Rosetta 3.3
Functions | Variables
color_pdb Namespace Reference

Functions

def Help

Variables

list pdbfile = sys.argv[1]
list tagfile = sys.argv[2]
tuple data = open(tagfile,'r')
tuple lines = string.split(data,'\n')
list tags = []
float sumcolor = 0.0
tuple token = string.split(i)
tuple res = int( i[22:26] )
float temp = 0.0
 find residue number
string temps = "% 4.2f"
list i = i[0:61]

Function Documentation

def color_pdb::Help ( )

Variable Documentation

tuple color_pdb::data = open(tagfile,'r')
list color_pdb::i = i[0:61]

Referenced by numeric::interpolation::spline::CompoundInterpolator::add_range(), already_minimized(), ObjexxFCL::ChunkVector< T >::append(), UBQ_E2Mover::apply(), FloppyTailMover::apply(), LigandRepackMinimizeProtocol::apply(), AnchorFinderMover::apply(), APDBCMover::apply(), MRMover::apply_makefrags(), utility::keys::SmallKeyMap< K, T >::assign(), utility::keys::ClassKeyMap< K, T, C >::assign(), ObjexxFCL::ChunkVector< T >::assign(), ObjexxFCL::Chunk< T >::assign(), ObjexxFCL::CArrayP< T >::assign(), ObjexxFCL::CArray< T >::assign(), IAMover::assign_IA_mover(), average(), numeric::average_link_clustering(), average_score_components(), Benchmark::Benchmark(), numeric::interpolation::periodic_range::periodic_value::half::bin(), numeric::interpolation::periodic_range::periodic_value::full::bin(), numeric::interpolation::periodic_range::half::bin(), numeric::interpolation::periodic_range::full::bin(), utility::BitVector< B >::BitVector(), ca_to_allatom_main(), numeric::model_quality::calc_rms(), ObjexxFCL::CArray< T >::CArray(), ObjexxFCL::CArrayP< T >::CArrayP(), utility::options::OptionCollection::check_specs(), utility::options::OptionCollection::check_values(), ObjexxFCL::Chunk< T >::Chunk(), ObjexxFCL::ChunkVector< T >::ChunkVector(), utility::keys::ClassKeyMap< K, T, C >::ClassKeyMap(), utility::options::OptionCollection::cleaned(), utility::tag::Tag::clone(), numeric::MultiDimensionalHistogram::collapse(), numeric::model_quality::COMAS(), numeric::complete_link_clustering(), ObjexxFCL::Fstring::compress(), ObjexxFCL::Cstring::compress(), utility::signals::SignalHub< ReturnType, Signal >::connect(), ObjexxFCL::IndexRange::contain(), core_init_with_additional_options(), correlation_coefficient(), create_bp_jump_database_test(), utility::PeriodicSplineReader::dF(), numeric::interpolation::spline::CubicSpline::dF(), numeric::interpolation::spline::BicubicSpline::dFdx(), numeric::interpolation::spline::BicubicSpline::dFdy(), numeric::MultiDimensionalHistogram::dim_labels(), utility::signals::SignalHub< ReturnType, Signal >::disconnect(), ObjexxFCL::distance(), ObjexxFCL::distance_squared(), basic::JsonEmitter::do_indent(), basic::YamlEmitter::do_indent(), ObjexxFCL::dot(), ObjexxFCL::dot_product(), numeric::eigenvalue_jacobi(), numeric::eigenvector_jacobi(), numeric::MultiDimensionalHistogram::end(), basic::Emitter::end(), ObjexxFCL::equali(), basic::Emitter::escape_string(), Benchmark::executeAllBenchmarks(), utility::PeriodicSplineReader::F(), numeric::interpolation::spline::CubicSpline::F(), numeric::interpolation::spline::BicubicSpline::F(), ObjexxFCL::FArray< double >::FArray(), ObjexxFCL::FArray1D< double >::FArray1D(), MRMover::fast_loopclose(), numeric::interpolation::spline::BicubicSpline::FdF(), numeric::fourier::fft(), numeric::fourier::fft2(), numeric::fourier::fft3(), utility::file::file_delete(), utility::Inline_File_Provider::file_exists(), ObjexxFCL::Fstring::find(), ObjexxFCL::Cstring::find(), utility::signals::SignalHub< ReturnType, Signal >::find_connection(), ObjexxFCL::Fstring::find_first_not_of(), ObjexxFCL::Fstring::find_first_of(), utility::options::OptionCollection::find_key_cl(), ObjexxFCL::Fstring::find_last(), ObjexxFCL::Cstring::find_last(), ObjexxFCL::Fstring::find_last_non_whitespace(), ObjexxFCL::Fstring::find_last_not_of(), ObjexxFCL::Fstring::find_last_of(), ObjexxFCL::Fstring::find_last_whitespace(), ObjexxFCL::Fstring::find_non_whitespace(), ObjexxFCL::Fstring::find_whitespace(), numeric::model_quality::findUU(), basic::Tracer::flush_all_channels(), basic::database::full_name(), ObjexxFCL::fmt::G(), utility::keys::KeyLookup< K >::gen(), gen_pep_bb_sequential(), numeric::random::mt19937_RG::gen_rand_all(), numeric::get_cluster_data(), numeric::MathMatrix< core::Real >::get_col(), numeric::interpolation::spline::SplineGenerator::get_interpolator(), utility::Inline_File_Provider::get_istream(), get_n_pep_nbrs(), utility::tag::Tag::getOption(), Benchmark::getReport(), utility::tag::Tag::getTags(), ObjexxFCL::Fstring::has(), ObjexxFCL::Cstring::has(), ObjexxFCL::Fstring::has_any_of(), ObjexxFCL::Cstring::has_any_of(), utility::options::VectorOption_T_< BooleanVectorOptionKey, bool >::has_any_of_characters(), utility::options::ScalarOption_T_< PathOptionKey, file::PathName >::has_any_of_characters(), utility::tag::Tag::hasOption(), numeric::fourier::ifft(), numeric::fourier::ifft2(), numeric::fourier::ifft3(), numeric::random::mt19937_RG::init_by_array(), UBQ_E2Mover::init_on_new_input(), FloppyTailMover::init_on_new_input(), numeric::random::mt19937_RG::initial_mask(), numeric::random::RandomGenerator::initializeRandomGenerators(), utility::keys::SmallKeyMap< K, T >::insert(), utility::keys::ClassKeyMap< K, T, C >::insert(), numeric::interpolation::spline::CompoundInterpolator::interpolate(), utility::signals::SignalHub< ReturnType, Signal >::invalidate_all(), numeric::MathMatrix< core::Real >::inverse_diagonal_matrix(), numeric::MathMatrix< core::Real >::inverse_square_matrix(), numeric::MathMatrix< core::Real >::inverse_tridiagonal_matrix(), ObjexxFCL::is_any_of(), ObjexxFCL::FArray< double >::is_default(), numeric::MathMatrix< core::Real >::is_diagonal(), ObjexxFCL::FArray2< double >::is_identity(), numeric::IntervalSet< double >::is_inside(), utility::is_string_numeric(), numeric::MathMatrix< core::Real >::is_tri_diagonal(), ObjexxFCL::FArray< double >::is_uniform(), ObjexxFCL::FArray< double >::is_zero(), numeric::jacobi(), utility::keys::KeyLookup< K >::key(), ObjexxFCL::KeyFArray1D< T >::KeyFArray1D(), numeric::fourier::kiss_fftnd(), ObjexxFCL::Fstring::left_justify(), ObjexxFCL::Cstring::left_justify(), utility::options::VectorOption_T_< BooleanVectorOptionKey, bool >::legal_string(), utility::options::ScalarOption_T_< PathOptionKey, file::PathName >::legal_string(), ObjexxFCL::Fstring::len_trim(), ObjexxFCL::Cstring::len_trim(), ObjexxFCL::Fstring::len_trim_whitespace(), ObjexxFCL::Cstring::len_trim_whitespace(), ObjexxFCL::FArray1< double >::length(), ObjexxFCL::ChunkVector< T >::length(), ObjexxFCL::CArrayP< T >::length(), ObjexxFCL::CArray< T >::length(), numeric::IntervalSet< double >::length(), ObjexxFCL::FArray1< double >::length_squared(), ObjexxFCL::ChunkVector< T >::length_squared(), ObjexxFCL::CArrayP< T >::length_squared(), ObjexxFCL::CArray< T >::length_squared(), ObjexxFCL::lowercase(), ObjexxFCL::Fstring::lowercase(), ObjexxFCL::Cstring::lowercase(), ObjexxFCL::lowercased(), main(), match_main(), numeric::model_quality::MatrixMult(), numeric::model_quality::maxsub(), numeric::MultiDimensionalHistogram::mean_squared_error(), minimize_with_constraints(), mutate_random_residue(), my_main(), utility::options::OptionCollection::n_part(), ObjexxFCL::ChunkVector< T >::non_preserving_resize(), ObjexxFCL::Chunk< T >::non_preserving_resize(), numeric::MultiDimensionalHistogram::num_bins(), ObjexxFCL::operator!=(), utility::keys::SmallKeyMap< K, T >::operator()(), utility::keys::ClassKeyMap< K, T, C >::operator()(), ObjexxFCL::KeyFArray1D< T >::operator()(), ObjexxFCL::FArray1P< T >::operator()(), ObjexxFCL::FArray1D< double >::operator()(), ObjexxFCL::FArray1A< T >::operator()(), ObjexxFCL::FArray1< double >::operator()(), numeric::operator*(), ObjexxFCL::ubyte::operator*=(), ObjexxFCL::FArray2< double >::operator*=(), ObjexxFCL::FArray< double >::operator*=(), ObjexxFCL::ChunkVector< T >::operator*=(), ObjexxFCL::Chunk< T >::operator*=(), ObjexxFCL::CArrayP< T >::operator*=(), ObjexxFCL::CArray< T >::operator*=(), ObjexxFCL::byte::operator*=(), numeric::MathMatrix< core::Real >::operator*=(), utility::BitVector< B >::operator+=(), ObjexxFCL::ubyte::operator+=(), ObjexxFCL::FArray< double >::operator+=(), ObjexxFCL::ChunkVector< T >::operator+=(), ObjexxFCL::Chunk< T >::operator+=(), ObjexxFCL::CArrayP< T >::operator+=(), ObjexxFCL::CArray< T >::operator+=(), ObjexxFCL::byte::operator+=(), utility::operator-(), utility::BitVector< B >::operator-=(), utility::BitSet< B >::operator-=(), ObjexxFCL::ubyte::operator-=(), ObjexxFCL::FArray< double >::operator-=(), ObjexxFCL::ChunkVector< T >::operator-=(), ObjexxFCL::Chunk< T >::operator-=(), ObjexxFCL::CArrayP< T >::operator-=(), ObjexxFCL::CArray< T >::operator-=(), ObjexxFCL::byte::operator-=(), ObjexxFCL::ubyte::operator/=(), ObjexxFCL::FArray< double >::operator/=(), ObjexxFCL::ChunkVector< T >::operator/=(), ObjexxFCL::Chunk< T >::operator/=(), ObjexxFCL::CArrayP< T >::operator/=(), ObjexxFCL::CArray< T >::operator/=(), ObjexxFCL::byte::operator/=(), ObjexxFCL::operator<(), operator<<(), utility::options::operator<<(), ObjexxFCL::operator<<(), numeric::operator<<(), ObjexxFCL::operator<=(), utility::keys::SmallKeyVector< PathVectorOptionKey, PathVectorOption >::operator=(), utility::keys::SmallKeyMap< K, T >::operator=(), utility::keys::KeyVector< K, T >::operator=(), utility::keys::ClassKeyVector< K, T, C >::operator=(), utility::keys::ClassKeyMap< K, T, C >::operator=(), ObjexxFCL::ubyte::operator=(), ObjexxFCL::FArray< double >::operator=(), ObjexxFCL::ChunkVector< T >::operator=(), ObjexxFCL::Chunk< T >::operator=(), ObjexxFCL::CArrayP< T >::operator=(), ObjexxFCL::CArray< T >::operator=(), ObjexxFCL::byte::operator=(), basic::svd::SVD_Solver::operator=(), basic::datacache::DataCache< CacheableData >::operator=(), ObjexxFCL::operator==(), ObjexxFCL::operator>(), ObjexxFCL::operator>=(), ObjexxFCL::fmt::operator>>(), utility::keys::SmallKeyVector< PathVectorOptionKey, PathVectorOption >::operator[](), utility::keys::SmallKeyMap< K, T >::operator[](), utility::keys::ClassKeyVector< K, T, C >::operator[](), utility::keys::ClassKeyMap< K, T, C >::operator[](), ObjexxFCL::KeyFArray6D< T >::operator[](), ObjexxFCL::KeyFArray5D< T >::operator[](), ObjexxFCL::KeyFArray4D< T >::operator[](), ObjexxFCL::KeyFArray3D< T >::operator[](), ObjexxFCL::KeyFArray2D< T >::operator[](), ObjexxFCL::KeyFArray1D< T >::operator[](), ObjexxFCL::FArray6D< T >::operator[](), ObjexxFCL::FArray5D< T >::operator[](), ObjexxFCL::FArray4D< T >::operator[](), ObjexxFCL::FArray3D< T >::operator[](), ObjexxFCL::FArray2D< double >::operator[](), ObjexxFCL::FArray1D< double >::operator[](), ObjexxFCL::FArray< double >::operator[](), ObjexxFCL::Cstring::operator[](), ObjexxFCL::Chunk< T >::operator[](), ObjexxFCL::CArrayP< T >::operator[](), ObjexxFCL::CArray< T >::operator[](), utility::BitVector< B >::operator|=(), MRMover::pack_missing_sidechains(), pep_rmsd_analysis(), numeric::random::mt19937_RG::period_certification(), positions_incompatible_with_task(), utility::options::OptionCollection::prefix(), print_ddgs(), print_pep_analysis(), print_pep_csts(), basic::prof_show(), numeric::random::random_permutation(), numeric::IntervalSet< double >::random_point(), numeric::random::WeightedSampler::random_sample(), numeric::random::RandomGenerator::RandomGenerator(), utility::PeriodicSplineReader::read(), ObjexxFCL::read_binary(), utility::signals::BufferedSignalHub< ReturnType, Signal >::release_buffer(), utility::keys::KeyLookup< K >::remove(), utility::signals::SignalHub< ReturnType, Signal >::remove_invalid(), numeric::MathMatrix< core::Real >::replace_col(), ObjexxFCL::Chunk< T >::reserve(), numeric::MultiDimensionalHistogram::reset_counts(), ObjexxFCL::ChunkVector< T >::resize(), ObjexxFCL::Chunk< T >::resize(), ObjexxFCL::CArrayP< T >::resize(), ObjexxFCL::CArray< T >::resize(), numeric::fourier::kiss_fftndr_state::resize(), numeric::fourier::kiss_fftnd_state::resize(), numeric::fourier::kiss_fftr_state::resize(), numeric::fourier::kiss_fft_state::resize(), numeric::random::RandomGenerator::restoreAllStates(), numeric::random::mt19937_RG::restoreState(), ObjexxFCL::Fstring::right_justify(), ObjexxFCL::Cstring::right_justify(), ObjexxFCL::FArray2< double >::right_multiply_by_transpose(), numeric::model_quality::rmsfitca2(), numeric::model_quality::rmsfitca3(), rna_sequence_recovery_metrics(), numeric::model_quality::rsym_evector(), numeric::model_quality::rsym_rotation(), SmallMoverBenchmark::run(), ShearMoverBenchmark::run(), ScoreBenchmark::run(), MinimizerBenchmark< sft, TScale >::run(), LigandDockScriptBenchmark::run(), LigandDockBenchmark::run(), DockingBenchmark< dock, TScale >::run(), DesignBenchmark::run(), run_pep_prep(), basic::svd::SVD_Solver::run_score_svd_on_matrix(), basic::svd::SVD_Solver::run_score_svd_without_solving(), RunPepSpec(), numeric::random::RandomGenerator::saveAllStates(), numeric::random::mt19937_RG::saveState(), utility::signals::SignalHub< ReturnType, Signal >::send(), sequence_tolerance_main(), ObjexxFCL::FArray2< double >::set_diagonal(), basic::Emitter::set_indent(), basic::svd::SVD_Solver::set_matrix_A(), numeric::interpolation::Histogram< X, Y >::set_params(), numeric::MathMatrix< core::Real >::set_unit(), basic::svd::SVD_Solver::set_vector_b(), numeric::random::mt19937_RG::setSeed(), MinimizerBenchmark< sft, TScale >::setUp(), setup_ca_constraints(), basic::setup_tag2string(), numeric::random::sfmt_idxof(), shift_angles(), utility::options::OptionCollection::show_accessed_options(), utility::options::show_accessed_options_T(), utility::options::OptionCollection::show_all(), utility::options::OptionCollection::show_all_hier(), utility::options::OptionCollection::show_help(), utility::options::OptionCollection::show_help_hier(), utility::options::OptionCollection::show_inaccessed_user_options(), utility::options::OptionCollection::show_table_text(), utility::options::OptionCollection::show_table_Wiki(), utility::options::OptionCollection::show_user(), ObjexxFCL::Chunk< T >::shrink(), numeric::single_link_clustering(), utility::tag::Tag::size(), utility::keys::SmallKeyMap< K, T >::SmallKeyMap(), utility::keys::ClassKeyVector< K, T, C >::sort(), utility::IndirectSorter< DataContainerType, ComparatorType >::sort(), numeric::interpolation::spline::spline_second_derivative(), utility::split(), utility::split_to_list(), numeric::MultiDimensionalHistogram::start(), basic::options::start_files(), store_energies(), utility::string2float(), utility::string2int(), utility::string_split(), utility::options::OptionCollection::suffix(), sum(), basic::svd::SVD_Solver::SVD_Solver(), ObjexxFCL::fmt::SW(), numeric::MathMatrix< core::Real >::swap_cols(), numeric::MathMatrix< core::Real >::swap_rows(), ObjexxFCL::FArray2< double >::symmetric(), basic::ComparingTracer::t_flush(), ObjexxFCL::FArray2< double >::to_diag(), ObjexxFCL::FArray2< double >::to_identity(), numeric::interpolation::spline::CubicSpline::train(), ObjexxFCL::FArray2< double >::transpose(), numeric::MathMatrix< core::Real >::transpose(), ObjexxFCL::transposed(), utility::options::OptionCollection::trim(), MRMover::trim_target_pose(), utility::options::OptionCollection::trimmed(), utility::file::trytry_ifstream_open(), utility::file::trytry_ofstream_open(), ObjexxFCL::unique(), ObjexxFCL::uniqued(), ObjexxFCL::uppercase(), ObjexxFCL::Fstring::uppercase(), ObjexxFCL::Cstring::uppercase(), ObjexxFCL::uppercased(), vector1_repr(), vector1_set(), utility::options::OptionCollection::wrapped(), utility::tag::Tag::write(), ObjexxFCL::write_binary(), basic::Emitter::write_raw(), numeric::random::RandomGenerator::~RandomGenerator(), and basic::Tracer::~Tracer().

tuple color_pdb::lines = string.split(data,'\n')
list color_pdb::pdbfile = sys.argv[1]
tuple color_pdb::res = int( i[22:26] )
tuple color_pdb::sumcolor = 0.0
list color_pdb::tagfile = sys.argv[2]
list color_pdb::tags = []
list color_pdb::temp = 0.0
string color_pdb::temps = "% 4.2f"
tuple color_pdb::token = string.split(i)
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