constel¶
Bindings for protocols::constel namespace
- class pyrosetta.rosetta.protocols.constel.ChainTerm¶
Bases:
pybind11_object
- get_cid(self: pyrosetta.rosetta.protocols.constel.ChainTerm) str ¶
cid_ accessor
C++: protocols::constel::ChainTerm::get_cid() const –> char
- get_cps(self: pyrosetta.rosetta.protocols.constel.ChainTerm) int ¶
c_ps_ accessor
C++: protocols::constel::ChainTerm::get_cps() const –> unsigned long
- get_nps(self: pyrosetta.rosetta.protocols.constel.ChainTerm) int ¶
n_ps_ accessor
C++: protocols::constel::ChainTerm::get_nps() const –> unsigned long
- print(self: pyrosetta.rosetta.protocols.constel.ChainTerm, t: pyrosetta.rosetta.basic.Tracer) None ¶
prints this chain’s info to tracer t
C++: protocols::constel::ChainTerm::print(class basic::Tracer &) const –> void
- class pyrosetta.rosetta.protocols.constel.ExcludedFilter¶
Bases:
pybind11_object
- static hasnt_excluded(: pyrosetta.rosetta.core.pose.Pose, cnl: pyrosetta.rosetta.utility.vector1_unsigned_long) bool ¶
C++: protocols::constel::ExcludedFilter::hasnt_excluded(const class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> bool
- static init(ps: pyrosetta.rosetta.core.pose.Pose, ex_fname: str) None ¶
C++: protocols::constel::ExcludedFilter::init(class core::pose::Pose &, const std::string &) –> void
- class pyrosetta.rosetta.protocols.constel.FilterByAmphetamine¶
Bases:
pybind11_object
Class to filter out constellations that cannot (putatively) be rescued by amphetamine.
- static is_satisfied(ps: pyrosetta.rosetta.core.pose.Pose, cnl: pyrosetta.rosetta.utility.vector1_unsigned_long) bool ¶
C++: protocols::constel::FilterByAmphetamine::is_satisfied(const class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> bool
- class pyrosetta.rosetta.protocols.constel.FilterByHistamine¶
Bases:
pybind11_object
Class to filter out constellations that cannot (putatively) be rescued by histamine.
- static is_satisfied(ps: pyrosetta.rosetta.core.pose.Pose, cnl: pyrosetta.rosetta.utility.vector1_unsigned_long) bool ¶
C++: protocols::constel::FilterByHistamine::is_satisfied(const class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> bool
- class pyrosetta.rosetta.protocols.constel.FilterByIndoleCOO¶
Bases:
pybind11_object
Class to filter out constellations that cannot (putatively) be rescued by compounds containing indole and a carboxylic group.
- static is_satisfied(ps: pyrosetta.rosetta.core.pose.Pose, cnl: pyrosetta.rosetta.utility.vector1_unsigned_long) bool ¶
C++: protocols::constel::FilterByIndoleCOO::is_satisfied(const class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> bool
- class pyrosetta.rosetta.protocols.constel.FilterByProxTerm¶
Bases:
pybind11_object
- static init(ps: pyrosetta.rosetta.core.pose.Pose, max_ct_dist: float, max_tt_dist: float, nres: int) None ¶
filter initialization
C++: protocols::constel::FilterByProxTerm::init(const class core::pose::Pose &, double, double, unsigned long) –> void
- static is_satisfied(ps: pyrosetta.rosetta.core.pose.Pose, cnl: pyrosetta.rosetta.utility.vector1_unsigned_long) bool ¶
tells whether a constellation satisfies the filter
C++: protocols::constel::FilterByProxTerm::is_satisfied(const class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> bool
- class pyrosetta.rosetta.protocols.constel.FilterBySASA¶
Bases:
pybind11_object
- static has_low_per_atom_sasa(ps: pyrosetta.rosetta.core.pose.Pose, cnl: pyrosetta.rosetta.utility.vector1_unsigned_long) bool ¶
Tells whether a constellation has a sufficiently low per-atom SASA
C++: protocols::constel::FilterBySASA::has_low_per_atom_sasa(const class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> bool
- static init(smax: float, ps: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::constel::FilterBySASA::init(const double, const class core::pose::Pose &) –> void
- class pyrosetta.rosetta.protocols.constel.FilterByTryptamine¶
Bases:
pybind11_object
Class to filter out constellations that cannot (putatively) be rescued by tryptamine.
- static is_satisfied(ps: pyrosetta.rosetta.core.pose.Pose, cnl: pyrosetta.rosetta.utility.vector1_unsigned_long) bool ¶
C++: protocols::constel::FilterByTryptamine::is_satisfied(const class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> bool
- class pyrosetta.rosetta.protocols.constel.HBondCommon¶
Bases:
pybind11_object
A class to hold data structures and functions shared by filters that consider hydrogen bonding.
- static is_rmoi_hbonded(ps: pyrosetta.rosetta.core.pose.Pose, cnl: pyrosetta.rosetta.utility.vector1_unsigned_long, im: int, is_donor: bool, hb_atoms: pyrosetta.rosetta.utility.vector1_std_string) bool ¶
Tells whether a residue’s moiety forms hydrogen bonds.
C++: protocols::constel::HBondCommon::is_rmoi_hbonded(const class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const unsigned long, const bool, const class utility::vector1<std::string, class std::allocator<std::string > > &) –> bool
- class pyrosetta.rosetta.protocols.constel.MasterFilter¶
Bases:
pybind11_object
- static is_constel_valid(ps: pyrosetta.rosetta.core.pose.Pose, cnl: pyrosetta.rosetta.utility.vector1_unsigned_long) bool ¶
Tells whether a constellation is valid.
C++: protocols::constel::MasterFilter::is_constel_valid(const class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> bool
- class pyrosetta.rosetta.protocols.constel.NeighTeller¶
Bases:
pybind11_object
- is_neigh_tree(self: pyrosetta.rosetta.protocols.constel.NeighTeller, set: pyrosetta.rosetta.utility.vector1_unsigned_long, ps: pyrosetta.rosetta.core.pose.Pose) bool ¶
: tells whether a set of residues form a tree of neighbors.
C++: protocols::constel::NeighTeller::is_neigh_tree(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const class core::pose::Pose &) –> bool
- isneigh(self: pyrosetta.rosetta.protocols.constel.NeighTeller, tgt: pyrosetta.rosetta.core.conformation.Residue, prb: pyrosetta.rosetta.core.conformation.Residue, ref_pose: pyrosetta.rosetta.core.pose.Pose) bool ¶
: tells whether a probe residue is a neighbor of a target residue.
C++: protocols::constel::NeighTeller::isneigh(const class core::conformation::Residue &, const class core::conformation::Residue &, const class core::pose::Pose &) –> bool
- class pyrosetta.rosetta.protocols.constel.OrientCommon¶
Bases:
pybind11_object
A class to hold data structures and functions common to filters that consider how groups of atoms within a constellation are oriented.
- static is_closer_to_tgt(low: pyrosetta.rosetta.numeric.xyzVector_double_t, hi: pyrosetta.rosetta.numeric.xyzVector_double_t, tgt: pyrosetta.rosetta.numeric.xyzVector_double_t) bool ¶
Tells whether atom ‘low’ is closer to atom ‘tgt’ than atom ‘hi’ is.
C++: protocols::constel::OrientCommon::is_closer_to_tgt(const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &) –> bool
- class pyrosetta.rosetta.protocols.constel.PresenceCommon¶
Bases:
pybind11_object
A class to hold data structures and functions shared by filters that check whether the amino acids and atoms they require in the constellation are indeed present.
- static are_aa_pres(ps: pyrosetta.rosetta.core.pose.Pose, cnl: pyrosetta.rosetta.utility.vector1_unsigned_long, aa_typs: pyrosetta.rosetta.utility.vector1_core_chemical_AA, aa_idxs: pyrosetta.rosetta.utility.vector1_unsigned_long) bool ¶
Records the presence of given amino acid types in a given constellation.
C++: protocols::constel::PresenceCommon::are_aa_pres(const class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const class utility::vector1<enum core::chemical::AA, class std::allocator<enum core::chemical::AA> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> bool
- static are_atoms_pres(res: pyrosetta.rosetta.core.conformation.Residue, anams: pyrosetta.rosetta.utility.vector1_std_string, aidxs: pyrosetta.rosetta.utility.vector1_unsigned_long) bool ¶
Records the presence of given atoms in a given residue.
C++: protocols::constel::PresenceCommon::are_atoms_pres(const class core::conformation::Residue &, const class utility::vector1<std::string, class std::allocator<std::string > > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> bool
- class pyrosetta.rosetta.protocols.constel.ResMut¶
Bases:
pybind11_object
A class to represent the mutation of a residue.
- property cid¶
- property eaa¶
- property pdbn¶
- property psn¶
- property saa¶
- class pyrosetta.rosetta.protocols.constel.ResidueMask¶
Bases:
pybind11_object
- assign(self: pyrosetta.rosetta.protocols.constel.ResidueMask, : pyrosetta.rosetta.protocols.constel.ResidueMask) pyrosetta.rosetta.protocols.constel.ResidueMask ¶
C++: protocols::constel::ResidueMask::operator=(const class protocols::constel::ResidueMask &) –> class protocols::constel::ResidueMask &
- print(self: pyrosetta.rosetta.protocols.constel.ResidueMask, os: pyrosetta.rosetta.std.ostream) None ¶
C++: protocols::constel::ResidueMask::print(std::ostream &) const –> void
- class pyrosetta.rosetta.protocols.constel.SingResCnlCrea¶
Bases:
pybind11_object
- static init(stripped: bool) None ¶
initializes the static members of this class
C++: protocols::constel::SingResCnlCrea::init(bool) –> void
- static list_allowable_mutations(starting_aa: str) pyrosetta.rosetta.utility.vector1_char ¶
- Lists the amino acid types that a given amino acid type can be
reduced to.
C++: protocols::constel::SingResCnlCrea::list_allowable_mutations(const char) –> class utility::vector1<char, class std::allocator<char> >
- static strip_atoms(pose: pyrosetta.rosetta.core.pose.Pose, seqpos: int, target_aa: str) None ¶
- sets occupancy to zero for constellation atoms that are not
to be printed on output.
C++: protocols::constel::SingResCnlCrea::strip_atoms(class core::pose::Pose &, unsigned long, const char) –> void
- static stripped() bool ¶
C++: protocols::constel::SingResCnlCrea::stripped() –> bool
- static zero_occ_for_deleted_atoms(pose: pyrosetta.rosetta.core.pose.Pose, seqpos: int, target_aa: str) None ¶
sets occupancy to zero for a residue’s non-constellation atoms.
C++: protocols::constel::SingResCnlCrea::zero_occ_for_deleted_atoms(class core::pose::Pose &, unsigned long, const char) –> void
- pyrosetta.rosetta.protocols.constel.at_interface(ps: pyrosetta.rosetta.core.pose.Pose, cnl: pyrosetta.rosetta.utility.vector1_unsigned_long) bool ¶
C++: protocols::constel::at_interface(const class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> bool
- pyrosetta.rosetta.protocols.constel.cnl_com(cnl: pyrosetta.rosetta.utility.vector1_unsigned_long, ps: pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.numeric.xyzVector_double_t ¶
returns the center of mass of a constellation
C++: protocols::constel::cnl_com(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const class core::pose::Pose &) –> class numeric::xyzVector<double>
- pyrosetta.rosetta.protocols.constel.has_aromatic(ps: pyrosetta.rosetta.core.pose.Pose, cnl: pyrosetta.rosetta.utility.vector1_unsigned_long) bool ¶
C++: protocols::constel::has_aromatic(const class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> bool
- pyrosetta.rosetta.protocols.constel.has_prox_termini(ps: pyrosetta.rosetta.core.pose.Pose, chain: pyrosetta.rosetta.protocols.constel.ChainTerm, NRES: int, DMAX2: float) bool ¶
tells whether a chain has proximal termini
C++: protocols::constel::has_prox_termini(const class core::pose::Pose &, const class protocols::constel::ChainTerm &, unsigned long, double) –> bool
- pyrosetta.rosetta.protocols.constel.mk_neigh_list(tgtnum: int, neighs: pyrosetta.rosetta.utility.vector1_bool, ps: pyrosetta.rosetta.core.pose.Pose) None ¶
Creates the list of residues that are neighbors of a given residue.
C++: protocols::constel::mk_neigh_list(const unsigned long, class utility::vector1<bool, class std::allocator<bool> > &, class core::pose::Pose &) –> void
- pyrosetta.rosetta.protocols.constel.out_pair_constel(mut1: pyrosetta.rosetta.protocols.constel.ResMut, mut2: pyrosetta.rosetta.protocols.constel.ResMut, ps: pyrosetta.rosetta.core.pose.Pose) None ¶
Outputs to file a constellation obtained from mutating a pair of residues
C++: protocols::constel::out_pair_constel(const struct protocols::constel::ResMut &, const struct protocols::constel::ResMut &, class core::pose::Pose &) –> void
- pyrosetta.rosetta.protocols.constel.out_triple_constel(mut1: pyrosetta.rosetta.protocols.constel.ResMut, mut2: pyrosetta.rosetta.protocols.constel.ResMut, mut3: pyrosetta.rosetta.protocols.constel.ResMut, ps: pyrosetta.rosetta.core.pose.Pose) None ¶
Outputs to file a constellation obtained from mutating a triple of residues
C++: protocols::constel::out_triple_constel(const struct protocols::constel::ResMut &, const struct protocols::constel::ResMut &, const struct protocols::constel::ResMut &, class core::pose::Pose &) –> void
- pyrosetta.rosetta.protocols.constel.pair_constel_set(*args, **kwargs)¶
Overloaded function.
pair_constel_set(target_pdb_number: int, target_pdb_chain: str, pose_init: pyrosetta.rosetta.core.pose.Pose) -> None
Searches pair-constellations by target residue.
C++: protocols::constel::pair_constel_set(const int, const char, class core::pose::Pose &) –> void
pair_constel_set(tgtmuts: str, pose_init: pyrosetta.rosetta.core.pose.Pose) -> None
Searches pair-constellations by mutation pair.
C++: protocols::constel::pair_constel_set(const std::string &, class core::pose::Pose &) –> void
- pyrosetta.rosetta.protocols.constel.pair_constel_set_idx2(i: int, j: int, pose_init: pyrosetta.rosetta.core.pose.Pose) None ¶
Outputs all pair-constellations between a given pair of residues
C++: protocols::constel::pair_constel_set_idx2(const unsigned long, const unsigned long, const class core::pose::Pose &) –> void
- pyrosetta.rosetta.protocols.constel.target_constel(tgtcnl_fil: str, ps: pyrosetta.rosetta.core.pose.Pose) None ¶
Searches a single, target constellation.
C++: protocols::constel::target_constel(std::string &, class core::pose::Pose &) –> void
- pyrosetta.rosetta.protocols.constel.triple_constel_set(target_pdb_number: int, target_pdb_chain: str, pose_init: pyrosetta.rosetta.core.pose.Pose) None ¶
Searches triple-constellations by target residue.
C++: protocols::constel::triple_constel_set(const int, const char, class core::pose::Pose &) –> void
- pyrosetta.rosetta.protocols.constel.triple_constel_set_idx3(i: int, j: int, k: int, pose_init: pyrosetta.rosetta.core.pose.Pose) None ¶
Outputs all triple-constellations among a given triple of residues
C++: protocols::constel::triple_constel_set_idx3(const unsigned long, const unsigned long, const unsigned long, const class core::pose::Pose &) –> void