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import java.sql.*; |
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import java.io.*; |
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import tools.*; |
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|
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/** |
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* Package: tools |
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* Class: testGraph2Pml |
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* Author: Ioannis Filippis, filippis@molgen.mpg.de |
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* Date: 21/03/2006 |
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* |
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* Simple test class for visualizing contact graphs using Graph2Pml class plus |
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* PyMol class. Run PyMol with the -R option to run the server. |
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* |
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* Notes: |
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* - You can find the results from all examples here in |
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* /project/StruPPi/ioannis/workspace/aglappe/vis_examples/ |
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* |
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* Changelog: |
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* 28/03/06 modified by IF (more examples added) |
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* 27/03/06 modified by IF (functional with comments - added cgo examples) |
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* 21/03/06 first created by IF (non functional) |
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*/ |
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|
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public class testGraph2Pml { |
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|
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public static void main(String[] args) { |
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|
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String connFile = "/project/StruPPi/ioannis/cnfs/msdgraph.my.cnf", pdbFileName = "", molObjName = ""; |
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Graph2Pml graphPml = null; |
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PyMol pml = null; |
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|
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mySQLConnect SQLC = new mySQLConnect(); |
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SQLC.readConnectionFile(connFile); |
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Connection conn = SQLC.openConnection(); |
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|
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//Create a new output stream to the pymol server running at the localhost |
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//all commands will be send there |
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PrintWriter serverOutPw = new PrintWriter(new PymolServerOutputStream("http://"+Machine.getClient()+":9123"), true); |
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pml = new PyMol(serverOutPw); |
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|
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pml.openLog("test", "/home/filippis/Desktop"); |
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|
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//Edges as lines |
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//export the pdb file directly from msdsd and load it in pymol |
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pdbFileName = Msdsd2Pdb.export2File("1rx4", 20717, 52567, 9, "/project/StruPPi/ioannis/tmp"); |
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molObjName = pml.loadPDB(pdbFileName, "/project/StruPPi/ioannis/tmp"); |
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System.out.println(molObjName); |
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|
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//create a pymol contact graph object for the graph 33729 |
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//use only SC_SC edges with SC_SC edge weight and nodes that have SC_SC edges |
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//no further filtering in the edges based on the contact range is applied |
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//no user based graph filtering is applied |
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//the graph comes from msdsd |
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//normal edges will be utilised |
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//the graph will not be visualised as "directed" |
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graphPml = new Graph2Pml(serverOutPw, molObjName, 33729, "SC_SC", "SC_SC_in+SC_SC_out", "SC_SC", "true", "true", true, false, false, conn); |
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//draw nodes, edges, special residues but not surface |
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//the node size will be calculated based on the SC_SC_out field on asc order |
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//the node color will be calculated based on the BB_BB_out field not discretised |
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//all ALA nodes will be transparent |
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//all residues that do not have any SC interactions will be the special ones colored green |
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//all edges will be lines of width determined by the SC_SC field in asc order |
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//all edges lines will have color calculated based on the BB_BB_out field not discretised |
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//all edges lines with adjacent ALA's will have gaps |
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graphPml.draw(true, true, true, false); |
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graphPml.setNodeSizeMethod("SC_SC_out", false); |
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graphPml.setNodeColorMethod("BB_BB_out", false); |
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graphPml.setNodeTranspCondition("(res = \"ALA\")"); |
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graphPml.setSpecialRes("green", "SELECT cid, num FROM newmsdgraph.nodes WHERE (graph_id = 33729) AND (sc_sc_in+sc_sc_out = 0);"); |
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graphPml.setEdgeSizeMethod("SC_SC", false); |
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graphPml.setEdgeColorMethod("BB_BB", false); |
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graphPml.setEdgeGapCondition("(i_res = \"ALA\" OR j_res = \"ALA\")"); |
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//create the contact graph |
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graphPml.outputGraph(); |
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//save the image not ray-traced |
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pml.saveImage("test1", "/home/filippis/Desktop", false); |
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//if you want later to read the view from a log file |
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//pml.openLog("test1_log","/home/filippis/Desktop"); |
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//get the view |
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pml.getView("test1_view"); |
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//pml.closeLog(); |
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|
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// delete all and reload the structure |
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pml.delete("all", false); |
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pml.loadPDB(pdbFileName, "/project/StruPPi/ioannis/tmp"); |
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|
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//to check reversibility in setNodeSizeMethod, setEdgeSizeMethod |
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//and discretised coloring in setNodeColorMethod, setEdgeColorMethod |
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graphPml.setNodeSizeMethod("SC_SC_out", true); |
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graphPml.setNodeColorMethod("BB_BB_out", true); |
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graphPml.setEdgeSizeMethod("SC_SC", true); |
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graphPml.setEdgeColorMethod("BB_BB", true); |
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graphPml.outputGraph(); |
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//set view by reading a log file |
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//pml.getFileView("test2_view", "/home/filippis/Desktop/test1_log.pml"); |
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//pml.setView("test2_view"); |
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//set view based on the view of the first structure so that you can compare |
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//different graphs for the same structure |
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pml.setView("test1_view"); |
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pml.saveImage("test2","/home/filippis/Desktop", false); |
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|
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// delete all and reload the structure |
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pml.delete("all", false); |
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pml.loadPDB(pdbFileName, "/project/StruPPi/ioannis/tmp"); |
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|
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//just check user defined set/discretised colors |
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//all green nodes must become red |
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graphPml.setNodeColors(new String[] {"red", "magenta", "orange", "chocolate"}); |
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//switched red-green, yellow-blue |
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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"}); |
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graphPml.outputGraph(); |
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pml.setView("test1_view"); |
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pml.saveImage("test2a","/home/filippis/Desktop", false); |
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|
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pml.delete("all", false); |
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pml.loadPDB(pdbFileName, "/project/StruPPi/ioannis/tmp"); |
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|
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//to check node method for edge coloring when nodeColor method not discretised |
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graphPml.setUniformNodeSize(0.6); |
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graphPml.setNodeColorMethod("BB_BB_out", false); |
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graphPml.setUniformEdgeSize(4); |
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graphPml.setEdgeColorMethod("node", true); |
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graphPml.outputGraph(); |
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pml.setView("test1_view"); |
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pml.saveImage("test3","/home/filippis/Desktop", false); |
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|
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pml.delete("all", false); |
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pml.loadPDB(pdbFileName, "/project/StruPPi/ioannis/tmp"); |
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|
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//to check node method for edge coloring when nodeColor method is discretised |
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graphPml.setUniformNodeSize(0.6); |
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graphPml.setNodeColorMethod("BB_BB_out", true); |
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graphPml.setUniformEdgeSize(4); |
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graphPml.setEdgeColorMethod("node", true); |
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graphPml.outputGraph(); |
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pml.setView("test1_view"); |
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pml.saveImage("test4","/home/filippis/Desktop", false); |
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|
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pml.delete("all", false); |
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pml.loadPDB(pdbFileName, "/project/StruPPi/ioannis/tmp"); |
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|
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//to check node method for edge coloring when nodeColor method is uniform |
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graphPml.setUniformNodeSize(0.6); |
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graphPml.setUniformNodeColor("blue"); |
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graphPml.setUniformEdgeSize(4); |
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graphPml.setEdgeColorMethod("node", true); |
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graphPml.outputGraph(); |
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pml.setView("test1_view"); |
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pml.saveImage("test5","/home/filippis/Desktop", false); |
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|
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pml.delete("all", false); |
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pml.loadPDB(pdbFileName, "/project/StruPPi/ioannis/tmp"); |
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|
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//to check the trick of directionality with gapped lines for "half" edges |
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//for this purpose a SC_BB graph model is used that doesn't ensure bidirectionality |
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graphPml = new Graph2Pml(serverOutPw, molObjName, 33729, "SC_BB", "SC_BB_in+SC_BB_out", "SC_BB", "true", "true", true, false, true, conn); |
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graphPml.outputGraph(); |
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pml.setView("test1_view"); |
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pml.saveImage("test6","/home/filippis/Desktop", false); |
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|
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|
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pml.delete("all", false); |
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|
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//test multi-chain macromolecule with RNA also |
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pdbFileName = Msdsd2Pdb.export2File("1a0a", 1107, 2560, 1, "/project/StruPPi/ioannis/tmp"); |
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molObjName = pml.loadPDB(pdbFileName, "/project/StruPPi/ioannis/tmp"); |
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System.out.println(molObjName); |
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|
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graphPml = new Graph2Pml(serverOutPw, molObjName, 95, "SC_SC", "SC_SC_in+SC_SC_out", "SC_SC", "true", "true", true, false, false, conn); |
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graphPml.draw(true, true, false, false); |
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//color nodes based on the chains they belong to |
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graphPml.setChainNodeColor(); |
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graphPml.setNodeTransp(0.2); |
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graphPml.setUniformEdgeColor("red"); |
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graphPml.setUniformEdgeSize(4.5); |
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graphPml.setEdgeGap(0.5); |
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graphPml.outputGraph(); |
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pml.saveImage("test7","/home/filippis/Desktop", false); |
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pml.getView("test2_view"); |
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|
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pml.delete("all", false); |
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pml.loadPDB(pdbFileName, "/project/StruPPi/ioannis/tmp"); |
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|
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//color edges based on the chains they belong to |
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graphPml.draw(true, true, false, false); |
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graphPml.setUniformNodeColor("red"); |
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graphPml.setChainEdgeColor(); |
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graphPml.outputGraph(); |
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pml.setView("test2_view"); |
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pml.saveImage("test8","/home/filippis/Desktop", false); |
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|
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pml.delete("all", false); |
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pml.loadPDB(pdbFileName, "/project/StruPPi/ioannis/tmp"); |
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|
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//to check node method for edge coloring when nodeColor method is based on chain coloring |
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//also check the user defined chain colors for nodes |
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graphPml.setChainNodeColor(new String[] {"blue"}); |
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graphPml.setEdgeColorMethod("node", true); |
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graphPml.outputGraph(); |
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pml.setView("test2_view"); |
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pml.saveImage("test9","/home/filippis/Desktop", false); |
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|
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pml.delete("all", false); |
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pml.loadPDB(pdbFileName, "/project/StruPPi/ioannis/tmp"); |
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|
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//draw also surface - you can not see the graph anymore |
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graphPml.draw(true, true, false, true); |
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graphPml.setSurfTransp(0.7); |
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graphPml.outputGraph(); |
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pml.setView("test2_view"); |
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pml.saveImage("test10","/home/filippis/Desktop", false); |
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|
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try { Thread.sleep(10000); } catch (Exception e) {} |
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|
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//hide the surface, show the RNA also |
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//change the color of the nodes for each chain using the pymol defined list of nodes for each chain |
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pml.hideWhat("surface", "graphMol", false); |
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pml.showWhat("lines", "restMol", false); |
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graphPml.setNodesColorUniform("nodes_cidA","red"); |
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graphPml.setNodesColorUniform("nodes_cidA","yellow"); |
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|
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try { Thread.sleep(10000); } catch (Exception e) {} |
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|
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//if you believe that the objects contained in the list won't exceed the pymol command length limit, |
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//you can concatenate all objects as a single string selection and handle them all together |
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pml.concatList("nodes", "+", "nodesStr"); |
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pml.setNodeColor("blue", "nodesStr", true); |
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pml.selPml("nodes", "nodesStr", true, true); |
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|
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pml.delete("all", false); |
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pml.loadPDB(pdbFileName, "/project/StruPPi/ioannis/tmp"); |
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|
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//check a graph model with only inter-secondary-structure-elements SC_SC edges |
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//remember that all the nodes with SC_SC will be selected |
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//use default behaviour |
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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); |
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graphPml.draw(true, true, false, false); |
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graphPml.outputGraph(); |
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pml.setView("test2_view"); |
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pml.saveImage("test11","/home/filippis/Desktop", false); |
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|
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pml.delete("all", false); |
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|
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//CGO EDGES SECTION |
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pdbFileName = Msdsd2Pdb.export2File("1kj0", 21698, 55132, 9, "/project/StruPPi/ioannis/tmp"); |
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molObjName = pml.loadPDB(pdbFileName, "/project/StruPPi/ioannis/tmp"); |
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|
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//Cgo makes sense to be used with directed graph |
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graphPml = new Graph2Pml(serverOutPw, molObjName, 35666, "SC_SC", "SC_SC_in+SC_SC_out", "SC_SC", "true", "true", true, true, true, conn); |
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graphPml.draw(true, true, false, false); |
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graphPml.outputGraph(); |
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pml.saveImage("test12","/home/filippis/Desktop", false); |
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pml.getView("test3_view"); |
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|
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// delete all edges |
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pml.iterateList("edges", "edge"); |
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pml.delete("edge", true); |
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|
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graphPml.draw(false, true, false, false); |
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graphPml.setUniformCgoEdgeSize(0.2); |
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graphPml.setEdgeColorMethod("node", true); |
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graphPml.outputGraph(); |
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pml.setView("test3_view"); |
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pml.saveImage("test13","/home/filippis/Desktop", false); |
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|
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// delete all edges |
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pml.iterateList("edges", "edge"); |
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pml.delete("edge", true); |
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|
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graphPml.setEdgeSizeMethod("SC_SC", false); |
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graphPml.setEdgeColorMethod("BB_BB", false); |
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graphPml.outputGraph(); |
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pml.setView("test3_view"); |
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pml.saveImage("test14","/home/filippis/Desktop", false); |
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|
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pml.iterateList("edges", "edge"); |
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pml.delete("edge", true); |
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|
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graphPml.setEdgeSizeMethod("SC_SC", true); |
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graphPml.setEdgeColorMethod("BB_BB", true); |
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graphPml.outputGraph(); |
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pml.setView("test3_view"); |
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pml.saveImage("test15","/home/filippis/Desktop", false); |
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|
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pml.delete("all", false); |
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pml.loadPDB(pdbFileName, "/project/StruPPi/ioannis/tmp"); |
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|
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//to check node method for edge coloring when nodeColor method not discretised |
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graphPml.draw(true, true, false, false); |
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graphPml.setUniformNodeSize(0.6); |
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graphPml.setNodeColorMethod("BB_BB_out", false); |
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graphPml.setUniformEdgeSize(0.4); |
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graphPml.setEdgeColorMethod("node", true); |
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graphPml.outputGraph(); |
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pml.setView("test3_view"); |
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pml.saveImage("test16","/home/filippis/Desktop", false); |
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|
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pml.delete("all", false); |
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pml.loadPDB(pdbFileName, "/project/StruPPi/ioannis/tmp"); |
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|
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//to check node method for edge coloring when nodeColor method not discretised |
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graphPml.setUniformNodeSize(0.6); |
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graphPml.setNodeColorMethod("BB_BB_out", true); |
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graphPml.setUniformEdgeSize(0.4); |
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graphPml.setEdgeColorMethod("node", true); |
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graphPml.outputGraph(); |
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pml.setView("test3_view"); |
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pml.saveImage("test17","/home/filippis/Desktop", false); |
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|
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pml.delete("all", false); |
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pml.loadPDB(pdbFileName, "/project/StruPPi/ioannis/tmp"); |
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|
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//see "real" half-edges |
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graphPml = new Graph2Pml(serverOutPw, molObjName, 35666, "SC_BB", "SC_BB_in+SC_BB_out", "SC_BB", "true", "true", true, true, true, conn); |
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graphPml.outputGraph(); |
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pml.setView("test3_view"); |
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pml.saveImage("test18","/home/filippis/Desktop", false); |
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|
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pml.delete("all", false); |
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|
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//test multi-chain macromolecule with RNA also |
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pdbFileName = "1a0a_1107_2560.pdb"; |
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molObjName = pml.loadPDB(pdbFileName, "/project/StruPPi/ioannis/tmp"); |
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System.out.println(molObjName); |
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|
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graphPml = new Graph2Pml(serverOutPw, molObjName, 95, "SC_SC", "SC_SC_in+SC_SC_out", "SC_SC", "true", "true", true, true, true, conn); |
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graphPml.draw(true, true, false, false); |
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graphPml.setNodeColorMethod("SC_SC_out", false); |
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graphPml.setNodeTransp(0); |
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graphPml.setEdgeSizeMethod("SC_SC", false); |
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graphPml.setChainEdgeColor(new String[] {"yellow","red"}); |
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graphPml.outputGraph(); |
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pml.saveImage("test19","/home/filippis/Desktop", false); |
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|
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pml.delete("all", false); |
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|
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pdbFileName = "1rx4_20717_52567.pdb"; |
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pml.loadPDB(pdbFileName, "/project/StruPPi/ioannis/tmp"); |
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|
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graphPml = new Graph2Pml(serverOutPw, molObjName, 33729, "SC_SC", "SC_SC_in+SC_SC_out", "SC_SC", "true", "true", true, true, true, conn); |
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graphPml.draw(true, true, false, false); |
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graphPml.setNodeSizeMethod("SC_SC_out", false); |
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graphPml.setNodeColorMethod("SC_SC_out", false); |
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graphPml.setNodeTransp(0.6); |
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graphPml.setEdgeSizeMethod("SC_SC", false); |
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graphPml.setEdgeColorMethod("SC_SC", false); |
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graphPml.outputGraph(); |
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pml.saveImage("test20","/home/filippis/Desktop", false); |
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|
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pml.delete("all", false); |
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pdbFileName = "1kj0_21698_55132.pdb"; |
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pml.loadPDB(pdbFileName, "/project/StruPPi/ioannis/tmp"); |
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|
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//check the setNodeSizeRange method |
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graphPml = new Graph2Pml(serverOutPw, molObjName, 35666, "SC_SC", "SC_SC_in+SC_SC_out", "SC_SC", "true", "true", true, true, true, conn); |
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graphPml.draw(true, false, false, false); |
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graphPml.setChainColors(new String[] {"red"}); |
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graphPml.setNodeSizeMethod("SC_SC_out", false); |
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graphPml.setNodeSizeRange(new double[] {0.6, 1.2}); |
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graphPml.outputGraph(); |
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pml.saveImage("test21","/home/filippis/Desktop", false); |
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|
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pml.delete("all", false); |
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pdbFileName = "1kj0_21698_55132.pdb"; |
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pml.loadPDB(pdbFileName, "/project/StruPPi/ioannis/tmp"); |
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|
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//check the setDefaults method |
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graphPml.setDefaults(new String[] {"nodeSizeRange", "chainColors"}); |
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graphPml.outputGraph(); |
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pml.saveImage("test22","/home/filippis/Desktop", false); |
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|
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pml.closeLog(); |
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|
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SQLC.closeConnection(conn); |
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|
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} |
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|
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} // end of class testGraph2Pml |
