Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
PymolBindingModel	42	54	24	0.00%	Show methods

Class PymolBindingModel

Class PymolBindingModel	Line # 42	Total Statements 54	Complexity 24	TOTAL Coverage 0.00%
PymolBindingModel(StructureViewerBase,StructureSelectionManager,PDBEntry[],SequenceI[][])   PymolBindingModel(StructureViewerBase,StructureSelectionManager,PDBEntry[],SequenceI[][])	7373	4.04	1.01	0.0 0.00%
getStructureFiles() : String[]   getStructureFiles() : String[]	8383	1.01	1.01	0.0 0.00%
highlightAtoms(List<AtomSpec>) : void   highlightAtoms(List<AtomSpec>) : void	8989	10.010	2.02	0.0 0.00%
getSequenceRenderer(AlignmentViewPanel) : SequenceRenderer   getSequenceRenderer(AlignmentViewPanel) : SequenceRenderer	114114	1.01	1.01	0.0 0.00%
executeCommand(StructureCommandI,boolean) : List<String>   executeCommand(StructureCommandI,boolean) : List<String>	120120	1.01	1.01	0.0 0.00%
getModelIdForFile(String) : String   getModelIdForFile(String) : String	128128	1.01	2.02	0.0 0.00%
getViewerType() : ViewerType   getViewerType() : ViewerType	134134	1.01	1.01	0.0 0.00%
isViewerRunning() : boolean   isViewerRunning() : boolean	140140	1.01	1.01	0.0 0.00%
closeViewer(boolean) : void   closeViewer(boolean) : void	146146	2.02	1.01	0.0 0.00%
launchPymol() : boolean   launchPymol() : boolean	153153	7.07	3.03	0.0 0.00%
openFile(PDBEntry) : void   openFile(PDBEntry) : void	173173	18.018	6.06	0.0 0.00%
getModelId(int,String) : String   getModelId(int,String) : String	215215	1.01	1.01	0.0 0.00%
getSessionFileExtension() : String   getSessionFileExtension() : String	227227	1.01	1.01	0.0 0.00%
getHelpURL() : String   getHelpURL() : String	233233	1.01	1.01	0.0 0.00%
sendFeaturesToViewer(AlignmentViewPanel) : int   sendFeaturesToViewer(AlignmentViewPanel) : int	246246	4.04	1.01	0.0 0.00%

 

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1		/*
2		* Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3		* Copyright (C) $$Year-Rel$$ The Jalview Authors
4		*
5		* This file is part of Jalview.
6		*
7		* Jalview is free software: you can redistribute it and/or
8		* modify it under the terms of the GNU General Public License
9		* as published by the Free Software Foundation, either version 3
10		* of the License, or (at your option) any later version.
11		*
12		* Jalview is distributed in the hope that it will be useful, but
13		* WITHOUT ANY WARRANTY; without even the implied warranty
14		* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15		* PURPOSE. See the GNU General Public License for more details.
16		*
17		* You should have received a copy of the GNU General Public License
18		* along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19		* The Jalview Authors are detailed in the 'AUTHORS' file.
20		*/
21		package jalview.gui;
22
23		import java.util.ArrayList;
24		import java.util.HashMap;
25		import java.util.List;
26		import java.util.Map;
27
28		import jalview.api.AlignmentViewPanel;
29		import jalview.bin.Console;
30		import jalview.datamodel.PDBEntry;
31		import jalview.datamodel.SequenceI;
32		import jalview.ext.pymol.PymolCommands;
33		import jalview.ext.pymol.PymolManager;
34		import jalview.gui.StructureViewer.ViewerType;
35		import jalview.structure.AtomSpec;
36		import jalview.structure.AtomSpecModel;
37		import jalview.structure.StructureCommand;
38		import jalview.structure.StructureCommandI;
39		import jalview.structure.StructureSelectionManager;
40		import jalview.structures.models.AAStructureBindingModel;
41
		0% Uncovered Elements: 83 (83) Complexity: 24 Complexity Density: 0.44
42		public class PymolBindingModel extends AAStructureBindingModel
43		{
44		/*
45		* format for labels shown on structures when mousing over sequence;
46		* see https://pymolwiki.org/index.php/Label#examples
47		* left not final so customisable e.g. with a Groovy script
48		*/
49		private static String LABEL_FORMAT = "\"%s %s\" % (resn,resi)";
50
51		private PymolManager pymolManager;
52
53		/*
54		* full paths to structure files opened in PyMOL
55		*/
56		List<String> structureFiles = new ArrayList<>();
57
58		/*
59		* lookup from file path to PyMOL object name
60		*/
61		Map<String, String> pymolObjects = new HashMap<>();
62
63		private String lastLabelSpec;
64
65		/**
66		* Constructor
67		*
68		* @param viewer
69		* @param ssm
70		* @param pdbentry
71		* @param sequenceIs
72		*/
		0% Uncovered Elements: 4 (4) Complexity: 1 Complexity Density: 0.25
73	0	public PymolBindingModel(StructureViewerBase viewer,...
74		StructureSelectionManager ssm, PDBEntry[] pdbentry,
75		SequenceI[][] sequenceIs)
76		{
77	0	super(ssm, pdbentry, sequenceIs, null);
78	0	pymolManager = new PymolManager();
79	0	setStructureCommands(new PymolCommands());
80	0	setViewer(viewer);
81		}
82
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
83	0	@Override...
84		public String[] getStructureFiles()
85		{
86	0	return structureFiles.toArray(new String[structureFiles.size()]);
87		}
88
		0% Uncovered Elements: 12 (12) Complexity: 2 Complexity Density: 0.2
89	0	@Override...
90		public void highlightAtoms(List<AtomSpec> atoms)
91		{
92		/*
93		* https://pymolwiki.org/index.php/indicate#examples
94		*/
95	0	StringBuilder sb = new StringBuilder();
96	0	for (AtomSpec atom : atoms)
97		{
98		// todo promote to StructureCommandsI.showLabel()
99	0	String modelId = getModelIdForFile(atom.getPdbFile());
100	0	sb.append(String.format(" %s//%s/%d/*", modelId, atom.getChain(),
101		atom.getPdbResNum()));
102		}
103	0	String labelSpec = sb.toString();
104	0	if (labelSpec.equals(lastLabelSpec))
105		{
106	0	return;
107		}
108	0	StructureCommandI command = new StructureCommand("indicate", labelSpec);
109	0	executeCommand(command, false);
110
111	0	lastLabelSpec = labelSpec;
112		}
113
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
114	0	@Override...
115		public SequenceRenderer getSequenceRenderer(AlignmentViewPanel avp)
116		{
117	0	return new SequenceRenderer(avp.getAlignViewport());
118		}
119
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
120	0	@Override...
121		protected List<String> executeCommand(StructureCommandI command,
122		boolean getReply)
123		{
124		// jalview.bin.Console.outPrintln(command.toString()); // debug
125	0	return pymolManager.sendCommand(command, getReply);
126		}
127
		0% Uncovered Elements: 3 (3) Complexity: 2 Complexity Density: 2
128	0	@Override...
129		protected String getModelIdForFile(String file)
130		{
131	0	return pymolObjects.containsKey(file) ? pymolObjects.get(file) : "";
132		}
133
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
134	0	@Override...
135		protected ViewerType getViewerType()
136		{
137	0	return ViewerType.PYMOL;
138		}
139
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
140	0	@Override...
141		public boolean isViewerRunning()
142		{
143	0	return pymolManager != null && pymolManager.isPymolLaunched();
144		}
145
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
146	0	@Override...
147		public void closeViewer(boolean closePymol)
148		{
149	0	super.closeViewer(closePymol);
150	0	pymolManager = null;
151		}
152
		0% Uncovered Elements: 11 (11) Complexity: 3 Complexity Density: 0.43
153	0	public boolean launchPymol()...
154		{
155	0	if (pymolManager.isPymolLaunched())
156		{
157	0	return true;
158		}
159
160	0	Process pymol = pymolManager.launchPymol();
161	0	if (pymol != null)
162		{
163		// start listening for PyMOL selections - how??
164	0	startExternalViewerMonitor(pymol);
165		}
166		else
167		{
168	0	Console.error("Failed to launch PyMOL!");
169		}
170	0	return pymol != null;
171		}
172
		0% Uncovered Elements: 24 (24) Complexity: 6 Complexity Density: 0.33
173	0	public void openFile(PDBEntry pe)...
174		{
175		// todo : check not already open, remap / rename, etc
176	0	String file = pe.getFile();
177	0	StructureCommandI cmd = getCommandGenerator().loadFile(file);
178
179		/*
180		* a second parameter sets the pdbid as the loaded PyMOL object name
181		*/
182	0	String pdbId = pe.getId();
183	0	try
184		{
185	0	String safePDBId = java.net.URLEncoder.encode(pdbId, "UTF-8");
186	0	pdbId = safePDBId.replace('%', '_');
187	0	pdbId = pdbId.replace("-", "__");
188	0	char fc = pdbId.charAt(0);
189		// put an 's' before any numerics
190	0	if (fc >= '0' && fc <= '9')
191		{
192	0	pdbId = 's' + pdbId;
193		}
194		// pdbId.replace('-', 0)
195		} catch (Exception x)
196		{
197	0	Console.error("Unxpected encoding exception for '" + pdbId + "'", x);
198		}
199	0	cmd.addParameter(pdbId);
200
201	0	executeCommand(cmd, false);
202
203	0	pymolObjects.put(file, pdbId);
204	0	if (!structureFiles.contains(file))
205		{
206	0	structureFiles.add(file);
207		}
208	0	if (getSsm() != null)
209		{
210	0	getSsm().addStructureViewerListener(this);
211		}
212
213		}
214
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
215	0	@Override...
216		protected String getModelId(int pdbfnum, String file)
217		{
218	0	return file;
219		}
220
221		/**
222		* Returns the file extension to use for a saved viewer session file (.pse)
223		*
224		* @return
225		* @see https://pymolwiki.org/index.php/Save
226		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
227	0	@Override...
228		public String getSessionFileExtension()
229		{
230	0	return ".pse";
231		}
232
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
233	0	@Override...
234		public String getHelpURL()
235		{
236	0	return "https://pymolwiki.org/";
237		}
238
239		/**
240		* Constructs and sends commands to set atom properties for visible Jalview
241		* features on residues mapped to structure
242		*
243		* @param avp
244		* @return
245		*/
		0% Uncovered Elements: 4 (4) Complexity: 1 Complexity Density: 0.25
246	0	public int sendFeaturesToViewer(AlignmentViewPanel avp)...
247		{
248		// todo pull up this and JalviewChimeraBinding variant
249	0	Map<String, Map<Object, AtomSpecModel>> featureValues = buildFeaturesMap(
250		avp);
251	0	List<StructureCommandI> commands = getCommandGenerator()
252		.setAttributes(featureValues);
253	0	executeCommands(commands, false, null);
254	0	return commands.size();
255		}
256
257		}