| 1 |
package proteinstructure; |
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import java.util.HashMap; |
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import java.util.ArrayList; |
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|
| 5 |
public class AA { |
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|
| 7 |
public static final String CONTACT_TYPE_C_ALPHA = "Ca"; |
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public static final String CONTACT_TYPE_C_BETA = "Cb"; |
| 9 |
|
| 10 |
public static String[] contactTypes() { |
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// NOTE: whenever a new contact type is added it needs to be added here as well as in ct2atoms |
| 12 |
String[] cts ={"ALL","BB","SC","Ca","Cb","Cg","C"}; |
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return cts; |
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} |
| 15 |
|
| 16 |
public static String[] singleAtomContactTypes() { |
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// NOTE: whenever a new contact type is added it needs to be added here as well as in ct2atoms |
| 18 |
String[] cts ={"Ca","Cb","Cg","C"}; |
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return cts; |
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} |
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|
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public static String[] multiAtomContactTypes() { |
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// NOTE: whenever a new contact type is added it needs to be added here as well as in ct2atoms |
| 24 |
String[] cts ={"ALL","BB","SC"}; |
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return cts; |
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} |
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|
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/** |
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* Returns true if given contact type is a valid one |
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* @param ct |
| 31 |
* @return |
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*/ |
| 33 |
public static boolean isValidCT(String ct){ |
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if (!ct.contains("/")){ |
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for (String validCt:contactTypes()){ |
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if (ct.equals(validCt)) return true; |
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} |
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} else { |
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String[] cts = ct.split("/"); |
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String i_ct = cts[0]; |
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String j_ct = cts[1]; |
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if (isValidCT(i_ct) && isValidCT(j_ct)) return true; |
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} |
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return false; |
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} |
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|
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/** |
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* Returns true if given contact type is a valid single atom contact type |
| 49 |
* @param ct |
| 50 |
* @return |
| 51 |
*/ |
| 52 |
public static boolean isValidSingleAtomCT(String ct) { |
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if (!ct.contains("/")){ |
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for (String validCt:singleAtomContactTypes()){ |
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if (ct.equals(validCt)) return true; |
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} |
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} else { |
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String[] cts = ct.split("/"); |
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String i_ct = cts[0]; |
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String j_ct = cts[1]; |
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if (isValidSingleAtomCT(i_ct) && isValidSingleAtomCT(j_ct)) return true; |
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} |
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return false; |
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} |
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|
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/** |
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* Returns true if given contact type is a valid multiple atom contact type |
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* @param ct |
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* @return |
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*/ |
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public static boolean isValidMultiAtomCT(String ct) { |
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if (!ct.contains("/")){ |
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for (String validCt:multiAtomContactTypes()){ |
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if (ct.equals(validCt)) return true; |
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} |
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} else { |
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String[] cts = ct.split("/"); |
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String i_ct = cts[0]; |
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String j_ct = cts[1]; |
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if (isValidMultiAtomCT(i_ct) && isValidMultiAtomCT(j_ct)) return true; |
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} |
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return false; |
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} |
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|
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private static HashMap<String,String> getThreeletter2oneletter() { |
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HashMap<String,String> three2oneletter = new HashMap<String,String>(); |
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three2oneletter.put("CYS", "C"); |
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three2oneletter.put("ASP", "D"); |
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three2oneletter.put("SER", "S"); |
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three2oneletter.put("GLN", "Q"); |
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three2oneletter.put("LYS", "K"); |
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three2oneletter.put("ILE", "I"); |
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three2oneletter.put("PRO", "P"); |
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three2oneletter.put("THR", "T"); |
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three2oneletter.put("PHE", "F"); |
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three2oneletter.put("ALA", "A"); |
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three2oneletter.put("GLY", "G"); |
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three2oneletter.put("HIS", "H"); |
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three2oneletter.put("GLU", "E"); |
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three2oneletter.put("LEU", "L"); |
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three2oneletter.put("ARG", "R"); |
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three2oneletter.put("TRP", "W"); |
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three2oneletter.put("VAL", "V"); |
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three2oneletter.put("ASN", "N"); |
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three2oneletter.put("TYR", "Y") ; |
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three2oneletter.put("MET", "M"); |
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return three2oneletter; |
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} |
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|
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public static String threeletter2oneletter(String three) { |
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HashMap<String,String> three2oneletter = getThreeletter2oneletter(); |
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return three2oneletter.get(three); |
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} |
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|
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private static HashMap<String,String> getOneletter2Threeletter(){ |
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HashMap<String,String> one2threeletter = new HashMap<String,String>(); |
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one2threeletter.put("C", "CYS"); |
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one2threeletter.put("D", "ASP"); |
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one2threeletter.put("S", "SER"); |
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one2threeletter.put("Q", "GLN"); |
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one2threeletter.put("K", "LYS"); |
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one2threeletter.put("I", "ILE"); |
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one2threeletter.put("P", "PRO"); |
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one2threeletter.put("T", "THR"); |
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one2threeletter.put("F", "PHE"); |
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one2threeletter.put("A", "ALA"); |
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one2threeletter.put("G", "GLY"); |
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one2threeletter.put("H", "HIS"); |
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one2threeletter.put("E", "GLU"); |
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one2threeletter.put("L", "LEU"); |
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one2threeletter.put("R", "ARG"); |
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one2threeletter.put("W", "TRP"); |
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one2threeletter.put("V", "VAL"); |
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one2threeletter.put("N", "ASN"); |
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one2threeletter.put("Y", "TYR"); |
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one2threeletter.put("M", "MET"); |
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return one2threeletter; |
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} |
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|
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public static String oneletter2threeletter(String one) { |
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HashMap<String,String> one2threeletter = getOneletter2Threeletter(); |
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return one2threeletter.get(one); |
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} |
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|
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public static ArrayList<String> aas() { |
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HashMap<String,String> three2oneletter = getThreeletter2oneletter(); |
| 147 |
ArrayList<String> aas = new ArrayList<String>(); |
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for (String aa:three2oneletter.keySet()) { |
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aas.add(aa); |
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} |
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return aas; |
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} |
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|
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public static HashMap<String,ArrayList<String>> getaas2atoms() { |
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HashMap<String,ArrayList<String>> aas2atoms = new HashMap<String,ArrayList<String>>(); |
| 156 |
aas2atoms.put("CYS", new ArrayList<String>()); |
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aas2atoms.get("CYS").add("SG"); |
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aas2atoms.get("CYS").add("CB"); |
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aas2atoms.get("CYS").add("O"); |
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aas2atoms.get("CYS").add("CA"); |
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aas2atoms.get("CYS").add("C"); |
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aas2atoms.get("CYS").add("N"); |
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aas2atoms.put("ASP", new ArrayList<String>()); |
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aas2atoms.get("ASP").add("N"); |
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aas2atoms.get("ASP").add("CB"); |
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aas2atoms.get("ASP").add("OD2"); |
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aas2atoms.get("ASP").add("CG"); |
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aas2atoms.get("ASP").add("CA"); |
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aas2atoms.get("ASP").add("C"); |
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aas2atoms.get("ASP").add("O"); |
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aas2atoms.get("ASP").add("OD1"); |
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aas2atoms.put("SER", new ArrayList<String>()); |
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aas2atoms.get("SER").add("C"); |
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aas2atoms.get("SER").add("N"); |
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aas2atoms.get("SER").add("CA"); |
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aas2atoms.get("SER").add("O"); |
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aas2atoms.get("SER").add("CB"); |
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aas2atoms.get("SER").add("OG"); |
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aas2atoms.put("GLN", new ArrayList<String>()); |
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aas2atoms.get("GLN").add("CA"); |
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aas2atoms.get("GLN").add("CG"); |
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aas2atoms.get("GLN").add("N"); |
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aas2atoms.get("GLN").add("NE2"); |
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aas2atoms.get("GLN").add("OE1"); |
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aas2atoms.get("GLN").add("CD"); |
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aas2atoms.get("GLN").add("C"); |
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aas2atoms.get("GLN").add("O"); |
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aas2atoms.get("GLN").add("CB"); |
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aas2atoms.put("LYS", new ArrayList<String>()); |
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aas2atoms.get("LYS").add("C"); |
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aas2atoms.get("LYS").add("CA"); |
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aas2atoms.get("LYS").add("N"); |
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aas2atoms.get("LYS").add("O"); |
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aas2atoms.get("LYS").add("CB"); |
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aas2atoms.get("LYS").add("CG"); |
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aas2atoms.get("LYS").add("CD"); |
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aas2atoms.get("LYS").add("CE"); |
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aas2atoms.get("LYS").add("NZ"); |
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aas2atoms.put("ASN", new ArrayList<String>()); |
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aas2atoms.get("ASN").add("ND2"); |
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aas2atoms.get("ASN").add("OD1"); |
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aas2atoms.get("ASN").add("CB"); |
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aas2atoms.get("ASN").add("O"); |
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aas2atoms.get("ASN").add("CG"); |
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aas2atoms.get("ASN").add("C"); |
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aas2atoms.get("ASN").add("CA"); |
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aas2atoms.get("ASN").add("N"); |
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aas2atoms.put("PRO", new ArrayList<String>()); |
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aas2atoms.get("PRO").add("O"); |
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aas2atoms.get("PRO").add("C"); |
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aas2atoms.get("PRO").add("CB"); |
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aas2atoms.get("PRO").add("CG"); |
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aas2atoms.get("PRO").add("CA"); |
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aas2atoms.get("PRO").add("CD"); |
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aas2atoms.get("PRO").add("N"); |
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aas2atoms.put("THR", new ArrayList<String>()); |
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aas2atoms.get("THR").add("CA"); |
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aas2atoms.get("THR").add("N"); |
| 219 |
aas2atoms.get("THR").add("C"); |
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aas2atoms.get("THR").add("CG2"); |
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aas2atoms.get("THR").add("OG1"); |
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aas2atoms.get("THR").add("CB"); |
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aas2atoms.get("THR").add("O"); |
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aas2atoms.put("PHE", new ArrayList<String>()); |
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aas2atoms.get("PHE").add("O"); |
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aas2atoms.get("PHE").add("CE2"); |
| 227 |
aas2atoms.get("PHE").add("CE1"); |
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aas2atoms.get("PHE").add("CG"); |
| 229 |
aas2atoms.get("PHE").add("C"); |
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aas2atoms.get("PHE").add("N"); |
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aas2atoms.get("PHE").add("CA"); |
| 232 |
aas2atoms.get("PHE").add("CB"); |
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aas2atoms.get("PHE").add("CD2"); |
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aas2atoms.get("PHE").add("CD1"); |
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aas2atoms.get("PHE").add("CZ"); |
| 236 |
aas2atoms.put("ALA", new ArrayList<String>()); |
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aas2atoms.get("ALA").add("CA"); |
| 238 |
aas2atoms.get("ALA").add("C"); |
| 239 |
aas2atoms.get("ALA").add("N"); |
| 240 |
aas2atoms.get("ALA").add("CB"); |
| 241 |
aas2atoms.get("ALA").add("O"); |
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aas2atoms.put("HIS", new ArrayList<String>()); |
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aas2atoms.get("HIS").add("CE1"); |
| 244 |
aas2atoms.get("HIS").add("CD2"); |
| 245 |
aas2atoms.get("HIS").add("ND1"); |
| 246 |
aas2atoms.get("HIS").add("CG"); |
| 247 |
aas2atoms.get("HIS").add("CB"); |
| 248 |
aas2atoms.get("HIS").add("O"); |
| 249 |
aas2atoms.get("HIS").add("C"); |
| 250 |
aas2atoms.get("HIS").add("CA"); |
| 251 |
aas2atoms.get("HIS").add("N"); |
| 252 |
aas2atoms.get("HIS").add("NE2"); |
| 253 |
aas2atoms.put("GLY", new ArrayList<String>()); |
| 254 |
aas2atoms.get("GLY").add("N"); |
| 255 |
aas2atoms.get("GLY").add("CA"); |
| 256 |
aas2atoms.get("GLY").add("C"); |
| 257 |
aas2atoms.get("GLY").add("O"); |
| 258 |
aas2atoms.put("ILE", new ArrayList<String>()); |
| 259 |
aas2atoms.get("ILE").add("CG2"); |
| 260 |
aas2atoms.get("ILE").add("CD1"); |
| 261 |
aas2atoms.get("ILE").add("O"); |
| 262 |
aas2atoms.get("ILE").add("N"); |
| 263 |
aas2atoms.get("ILE").add("CA"); |
| 264 |
aas2atoms.get("ILE").add("C"); |
| 265 |
aas2atoms.get("ILE").add("CB"); |
| 266 |
aas2atoms.get("ILE").add("CG1"); |
| 267 |
aas2atoms.put("LEU", new ArrayList<String>()); |
| 268 |
aas2atoms.get("LEU").add("N"); |
| 269 |
aas2atoms.get("LEU").add("CA"); |
| 270 |
aas2atoms.get("LEU").add("C"); |
| 271 |
aas2atoms.get("LEU").add("O"); |
| 272 |
aas2atoms.get("LEU").add("CB"); |
| 273 |
aas2atoms.get("LEU").add("CG"); |
| 274 |
aas2atoms.get("LEU").add("CD2"); |
| 275 |
aas2atoms.get("LEU").add("CD1"); |
| 276 |
aas2atoms.put("ARG", new ArrayList<String>()); |
| 277 |
aas2atoms.get("ARG").add("NH2"); |
| 278 |
aas2atoms.get("ARG").add("CZ"); |
| 279 |
aas2atoms.get("ARG").add("NE"); |
| 280 |
aas2atoms.get("ARG").add("CD"); |
| 281 |
aas2atoms.get("ARG").add("CG"); |
| 282 |
aas2atoms.get("ARG").add("C"); |
| 283 |
aas2atoms.get("ARG").add("CA"); |
| 284 |
aas2atoms.get("ARG").add("N"); |
| 285 |
aas2atoms.get("ARG").add("NH1"); |
| 286 |
aas2atoms.get("ARG").add("CB"); |
| 287 |
aas2atoms.get("ARG").add("O"); |
| 288 |
aas2atoms.put("TRP", new ArrayList<String>()); |
| 289 |
aas2atoms.get("TRP").add("CE2"); |
| 290 |
aas2atoms.get("TRP").add("CA"); |
| 291 |
aas2atoms.get("TRP").add("C"); |
| 292 |
aas2atoms.get("TRP").add("O"); |
| 293 |
aas2atoms.get("TRP").add("CB"); |
| 294 |
aas2atoms.get("TRP").add("CG"); |
| 295 |
aas2atoms.get("TRP").add("CD1"); |
| 296 |
aas2atoms.get("TRP").add("CD2"); |
| 297 |
aas2atoms.get("TRP").add("CH2"); |
| 298 |
aas2atoms.get("TRP").add("CZ3"); |
| 299 |
aas2atoms.get("TRP").add("CZ2"); |
| 300 |
aas2atoms.get("TRP").add("CE3"); |
| 301 |
aas2atoms.get("TRP").add("NE1"); |
| 302 |
aas2atoms.get("TRP").add("N"); |
| 303 |
aas2atoms.put("VAL", new ArrayList<String>()); |
| 304 |
aas2atoms.get("VAL").add("CG1"); |
| 305 |
aas2atoms.get("VAL").add("CB"); |
| 306 |
aas2atoms.get("VAL").add("O"); |
| 307 |
aas2atoms.get("VAL").add("C"); |
| 308 |
aas2atoms.get("VAL").add("CA"); |
| 309 |
aas2atoms.get("VAL").add("N"); |
| 310 |
aas2atoms.get("VAL").add("CG2"); |
| 311 |
aas2atoms.put("GLU", new ArrayList<String>()); |
| 312 |
aas2atoms.get("GLU").add("C"); |
| 313 |
aas2atoms.get("GLU").add("N"); |
| 314 |
aas2atoms.get("GLU").add("CA"); |
| 315 |
aas2atoms.get("GLU").add("OE2"); |
| 316 |
aas2atoms.get("GLU").add("OE1"); |
| 317 |
aas2atoms.get("GLU").add("CD"); |
| 318 |
aas2atoms.get("GLU").add("CG"); |
| 319 |
aas2atoms.get("GLU").add("CB"); |
| 320 |
aas2atoms.get("GLU").add("O"); |
| 321 |
aas2atoms.put("TYR", new ArrayList<String>()); |
| 322 |
aas2atoms.get("TYR").add("CD2"); |
| 323 |
aas2atoms.get("TYR").add("CD1"); |
| 324 |
aas2atoms.get("TYR").add("OH"); |
| 325 |
aas2atoms.get("TYR").add("CZ"); |
| 326 |
aas2atoms.get("TYR").add("CE2"); |
| 327 |
aas2atoms.get("TYR").add("N"); |
| 328 |
aas2atoms.get("TYR").add("CA"); |
| 329 |
aas2atoms.get("TYR").add("C"); |
| 330 |
aas2atoms.get("TYR").add("O"); |
| 331 |
aas2atoms.get("TYR").add("CB"); |
| 332 |
aas2atoms.get("TYR").add("CG"); |
| 333 |
aas2atoms.get("TYR").add("CE1"); |
| 334 |
aas2atoms.put("MET", new ArrayList<String>()); |
| 335 |
aas2atoms.get("MET").add("CA"); |
| 336 |
aas2atoms.get("MET").add("O"); |
| 337 |
aas2atoms.get("MET").add("C"); |
| 338 |
aas2atoms.get("MET").add("CB"); |
| 339 |
aas2atoms.get("MET").add("CE"); |
| 340 |
aas2atoms.get("MET").add("N"); |
| 341 |
aas2atoms.get("MET").add("CG"); |
| 342 |
aas2atoms.get("MET").add("SD"); |
| 343 |
return aas2atoms; |
| 344 |
|
| 345 |
} |
| 346 |
|
| 347 |
public static HashMap<String,String[]> ct2atoms(String ct) { |
| 348 |
ArrayList<String> aas = aas(); |
| 349 |
HashMap<String,String[]> ct2atoms = new HashMap<String,String[]>(); |
| 350 |
if (ct.equals("Ca")){ |
| 351 |
String[] atoms = {"CA"}; |
| 352 |
for (String aa:aas) { |
| 353 |
ct2atoms.put(aa, atoms); |
| 354 |
} |
| 355 |
} |
| 356 |
else if (ct.equals("Cb")){ |
| 357 |
String[] atoms = {"CB"}; |
| 358 |
for (String aa:aas) { |
| 359 |
ct2atoms.put(aa, atoms); |
| 360 |
} |
| 361 |
atoms = new String[1]; |
| 362 |
atoms[0]="CA"; |
| 363 |
ct2atoms.put("GLY", atoms); |
| 364 |
} |
| 365 |
else if (ct.equals("C")){ |
| 366 |
String[] atoms = {"C"}; |
| 367 |
for (String aa:aas) { |
| 368 |
ct2atoms.put(aa, atoms); |
| 369 |
} |
| 370 |
} |
| 371 |
else if (ct.equals("Cg")){ |
| 372 |
String[] atoms = {"SG"}; |
| 373 |
ct2atoms.put("CYS", atoms); |
| 374 |
atoms = new String[1]; |
| 375 |
atoms[0]= "CG"; |
| 376 |
ct2atoms.put("ASP", atoms); |
| 377 |
atoms = new String[1]; |
| 378 |
atoms[0]="OG"; |
| 379 |
ct2atoms.put("SER", atoms); |
| 380 |
atoms = new String[1]; |
| 381 |
atoms[0]="CG"; |
| 382 |
ct2atoms.put("GLN", atoms); |
| 383 |
atoms = new String[1]; |
| 384 |
atoms[0]="CD"; |
| 385 |
ct2atoms.put("LYS", atoms); |
| 386 |
atoms = new String[1]; |
| 387 |
atoms[0]="CG1"; |
| 388 |
ct2atoms.put("ILE", atoms); |
| 389 |
atoms = new String[1]; |
| 390 |
atoms[0]="CG"; |
| 391 |
ct2atoms.put("PRO", atoms); |
| 392 |
atoms = new String[1]; |
| 393 |
atoms[0]="OG1"; |
| 394 |
ct2atoms.put("THR", atoms); |
| 395 |
atoms = new String[1]; |
| 396 |
atoms[0]="CG"; |
| 397 |
ct2atoms.put("PHE", atoms); |
| 398 |
ct2atoms.put("ALA", new String[0]); |
| 399 |
ct2atoms.put("GLY", new String[0]); |
| 400 |
atoms = new String[1]; |
| 401 |
atoms[0]="CG"; |
| 402 |
ct2atoms.put("HIS", atoms); |
| 403 |
atoms = new String[1]; |
| 404 |
atoms[0]="CG"; |
| 405 |
ct2atoms.put("GLU", atoms); |
| 406 |
atoms = new String[1]; |
| 407 |
atoms[0]="CG"; |
| 408 |
ct2atoms.put("LEU", atoms); |
| 409 |
atoms = new String[1]; |
| 410 |
atoms[0]="NE"; |
| 411 |
ct2atoms.put("ARG", atoms); |
| 412 |
atoms = new String[1]; |
| 413 |
atoms[0]="CD2"; |
| 414 |
ct2atoms.put("TRP", atoms); |
| 415 |
atoms = new String[1]; |
| 416 |
atoms[0]="CG1"; |
| 417 |
ct2atoms.put("VAL", atoms); |
| 418 |
atoms = new String[1]; |
| 419 |
atoms[0]="CG"; |
| 420 |
ct2atoms.put("ASN", atoms); |
| 421 |
atoms = new String[1]; |
| 422 |
atoms[0]="CG"; |
| 423 |
ct2atoms.put("TYR", atoms); |
| 424 |
atoms = new String[1]; |
| 425 |
atoms[0]="CG"; |
| 426 |
ct2atoms.put("MET", atoms); |
| 427 |
} |
| 428 |
else if (ct.equals("BB")){ |
| 429 |
String[] atoms = {"CA", "N", "C", "O"}; |
| 430 |
for (String aa:aas) { |
| 431 |
ct2atoms.put(aa, atoms); |
| 432 |
} |
| 433 |
} |
| 434 |
else if (ct.equals("SC")){ |
| 435 |
HashMap<String,ArrayList<String>> aas2atoms = getaas2atoms(); |
| 436 |
for (String aa:aas) { |
| 437 |
ArrayList<String> SCatoms =aas2atoms.get(aa); |
| 438 |
SCatoms.remove("CA"); |
| 439 |
SCatoms.remove("N"); |
| 440 |
SCatoms.remove("C"); |
| 441 |
SCatoms.remove("O"); |
| 442 |
String[] SCatomsar= new String[SCatoms.size()]; |
| 443 |
SCatomsar=SCatoms.toArray(SCatomsar); |
| 444 |
ct2atoms.put(aa, SCatomsar); |
| 445 |
} |
| 446 |
} |
| 447 |
else if (ct.equals("ALL")){ |
| 448 |
HashMap<String,ArrayList<String>> aas2atoms = getaas2atoms(); |
| 449 |
for (String aa:aas) { |
| 450 |
ArrayList<String> ALLatoms = aas2atoms.get(aa); |
| 451 |
String[] ALLatomsar= new String[ALLatoms.size()]; |
| 452 |
ALLatomsar=ALLatoms.toArray(ALLatomsar); |
| 453 |
ct2atoms.put(aa,ALLatomsar); |
| 454 |
} |
| 455 |
} |
| 456 |
return ct2atoms; |
| 457 |
} |
| 458 |
} |
