constel

Bindings for protocols::constel namespace

class pyrosetta.rosetta.protocols.constel.ChainTerm

Bases: pybind11_builtins.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_builtins.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_builtins.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_builtins.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_builtins.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_builtins.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_builtins.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_builtins.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_builtins.pybind11_object

A class to hold data structures and functions shared by filters that consider hydrogen bonding.

static init() None

C++: protocols::constel::HBondCommon::init() –> void

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_builtins.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_builtins.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_builtins.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_builtins.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_builtins.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_builtins.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_builtins.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.

  1. 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

  1. 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