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Rosetta
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Looks through a PDB file and outputs disulfide formation scores. More...
#include <devel/init.hh>#include <utility/vector1.hh>#include <fstream>#include <basic/options/util.hh>#include <basic/options/keys/in.OptionKeys.gen.hh>#include <basic/options/keys/out.OptionKeys.gen.hh>#include <basic/options/keys/blivens.OptionKeys.gen.hh>#include <basic/options/option.hh>#include <core/pose/Pose.hh>#include <core/conformation/Residue.hh>#include <core/chemical/ResidueType.hh>#include <core/io/pdb/pdb_writer.hh>#include <core/scoring/disulfides/CentroidDisulfidePotential.hh>#include <core/pose/PDBInfo.hh>#include <core/scoring/dssp/Dssp.hh>#include <apps/pilot/blivens/disulfides.hh>#include <numeric/random/random.hh>#include <basic/Tracer.hh>#include <core/import_pose/import_pose.hh>#include <protocols/jumping/StrandPairing.hh>Classes | |
| class | PairScore |
Functions | |
| int | usage (char *msg) |
| int | main (int argc, char *argv[]) |
Variables | |
| static basic::Tracer | TR ("pilot_apps.blivens.disulfide_scorer") |
Looks through a PDB file and outputs disulfide formation scores.
Outputs scores for all detected disulfide bonds. Also outputs non-bonded pairs with probability 'nds_prob'. Thus if nds_prob=0 only disulfide bonds will be output, while if prob=1 the output will span all n*(n-1)/2 pairs of residues in the protein.
Similarly, non-disulfide bonded cysteines are output with probability 'cys_prob'. Note that cysteines are excluded from the nds_prob output because of this second option.
The expected number of nonbonded pairs output is prob*n*(n-1)/2
| int main | ( | int | argc, |
| char * | argv[] | ||
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References actual_disulfide(), argv, basic::options::OptionKeys::blivens::disulfide_scorer::cys_prob, blivens::disulfide_scorer::cys_prob(), basic::options::OptionKeys::in::file::dssp, test.T009_Exceptions::e, create_a3b_hbs::i, basic::init(), create_a3b_hbs::j, in::file::l(), blivens::disulfide_scorer::nds_prob(), out::file::o(), option, erraser_single_res_analysis::out, lactamize::outfile, pdbs, beta_nonlocal::pose, PairScore::printHeader(), spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib::prob, in::file::s(), legacy_score_vs_rmsd::scores, basic::options::start_files(), TR, numeric::random::uniform(), usage(), basic::options::OptionKeys::inout::dbms::user, and basic::Tracer::Warning.
| int usage | ( | char * | msg | ) |
References basic::Tracer::Error, utility::options::OptionKeys::options::exit, and TR.
Referenced by main().
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1.9.1