Residue¶

class rnamake.residue.Bead(center, btype)[source]¶

Bases: object

Bead class stores information related to keeping track of steric clashes between residues during building. They are never used outside the Residue class

Parameters:	btype (BeadType) – type of the bead either Phos(Phosphate), Sugar or Base, of the atoms used generate the center center (numpy array) – The geometric center of the group of atoms

copy()[source]¶

returns a deep copy of current bead object

Returns:	copy of bead object
Return type:	Bead

type_name()[source]¶

returns name of btype in string form

Returns:	name of btype type
Return type:	str

class rnamake.residue.BeadType[source]¶

Bases: object

BeadType is an ENUM type. This is to specify which center of atoms each bead represents.

Phosphate (0): P, OP1, OP2

Sugar (1): O5’,C5’,C4’,O4’,C3’,O3’,C1’,C2’,O2’

Base (2): All remaining atoms

class rnamake.residue.Residue(rtype, name, num, chain_id, i_code='')[source]¶

Bases: object

Store residue information from pdb file, stores all Atom objects that belong to residue. Implementation is designed to be extremely lightweight.

Parameters:	rtype (residue_type.ResidueType) – residue type, stores information about residue name (str) – residue name num (int) – residue num chain_id (str) – chain identification i_code (str) – insertion code, optional argument if not supplied will be set to
Attributes:

atoms : atom.Atom: holds all atoms that belong to this residue object
name : str: name of residue, ex. ADE, GUA etc
num : int: residue num
rtype : residue_type.ResidueType: Information about residue type each nucleic acid has its own type
chain_id : str: chain indentification string, ex. ‘A’ or ‘B’
i_code: str: residue insertion code
uuid : uuid.uuid1: the unique id to indentify residue

Examples:

# generating a new residue
>>> rts = residue_type.ResidueTypeSet()
>>> rtype = rts.get_rtype_by_resname("ADE")
>>> r = Residue(rtype, "ADE", 1, "A")
>>> print r.name
A

#using test residue
>>> import rnamake.unittests.instances
>>> r = rnamake.unittests.instances.residue()
>>> print r.name
G

>>> a = r.get_atom("C1'")
>>> print a.coords
[-23.806 -50.289  86.732]

>>> r.get_beads()
[<Bead(btype='SUGAR', center='-24.027 -48.5001111111 86.368')>, <Bead(btype='BASE', center='-21.2186363636 -52.048 85.1157272727')>]

#a fast way of saving coordinate information to file
>>> r.to_str()
"GUA,G,103,A,,N,N,N,O5' -26.469 -47.756 84.669,C5' -25.05 -47.579 84.775,C4' -24.521 -48.156 86.068,O4' -24.861 -49.568 86.118,C3' -23.009 -48.119 86.281,O3' -22.548 -46.872 86.808,C1' -23.806 -50.289 86.732,C2' -22.812 -49.259 87.269,O2' -23.167 -48.903 88.592,N1 -19.538 -52.485 85.025,C2 -19.717 -51.643 86.097,N2 -18.624 -51.354 86.809,N3 -20.884 -51.124 86.445,C4 -21.881 -51.521 85.623,C5 -21.811 -52.356 84.527,C6 -20.546 -52.91 84.164,O6 -20.273 -53.677 83.228,N7 -23.063 -52.513 83.947,C8 -23.858 -51.786 84.686,N9 -23.21 -51.159 85.722,"

#get PDB formmated coordinates back out
>>> r.to_pdb_str()
ATOM      1 O5'  G   A 103     -26.469 -47.756  84.669  1.00  0.00
ATOM      2 C5'  G   A 103     -25.050 -47.579  84.775  1.00  0.00
ATOM      3 C4'  G   A 103     -24.521 -48.156  86.068  1.00  0.00
ATOM      4 O4'  G   A 103     -24.861 -49.568  86.118  1.00  0.00
ATOM      5 C3'  G   A 103     -23.009 -48.119  86.281  1.00  0.00
ATOM      6 O3'  G   A 103     -22.548 -46.872  86.808  1.00  0.00
.
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.

connected_to(res, cutoff=3.0)[source]¶

Determine if another residue is connected to this residue, returns 0 if res is not connected to self, returns 1 if connection is going from 5’ to 3’ and returns -1 if connection is going from 3’ to 5’

Parameters:	res (Residue) – another residue cutoff (int) – distance to be considered connected, default: 3 Angstroms
Return type:	int

copy()[source]¶

performs a deep copy of Residue object

Return type:	Residue
Examples:

>>> import rnamake.unittests.instances
>>> r = rnamake.unittests.instances.residue()
>>> r_copy = r.copy()
>>> r_copy.name
G

get_atom(atom_name)[source]¶

get atom object by its name

Parameters:	atom_name (str) – name

Examples:

>>> r = rnamake.unittests.instances.residue()
>>> a = r.get_atom("C1'")
>>> print a.coords
[-23.806 -50.289  86.732]

get_beads()[source]¶

Generates steric beads required for checking for steric clashes between motifs. Each residues has three beads modeled after the typical three bead models used in coarse grain modeling. The three beads are:

Phosphate: P, OP1, OP2

Sugar : O5’,C5’,C4’,O4’,C3’,O3’,C1’,C2’,O2’

Base : All remaining atoms

if there are for example no phosphate atoms only 2 beads will be returned.

>>> import rnamake.unittests.instances
>>> r = rnamake.unittests.instances.residue()
>>> r.get_beads()
[<Bead(btype='SUGAR', center='-24.027 -48.5001111111 86.368')>, <Bead(btype='BASE', center='-21.2186363636 -52.048 85.1157272727')>]

new_uuid()[source]¶: give residue a new unique indentifier code. There is probably no reason why you should call this unless writing a new, motif structure.

setup_atoms(atoms)[source]¶

put atoms in correct positon in internal atom list, also corrects some named atom names to their correct name

Parameters:	atoms (list of Atom objects) – list of atom objects that are to be part of this residue

short_name()[source]¶

gets letter of residue, i.e. A or G etc

Returns:	letter for residue
Return type:	str

to_pdb(fname='residue.pdb')[source]¶

Writes a PDB string formmated verision of this Residue object to file

Parameters:	fname (str) – filename of output PDB file, default=”chain.pdb”
Returns:	None

to_pdb_str(acount=1, return_acount=0, rnum=-1, chain_id='')[source]¶

returns pdb formatted string of residue’s coordinate information

Parameters:	acount (int) – current atom index, default: 1 return_acount (int) – final atom index after current atoms, default: 0 rnum (int) – starting residue number, default: -1 chain_id (str) – the chain id of the chain, i.e. “A”, “B” etc
Return type:	str
Examples:

>>> import rnamake.unittests.instances
>>> r = rnamake.unittests.instances.residue()
>>> r.to_pdb_str()
ATOM      1 O5'  G   A 103     -26.469 -47.756  84.669  1.00  0.00
ATOM      2 C5'  G   A 103     -25.050 -47.579  84.775  1.00  0.00
ATOM      3 C4'  G   A 103     -24.521 -48.156  86.068  1.00  0.00
ATOM      4 O4'  G   A 103     -24.861 -49.568  86.118  1.00  0.00
ATOM      5 C3'  G   A 103     -23.009 -48.119  86.281  1.00  0.00
ATOM      6 O3'  G   A 103     -22.548 -46.872  86.808  1.00  0.00
.
.
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to_str()[source]¶

stringifes residue object

Returns:	stringified residue object

>>> import rnamake.unittests.instances
>>> r = rnamake.unittests.instances.residue()
>>> r.to_str()
"GUA,G,103,A,,N,N,N,O5' -26.469 -47.756 84.669,C5' -25.05 -47.579 84.775,C4' -24.521 -48.156 86.068,O4' -24.861 -49.568 86.118,C3' -23.009 -48.119 86.281,O3' -22.548 -46.872 86.808,C1' -23.806 -50.289 86.732,C2' -22.812 -49.259 87.269,O2' -23.167 -48.903 88.592,N1 -19.538 -52.485 85.025,C2 -19.717 -51.643 86.097,N2 -18.624 -51.354 86.809,N3 -20.884 -51.124 86.445,C4 -21.881 -51.521 85.623,C5 -21.811 -52.356 84.527,C6 -20.546 -52.91 84.164,O6 -20.273 -53.677 83.228,N7 -23.063 -52.513 83.947,C8 -23.858 -51.786 84.686,N9 -23.21 -51.159 85.722,"