Molecule


1   package JSci.chemistry;
2   
3   import java.util.Collections  ;
4   import java.util.HashSet  ;
5   import java.util.Set  ;
6   import JSci.physics.*;
7   
8   /**
9   * A class representing molecules.
10  * @version 0.2
11  * @author Mark Hale
12  */
13  public class Molecule extends Particle {
14          /**
15          * Atoms.
16          */
17          private final Set   atoms = new HashSet  ();
18          /**
19          * Constructs a molecule from a chemical formula.
20          */
21          public Molecule(String   formula) {
22                  if(formula == null || formula.length() == 0)
23                          throw new IllegalArgumentException  ("Formula cannot be null or empty.");
24                  int startPos = 0, endPos;
25                  boolean isNumber = false;
26                  String   symbol = null;
27                  int count;
28                  for(int i=1; i<formula.length(); i++) {
29                          char ch = formula.charAt(i);
30                          if(Character.isUpperCase(ch)) {
31                                  endPos = i;
32                                  if(isNumber) {
33                                          count = Integer.parseInt(formula.substring(startPos, endPos));
34                                          isNumber = false;
35                                  } else {
36                                          symbol = formula.substring(startPos, endPos);
37                                          count = 1;
38                                  }
39                                  String   name = PeriodicTable.getName(symbol);
40                                  if(name != null) {
41                                          Element element = PeriodicTable.getElement(name);
42                                          for(int j=0; j<count; j++)
43                                                  atoms.add(new Atom(element));
44                                  }
45                                  startPos = endPos;
46                          } else if(!isNumber && Character.isDigit(ch)) {
47                                  isNumber = true;
48                                  endPos = i;
49                                  symbol = formula.substring(startPos, endPos);
50                                  startPos = endPos;
51                          }
52                  }
53                  endPos = formula.length();
54                  if(isNumber) {
55                          count = Integer.parseInt(formula.substring(startPos, endPos));
56                          isNumber = false;
57                  } else {
58                          symbol = formula.substring(startPos, endPos);
59                          count = 1;
60                  }
61                  String   name = PeriodicTable.getName(symbol);
62                  if(name != null) {
63                          Element element = PeriodicTable.getElement(name);
64                          for(int j=0; j<count; j++)
65                                  atoms.add(new Atom(element));
66                  }
67          }
68          /**
69          * Constructs a molecule from two atoms.
70          */
71          public Molecule(Atom a, Atom b) {
72                  atoms.add(a);
73                  atoms.add(b);
74          }
75          /**
76          * Constructs a molecule from an array of atoms.
77          */
78          public Molecule(Atom a[]) {
79                  for(int i=0; i<a.length; i++)
80                          atoms.add(a[i]);
81          }
82          /**
83          * Returns the atoms in this molecule.
84          */
85          public Set   getAtoms() {
86                  return Collections.unmodifiableSet(atoms);
87          }
88          /**
89          * Binds with an atom.
90          * @return this.
91          */
92          public Molecule bind(Atom a) {
93                  atoms.add(a);
94                  return this;
95          }
96          /**
97          * Binds with a molecule.
98          * @return this.
99          */
100         public Molecule bind(Molecule m) {
101                 atoms.addAll(m.atoms);
102                 return this;
103         }
104 }
105 
106
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