 ../
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jars/
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1309
(11 years ago)
by jmduarteg:
New jar for uniprot JAPI
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modelit/
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1301
(11 years ago)
by hstehr:
overwriting default contactTypes.dat with the one needed for CMView release versions (only contains standard contact types). The old version with all esoteric contact types is renamed to contactTypes.all.dat
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reconstruct/
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992
(12 years ago)
by jmduarteg:
Removed unneeded code
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scripts/
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1289
(11 years ago)
by jmduarteg:
Introduced constant for formatdb executable
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src/
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1329
(11 years ago)
by jmduarteg:
Important change: now the PDB file reader will try to read and fix the numbering of PDB files. Whenever the alignment is wrong it will realign and renumber using the jaligner package. The result of reading original PDB files now will be the same as that of reading CIF files, including proper mapping of classical PDB numbers to SEQRES residue serials (as in CIF).
There is one change of behaviour in comparison to before: when no SEQRES present the sequence is taken to be that of ATOM lines instead of padding it with Xs.
Still in this version the re-alignment is not perfect as there are some times when ambiguities occur and they are not solved (e.g. in 2nwr where alignment in an unobserved loop can be at two possible places for a GLY). That is anyway a rather minor problem (coordinates are still fine, just the chain is not ordered correctly at 1 or 2 points) and rare (~1% of files)
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.classpath
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1291
(11 years ago)
by cvehlow:
Control database access! for CGAP
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.project
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1065
(12 years ago)
by hstehr:
reverting changes to .project and .classpath which were accidentally committed
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LICENSE
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974
(12 years ago)
by duarte:
Adding license files
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Manifest.txt
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968
(12 years ago)
by duarte:
Updated make-aglappe script (and renamed to make-owl).
Changed aglappe strings to OWL (following new name of library)
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gpl.txt
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974
(12 years ago)
by duarte:
Adding license files
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