 ../
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scoring/
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1287
(11 years ago)
by matt4077:
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alignment/
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1305
(11 years ago)
by jmduarteg:
Renaming all xxxxError named exceptions to xxxxException. Long overdue thing (was historical because it came from python). Learnt just recently that java does have a concept of Error too.
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features/
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1306
(11 years ago)
by jmduarteg:
Added Serializable interface to many classes. To be able to serialize classes containing objects of these types.
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graphs/
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1316
(11 years ago)
by jmduarteg:
Got rid (finally!) of AAinfo. Its functionality is now in ContactType and AminoAcid.
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PdbLoadError.java
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1005
(12 years ago)
by hstehr:
refactoring: renaming proteinstructure to structure and tools to util; moving connections,features,runners,sequence,structure,util to owl.core
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PolResidue.java
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1005
(12 years ago)
by hstehr:
refactoring: renaming proteinstructure to structure and tools to util; moving connections,features,runners,sequence,structure,util to owl.core
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Polymer.java
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1005
(12 years ago)
by hstehr:
refactoring: renaming proteinstructure to structure and tools to util; moving connections,features,runners,sequence,structure,util to owl.core
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BackboneCoords.java
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1009
(12 years ago)
by hstehr:
refactoring: moved many many classes to more appropriate packages; created new packages owl.core.sequence.alignment, owl.core.structure.alignment, owl.core.structure.features
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aapairsBounds.dat
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1012
(12 years ago)
by hstehr:
bugfix: hard-coded paths to files aapairsBounds.dat and contactTypes.dat had to be updated following the refactoring (this was already fixed by previous commit); introduced proper error messags if files are not found
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symop.lib
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1179
(11 years ago)
by jmduarteg:
New classes to parse and store crystallographic space groups info.
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vdw.radii
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1247
(11 years ago)
by jmduarteg:
Implemented our own ASA calculation! Taken from Bosco's python implementation, thanks again Bosco!
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Atom.java
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1248
(11 years ago)
by jmduarteg:
Now using our own ASA calculation instead of NACCESS for the interface areas calculation. We are slower than NACCESS but at least don't depend on it anymore, old NACCESS methods can still be used.
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Asa.java
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1255
(11 years ago)
by jmduarteg:
Minor changes to the test.
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AtomRadii.java
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1258
(11 years ago)
by jmduarteg:
Fixed bug: now we properly parse from pisa both the orthonormal and the crystal coords operators.
Added a test for SpaceGroup to test for proper parsing of algebraic strings
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InterfaceRimCore.java
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1264
(11 years ago)
by jmduarteg:
Added printing of rim and core residues methods.
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SymoplibParser.java
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1281
(11 years ago)
by jmduarteg:
Now checking that the space group read from file/db is correct, if not PdbLoadError thrown.
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PdbUnitCell.java
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1284
(11 years ago)
by cvehlow:
Overrides removed
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contactTypes.dat
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1302
(11 years ago)
by hstehr:
adding ALL_H contact type to contactTypes.dat because otherwise AAinfo.isValidAtomWithOXT() breaks with a NullPointerException
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PdbAsymUnit.java
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1305
(11 years ago)
by jmduarteg:
Renaming all xxxxError named exceptions to xxxxException. Long overdue thing (was historical because it came from python). Learnt just recently that java does have a concept of Error too.
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TemplateList.java
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1305
(11 years ago)
by jmduarteg:
Renaming all xxxxError named exceptions to xxxxException. Long overdue thing (was historical because it came from python). Learnt just recently that java does have a concept of Error too.
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PdbChainCodeNotFoundException.java
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1305
(11 years ago)
by jmduarteg:
Renaming all xxxxError named exceptions to xxxxException. Long overdue thing (was historical because it came from python). Learnt just recently that java does have a concept of Error too.
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ConformationsNotSameSizeException.java
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1305
(11 years ago)
by jmduarteg:
Renaming all xxxxError named exceptions to xxxxException. Long overdue thing (was historical because it came from python). Learnt just recently that java does have a concept of Error too.
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PdbaseInconsistencyException.java
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1305
(11 years ago)
by jmduarteg:
Renaming all xxxxError named exceptions to xxxxException. Long overdue thing (was historical because it came from python). Learnt just recently that java does have a concept of Error too.
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PdbSet.java
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1305
(11 years ago)
by jmduarteg:
Renaming all xxxxError named exceptions to xxxxException. Long overdue thing (was historical because it came from python). Learnt just recently that java does have a concept of Error too.
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Template.java
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1305
(11 years ago)
by jmduarteg:
Renaming all xxxxError named exceptions to xxxxException. Long overdue thing (was historical because it came from python). Learnt just recently that java does have a concept of Error too.
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PdbCodeNotFoundException.java
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1305
(11 years ago)
by jmduarteg:
Renaming all xxxxError named exceptions to xxxxException. Long overdue thing (was historical because it came from python). Learnt just recently that java does have a concept of Error too.
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SpaceGroup.java
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1306
(11 years ago)
by jmduarteg:
Added Serializable interface to many classes. To be able to serialize classes containing objects of these types.
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CrystalCell.java
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1306
(11 years ago)
by jmduarteg:
Added Serializable interface to many classes. To be able to serialize classes containing objects of these types.
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ContactType.java
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1316
(11 years ago)
by jmduarteg:
Got rid (finally!) of AAinfo. Its functionality is now in ContactType and AminoAcid.
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AminoAcid.java
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1316
(11 years ago)
by jmduarteg:
Got rid (finally!) of AAinfo. Its functionality is now in ContactType and AminoAcid.
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Pdb.java
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1316
(11 years ago)
by jmduarteg:
Got rid (finally!) of AAinfo. Its functionality is now in ContactType and AminoAcid.
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Residue.java
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1316
(11 years ago)
by jmduarteg:
Got rid (finally!) of AAinfo. Its functionality is now in ContactType and AminoAcid.
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PdbasePdb.java
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1316
(11 years ago)
by jmduarteg:
Got rid (finally!) of AAinfo. Its functionality is now in ContactType and AminoAcid.
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CiffilePdb.java
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1316
(11 years ago)
by jmduarteg:
Got rid (finally!) of AAinfo. Its functionality is now in ContactType and AminoAcid.
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PdbfilePdb.java
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1316
(11 years ago)
by jmduarteg:
Got rid (finally!) of AAinfo. Its functionality is now in ContactType and AminoAcid.
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ChainInterface.java
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1319
(11 years ago)
by jmduarteg:
Removed the serialize/deserialize methods (now in Goodies)
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ChainInterfaceList.java
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1319
(11 years ago)
by jmduarteg:
Removed the serialize/deserialize methods (now in Goodies)
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AtomType.java
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1320
(11 years ago)
by jmduarteg:
Added atom types that appear in HET residues and details to docs
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