 ../
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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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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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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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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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Nucleotide.java
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1321
(11 years ago)
by jmduarteg:
New enum for nucleotides
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Pdb.java
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1324
(11 years ago)
by jmduarteg:
A few bug fixes and improvements in pdb data parsing.
- bug fix: in some cases exptl method field has more than 1 value (e.g. 2krl). In cif files this was causing a null pointer. We now parse it properly (taking first one as the exptl method) in both cif and pdb files
- improved very slightly the cif file parser moving out of loops the index getters
- drop fullLength as a field in Pdb, now we have only getFullLength()
- pdb file atom parsing is now column based and not regex based (hopefully will make it slightly faster)
- now parsing the element column of pdb files: now the atom type detection comes from the appropriate field in pdb/cif/pdbase. If in pdb file and not present we still try to guess it as before
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Atom.java
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1324
(11 years ago)
by jmduarteg:
A few bug fixes and improvements in pdb data parsing.
- bug fix: in some cases exptl method field has more than 1 value (e.g. 2krl). In cif files this was causing a null pointer. We now parse it properly (taking first one as the exptl method) in both cif and pdb files
- improved very slightly the cif file parser moving out of loops the index getters
- drop fullLength as a field in Pdb, now we have only getFullLength()
- pdb file atom parsing is now column based and not regex based (hopefully will make it slightly faster)
- now parsing the element column of pdb files: now the atom type detection comes from the appropriate field in pdb/cif/pdbase. If in pdb file and not present we still try to guess it as before
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PdbasePdb.java
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1324
(11 years ago)
by jmduarteg:
A few bug fixes and improvements in pdb data parsing.
- bug fix: in some cases exptl method field has more than 1 value (e.g. 2krl). In cif files this was causing a null pointer. We now parse it properly (taking first one as the exptl method) in both cif and pdb files
- improved very slightly the cif file parser moving out of loops the index getters
- drop fullLength as a field in Pdb, now we have only getFullLength()
- pdb file atom parsing is now column based and not regex based (hopefully will make it slightly faster)
- now parsing the element column of pdb files: now the atom type detection comes from the appropriate field in pdb/cif/pdbase. If in pdb file and not present we still try to guess it as before
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CiffilePdb.java
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1324
(11 years ago)
by jmduarteg:
A few bug fixes and improvements in pdb data parsing.
- bug fix: in some cases exptl method field has more than 1 value (e.g. 2krl). In cif files this was causing a null pointer. We now parse it properly (taking first one as the exptl method) in both cif and pdb files
- improved very slightly the cif file parser moving out of loops the index getters
- drop fullLength as a field in Pdb, now we have only getFullLength()
- pdb file atom parsing is now column based and not regex based (hopefully will make it slightly faster)
- now parsing the element column of pdb files: now the atom type detection comes from the appropriate field in pdb/cif/pdbase. If in pdb file and not present we still try to guess it as before
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PdbfilePdb.java
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1324
(11 years ago)
by jmduarteg:
A few bug fixes and improvements in pdb data parsing.
- bug fix: in some cases exptl method field has more than 1 value (e.g. 2krl). In cif files this was causing a null pointer. We now parse it properly (taking first one as the exptl method) in both cif and pdb files
- improved very slightly the cif file parser moving out of loops the index getters
- drop fullLength as a field in Pdb, now we have only getFullLength()
- pdb file atom parsing is now column based and not regex based (hopefully will make it slightly faster)
- now parsing the element column of pdb files: now the atom type detection comes from the appropriate field in pdb/cif/pdbase. If in pdb file and not present we still try to guess it as before
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