHERE (graph_id = 33729) AND (sc_sc_in+sc_sc_out = 0);");
63			graphPml.setEdgeSizeMethod("SC_SC", false);
64			graphPml.setEdgeColorMethod("BB_BB", false);
65			graphPml.setEdgeGapCondition("(i_res = \"ALA\" OR j_res = \"ALA\")");
66			//create the contact graph
67			graphPml.outputGraph();
68			//save the image not ray-traced
69			pml.saveImage("test1","/home/filippis/Desktop", false);
70			//if you want later to read the view from a log file
71			//pml.openLog("test1_log","/home/filippis/Desktop");
72			//get the view
73			pml.getView("test1_view");
74			//pml.closeLog();
75
76			// delete all and reload the structure
77			pml.delete("all", false);
78			pml.loadPDB(pdbFileName, "/project/StruPPi/ioannis/tmp");
79
80			//to check reversibility in setNodeSizeMethod, setEdgeSizeMethod
81			//and discretised coloring in setNodeColorMethod, setEdgeColorMethod
82			graphPml.setNodeSizeMethod("SC_SC_out", true);
83			graphPml.setNodeColorMethod("BB_BB_out", true);
84			graphPml.setEdgeSizeMethod("SC_SC", true);
85			graphPml.setEdgeColorMethod("BB_BB", true);
86			graphPml.outputGraph();
87			//set view by reading a log file
88			//pml.getFileView("test2_view", "/home/filippis/Desktop/test1_log.pml");
89			//pml.setView("test2_view");
90			//set view based on the view of the first structure so that you can compare
91			//different graphs for the same structure
92			pml.setView("test1_view");
93			pml.saveImage("test2","/home/filippis/Desktop", false);
94
95			pml.delete("all", false);
96			pml.loadPDB(pdbFileName, "/project/StruPPi/ioannis/tmp");
97
98			//to check node method for edge coloring when nodeColor method not discretised
99			graphPml.setUniformNodeSize(0.6);
100			graphPml.setNodeColorMethod("BB_BB_out", false);
101			graphPml.setUniformEdgeSize(4);
102			graphPml.setEdgeColorMethod("node", true);
103			graphPml.outputGraph();
104			pml.setView("test1_view");
105			pml.saveImage("test3","/home/filippis/Desktop", false);
106
107			pml.delete("all", false);
108			pml.loadPDB(pdbFileName, "/project/StruPPi/ioannis/tmp");
109
110			//to check node method for edge coloring when nodeColor method is discretised
111			graphPml.setUniformNodeSize(0.6);
112			graphPml.setNodeColorMethod("BB_BB_out", true);
113			graphPml.setUniformEdgeSize(4);
114			graphPml.setEdgeColorMethod("node", true);
115			graphPml.outputGraph();
116			pml.setView("test1_view");
117			pml.saveImage("test4","/home/filippis/Desktop", false);
118
119			pml.delete("all", false);
120			pml.loadPDB(pdbFileName, "/project/StruPPi/ioannis/tmp");
121
122			//to check node method for edge coloring when nodeColor method is uniform
123			graphPml.setUniformNodeSize(0.6);
124			graphPml.setUniformNodeColor("blue");
125			graphPml.setUniformEdgeSize(4);
126			graphPml.setEdgeColorMethod("node", true);
127			graphPml.outputGraph();
128			pml.setView("test1_view");
129			pml.saveImage("test5","/home/filippis/Desktop", false);
130
131			pml.delete("all", false);
132			pml.loadPDB(pdbFileName, "/project/StruPPi/ioannis/tmp");
133
134			//to check the trick of directionality with gapped lines for "half" edges
135			//for this purpose a SC_BB graph model is used that doesn't ensure bidirectionality
136			graphPml = new Graph2Pml(serverOutPw, molObjName, 33729, "SC_BB", "SC_BB_in+SC_BB_out", "SC_BB", "true", "true", true, false, true, conn);
137			graphPml.outputGraph();
138			pml.setView("test1_view");
139			pml.saveImage("test6","/home/filippis/Desktop", false);
140
141
142			pml.delete("all", false);
143
144			//test multi-chain macromolecule with RNA also
145			pdbFileName = Msdsd2Pdb.export2File("1a0a", 1107, 2560, 1, "/project/StruPPi/ioannis/tmp");
146			molObjName = pml.loadPDB(pdbFileName, "/project/StruPPi/ioannis/tmp");
147			System.out.println(molObjName);
148
149			graphPml = new Graph2Pml(serverOutPw, molObjName, 95, "SC_SC", "SC_SC_in+SC_SC_out", "SC_SC", "true", "true", true, false, false, conn);
150			graphPml.draw(true, true, false, false);
151			//color nodes based on the chains they belong to
152			graphPml.setNodeColorMethod("chain", true);
153			graphPml.setNodeTransp(0.2);
154			graphPml.setUniformEdgeColor("red");
155			graphPml.setUniformEdgeSize(4.5);
156			graphPml.setEdgeGap(0.5);
157			graphPml.outputGraph();
158			pml.saveImage("test7","/home/filippis/Desktop", false);
159			pml.getView("test2_view");
160
161			pml.delete("all", false);
162			pml.loadPDB(pdbFileName, "/project/StruPPi/ioannis/tmp");
163
164			//color edges based on the chains they belong to
165			graphPml.draw(true, true, false, false);
166			graphPml.setUniformNodeColor("red");
167			graphPml.setEdgeColorMethod("chain", true);
168			graphPml.outputGraph();
169			pml.setView("test2_view");
170			pml.saveImage("test8","/home/filippis/Desktop", false);
171
172			pml.delete("all", false);
173			pml.loadPDB(pdbFileName, "/project/StruPPi/ioannis/tmp");
174
175			//to check node method for edge coloring when nodeColor method is based on chain coloring
176			graphPml.setNodeColorMethod("chain", true);
177			graphPml.setEdgeColorMethod("node", true);
178			graphPml.outputGraph();
179			pml.setView("test2_view");
180			pml.saveImage("test9","/home/filippis/Desktop", false);
181
182			pml.delete("all", false);
183			pml.loadPDB(pdbFileName, "/project/StruPPi/ioannis/tmp");
184
185			//draw also surface - you can not see the graph anymore
186			graphPml.draw(true, true, false, true);
187			graphPml.setSurfTransp(0.7);
188			graphPml.outputGraph();
189			pml.setView("test2_view");
190			pml.saveImage("test10","/home/filippis/Desktop", false);
191
192			try { Thread.sleep(10000); } catch (Exception e) {}
193
194			//hide the surface, show the RNA also
195			//change the color of the nodes for each chain using the pymol defined list of nodes for each chain
196			pml.hideWhat("surface", "graphMol", false);
197			pml.showWhat("lines", "restMol", false);
198			graphPml.setNodesColorUniform("nodes_cidA","red");
199			graphPml.setNodesColorUniform("nodes_cidA","yellow");
200
201			try { Thread.sleep(10000); } catch (Exception e) {}
202
203			//if you believe that the objects contained in the list won't exceed the pymol command length limit,
204			//you can concatenate all objects as a single string selection and handle them all together
205			pml.concatList("nodes", "+", "nodesStr");
206			pml.setNodeColor("blue", "nodesStr", true);
207			pml.selPml("nodes", "nodesStr", true, true);
208
209			pml.delete("all", false);
210			pml.loadPDB(pdbFileName, "/project/StruPPi/ioannis/tmp");
211
212			//check a graph model with only inter-secondary-structure-elements SC_SC edges
213			//remember that all the nodes with SC_SC will be selected
214			//use default behaviour
215			graphPml = new Graph2Pml(serverOutPw, molObjName, 95, "SC_SC", "SC_SC_in+SC_SC_out", "SC_SC", "(!((i_ssid = j_ssid) AND (i_sstype = j_sstype)))", "true", true, false, false, conn);
216			graphPml.draw(true, true, false, false);
217			graphPml.outputGraph();
218			pml.setView("test2_view");
219			pml.saveImage("test11","/home/filippis/Desktop", false);
220
221			pml.delete("all", false);
222
223	filippis	47	//CGO EDGES SECTION
224			pdbFileName = Msdsd2Pdb.export2File("1kj0", 21698, 55132, 9, "/project/StruPPi/ioannis/tmp");
225			molObjName = pml.loadPDB(pdbFileName, "/project/StruPPi/ioannis/tmp");
226
227			//Cgo makes sense to be used with directed graph
228			graphPml = new Graph2Pml(serverOutPw, molObjName, 35666, "SC_SC", "SC_SC_in+SC_SC_out", "SC_SC", "true", "true", true, true, true, conn);
229			graphPml.draw(true, true, false, false);
230			graphPml.outputGraph();
231			pml.saveImage("test12","/home/filippis/Desktop", false);
232			pml.getView("test3_view");
233
234			// delete all edges
235			pml.iterateList("edges", "edge");
236			pml.delete("edge", true);
237
238			graphPml.draw(false, true, false, false);
239			graphPml.setUniformCgoEdgeSize(0.2);
240			graphPml.setEdgeColorMethod("node", true);
241			graphPml.outputGraph();
242			pml.setView("test3_view");
243			pml.saveImage("test13","/home/filippis/Desktop", false);
244
245			// delete all edges
246			pml.iterateList("edges", "edge");
247			pml.delete("edge", true);
248
249			graphPml.setEdgeSizeMethod("SC_SC", false);
250			graphPml.setEdgeColorMethod("BB_BB", false);
251			graphPml.outputGraph();
252			pml.setView("test3_view");
253			pml.saveImage("test14","/home/filippis/Desktop", false);
254
255			pml.iterateList("edges", "edge");
256			pml.delete("edge", true);
257
258			graphPml.setEdgeSizeMethod("SC_SC", true);
259			graphPml.setEdgeColorMethod("BB_BB", true);
260			graphPml.outputGraph();
261			pml.setView("test3_view");
262			pml.saveImage("test15","/home/filippis/Desktop", false);
263
264			pml.delete("all", false);
265			pml.loadPDB(pdbFileName, "/project/StruPPi/ioannis/tmp");
266
267			//to check node method for edge coloring when nodeColor method not discretised
268			graphPml.draw(true, true, false, false);
269			graphPml.setUniformNodeSize(0.6);
270			graphPml.setNodeColorMethod("BB_BB_out", false);
271			graphPml.setUniformEdgeSize(0.4);
272			graphPml.setEdgeColorMethod("node", true);
273			graphPml.outputGraph();
274			pml.setView("test3_view");
275			pml.saveImage("test16","/home/filippis/Desktop", false);
276
277			pml.delete("all", false);
278			pml.loadPDB(pdbFileName, "/project/StruPPi/ioannis/tmp");
279
280			//to check node method for edge coloring when nodeColor method not discretised
281			graphPml.setUniformNodeSize(0.6);
282			graphPml.setNodeColorMethod("BB_BB_out", true);
283			graphPml.setUniformEdgeSize(0.4);
284			graphPml.setEdgeColorMethod("node", true);
285			graphPml.outputGraph();
286			pml.setView("test3_view");
287			pml.saveImage("test17","/home/filippis/Desktop", false);
288
289			pml.delete("all", false);
290			pml.loadPDB(pdbFileName, "/project/StruPPi/ioannis/tmp");
291
292			//see "real" half-edges
293			graphPml = new Graph2Pml(serverOutPw, molObjName, 35666, "SC_BB", "SC_BB_in+SC_BB_out", "SC_BB", "true", "true", true, true, true, conn);
294			graphPml.outputGraph();
295			pml.setView("test3_view");
296			pml.saveImage("test18","/home/filippis/Desktop", false);
297
298			pml.delete("all", false);
299
300			//test multi-chain macromolecule with RNA also
301			pdbFileName = "1a0a_1107_2560.pdb";
302			molObjName = pml.loadPDB(pdbFileName, "/project/StruPPi/ioannis/tmp");
303			System.out.println(molObjName);
304
305			graphPml = new Graph2Pml(serverOutPw, molObjName, 95, "SC_SC", "SC_SC_in+SC_SC_out", "SC_SC", "true", "true", true, true, true, conn);
306			graphPml.draw(true, true, false, false);
307			graphPml.setNodeColorMethod("SC_SC_out", false);
308			graphPml.setNodeTransp(0);
309			graphPml.setEdgeSizeMethod("SC_SC", false);
310			graphPml.setEdgeColorMethod("chain", true);
311			graphPml.outputGraph();
312			pml.saveImage("test19","/home/filippis/Desktop", false);
313
314			pml.delete("all", false);
315
316			pdbFileName = "1rx4_20717_52567.pdb";
317			pml.loadPDB(pdbFileName, "/project/StruPPi/ioannis/tmp");
318
319			graphPml = new Graph2Pml(serverOutPw, molObjName, 33729, "SC_SC", "SC_SC_in+SC_SC_out", "SC_SC", "true", "true", true, true, true, conn);
320			graphPml.draw(true, true, false, false);
321			graphPml.setNodeSizeMethod("SC_SC_out", false);
322			graphPml.setNodeColorMethod("SC_SC_out", false);
323			graphPml.setNodeTransp(0.6);
324			graphPml.setEdgeSizeMethod("SC_SC", false);
325			graphPml.setEdgeColorMethod("SC_SC", false);
326			graphPml.outputGraph();
327			pml.saveImage("test20","/home/filippis/Desktop", false);
328
329	filippis	42	SQLC.closeConnection(conn);
330
331			}
332
333	filippis	45	} // end of class testGraph2Pml