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.
 * 
 * Notes:
 * - You can find the results from all examples here in 
 *   /project/StruPPi/ioannis/workspace/aglappe/vis_examples/
 * 
 * Changelog:
 * 28/03/06 modified by IF (more examples added)
 * 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);

                pml.openLog("test", "/home/filippis/Desktop");
                
                //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);
                
                // delete all and reload the structure
                pml.delete("all", false);
                pml.loadPDB(pdbFileName, "/project/StruPPi/ioannis/tmp");
                
                //just check user defined set/discretised colors
                //all green nodes must become red
                graphPml.setNodeColors(new String[] {"red", "magenta", "orange", "chocolate"});
                //switched red-green, yellow-blue
                graphPml.setEdgeColors(new String[] {"red", "green", "yellow", "blue", "violet", "cyan", "salmon", "lime", "pink", "slate", "magenta", "orange", "marine", "olive", "purple", "teal", "forest", "firebrick", "chocolate", "wheat", "white", "grey"});
            graphPml.outputGraph();
                pml.setView("test1_view");
                pml.saveImage("test2a","/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.setChainNodeColor();
                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.setChainEdgeColor();
                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
                //also check the user defined chain colors for nodes
                graphPml.setChainNodeColor(new String[] {"blue"});
                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.setChainEdgeColor(new String[] {"yellow","red"});
                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);
                
                pml.delete("all", false);
                pdbFileName = "1kj0_21698_55132.pdb";
                pml.loadPDB(pdbFileName, "/project/StruPPi/ioannis/tmp");
                
                //check the setNodeSizeRange method
                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, false, false, false);
                graphPml.setChainColors(new String[] {"red"});
                graphPml.setNodeSizeMethod("SC_SC_out", false);
                graphPml.setNodeSizeRange(new double[] {0.6, 1.2});
                graphPml.outputGraph();
                pml.saveImage("test21","/home/filippis/Desktop", false);
                
                pml.delete("all", false);
                pdbFileName = "1kj0_21698_55132.pdb";
                pml.loadPDB(pdbFileName, "/project/StruPPi/ioannis/tmp");
                
                //check the setDefaults method
                graphPml.setDefaults(new String[] {"nodeSizeRange", "chainColors"});
                graphPml.outputGraph();
                pml.saveImage("test22","/home/filippis/Desktop", false);
                
                pml.closeLog();
                
                SQLC.closeConnection(conn);     

    }

} // end of class testGraph2Pml
Revision:	50
Committed:	Tue Mar 28 15:05:31 2006 UTC (18 years, 6 months ago) by filippis
File size:	15457 byte(s)
Log Message:	More examples added and the current ones modified according to Graph2Pml changes
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	filippis	50	* Notes:
15			* - You can find the results from all examples here in
16			* /project/StruPPi/ioannis/workspace/aglappe/vis_examples/
17			*
18	filippis	45	* Changelog:
19	filippis	50	* 28/03/06 modified by IF (more examples added)
20	filippis	47	* 27/03/06 modified by IF (functional with comments - added cgo examples)
21	filippis	45	* 21/03/06 first created by IF (non functional)
22			*/
23
24	filippis	42	public class testGraph2Pml {
25
26			public static void main(String[] args) {
27	filippis	45
28			String connFile = "/project/StruPPi/ioannis/cnfs/msdgraph.my.cnf", pdbFileName = "", molObjName = "";
29			Graph2Pml graphPml = null;
30			PyMol pml = null;
31
32	filippis	42	mySQLConnect SQLC = new mySQLConnect();
33			SQLC.readConnectionFile(connFile);
34			Connection conn = SQLC.openConnection();
35
36	filippis	45	//Create a new output stream to the pymol server running at the localhost
37			//all commands will be send there
38			PrintWriter serverOutPw = new PrintWriter(new PymolServerOutputStream("http://"+Machine.getClient()+":9123"), true);
39			pml = new PyMol(serverOutPw);
40	filippis	50
41			pml.openLog("test", "/home/filippis/Desktop");
42	filippis	45
43	filippis	47	//Edges as lines
44	filippis	45	//export the pdb file directly from msdsd and load it in pymol
45			pdbFileName = Msdsd2Pdb.export2File("1rx4", 20717, 52567, 9, "/project/StruPPi/ioannis/tmp");
46			molObjName = pml.loadPDB(pdbFileName, "/project/StruPPi/ioannis/tmp");
47	filippis	42	System.out.println(molObjName);
48	filippis	45
49			//create a pymol contact graph object for the graph 33729
50			//use only SC_SC edges with SC_SC edge weight and nodes that have SC_SC edges
51			//no further filtering in the edges based on the contact range is applied
52			//no user based graph filtering is applied
53			//the graph comes from msdsd
54			//normal edges will be utilised
55			//the graph will not be visualised as "directed"
56			graphPml = new Graph2Pml(serverOutPw, molObjName, 33729, "SC_SC", "SC_SC_in+SC_SC_out", "SC_SC", "true", "true", true, false, false, conn);
57			//draw nodes, edges, special residues but not surface
58			//the node size will be calculated based on the SC_SC_out field on asc order
59			//the node color will be calculated based on the BB_BB_out field not discretised
60			//all ALA nodes will be transparent
61			//all residues that do not have any SC interactions will be the special ones colored green
62			//all edges will be lines of width determined by the SC_SC field in asc order
63			//all edges lines will have color calculated based on the BB_BB_out field not discretised
64			//all edges lines with adjacent ALA's will have gaps
65			graphPml.draw(true, true, true, false);
66			graphPml.setNodeSizeMethod("SC_SC_out", false);
67			graphPml.setNodeColorMethod("BB_BB_out", false);
68			graphPml.setNodeTranspCondition("(res = \"ALA\")");
69			graphPml.setSpecialRes("green", "SELECT cid, num FROM newmsdgraph.nodes WHERE (graph_id = 33729) AND (sc_sc_in+sc_sc_out = 0);");
70			graphPml.setEdgeSizeMethod("SC_SC", false);
71			graphPml.setEdgeColorMethod("BB_BB", false);
72			graphPml.setEdgeGapCondition("(i_res = \"ALA\" OR j_res = \"ALA\")");
73			//create the contact graph
74			graphPml.outputGraph();
75			//save the image not ray-traced
76	filippis	50	pml.saveImage("test1", "/home/filippis/Desktop", false);
77	filippis	45	//if you want later to read the view from a log file
78			//pml.openLog("test1_log","/home/filippis/Desktop");
79			//get the view
80			pml.getView("test1_view");
81			//pml.closeLog();
82
83			// delete all and reload the structure
84			pml.delete("all", false);
85			pml.loadPDB(pdbFileName, "/project/StruPPi/ioannis/tmp");
86
87			//to check reversibility in setNodeSizeMethod, setEdgeSizeMethod
88			//and discretised coloring in setNodeColorMethod, setEdgeColorMethod
89			graphPml.setNodeSizeMethod("SC_SC_out", true);
90			graphPml.setNodeColorMethod("BB_BB_out", true);
91			graphPml.setEdgeSizeMethod("SC_SC", true);
92			graphPml.setEdgeColorMethod("BB_BB", true);
93			graphPml.outputGraph();
94			//set view by reading a log file
95			//pml.getFileView("test2_view", "/home/filippis/Desktop/test1_log.pml");
96			//pml.setView("test2_view");
97			//set view based on the view of the first structure so that you can compare
98			//different graphs for the same structure
99			pml.setView("test1_view");
100			pml.saveImage("test2","/home/filippis/Desktop", false);
101
102	filippis	50	// delete all and reload the structure
103	filippis	45	pml.delete("all", false);
104			pml.loadPDB(pdbFileName, "/project/StruPPi/ioannis/tmp");
105
106	filippis	50	//just check user defined set/discretised colors
107			//all green nodes must become red
108			graphPml.setNodeColors(new String[] {"red", "magenta", "orange", "chocolate"});
109			//switched red-green, yellow-blue
110			graphPml.setEdgeColors(new String[] {"red", "green", "yellow", "blue", "violet", "cyan", "salmon", "lime", "pink", "slate", "magenta", "orange", "marine", "olive", "purple", "teal", "forest", "firebrick", "chocolate", "wheat", "white", "grey"});
111			graphPml.outputGraph();
112			pml.setView("test1_view");
113			pml.saveImage("test2a","/home/filippis/Desktop", false);
114
115			pml.delete("all", false);
116			pml.loadPDB(pdbFileName, "/project/StruPPi/ioannis/tmp");
117
118	filippis	45	//to check node method for edge coloring when nodeColor method not discretised
119			graphPml.setUniformNodeSize(0.6);
120			graphPml.setNodeColorMethod("BB_BB_out", false);
121			graphPml.setUniformEdgeSize(4);
122			graphPml.setEdgeColorMethod("node", true);
123			graphPml.outputGraph();
124			pml.setView("test1_view");
125			pml.saveImage("test3","/home/filippis/Desktop", false);
126
127			pml.delete("all", false);
128			pml.loadPDB(pdbFileName, "/project/StruPPi/ioannis/tmp");
129
130			//to check node method for edge coloring when nodeColor method is discretised
131			graphPml.setUniformNodeSize(0.6);
132			graphPml.setNodeColorMethod("BB_BB_out", true);
133			graphPml.setUniformEdgeSize(4);
134			graphPml.setEdgeColorMethod("node", true);
135			graphPml.outputGraph();
136			pml.setView("test1_view");
137			pml.saveImage("test4","/home/filippis/Desktop", false);
138
139			pml.delete("all", false);
140			pml.loadPDB(pdbFileName, "/project/StruPPi/ioannis/tmp");
141
142			//to check node method for edge coloring when nodeColor method is uniform
143			graphPml.setUniformNodeSize(0.6);
144			graphPml.setUniformNodeColor("blue");
145			graphPml.setUniformEdgeSize(4);
146			graphPml.setEdgeColorMethod("node", true);
147			graphPml.outputGraph();
148			pml.setView("test1_view");
149			pml.saveImage("test5","/home/filippis/Desktop", false);
150
151			pml.delete("all", false);
152			pml.loadPDB(pdbFileName, "/project/StruPPi/ioannis/tmp");
153
154			//to check the trick of directionality with gapped lines for "half" edges
155			//for this purpose a SC_BB graph model is used that doesn't ensure bidirectionality
156			graphPml = new Graph2Pml(serverOutPw, molObjName, 33729, "SC_BB", "SC_BB_in+SC_BB_out", "SC_BB", "true", "true", true, false, true, conn);
157			graphPml.outputGraph();
158			pml.setView("test1_view");
159			pml.saveImage("test6","/home/filippis/Desktop", false);
160
161
162			pml.delete("all", false);
163
164			//test multi-chain macromolecule with RNA also
165			pdbFileName = Msdsd2Pdb.export2File("1a0a", 1107, 2560, 1, "/project/StruPPi/ioannis/tmp");
166			molObjName = pml.loadPDB(pdbFileName, "/project/StruPPi/ioannis/tmp");
167			System.out.println(molObjName);
168
169			graphPml = new Graph2Pml(serverOutPw, molObjName, 95, "SC_SC", "SC_SC_in+SC_SC_out", "SC_SC", "true", "true", true, false, false, conn);
170			graphPml.draw(true, true, false, false);
171			//color nodes based on the chains they belong to
172	filippis	50	graphPml.setChainNodeColor();
173	filippis	45	graphPml.setNodeTransp(0.2);
174			graphPml.setUniformEdgeColor("red");
175			graphPml.setUniformEdgeSize(4.5);
176			graphPml.setEdgeGap(0.5);
177			graphPml.outputGraph();
178			pml.saveImage("test7","/home/filippis/Desktop", false);
179			pml.getView("test2_view");
180
181			pml.delete("all", false);
182			pml.loadPDB(pdbFileName, "/project/StruPPi/ioannis/tmp");
183
184			//color edges based on the chains they belong to
185			graphPml.draw(true, true, false, false);
186			graphPml.setUniformNodeColor("red");
187	filippis	50	graphPml.setChainEdgeColor();
188	filippis	45	graphPml.outputGraph();
189			pml.setView("test2_view");
190			pml.saveImage("test8","/home/filippis/Desktop", false);
191
192			pml.delete("all", false);
193			pml.loadPDB(pdbFileName, "/project/StruPPi/ioannis/tmp");
194
195	filippis	50	//to check node method for edge coloring when nodeColor method is based on chain coloring
196			//also check the user defined chain colors for nodes
197			graphPml.setChainNodeColor(new String[] {"blue"});
198	filippis	45	graphPml.setEdgeColorMethod("node", true);
199			graphPml.outputGraph();
200			pml.setView("test2_view");
201			pml.saveImage("test9","/home/filippis/Desktop", false);
202
203			pml.delete("all", false);
204			pml.loadPDB(pdbFileName, "/project/StruPPi/ioannis/tmp");
205
206			//draw also surface - you can not see the graph anymore
207			graphPml.draw(true, true, false, true);
208			graphPml.setSurfTransp(0.7);
209			graphPml.outputGraph();
210			pml.setView("test2_view");
211			pml.saveImage("test10","/home/filippis/Desktop", false);
212
213			try { Thread.sleep(10000); } catch (Exception e) {}
214
215			//hide the surface, show the RNA also
216			//change the color of the nodes for each chain using the pymol defined list of nodes for each chain
217			pml.hideWhat("surface", "graphMol", false);
218			pml.showWhat("lines", "restMol", false);
219			graphPml.setNodesColorUniform("nodes_cidA","red");
220			graphPml.setNodesColorUniform("nodes_cidA","yellow");
221
222			try { Thread.sleep(10000); } catch (Exception e) {}
223
224			//if you believe that the objects contained in the list won't exceed the pymol command length limit,
225			//you can concatenate all objects as a single string selection and handle them all together
226			pml.concatList("nodes", "+", "nodesStr");
227			pml.setNodeColor("blue", "nodesStr", true);
228			pml.selPml("nodes", "nodesStr", true, true);
229
230			pml.delete("all", false);
231			pml.loadPDB(pdbFileName, "/project/StruPPi/ioannis/tmp");
232
233			//check a graph model with only inter-secondary-structure-elements SC_SC edges
234			//remember that all the nodes with SC_SC will be selected
235			//use default behaviour
236			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);
237			graphPml.draw(true, true, false, false);
238			graphPml.outputGraph();
239			pml.setView("test2_view");
240			pml.saveImage("test11","/home/filippis/Desktop", false);
241
242			pml.delete("all", false);
243
244	filippis	47	//CGO EDGES SECTION
245			pdbFileName = Msdsd2Pdb.export2File("1kj0", 21698, 55132, 9, "/project/StruPPi/ioannis/tmp");
246			molObjName = pml.loadPDB(pdbFileName, "/project/StruPPi/ioannis/tmp");
247
248			//Cgo makes sense to be used with directed graph
249			graphPml = new Graph2Pml(serverOutPw, molObjName, 35666, "SC_SC", "SC_SC_in+SC_SC_out", "SC_SC", "true", "true", true, true, true, conn);
250			graphPml.draw(true, true, false, false);
251			graphPml.outputGraph();
252			pml.saveImage("test12","/home/filippis/Desktop", false);
253			pml.getView("test3_view");
254
255			// delete all edges
256			pml.iterateList("edges", "edge");
257			pml.delete("edge", true);
258
259			graphPml.draw(false, true, false, false);
260			graphPml.setUniformCgoEdgeSize(0.2);
261			graphPml.setEdgeColorMethod("node", true);
262			graphPml.outputGraph();
263			pml.setView("test3_view");
264			pml.saveImage("test13","/home/filippis/Desktop", false);
265
266			// delete all edges
267			pml.iterateList("edges", "edge");
268			pml.delete("edge", true);
269
270			graphPml.setEdgeSizeMethod("SC_SC", false);
271			graphPml.setEdgeColorMethod("BB_BB", false);
272			graphPml.outputGraph();
273			pml.setView("test3_view");
274			pml.saveImage("test14","/home/filippis/Desktop", false);
275
276			pml.iterateList("edges", "edge");
277			pml.delete("edge", true);
278
279			graphPml.setEdgeSizeMethod("SC_SC", true);
280			graphPml.setEdgeColorMethod("BB_BB", true);
281			graphPml.outputGraph();
282			pml.setView("test3_view");
283			pml.saveImage("test15","/home/filippis/Desktop", false);
284
285			pml.delete("all", false);
286			pml.loadPDB(pdbFileName, "/project/StruPPi/ioannis/tmp");
287
288			//to check node method for edge coloring when nodeColor method not discretised
289			graphPml.draw(true, true, false, false);
290			graphPml.setUniformNodeSize(0.6);
291			graphPml.setNodeColorMethod("BB_BB_out", false);
292			graphPml.setUniformEdgeSize(0.4);
293			graphPml.setEdgeColorMethod("node", true);
294			graphPml.outputGraph();
295			pml.setView("test3_view");
296			pml.saveImage("test16","/home/filippis/Desktop", false);
297
298			pml.delete("all", false);
299			pml.loadPDB(pdbFileName, "/project/StruPPi/ioannis/tmp");
300
301			//to check node method for edge coloring when nodeColor method not discretised
302			graphPml.setUniformNodeSize(0.6);
303			graphPml.setNodeColorMethod("BB_BB_out", true);
304			graphPml.setUniformEdgeSize(0.4);
305			graphPml.setEdgeColorMethod("node", true);
306			graphPml.outputGraph();
307			pml.setView("test3_view");
308			pml.saveImage("test17","/home/filippis/Desktop", false);
309
310			pml.delete("all", false);
311			pml.loadPDB(pdbFileName, "/project/StruPPi/ioannis/tmp");
312
313			//see "real" half-edges
314			graphPml = new Graph2Pml(serverOutPw, molObjName, 35666, "SC_BB", "SC_BB_in+SC_BB_out", "SC_BB", "true", "true", true, true, true, conn);
315			graphPml.outputGraph();
316			pml.setView("test3_view");
317			pml.saveImage("test18","/home/filippis/Desktop", false);
318
319			pml.delete("all", false);
320
321			//test multi-chain macromolecule with RNA also
322			pdbFileName = "1a0a_1107_2560.pdb";
323			molObjName = pml.loadPDB(pdbFileName, "/project/StruPPi/ioannis/tmp");
324			System.out.println(molObjName);
325
326			graphPml = new Graph2Pml(serverOutPw, molObjName, 95, "SC_SC", "SC_SC_in+SC_SC_out", "SC_SC", "true", "true", true, true, true, conn);
327			graphPml.draw(true, true, false, false);
328			graphPml.setNodeColorMethod("SC_SC_out", false);
329			graphPml.setNodeTransp(0);
330			graphPml.setEdgeSizeMethod("SC_SC", false);
331	filippis	50	graphPml.setChainEdgeColor(new String[] {"yellow","red"});
332	filippis	47	graphPml.outputGraph();
333			pml.saveImage("test19","/home/filippis/Desktop", false);
334
335			pml.delete("all", false);
336
337			pdbFileName = "1rx4_20717_52567.pdb";
338			pml.loadPDB(pdbFileName, "/project/StruPPi/ioannis/tmp");
339
340			graphPml = new Graph2Pml(serverOutPw, molObjName, 33729, "SC_SC", "SC_SC_in+SC_SC_out", "SC_SC", "true", "true", true, true, true, conn);
341			graphPml.draw(true, true, false, false);
342			graphPml.setNodeSizeMethod("SC_SC_out", false);
343			graphPml.setNodeColorMethod("SC_SC_out", false);
344			graphPml.setNodeTransp(0.6);
345			graphPml.setEdgeSizeMethod("SC_SC", false);
346			graphPml.setEdgeColorMethod("SC_SC", false);
347			graphPml.outputGraph();
348			pml.saveImage("test20","/home/filippis/Desktop", false);
349
350	filippis	50	pml.delete("all", false);
351			pdbFileName = "1kj0_21698_55132.pdb";
352			pml.loadPDB(pdbFileName, "/project/StruPPi/ioannis/tmp");
353
354			//check the setNodeSizeRange method
355			graphPml = new Graph2Pml(serverOutPw, molObjName, 35666, "SC_SC", "SC_SC_in+SC_SC_out", "SC_SC", "true", "true", true, true, true, conn);
356			graphPml.draw(true, false, false, false);
357			graphPml.setChainColors(new String[] {"red"});
358			graphPml.setNodeSizeMethod("SC_SC_out", false);
359			graphPml.setNodeSizeRange(new double[] {0.6, 1.2});
360			graphPml.outputGraph();
361			pml.saveImage("test21","/home/filippis/Desktop", false);
362
363			pml.delete("all", false);
364			pdbFileName = "1kj0_21698_55132.pdb";
365			pml.loadPDB(pdbFileName, "/project/StruPPi/ioannis/tmp");
366
367			//check the setDefaults method
368			graphPml.setDefaults(new String[] {"nodeSizeRange", "chainColors"});
369			graphPml.outputGraph();
370			pml.saveImage("test22","/home/filippis/Desktop", false);
371
372			pml.closeLog();
373
374	filippis	42	SQLC.closeConnection(conn);
375
376			}
377
378	filippis	45	} // end of class testGraph2Pml