trunk/proteinstructure/Graph.java

package proteinstructure;

import java.io.FileOutputStream;
import java.io.PrintStream;
import java.io.IOException;
import java.util.TreeMap;
import java.util.HashMap;

/**
 * A residue interaction graph derived from a single chain pdb protein structure
 * 
 * @author              Jose Duarte
 * Class:               Graph
 * Package:             proteinstructure
 */
public class Graph {

        public final static String GRAPHFILEFORMATVERSION = "1.0";
        
        public ContactList contacts; // we keep it public to be able to re-reference the object directly (getContacts() copies it)
        
        protected TreeMap<Integer,String> nodes; // nodes is a TreeMap of residue serials to residue types (3 letter code)
        protected String sequence;                              // the full sequence (with unobserved residues and non-standard aas ='X')
        protected String pdbCode;
        protected String chainCode;
        protected String pdbChainCode;
        protected double cutoff;
        protected String ct;                                    // the contact type
        protected boolean directed;
        
        // fullLength is length of full sequence or:
        // -if sequence not provided (when reading from db): length of everything except possible unobserved residues at end of chain
        // -if sequence and nodes not provided (when reading from file and sequence field missing): length except possible unobserved residues at end of chain and possible nodes without contacts at end of chain
        protected int fullLength; 
        protected int obsLength;  // length without unobserved, non standard aas 
        
        protected int numContacts;
        
        protected boolean modified;
        
        public Graph() {
                
        }
                
        /**
         * Constructs Graph object by passing ArrayList with contacts and TreeMap with nodes (res serials and types)
         * Must also pass contact type, cutoff, pdbCode and chainCode
         * @param contacts
         * @param nodes
         * @param sequence
         * @param cutoff
         * @param ct
         * @param pdbCode
         * @param chainCode
         */
        public Graph (ContactList contacts, TreeMap<Integer,String> nodes, String sequence, double cutoff,String ct, String pdbCode, String chainCode, String pdbChainCode) {
                this.contacts=contacts;
                this.cutoff=cutoff;
                this.nodes=nodes;
                this.sequence=sequence;
                this.pdbCode=pdbCode;
                this.chainCode=chainCode;
                this.pdbChainCode=pdbChainCode;
                this.ct=ct;
                this.fullLength=sequence.length();
                this.obsLength=nodes.size();
                this.numContacts=contacts.size();
                this.modified=false;
                this.directed=false;
                if (ct.contains("/")){
                        directed=true;
                }
        }
        

        //TODO implement (from python) write_graph_to_db, do we really need it here??
                
        public void write_graph_to_file (String outfile) throws IOException {
                PrintStream Out = new PrintStream(new FileOutputStream(outfile));
                Out.println("#AGLAPPE GRAPH FILE ver: "+GRAPHFILEFORMATVERSION);
                Out.println("#SEQUENCE: "+sequence);
                Out.println("#PDB: "+pdbCode);
                Out.println("#PDB CHAIN CODE: "+pdbChainCode);
                Out.println("#CHAIN: "+chainCode);
                Out.println("#CT: "+ct);
                Out.println("#CUTOFF: "+cutoff);
                for (Contact pair:contacts){
                        int i_resser=pair.i;
                        int j_resser=pair.j;
                        Out.println(i_resser+"\t"+j_resser);
                }
                Out.close();            
        }
        
        /**
         * Gets list of contacts as a new ContactList (deep copied)
         * 
         */
        public ContactList getContacts(){
                ContactList newContacts = new ContactList();
                for (Contact cont:contacts){
                        newContacts.add(new Contact(cont.i,cont.j));
                }
                return newContacts;
        }
        
        /**
         * Gets TreeMap of nodes, deep copying  
         * 
         */
        public TreeMap<Integer,String> getNodes(){
                TreeMap<Integer,String> newNodes = new TreeMap<Integer,String>();
                for (int resser:nodes.keySet()){
                        newNodes.put(resser, nodes.get(resser));
                }
                return newNodes;
        }
        
        /**
         * Deep copies this Graph object returning new one
         * @return
         */
        public Graph copy(){
                return new Graph(getContacts(),getNodes(),sequence,cutoff,ct,pdbCode,chainCode,pdbChainCode);           
        }
        
        /**
         * Returns an int matrix with 1s for contacts and 0s for non contacts, i.e. the contact map
         * In non-crossed cases this should give us the upper half matrix (contacts are only j>i)
         * In crossed cases this gives us a full matrix (contacts are both j>i and i>j since they are directed)
         * @return
         */
        public int[][] getIntMatrix(){
                // this initialises the matrix to 0 (i.e. no contact)
                int[][] cm = new int[fullLength][fullLength];
                // we put a 1 for all given contacts
                for (Contact cont:contacts){
                        int i_resser = cont.i;
                        int j_resser = cont.j;
                        cm[i_resser-1][j_resser-1]=1;
                }
                return cm;
        }

        /**
         * Gets a node's residue type given the residue serial
         * @param resser
         * @return
         */
        public String getResType(int resser){
                return nodes.get(resser);
        }
        
        /**
         * Gets node neighbourhood given a residue serial
         * @param resser
         * @return
         */
        public NodeNbh getNodeNbh(int resser){
                NodeNbh nbh = new NodeNbh(resser, getResType(resser));
                //this could be implemented using the contact map matrix and scanning through 1 column/row
                //it would be just slightly faster, here we do 2*numContacts iterations, using matrix would be only fullLength iterations
                //however we would then have the overhead of creating the matrix
                for (Contact cont:contacts){
                        if (cont.i==resser) nbh.put(cont.j, nodes.get(cont.j));
                        if (cont.j==resser) nbh.put(cont.i, nodes.get(cont.i));
                }
                return nbh;
        }
        
        /**
         * Gets edge neighbourhood (common neighbourhood) given a residue serial pair
         * @param i_resser
         * @param j_resser
         * @return
         */
        public EdgeNbh getEdgeNbh(int i_resser, int j_resser){
                EdgeNbh nbh = new EdgeNbh(i_resser, getResType(i_resser), j_resser, getResType(j_resser));
                NodeNbh i_nbhd = getNodeNbh(i_resser);
                NodeNbh j_nbhd = getNodeNbh(j_resser);
                if (j_nbhd.size()>=i_nbhd.size()) { //with this we will be slightly faster, always iterating through smallest TreeMap
                        for (int resser:i_nbhd.keySet()) {
                                if (j_nbhd.containsKey(resser)) nbh.put(resser, i_nbhd.get(resser));
                        }
                } else {
                        for (int resser:j_nbhd.keySet()) {
                                if (i_nbhd.containsKey(resser)) nbh.put(resser, j_nbhd.get(resser));                    
                        }
                }
                return nbh;
        }

        public void addEdge(Contact cont){
                contacts.add(cont);
                numContacts++;
                modified=true;
        }
        
        public void delEdge(Contact cont){
                contacts.remove(cont);
                numContacts--;
                modified=true;
        }
        
        public void restrictContactsToMaxRange(int range){
                ContactList edgesToDelete = new ContactList();
                for (Contact cont:contacts){
                        if (cont.getRange()>range) edgesToDelete.add(cont);
                }
                for (Contact cont:edgesToDelete){
                        delEdge(cont);
                }
        }
        
        public void restrictContactsToMinRange(int range){
                ContactList edgesToDelete = new ContactList();
                for (Contact cont:contacts){
                        if (cont.getRange()<range) edgesToDelete.add(cont);
                }
                for (Contact cont:edgesToDelete){
                        delEdge(cont);
                }
        }

        /**
         * Returns a HashMap with all edge neighbourhood sizes (if they are >0) for each cell in the contact map
         * @return
         */
        public HashMap<Contact,Integer> getAllEdgeNbhSizes() {
                HashMap<Contact,Integer> sizes = new HashMap<Contact, Integer>();
                if (!directed) {
                        for (int i=1; i<fullLength;i++){
                                for (int j=i+1; j<fullLength;j++){
                                        int size = getEdgeNbh(i, j).size();
                                        if (size>0)     sizes.put(new Contact(i,j), size);
                                }
                        }                       
                } else {
                        for (int i=1; i<fullLength;i++){
                                for (int j=1; j<fullLength;j++){
                                        if (i!=j){
                                                int size = getEdgeNbh(i, j).size();
                                                if (size>0) sizes.put(new Contact(i,j), size);
                                        }
                                }
                        }
                }
                return sizes;
        }

        //TODO not sure what kind of return we want, for now is a HashMap with three graph objects 
        public HashMap<String,Graph> compare(Graph other) throws Exception{
                //first check that other has same sequence than this, otherwise throw exception
                if (!this.sequence.equals(other.sequence)){
                        //TODO throw specific exception
                        throw new Exception("Sequence of 2 graphs to compare differ, can't compare them.");
                }
                ContactList common = new ContactList();
                ContactList onlythis = new ContactList();
                ContactList onlyother = new ContactList();
                for (Contact cont:this.contacts){
                        if (other.contacts.contains(cont)) {
                                common.add(cont);
                        } else{
                                onlythis.add(cont);
                        }
                }
                for (Contact cont:other.contacts){
                        if (!this.contacts.contains(cont)){
                                onlyother.add(cont);
                        }
                }
                Graph commongraph = new Graph (common,getNodes(),sequence,cutoff,ct,pdbCode,chainCode,pdbChainCode);
                Graph onlythisgraph = new Graph (onlythis,getNodes(),sequence,cutoff,ct,pdbCode,chainCode,pdbChainCode);
                Graph onlyothergraph = new Graph (onlyother,getNodes(),sequence,cutoff,ct,other.pdbCode,other.chainCode,other.pdbChainCode);
                HashMap<String,Graph> result = new HashMap<String,Graph>();
                result.put("common", commongraph);
                result.put("onlythis", onlythisgraph);
                result.put("onlyother",onlyothergraph);
                return result;
        }
        
        public boolean isModified(){
                return modified;
        }
        
        public boolean isDirected(){
                return directed;
        }
        
        public String getPdbCode() {
                return pdbCode;
        }
        
        public String getPdbChainCode(){
                return pdbChainCode;
        }
        
        public String getChainCode(){
                return chainCode;
        }
        
        public String getSequence(){
                return sequence;
        }
        
        public int getFullLength(){
                return fullLength;
        }
        
        public int getObsLength(){
                return obsLength;
        }
        
        public int getNumContacts(){
                // in theory we could return just numContacts, because we have taken care of updating it every time contacts changed
                // however we call directly contacts.size() as I feel is safer
                return contacts.size(); 
        }
        
        public String getContactType() {
                return ct;
        }
        
        public double getCutoff(){
                return cutoff;
        }
}
Revision:	208
Committed:	Wed Jun 27 14:42:12 2007 UTC (17 years, 3 months ago) by duarte
File size:	9518 byte(s)
Log Message:	FIXED BUGS: - directed was not set when reading from cm file - pdbChainCode not set when reading from db given pdbCode - filling pdbresser2resser and resser2pdbresser hashmaps also in reading from pdb file - using "A" as chainCode when reading from pdb file - some error handling for file formats: new exception classes GraphFileFormatError and PdbfileFormatError
Line	User	Rev	File contents
1	duarte	123	package proteinstructure;
2	duarte	191
3	duarte	123	import java.io.FileOutputStream;
4			import java.io.PrintStream;
5			import java.io.IOException;
6	duarte	129	import java.util.TreeMap;
7	duarte	189	import java.util.HashMap;
8	duarte	123
9	duarte	207	/**
10			* A residue interaction graph derived from a single chain pdb protein structure
11			*
12			* @author Jose Duarte
13			* Class: Graph
14			* Package: proteinstructure
15			*/
16	duarte	123	public class Graph {
17
18	duarte	144	public final static String GRAPHFILEFORMATVERSION = "1.0";
19	duarte	206
20	duarte	207	public ContactList contacts; // we keep it public to be able to re-reference the object directly (getContacts() copies it)
21	duarte	123
22	duarte	207	protected TreeMap<Integer,String> nodes; // nodes is a TreeMap of residue serials to residue types (3 letter code)
23			protected String sequence; // the full sequence (with unobserved residues and non-standard aas ='X')
24			protected String pdbCode;
25			protected String chainCode;
26	duarte	208	protected String pdbChainCode;
27	duarte	207	protected double cutoff;
28			protected String ct; // the contact type
29	duarte	208	protected boolean directed;
30	duarte	207
31	duarte	159	// fullLength is length of full sequence or:
32			// -if sequence not provided (when reading from db): length of everything except possible unobserved residues at end of chain
33			// -if sequence and nodes not provided (when reading from file and sequence field missing): length except possible unobserved residues at end of chain and possible nodes without contacts at end of chain
34	duarte	207	protected int fullLength;
35			protected int obsLength; // length without unobserved, non standard aas
36	duarte	159
37	duarte	207	protected int numContacts;
38	duarte	159
39	duarte	207	protected boolean modified;
40	duarte	175
41	duarte	207	public Graph() {
42
43			}
44
45	duarte	134	/**
46			* Constructs Graph object by passing ArrayList with contacts and TreeMap with nodes (res serials and types)
47	duarte	206	* Must also pass contact type, cutoff, pdbCode and chainCode
48	duarte	134	* @param contacts
49			* @param nodes
50			* @param sequence
51			* @param cutoff
52			* @param ct
53	duarte	206	* @param pdbCode
54			* @param chainCode
55	duarte	134	*/
56	duarte	206	public Graph (ContactList contacts, TreeMap<Integer,String> nodes, String sequence, double cutoff,String ct, String pdbCode, String chainCode, String pdbChainCode) {
57	duarte	123	this.contacts=contacts;
58			this.cutoff=cutoff;
59	duarte	129	this.nodes=nodes;
60			this.sequence=sequence;
61	duarte	206	this.pdbCode=pdbCode;
62			this.chainCode=chainCode;
63			this.pdbChainCode=pdbChainCode;
64	duarte	123	this.ct=ct;
65	duarte	159	this.fullLength=sequence.length();
66			this.obsLength=nodes.size();
67			this.numContacts=contacts.size();
68	duarte	175	this.modified=false;
69	duarte	208	this.directed=false;
70	duarte	129	if (ct.contains("/")){
71			directed=true;
72			}
73	duarte	123	}
74	duarte	135
75	duarte	129
76	duarte	135	//TODO implement (from python) write_graph_to_db, do we really need it here??
77
78	duarte	144	public void write_graph_to_file (String outfile) throws IOException {
79			PrintStream Out = new PrintStream(new FileOutputStream(outfile));
80	duarte	208	Out.println("#AGLAPPE GRAPH FILE ver: "+GRAPHFILEFORMATVERSION);
81	duarte	144	Out.println("#SEQUENCE: "+sequence);
82	duarte	206	Out.println("#PDB: "+pdbCode);
83			Out.println("#PDB CHAIN CODE: "+pdbChainCode);
84			Out.println("#CHAIN: "+chainCode);
85	duarte	144	Out.println("#CT: "+ct);
86			Out.println("#CUTOFF: "+cutoff);
87			for (Contact pair:contacts){
88			int i_resser=pair.i;
89			int j_resser=pair.j;
90			Out.println(i_resser+"\t"+j_resser);
91			}
92			Out.close();
93			}
94	duarte	175
95	duarte	159	/**
96	duarte	175	* Gets list of contacts as a new ContactList (deep copied)
97			*
98			*/
99			public ContactList getContacts(){
100			ContactList newContacts = new ContactList();
101			for (Contact cont:contacts){
102			newContacts.add(new Contact(cont.i,cont.j));
103			}
104			return newContacts;
105			}
106
107			/**
108			* Gets TreeMap of nodes, deep copying
109			*
110			*/
111			public TreeMap<Integer,String> getNodes(){
112			TreeMap<Integer,String> newNodes = new TreeMap<Integer,String>();
113			for (int resser:nodes.keySet()){
114			newNodes.put(resser, nodes.get(resser));
115			}
116			return newNodes;
117			}
118
119			/**
120			* Deep copies this Graph object returning new one
121			* @return
122			*/
123			public Graph copy(){
124	duarte	206	return new Graph(getContacts(),getNodes(),sequence,cutoff,ct,pdbCode,chainCode,pdbChainCode);
125	duarte	175	}
126
127			/**
128	duarte	159	* Returns an int matrix with 1s for contacts and 0s for non contacts, i.e. the contact map
129			* In non-crossed cases this should give us the upper half matrix (contacts are only j>i)
130			* In crossed cases this gives us a full matrix (contacts are both j>i and i>j since they are directed)
131			* @return
132			*/
133			public int[][] getIntMatrix(){
134			// this initialises the matrix to 0 (i.e. no contact)
135			int[][] cm = new int[fullLength][fullLength];
136			// we put a 1 for all given contacts
137			for (Contact cont:contacts){
138			int i_resser = cont.i;
139			int j_resser = cont.j;
140			cm[i_resser-1][j_resser-1]=1;
141	duarte	129	}
142			return cm;
143			}
144	duarte	159
145	duarte	165	/**
146	duarte	179	* Gets a node's residue type given the residue serial
147			* @param resser
148			* @return
149			*/
150			public String getResType(int resser){
151			return nodes.get(resser);
152			}
153
154			/**
155	duarte	165	* Gets node neighbourhood given a residue serial
156			* @param resser
157			* @return
158			*/
159	duarte	179	public NodeNbh getNodeNbh(int resser){
160			NodeNbh nbh = new NodeNbh(resser, getResType(resser));
161	duarte	165	//this could be implemented using the contact map matrix and scanning through 1 column/row
162			//it would be just slightly faster, here we do 2*numContacts iterations, using matrix would be only fullLength iterations
163	duarte	179	//however we would then have the overhead of creating the matrix
164	duarte	165	for (Contact cont:contacts){
165			if (cont.i==resser) nbh.put(cont.j, nodes.get(cont.j));
166			if (cont.j==resser) nbh.put(cont.i, nodes.get(cont.i));
167			}
168			return nbh;
169			}
170
171			/**
172			* Gets edge neighbourhood (common neighbourhood) given a residue serial pair
173			* @param i_resser
174			* @param j_resser
175			* @return
176			*/
177	duarte	179	public EdgeNbh getEdgeNbh(int i_resser, int j_resser){
178			EdgeNbh nbh = new EdgeNbh(i_resser, getResType(i_resser), j_resser, getResType(j_resser));
179			NodeNbh i_nbhd = getNodeNbh(i_resser);
180			NodeNbh j_nbhd = getNodeNbh(j_resser);
181	duarte	175	if (j_nbhd.size()>=i_nbhd.size()) { //with this we will be slightly faster, always iterating through smallest TreeMap
182			for (int resser:i_nbhd.keySet()) {
183			if (j_nbhd.containsKey(resser)) nbh.put(resser, i_nbhd.get(resser));
184			}
185			} else {
186			for (int resser:j_nbhd.keySet()) {
187			if (i_nbhd.containsKey(resser)) nbh.put(resser, j_nbhd.get(resser));
188			}
189	duarte	165	}
190			return nbh;
191			}
192
193	duarte	175	public void addEdge(Contact cont){
194			contacts.add(cont);
195			numContacts++;
196			modified=true;
197			}
198
199			public void delEdge(Contact cont){
200			contacts.remove(cont);
201			numContacts--;
202			modified=true;
203			}
204
205			public void restrictContactsToMaxRange(int range){
206	duarte	179	ContactList edgesToDelete = new ContactList();
207	duarte	175	for (Contact cont:contacts){
208	duarte	179	if (cont.getRange()>range) edgesToDelete.add(cont);
209	duarte	175	}
210	duarte	179	for (Contact cont:edgesToDelete){
211			delEdge(cont);
212			}
213	duarte	175	}
214
215			public void restrictContactsToMinRange(int range){
216	duarte	179	ContactList edgesToDelete = new ContactList();
217	duarte	175	for (Contact cont:contacts){
218	duarte	179	if (cont.getRange()<range) edgesToDelete.add(cont);
219	duarte	175	}
220	duarte	179	for (Contact cont:edgesToDelete){
221			delEdge(cont);
222			}
223	duarte	175	}
224	duarte	189
225	duarte	191	/**
226			* Returns a HashMap with all edge neighbourhood sizes (if they are >0) for each cell in the contact map
227			* @return
228			*/
229			public HashMap<Contact,Integer> getAllEdgeNbhSizes() {
230			HashMap<Contact,Integer> sizes = new HashMap<Contact, Integer>();
231			if (!directed) {
232			for (int i=1; i<fullLength;i++){
233			for (int j=i+1; j<fullLength;j++){
234			int size = getEdgeNbh(i, j).size();
235			if (size>0) sizes.put(new Contact(i,j), size);
236			}
237			}
238			} else {
239			for (int i=1; i<fullLength;i++){
240			for (int j=1; j<fullLength;j++){
241			if (i!=j){
242			int size = getEdgeNbh(i, j).size();
243			if (size>0) sizes.put(new Contact(i,j), size);
244			}
245			}
246			}
247			}
248			return sizes;
249			}
250
251	duarte	189	//TODO not sure what kind of return we want, for now is a HashMap with three graph objects
252			public HashMap<String,Graph> compare(Graph other) throws Exception{
253			//first check that other has same sequence than this, otherwise throw exception
254			if (!this.sequence.equals(other.sequence)){
255			//TODO throw specific exception
256			throw new Exception("Sequence of 2 graphs to compare differ, can't compare them.");
257			}
258			ContactList common = new ContactList();
259			ContactList onlythis = new ContactList();
260			ContactList onlyother = new ContactList();
261			for (Contact cont:this.contacts){
262			if (other.contacts.contains(cont)) {
263			common.add(cont);
264			} else{
265			onlythis.add(cont);
266			}
267			}
268			for (Contact cont:other.contacts){
269			if (!this.contacts.contains(cont)){
270			onlyother.add(cont);
271			}
272			}
273	duarte	206	Graph commongraph = new Graph (common,getNodes(),sequence,cutoff,ct,pdbCode,chainCode,pdbChainCode);
274			Graph onlythisgraph = new Graph (onlythis,getNodes(),sequence,cutoff,ct,pdbCode,chainCode,pdbChainCode);
275			Graph onlyothergraph = new Graph (onlyother,getNodes(),sequence,cutoff,ct,other.pdbCode,other.chainCode,other.pdbChainCode);
276	duarte	189	HashMap<String,Graph> result = new HashMap<String,Graph>();
277			result.put("common", commongraph);
278			result.put("onlythis", onlythisgraph);
279			result.put("onlyother",onlyothergraph);
280			return result;
281			}
282	duarte	206
283			public boolean isModified(){
284			return modified;
285			}
286
287			public boolean isDirected(){
288			return directed;
289			}
290
291			public String getPdbCode() {
292			return pdbCode;
293			}
294
295			public String getPdbChainCode(){
296			return pdbChainCode;
297			}
298
299			public String getChainCode(){
300			return chainCode;
301			}
302
303			public String getSequence(){
304			return sequence;
305			}
306
307			public int getFullLength(){
308			return fullLength;
309			}
310
311			public int getObsLength(){
312			return obsLength;
313			}
314
315			public int getNumContacts(){
316			// in theory we could return just numContacts, because we have taken care of updating it every time contacts changed
317			// however we call directly contacts.size() as I feel is safer
318			return contacts.size();
319			}
320
321			public String getContactType() {
322			return ct;
323			}
324
325			public double getCutoff(){
326			return cutoff;
327			}
328	duarte	123	}