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root/owl/trunk/src/owl/core/structure
r1305
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features/ 1226 (11 years ago) by hstehr: Refactoring of SiftsConnection and SiftsFeature, now implementing Uniprot2Pdb
scoring/ 1287 (11 years ago) by matt4077:
alignment/ 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.
graphs/ 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.
ContactType.java 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
PdbLoadError.java 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
PolResidue.java 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
Polymer.java 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
BackboneCoords.java 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
aapairsBounds.dat 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
AAinfo.java 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
AminoAcid.java 1094 (11 years ago) by jmduarteg: Implemented reduced alphabets in AminoAcid class and modified entropy calculation to allow reduced alphabets.
symop.lib 1179 (11 years ago) by jmduarteg: New classes to parse and store crystallographic space groups info.
vdw.radii 1247 (11 years ago) by jmduarteg: Implemented our own ASA calculation! Taken from Bosco's python implementation, thanks again Bosco!
AtomType.java 1247 (11 years ago) by jmduarteg: Implemented our own ASA calculation! Taken from Bosco's python implementation, thanks again Bosco!
Atom.java 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.
Asa.java 1255 (11 years ago) by jmduarteg: Minor changes to the test.
Residue.java 1256 (11 years ago) by jmduarteg: Now reporting on percent burial too
AtomRadii.java 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
InterfaceRimCore.java 1264 (11 years ago) by jmduarteg: Added printing of rim and core residues methods.
CrystalCell.java 1269 (11 years ago) by jmduarteg: Fixed bug in SpaceGroupTest. Now it works and test passes. Introduced checking for clashes in interfaces. Added it to the PdbAsymUnitTest
SpaceGroup.java 1270 (11 years ago) by jmduarteg: Fixed bug: was still not converting well algebraic transformations to matrix: was failing for transformations with terms like "X-Y+1/3"
SymoplibParser.java 1281 (11 years ago) by jmduarteg: Now checking that the space group read from file/db is correct, if not PdbLoadError thrown.
PdbUnitCell.java 1284 (11 years ago) by cvehlow: Overrides removed
ChainInterface.java 1296 (11 years ago) by jmduarteg: Bringing back the PISA classes for interface, molecule and residues. We store things first into them and only then convert to our own ChainInterface if needed. This is a much better approach less prone to errors. Tests pass.
ChainInterfaceList.java 1296 (11 years ago) by jmduarteg: Bringing back the PISA classes for interface, molecule and residues. We store things first into them and only then convert to our own ChainInterface if needed. This is a much better approach less prone to errors. Tests pass.
contactTypes.dat 1302 (11 years ago) by hstehr: adding ALL_H contact type to contactTypes.dat because otherwise AAinfo.isValidAtomWithOXT() breaks with a NullPointerException
PdbAsymUnit.java 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.
TemplateList.java 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.
PdbChainCodeNotFoundException.java 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.
Pdb.java 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.
ConformationsNotSameSizeException.java 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.
PdbaseInconsistencyException.java 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.
PdbSet.java 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.
Template.java 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.
PdbasePdb.java 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.
CiffilePdb.java 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.
PdbCodeNotFoundException.java 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.
PdbfilePdb.java 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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