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Rosetta Protocols
2014.16.56682
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Rosetta Protocols
2014.16.56682
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#include <AlignmentClustering.hh>
Public Member Functions | |
| AlignmentClustering () | |
| virtual | ~AlignmentClustering () |
| Deletes AlignmentClustering object More... | |
Private Member Functions | |
| vector1< AlignmentClusterOP > | cluster (vector1< vector1< Real > > &gdtmms, vector1< SequenceAlignment > &rankedAlignments, Real threshold_gdt) |
| Does the clustering More... | |
| map< string, Pose > | poses_from_cmd_line (utility::vector1< std::string > const &fn_list) |
| gathers the poses More... | |
| vector1< SequenceAlignment > | generateRankedAlignments (map< string, SequenceAlignment > &alns, Real THRESHOLD_FOR_E_VAL) |
| gets the aligment from file and ranks them. Some models do not have e-vals in ev_map because thy are too far down in ranking. As long as 10 models are in the hh_map or ev_map the ranking comes from there. More... | |
| protocols::comparative_modeling::AlignmentClustering::AlignmentClustering | ( | ) |
creates an alignment clustering object, this is in charge of clustering
References align_poses_naive(), in::file::alignment, cm::aln_format, protocols::comparative_modeling::PartialThreadingMover::apply(), utility::io::ozstream::close(), cluster, run::debug, core::pose::Pose::dump_pdb(), in::file::fasta, filename(), protocols::comparative_modeling::gather_coords(), gdtmm, core::pose::make_pose_from_sequence(), basic::options::option, option, overlap(), protocols::comparative_modeling::poses_from_cmd_line(), core::sequence::read_aln(), core::sequence::read_fasta_file(), read_fasta_file(), rsd_set_from_cmd_line(), sequence, in::file::template_pdb, core::pose::Pose::total_residue(), tr, xyz_gdtmm(), and core::scoring::xyz_gdtmm().
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virtual |
Deletes AlignmentClustering object
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private |
Does the clustering
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private |
gets the aligment from file and ranks them. Some models do not have e-vals in ev_map because thy are too far down in ranking. As long as 10 models are in the hh_map or ev_map the ranking comes from there.
References cm::ev_map, file_exists(), filename(), getline(), cm::hh_map, option, tr, user, and utility_exit_with_message.
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private |
gathers the poses
References end, utility::file_basename(), file_exists(), utility::file::file_exists(), core::import_pose::pose_from_pdb(), and rsd_set_from_cmd_line().
1.8.7