rapodaca / mx forked from metamolecular/mx

branch 66a98a3

To reproduce: http://gist.github.com/129352

Expected: test passes

Found: test throws with

 [java] 1) testMapperFromCopiedMolecule(Test)java.lang.ArrayIndexOutOfBoundsException: -1
 [java]     at java.util.ArrayList.get(ArrayList.java:323)
 [java]     at com.metamolecular.mx.query.DefaultQuery.<init>(DefaultQuery.java:64)
 [java]     at com.metamolecular.mx.map.DefaultMapper.<init>(DefaultMapper.java:54)
 [java]     at Test.testMapperFromCopiedMolecule(Test.java:13)
 [java]     at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
 [java]     at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
 [java]     at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
 [java]     at TestEnvironment.main(TestEnvironment.java:13)

 [java] FAILURES!!!
 [java] Tests run: 1,  Failures: 0,  Errors: 1

66a98a3

Expected molfile comment line to read:

Created with MX - http://rapodaca.github.com/mx

but got this instead:

Created with ChemWriter - http://metamolecular.com/chemwriter

1. [http://gist.github.com/129344](To reproduce)
   
2. Expected that test passes.
   
3. Saw that test fails.

To reproduce: http://gist.github.com/130536

Expected: test passes

Found: Test fails

MX should create binary fingerprints from arbitrary Molecules. A Fingerprinter interface and a PathFingerprinter default implementation should be given.

Neither MolfileReader nor MolfileWriter currently support atom values (V) in the properties block. For example:

[NO NAME]
  CHEMWRIT          2D
Created with MX - http://rapodaca.github.com/mx
  6  6  0  0  0  0  0  0  0  0  0 V2000
   -8.0649    0.7078    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1989    0.2078    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3329    0.7078    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3329    1.7078    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1989    2.2078    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.0649    1.7078    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  1  1  0  0  0  0
V    1 This is carbon 1
V    2 This is carbon 2
V    3 And this is carbon 3
M  END

A partially-implemented SMILES is not very useful and casts doubt on the completeness of other MX features. SMILESReader should be placed into a separate branch and worked on until it is fully implemented, then moved onto master and into subsequent releases.