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)
 * 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);
                
                //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);
                
                SQLC.closeConnection(conn);     

    }

} // end of class testGraph2Pml
Revision:	45
Committed:	Mon Mar 27 16:32:22 2006 UTC (18 years, 11 months ago) by filippis
File size:	9400 byte(s)
Log Message:	Graph2Pymol class now functional testGraph2Pymol class now functional with comments also PyMol class:python strings methods and removeList, concatList, refresh methods added Machine class: indentation
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			* 27/03/06 modified by IF (functional with comments)
16			* 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			//export the pdb file directly from msdsd and load it in pymol
37			pdbFileName = Msdsd2Pdb.export2File("1rx4", 20717, 52567, 9, "/project/StruPPi/ioannis/tmp");
38			molObjName = pml.loadPDB(pdbFileName, "/project/StruPPi/ioannis/tmp");
39	filippis	42	System.out.println(molObjName);
40	filippis	45
41			//create a pymol contact graph object for the graph 33729
42			//use only SC_SC edges with SC_SC edge weight and nodes that have SC_SC edges
43			//no further filtering in the edges based on the contact range is applied
44			//no user based graph filtering is applied
45			//the graph comes from msdsd
46			//normal edges will be utilised
47			//the graph will not be visualised as "directed"
48			graphPml = new Graph2Pml(serverOutPw, molObjName, 33729, "SC_SC", "SC_SC_in+SC_SC_out", "SC_SC", "true", "true", true, false, false, conn);
49			//draw nodes, edges, special residues but not surface
50			//the node size will be calculated based on the SC_SC_out field on asc order
51			//the node color will be calculated based on the BB_BB_out field not discretised
52			//all ALA nodes will be transparent
53			//all residues that do not have any SC interactions will be the special ones colored green
54			//all edges will be lines of width determined by the SC_SC field in asc order
55			//all edges lines will have color calculated based on the BB_BB_out field not discretised
56			//all edges lines with adjacent ALA's will have gaps
57			graphPml.draw(true, true, true, false);
58			graphPml.setNodeSizeMethod("SC_SC_out", false);
59			graphPml.setNodeColorMethod("BB_BB_out", false);
60			graphPml.setNodeTranspCondition("(res = \"ALA\")");
61			graphPml.setSpecialRes("green", "SELECT cid, num FROM newmsdgraph.nodes WHERE (graph_id = 33729) AND (sc_sc_in+sc_sc_out = 0);");
62			graphPml.setEdgeSizeMethod("SC_SC", false);
63			graphPml.setEdgeColorMethod("BB_BB", false);
64			graphPml.setEdgeGapCondition("(i_res = \"ALA\" OR j_res = \"ALA\")");
65			//create the contact graph
66			graphPml.outputGraph();
67			//save the image not ray-traced
68			pml.saveImage("test1","/home/filippis/Desktop", false);
69			//if you want later to read the view from a log file
70			//pml.openLog("test1_log","/home/filippis/Desktop");
71			//get the view
72			pml.getView("test1_view");
73			//pml.closeLog();
74
75			// delete all and reload the structure
76			pml.delete("all", false);
77			pml.loadPDB(pdbFileName, "/project/StruPPi/ioannis/tmp");
78
79			//to check reversibility in setNodeSizeMethod, setEdgeSizeMethod
80			//and discretised coloring in setNodeColorMethod, setEdgeColorMethod
81			graphPml.setNodeSizeMethod("SC_SC_out", true);
82			graphPml.setNodeColorMethod("BB_BB_out", true);
83			graphPml.setEdgeSizeMethod("SC_SC", true);
84			graphPml.setEdgeColorMethod("BB_BB", true);
85			graphPml.outputGraph();
86			//set view by reading a log file
87			//pml.getFileView("test2_view", "/home/filippis/Desktop/test1_log.pml");
88			//pml.setView("test2_view");
89			//set view based on the view of the first structure so that you can compare
90			//different graphs for the same structure
91			pml.setView("test1_view");
92			pml.saveImage("test2","/home/filippis/Desktop", false);
93
94			pml.delete("all", false);
95			pml.loadPDB(pdbFileName, "/project/StruPPi/ioannis/tmp");
96
97			//to check node method for edge coloring when nodeColor method not discretised
98			graphPml.setUniformNodeSize(0.6);
99			graphPml.setNodeColorMethod("BB_BB_out", false);
100			graphPml.setUniformEdgeSize(4);
101			graphPml.setEdgeColorMethod("node", true);
102			graphPml.outputGraph();
103			pml.setView("test1_view");
104			pml.saveImage("test3","/home/filippis/Desktop", false);
105
106			pml.delete("all", false);
107			pml.loadPDB(pdbFileName, "/project/StruPPi/ioannis/tmp");
108
109			//to check node method for edge coloring when nodeColor method is discretised
110			graphPml.setUniformNodeSize(0.6);
111			graphPml.setNodeColorMethod("BB_BB_out", true);
112			graphPml.setUniformEdgeSize(4);
113			graphPml.setEdgeColorMethod("node", true);
114			graphPml.outputGraph();
115			pml.setView("test1_view");
116			pml.saveImage("test4","/home/filippis/Desktop", false);
117
118			pml.delete("all", false);
119			pml.loadPDB(pdbFileName, "/project/StruPPi/ioannis/tmp");
120
121			//to check node method for edge coloring when nodeColor method is uniform
122			graphPml.setUniformNodeSize(0.6);
123			graphPml.setUniformNodeColor("blue");
124			graphPml.setUniformEdgeSize(4);
125			graphPml.setEdgeColorMethod("node", true);
126			graphPml.outputGraph();
127			pml.setView("test1_view");
128			pml.saveImage("test5","/home/filippis/Desktop", false);
129
130			pml.delete("all", false);
131			pml.loadPDB(pdbFileName, "/project/StruPPi/ioannis/tmp");
132
133			//to check the trick of directionality with gapped lines for "half" edges
134			//for this purpose a SC_BB graph model is used that doesn't ensure bidirectionality
135			graphPml = new Graph2Pml(serverOutPw, molObjName, 33729, "SC_BB", "SC_BB_in+SC_BB_out", "SC_BB", "true", "true", true, false, true, conn);
136			graphPml.outputGraph();
137			pml.setView("test1_view");
138			pml.saveImage("test6","/home/filippis/Desktop", false);
139
140
141			pml.delete("all", false);
142
143			//test multi-chain macromolecule with RNA also
144			pdbFileName = Msdsd2Pdb.export2File("1a0a", 1107, 2560, 1, "/project/StruPPi/ioannis/tmp");
145			molObjName = pml.loadPDB(pdbFileName, "/project/StruPPi/ioannis/tmp");
146			System.out.println(molObjName);
147
148			graphPml = new Graph2Pml(serverOutPw, molObjName, 95, "SC_SC", "SC_SC_in+SC_SC_out", "SC_SC", "true", "true", true, false, false, conn);
149			graphPml.draw(true, true, false, false);
150			//color nodes based on the chains they belong to
151			graphPml.setNodeColorMethod("chain", true);
152			graphPml.setNodeTransp(0.2);
153			graphPml.setUniformEdgeColor("red");
154			graphPml.setUniformEdgeSize(4.5);
155			graphPml.setEdgeGap(0.5);
156			graphPml.outputGraph();
157			pml.saveImage("test7","/home/filippis/Desktop", false);
158			pml.getView("test2_view");
159
160			pml.delete("all", false);
161			pml.loadPDB(pdbFileName, "/project/StruPPi/ioannis/tmp");
162
163			//color edges based on the chains they belong to
164			graphPml.draw(true, true, false, false);
165			graphPml.setUniformNodeColor("red");
166			graphPml.setEdgeColorMethod("chain", true);
167			graphPml.outputGraph();
168			pml.setView("test2_view");
169			pml.saveImage("test8","/home/filippis/Desktop", false);
170
171			pml.delete("all", false);
172			pml.loadPDB(pdbFileName, "/project/StruPPi/ioannis/tmp");
173
174			//to check node method for edge coloring when nodeColor method is based on chain coloring
175			graphPml.setNodeColorMethod("chain", true);
176			graphPml.setEdgeColorMethod("node", true);
177			graphPml.outputGraph();
178			pml.setView("test2_view");
179			pml.saveImage("test9","/home/filippis/Desktop", false);
180
181			pml.delete("all", false);
182			pml.loadPDB(pdbFileName, "/project/StruPPi/ioannis/tmp");
183
184			//draw also surface - you can not see the graph anymore
185			graphPml.draw(true, true, false, true);
186			graphPml.setSurfTransp(0.7);
187			graphPml.outputGraph();
188			pml.setView("test2_view");
189			pml.saveImage("test10","/home/filippis/Desktop", false);
190
191			try { Thread.sleep(10000); } catch (Exception e) {}
192
193			//hide the surface, show the RNA also
194			//change the color of the nodes for each chain using the pymol defined list of nodes for each chain
195			pml.hideWhat("surface", "graphMol", false);
196			pml.showWhat("lines", "restMol", false);
197			graphPml.setNodesColorUniform("nodes_cidA","red");
198			graphPml.setNodesColorUniform("nodes_cidA","yellow");
199
200			try { Thread.sleep(10000); } catch (Exception e) {}
201
202			//if you believe that the objects contained in the list won't exceed the pymol command length limit,
203			//you can concatenate all objects as a single string selection and handle them all together
204			pml.concatList("nodes", "+", "nodesStr");
205			pml.setNodeColor("blue", "nodesStr", true);
206			pml.selPml("nodes", "nodesStr", true, true);
207
208			pml.delete("all", false);
209			pml.loadPDB(pdbFileName, "/project/StruPPi/ioannis/tmp");
210
211			//check a graph model with only inter-secondary-structure-elements SC_SC edges
212			//remember that all the nodes with SC_SC will be selected
213			//use default behaviour
214			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);
215			graphPml.draw(true, true, false, false);
216			graphPml.outputGraph();
217			pml.setView("test2_view");
218			pml.saveImage("test11","/home/filippis/Desktop", false);
219
220			pml.delete("all", false);
221
222	filippis	42	SQLC.closeConnection(conn);
223
224			}
225
226	filippis	45	} // end of class testGraph2Pml