*
*/
-public class ChimeraResidue implements ChimeraStructuralObject, Comparable<ChimeraResidue> {
-
- /* Constants */
- public static final int SINGLE_LETTER = 0; // Display residues as a single
- // letter
- public static final int THREE_LETTER = 1; // Display residues as three letters
- public static final int FULL_NAME = 2; // Display full residue names
-
- private String type; // Residue type
- private String index; // Residue index
- private String chainId; // ChainID for this residue
- private int modelNumber; // model number for this residue
- private int subModelNumber; // sub-model number for this residue
- protected int residueNumber;
- protected String insertionCode;
- private ChimeraModel chimeraModel; // ChimeraModel the residue is part of
- private Object userData; // user data to associate with this residue
- // public static HashMap<String, String> aaNames = null; // a map of amino acid
- // names
- private static int displayType = THREE_LETTER; // the current display type
- private boolean selected = false; // the selection state
-
- /**
- * Constructor to create a new ChimeraResidue
- *
- * @param type
- * the residue type
- * @param index
- * the index of the residue
- * @param modelNumber
- * the model number this residue is part of
- */
- public ChimeraResidue(String type, String index, int modelNumber) {
- this(type, index, modelNumber, 0);
- }
-
- /**
- * Constructor to create a new ChimeraResidue
- *
- * @param type
- * the residue type
- * @param index
- * the index of the residue
- * @param modelNumber
- * the model number this residue is part of
- * @param subModelNumber
- * the sub-model number this residue is part of
- */
- public ChimeraResidue(String type, String index, int modelNumber, int subModelNumber) {
- this.type = type;
- this.index = index;
- this.modelNumber = modelNumber;
- this.subModelNumber = subModelNumber;
- splitInsertionCode(this.index);
- // if (aaNames == null) {
- // initNames();
- // }
- }
-
- /**
- * Constructor to create a new ChimeraResidue from an input line
- *
- * @param chimeraInputLine
- * a Chimera residue description
- */
- // invoked when listing (selected) residues: listr spec #0; lists level residue
- // Line: residue id #0:37.A type MET
- public ChimeraResidue(String chimeraInputLine) {
- // initNames();
- String[] split1 = chimeraInputLine.split(":");
-
- // First half has model number -- get the number
- int numberOffset = split1[0].indexOf('#');
- String model = split1[0].substring(numberOffset + 1);
- int decimalOffset = model.indexOf('.'); // Do we have a sub-model?
- try {
- this.subModelNumber = 0;
- if (decimalOffset > 0) {
- this.subModelNumber = Integer.parseInt(model.substring(decimalOffset + 1));
- this.modelNumber = Integer.parseInt(model.substring(0, decimalOffset));
- } else {
- this.modelNumber = Integer.parseInt(model);
- }
- } catch (Exception e) {
- LoggerFactory.getLogger(ChimeraResidue.class)
- .error("Unexpected return from Chimera: " + model);
- this.modelNumber = -1;
- }
-
- // Second half has residue info: index & type
- String[] rTokens = split1[1].split(" ");
- this.type = rTokens[2];
-
- String[] iTokens = rTokens[0].split("\\.");
- if (iTokens.length > 0) {
- this.index = iTokens[0];
-
- // Careful, might or might not have a chainID
- if (iTokens.length > 1)
- this.chainId = iTokens[1];
- else
- this.chainId = "_";
- } else
- this.index = rTokens[0];
-
- splitInsertionCode(this.index);
- }
-
- /**
- * Set the selected state for this residue
- *
- * @param selected
- * the selection state to set
- */
- public void setSelected(boolean selected) {
- this.selected = selected;
- }
-
- /**
- * Return the selected state of this residue
- *
- * @return the selected state
- */
- public boolean isSelected() {
- return selected;
- }
-
- /**
- * Return an array made up of this residue (required for ChimeraStructuralObject interface
- *
- * @return a List with this residue as its sole member
- */
- public List<ChimeraStructuralObject> getChildren() {
- List<ChimeraStructuralObject> v = new ArrayList<ChimeraStructuralObject>();
- v.add(this);
- return v;
- }
-
- /**
- * Return the string representation of this residue as follows: "<i>residue_name</i> <i>index</i>"
- * where <i>residue_name</i> could be either the single letter, three letter, or full name
- * representation of the amino acid.
- *
- * @return the string representation
- */
- public String displayName() {
- return toString();
- }
-
- /**
- * Return the string representation of this residue as follows: "<i>residue_name</i> <i>index</i>"
- * where <i>residue_name</i> could be either the single letter, three letter, or full name
- * representation of the amino acid.
- *
- * @return the string representation
- */
- public String toString() {
- if (displayType == FULL_NAME) {
- return (ChimUtils.toFullName(type) + " " + index);
- } else if (displayType == SINGLE_LETTER) {
- return (ChimUtils.toSingleLetter(type) + " " + index);
- } else if (displayType == THREE_LETTER) {
- return (ChimUtils.toThreeLetter(type) + " " + index);
- } else {
- return (type + " " + index);
- }
- }
-
- /**
- * Return the Chimera specification for this Residue
- *
- * @return Chimera specification
- */
- public String toSpec() {
- if (!chainId.equals("_"))
- return ("#" + modelNumber + ":" + index + "." + chainId);
- else
- return ("#" + modelNumber + ":" + index + ".");
- }
-
- /**
- * Get the index of this residue
- *
- * @return residue index
- */
- public String getIndex() {
- return this.index;
- }
-
- /**
- * Get the chainID for this residue
- *
- * @return String value of the chainId
- */
- public String getChainId() {
- return this.chainId;
- }
-
- /**
- * Get the type for this residue
- *
- * @return residue type
- */
- public String getType() {
- return this.type;
- }
-
- /**
- * Get the model number for this residue
- *
- * @return the model number
- */
- public int getModelNumber() {
- return this.modelNumber;
- }
-
- /**
- * Get the sub-model number for this residue
- *
- * @return the sub-model number
- */
- public int getSubModelNumber() {
- return this.subModelNumber;
- }
-
- /**
- * Get the model this residue is part of
- *
- * @return the ChimeraModel
- */
- public ChimeraModel getChimeraModel() {
- return this.chimeraModel;
- }
-
- /**
- * Set the model this residue is part of
- *
- * @param chimeraModel
- * the ChimeraModel this model is part of
- */
- public void setChimeraModel(ChimeraModel chimeraModel) {
- this.chimeraModel = chimeraModel;
- }
-
- /**
- * Get the user data for this residue
- *
- * @return user data
- */
- public Object getUserData() {
- return userData;
- }
-
- /**
- * Set the user data for this Residue
- *
- * @param data
- * the user data to associate with this residue
- */
- public void setUserData(Object data) {
- this.userData = data;
- }
-
- public int compareTo(ChimeraResidue c2) {
- if (residueNumber < c2.residueNumber)
- return -1;
- else if (residueNumber == c2.residueNumber) {
- if (insertionCode == null && c2.insertionCode == null)
- return 0;
- else if (insertionCode == null)
- return -1;
- else if (c2.insertionCode == null)
- return 1;
- return (insertionCode.compareTo(c2.insertionCode));
- }
- return 1;
- }
-
- public void splitInsertionCode(String residue) {
- // OK, split the index into number and insertion code
- Pattern p = Pattern.compile("(\\d*)([A-Z]?)");
- Matcher m = p.matcher(residue);
- if (m.matches()) {
- this.residueNumber = Integer.parseInt(m.group(1));
- if (m.groupCount() > 1)
- this.insertionCode = m.group(2);
- else
- this.insertionCode = null;
- }
- }
-
- /**********************************************
- * Static routines
- *********************************************/
-
- /**
- * Initialize the residue names
- */
- // private static void initNames() {
- // // Create our residue name table
- // aaNames = new HashMap<String, String>();
- // aaNames.put("ALA", "A Ala Alanine N[C@@H](C)C(O)=O");
- // aaNames.put("ARG", "R Arg Arginine N[C@@H](CCCNC(N)=N)C(O)=O");
- // aaNames.put("ASN", "N Asn Asparagine N[C@@H](CC(N)=O)C(O)=O");
- // aaNames.put("ASP", "D Asp Aspartic_acid N[C@@H](CC(O)=O)C(O)=O");
- // aaNames.put("CYS", "C Cys Cysteine N[C@@H](CS)C(O)=O");
- // aaNames.put("GLN", "Q Gln Glutamine N[C@H](C(O)=O)CCC(N)=O");
- // aaNames.put("GLU", "E Glu Glumatic_acid N[C@H](C(O)=O)CCC(O)=O");
- // aaNames.put("GLY", "G Gly Glycine NCC(O)=O");
- // aaNames.put("HIS", "H His Histidine N[C@@H](CC1=CN=CN1)C(O)=O");
- // aaNames.put("ILE", "I Ile Isoleucine N[C@]([C@H](C)CC)([H])C(O)=O");
- // aaNames.put("LEU", "L Leu Leucine N[C@](CC(C)C)([H])C(O)=O");
- // aaNames.put("LYS", "K Lys Lysine N[C@](CCCCN)([H])C(O)=O");
- // aaNames.put("DLY", "K Dly D-Lysine NCCCC[C@@H](N)C(O)=O");
- // aaNames.put("MET", "M Met Methionine N[C@](CCSC)([H])C(O)=O");
- // aaNames.put("PHE", "F Phe Phenylalanine N[C@](CC1=CC=CC=C1)([H])C(O)=O");
- // aaNames.put("PRO", "P Pro Proline OC([C@@]1([H])NCCC1)=O");
- // aaNames.put("SER", "S Ser Serine OC[C@](C(O)=O)([H])N");
- // aaNames.put("THR", "T Thr Threonine O[C@H](C)[C@](C(O)=O)([H])N");
- // aaNames.put("TRP", "W Trp Tryptophan N[C@@]([H])(CC1=CN([H])C2=C1C=CC=C2)C(O)=O");
- // aaNames.put("TYR", "Y Tyr Tyrosine N[C@@](C(O)=O)([H])CC1=CC=C(O)C=C1");
- // aaNames.put("VAL", "V Val Valine N[C@@](C(O)=O)([H])C(C)C");
- // aaNames.put("ASX", "B Asx Aspartic_acid_or_Asparagine");
- // aaNames.put("GLX", "Z Glx Glutamine_or_Glutamic_acid");
- // aaNames.put("XAA", "X Xaa Any_or_unknown_amino_acid");
- // aaNames.put("HOH", "HOH HOH Water [H]O[H]");
- // }
-
- /**
- * Set the display type.
- *
- * @param type
- * the display type
- */
- public static void setDisplayType(int type) {
- displayType = type;
- }
-
- public static int getDisplayType() {
- return displayType;
- }
-
- public boolean hasSelectedChildren() {
- return false;
- }
+public class ChimeraResidue implements ChimeraStructuralObject,
+ Comparable<ChimeraResidue>
+{
+
+ /* Constants */
+ public static final int SINGLE_LETTER = 0; // Display residues as a single
+ // letter
+
+ public static final int THREE_LETTER = 1; // Display residues as three letters
+
+ public static final int FULL_NAME = 2; // Display full residue names
+
+ private String type; // Residue type
+
+ private String index; // Residue index
+
+ private String chainId; // ChainID for this residue
+
+ private int modelNumber; // model number for this residue
+
+ private int subModelNumber; // sub-model number for this residue
+
+ protected int residueNumber;
+
+ protected String insertionCode;
+
+ private ChimeraModel chimeraModel; // ChimeraModel the residue is part of
+
+ private Object userData; // user data to associate with this residue
+
+ // public static HashMap<String, String> aaNames = null; // a map of amino
+ // acid
+ // names
+ private static int displayType = THREE_LETTER; // the current display type
+
+ private boolean selected = false; // the selection state
+
+ /**
+ * Constructor to create a new ChimeraResidue
+ *
+ * @param type
+ * the residue type
+ * @param index
+ * the index of the residue
+ * @param modelNumber
+ * the model number this residue is part of
+ */
+ public ChimeraResidue(String type, String index, int modelNumber)
+ {
+ this(type, index, modelNumber, 0);
+ }
+
+ /**
+ * Constructor to create a new ChimeraResidue
+ *
+ * @param type
+ * the residue type
+ * @param index
+ * the index of the residue
+ * @param modelNumber
+ * the model number this residue is part of
+ * @param subModelNumber
+ * the sub-model number this residue is part of
+ */
+ public ChimeraResidue(String type, String index, int modelNumber,
+ int subModelNumber)
+ {
+ this.type = type;
+ this.index = index;
+ this.modelNumber = modelNumber;
+ this.subModelNumber = subModelNumber;
+ splitInsertionCode(this.index);
+ // if (aaNames == null) {
+ // initNames();
+ // }
+ }
+
+ /**
+ * Constructor to create a new ChimeraResidue from an input line
+ *
+ * @param chimeraInputLine
+ * a Chimera residue description
+ */
+ // invoked when listing (selected) residues: listr spec #0; lists level
+ // residue
+ // Line: residue id #0:37.A type MET
+ public ChimeraResidue(String chimeraInputLine)
+ {
+ // initNames();
+ String[] split1 = chimeraInputLine.split(":");
+
+ // First half has model number -- get the number
+ int numberOffset = split1[0].indexOf('#');
+ String model = split1[0].substring(numberOffset + 1);
+ int decimalOffset = model.indexOf('.'); // Do we have a sub-model?
+ try
+ {
+ this.subModelNumber = 0;
+ if (decimalOffset > 0)
+ {
+ this.subModelNumber = Integer.parseInt(model
+ .substring(decimalOffset + 1));
+ this.modelNumber = Integer.parseInt(model.substring(0,
+ decimalOffset));
+ }
+ else
+ {
+ this.modelNumber = Integer.parseInt(model);
+ }
+ } catch (Exception e)
+ {
+ LoggerFactory.getLogger(ChimeraResidue.class).error(
+ "Unexpected return from Chimera: " + model);
+ this.modelNumber = -1;
+ }
+
+ // Second half has residue info: index & type
+ String[] rTokens = split1[1].split(" ");
+ this.type = rTokens[2];
+
+ String[] iTokens = rTokens[0].split("\\.");
+ if (iTokens.length > 0)
+ {
+ this.index = iTokens[0];
+
+ // Careful, might or might not have a chainID
+ if (iTokens.length > 1)
+ this.chainId = iTokens[1];
+ else
+ this.chainId = "_";
+ }
+ else
+ this.index = rTokens[0];
+
+ splitInsertionCode(this.index);
+ }
+
+ /**
+ * Set the selected state for this residue
+ *
+ * @param selected
+ * the selection state to set
+ */
+ public void setSelected(boolean selected)
+ {
+ this.selected = selected;
+ }
+
+ /**
+ * Return the selected state of this residue
+ *
+ * @return the selected state
+ */
+ public boolean isSelected()
+ {
+ return selected;
+ }
+
+ /**
+ * Return an array made up of this residue (required for
+ * ChimeraStructuralObject interface
+ *
+ * @return a List with this residue as its sole member
+ */
+ public List<ChimeraStructuralObject> getChildren()
+ {
+ List<ChimeraStructuralObject> v = new ArrayList<ChimeraStructuralObject>();
+ v.add(this);
+ return v;
+ }
+
+ /**
+ * Return the string representation of this residue as follows:
+ * "<i>residue_name</i> <i>index</i>" where <i>residue_name</i> could be
+ * either the single letter, three letter, or full name representation of the
+ * amino acid.
+ *
+ * @return the string representation
+ */
+ public String displayName()
+ {
+ return toString();
+ }
+
+ /**
+ * Return the string representation of this residue as follows:
+ * "<i>residue_name</i> <i>index</i>" where <i>residue_name</i> could be
+ * either the single letter, three letter, or full name representation of the
+ * amino acid.
+ *
+ * @return the string representation
+ */
+ public String toString()
+ {
+ if (displayType == FULL_NAME)
+ {
+ return (ChimUtils.toFullName(type) + " " + index);
+ }
+ else if (displayType == SINGLE_LETTER)
+ {
+ return (ChimUtils.toSingleLetter(type) + " " + index);
+ }
+ else if (displayType == THREE_LETTER)
+ {
+ return (ChimUtils.toThreeLetter(type) + " " + index);
+ }
+ else
+ {
+ return (type + " " + index);
+ }
+ }
+
+ /**
+ * Return the Chimera specification for this Residue
+ *
+ * @return Chimera specification
+ */
+ public String toSpec()
+ {
+ if (!chainId.equals("_"))
+ return ("#" + modelNumber + ":" + index + "." + chainId);
+ else
+ return ("#" + modelNumber + ":" + index + ".");
+ }
+
+ /**
+ * Get the index of this residue
+ *
+ * @return residue index
+ */
+ public String getIndex()
+ {
+ return this.index;
+ }
+
+ /**
+ * Get the chainID for this residue
+ *
+ * @return String value of the chainId
+ */
+ public String getChainId()
+ {
+ return this.chainId;
+ }
+
+ /**
+ * Get the type for this residue
+ *
+ * @return residue type
+ */
+ public String getType()
+ {
+ return this.type;
+ }
+
+ /**
+ * Get the model number for this residue
+ *
+ * @return the model number
+ */
+ public int getModelNumber()
+ {
+ return this.modelNumber;
+ }
+
+ /**
+ * Get the sub-model number for this residue
+ *
+ * @return the sub-model number
+ */
+ public int getSubModelNumber()
+ {
+ return this.subModelNumber;
+ }
+
+ /**
+ * Get the model this residue is part of
+ *
+ * @return the ChimeraModel
+ */
+ public ChimeraModel getChimeraModel()
+ {
+ return this.chimeraModel;
+ }
+
+ /**
+ * Set the model this residue is part of
+ *
+ * @param chimeraModel
+ * the ChimeraModel this model is part of
+ */
+ public void setChimeraModel(ChimeraModel chimeraModel)
+ {
+ this.chimeraModel = chimeraModel;
+ }
+
+ /**
+ * Get the user data for this residue
+ *
+ * @return user data
+ */
+ public Object getUserData()
+ {
+ return userData;
+ }
+
+ /**
+ * Set the user data for this Residue
+ *
+ * @param data
+ * the user data to associate with this residue
+ */
+ public void setUserData(Object data)
+ {
+ this.userData = data;
+ }
+
+ public int compareTo(ChimeraResidue c2)
+ {
+ if (residueNumber < c2.residueNumber)
+ return -1;
+ else if (residueNumber == c2.residueNumber)
+ {
+ if (insertionCode == null && c2.insertionCode == null)
+ return 0;
+ else if (insertionCode == null)
+ return -1;
+ else if (c2.insertionCode == null)
+ return 1;
+ return (insertionCode.compareTo(c2.insertionCode));
+ }
+ return 1;
+ }
+
+ public void splitInsertionCode(String residue)
+ {
+ // OK, split the index into number and insertion code
+ Pattern p = Pattern.compile("(\\d*)([A-Z]?)");
+ Matcher m = p.matcher(residue);
+ if (m.matches())
+ {
+ this.residueNumber = Integer.parseInt(m.group(1));
+ if (m.groupCount() > 1)
+ this.insertionCode = m.group(2);
+ else
+ this.insertionCode = null;
+ }
+ }
+
+ /**********************************************
+ * Static routines
+ *********************************************/
+
+ /**
+ * Initialize the residue names
+ */
+ // private static void initNames() {
+ // // Create our residue name table
+ // aaNames = new HashMap<String, String>();
+ // aaNames.put("ALA", "A Ala Alanine N[C@@H](C)C(O)=O");
+ // aaNames.put("ARG", "R Arg Arginine N[C@@H](CCCNC(N)=N)C(O)=O");
+ // aaNames.put("ASN", "N Asn Asparagine N[C@@H](CC(N)=O)C(O)=O");
+ // aaNames.put("ASP", "D Asp Aspartic_acid N[C@@H](CC(O)=O)C(O)=O");
+ // aaNames.put("CYS", "C Cys Cysteine N[C@@H](CS)C(O)=O");
+ // aaNames.put("GLN", "Q Gln Glutamine N[C@H](C(O)=O)CCC(N)=O");
+ // aaNames.put("GLU", "E Glu Glumatic_acid N[C@H](C(O)=O)CCC(O)=O");
+ // aaNames.put("GLY", "G Gly Glycine NCC(O)=O");
+ // aaNames.put("HIS", "H His Histidine N[C@@H](CC1=CN=CN1)C(O)=O");
+ // aaNames.put("ILE", "I Ile Isoleucine N[C@]([C@H](C)CC)([H])C(O)=O");
+ // aaNames.put("LEU", "L Leu Leucine N[C@](CC(C)C)([H])C(O)=O");
+ // aaNames.put("LYS", "K Lys Lysine N[C@](CCCCN)([H])C(O)=O");
+ // aaNames.put("DLY", "K Dly D-Lysine NCCCC[C@@H](N)C(O)=O");
+ // aaNames.put("MET", "M Met Methionine N[C@](CCSC)([H])C(O)=O");
+ // aaNames.put("PHE", "F Phe Phenylalanine N[C@](CC1=CC=CC=C1)([H])C(O)=O");
+ // aaNames.put("PRO", "P Pro Proline OC([C@@]1([H])NCCC1)=O");
+ // aaNames.put("SER", "S Ser Serine OC[C@](C(O)=O)([H])N");
+ // aaNames.put("THR", "T Thr Threonine O[C@H](C)[C@](C(O)=O)([H])N");
+ // aaNames.put("TRP",
+ // "W Trp Tryptophan N[C@@]([H])(CC1=CN([H])C2=C1C=CC=C2)C(O)=O");
+ // aaNames.put("TYR", "Y Tyr Tyrosine N[C@@](C(O)=O)([H])CC1=CC=C(O)C=C1");
+ // aaNames.put("VAL", "V Val Valine N[C@@](C(O)=O)([H])C(C)C");
+ // aaNames.put("ASX", "B Asx Aspartic_acid_or_Asparagine");
+ // aaNames.put("GLX", "Z Glx Glutamine_or_Glutamic_acid");
+ // aaNames.put("XAA", "X Xaa Any_or_unknown_amino_acid");
+ // aaNames.put("HOH", "HOH HOH Water [H]O[H]");
+ // }
+
+ /**
+ * Set the display type.
+ *
+ * @param type
+ * the display type
+ */
+ public static void setDisplayType(int type)
+ {
+ displayType = type;
+ }
+
+ public static int getDisplayType()
+ {
+ return displayType;
+ }
+
+ public boolean hasSelectedChildren()
+ {
+ return false;
+ }
}
git://source.jalview.org / jalview.git / blobdiff