Splice will now respect segment information even if sequence profiles are not set. Cosmetic log changes in the 3 splice integration tests

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cryst_design.cc with options added

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Fixing some of the build errors on Win64 platform

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FastDesign now prints a very useful table of the task factory

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Fix valgrind error on ResidueType unit tests. nbr_atom_ was being left uninitialized under non-params file construction, resulting in bad memory access under the unit tests. Add a consistent initialization value, and appropriate checking.

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If given a blueprint, SecondaryStructureFilter now scans the strand pairing and determines whether it is possible for all "E" residues to be paired. For these residues, DSSP will always return "L" because there is no hydrogen bonding. The wanted ss string is modified by converting unpaired residues to "h" (which means L or E). This does not change the behavior if a ss string is specified, or if a complete blueprint with 100% paired strands is specified. This change allows checking the secondary structure of partially-built sheets, which was not previously possible.

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DesignBySecondaryStructure now correctly eliminates ligands from the DSSP string

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Detect connectivity for crystal docking now works. Scores returned now correctly represent the weakest interface in the lattice.

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Carbohydrates & Lipids: updating centroid database files

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Fixing header-only build

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Make RandomGenerator default & copy constructors private. You must provide a magic number when constructing a RandomGenerator. Also, each RandomGenerator must have a unique magic number, so copies are a no-no. Praise/blame go to Per, who got me looking at the issue. (Unfortunately, this doesn't fix his problem.) No test changes expected, as no one was really violating these rules.

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Fix GasteigerAtomTyper unit tests. The source of the problem was a *reference* to a COP that was being passed around. While the underlying object was still existing, the COP object itself was getting deleted, resulting in bad memory access. This expressed itself (intermittantly) on Mac but not Linux due to differences in how the memory was being handled, and if the referenced memory was reused or not.

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Removing ‘using namespace std’ from some of the protocols .hh files

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For some reason, my clang version will not compile these files without the extra include(core/io/silent/ProteinSilentStruct.tmpl.hh) for files: test/core/io/silent/protein_silent.cxxtest.hh test/protocols/jumping/JumpSetup.cxxtest.hh

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GenericMonteCarlo can now write a progress_file with information on each step, its accept/reject status, the filter value and the pose sequence. no test changes expected

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Fixed bug in splice that caused it to disrespect delta length cutoff when iterate disabled. Changed get_disulf integration, so that it does not rely on the template to get the rigid body orientation of pose (this was the cause of a very rare error). Cleaned out some comments in RBOutMover.

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