Home       Trees       Indices       Help   
Module rosetta :: Module core :: Module pose :: Class PDBInfo
[hide private]
[frames] | no frames]

Class PDBInfo

object --+
         |
        PDBInfo

maintains pdb residue & atom information inside a Pose


Upon creation of new residue records, e.g. when calling the
 constructors without 'init' or appending/prepending residues, the
 chain id for the new records will be set to a character, currently
 '^', denoting "empty record".  This character may be looked up by
 calling the static method PDBInfo::empty_record().


Class implementation is biased towards simplicity and fast lookup.
 Residue/atom information are kept in vectors.  An internally maintained
 PDBPoseMap provides mapping from pdb -> pose residue numbering.  This
 causes residue mutators to be a bit more expensive due to map updates,
 but this is ok because they are typically called sparingly.  Accessors
 and mutators have overloaded method convention, while special mutators
 use .set_* convention.
Instance Methods [hide private]
 
__init__(*args, **kwargs)
Overloaded function.
a new object with type S, a subtype of T
__new__(T, S, ...)
unicode
__str__(rosetta.core.pose.PDBInfo)
str(x)
 
add_reslabel(...)
add_reslabel(self : rosetta.core.pose.PDBInfo, res : int, label : unicode) -> NoneType
 
add_unrecognized_atoms(...)
add_unrecognized_atoms(self : rosetta.core.pose.PDBInfo, UAs : rosetta.utility.vector1_core_pose_UnrecognizedAtomRecord) -> NoneType
 
alt_loc(*args, **kwargs)
Overloaded function.
 
append_res(*args, **kwargs)
Overloaded function.
 
assign(...)
assign(self : rosetta.core.pose.PDBInfo, info : rosetta.core.pose.PDBInfo) -> rosetta.core.pose.PDBInfo
 
attach_to(...)
attach_to(self : rosetta.core.pose.PDBInfo, conf : rosetta.core.conformation.Conformation) -> NoneType
 
bfactor(*args, **kwargs)
Overloaded function.
 
chain(*args, **kwargs)
Overloaded function.
 
clear_reslabel(...)
clear_reslabel(self : rosetta.core.pose.PDBInfo, res : int) -> NoneType
 
copy(...)
copy(self : rosetta.core.pose.PDBInfo, input_info : rosetta.core.pose.PDBInfo, copy_from : int, copy_to : int, start_from : int) -> NoneType
rosetta.core.io.CrystInfo
crystinfo(rosetta.core.pose.PDBInfo)
Returns the pdb crystinfo
 
delete_res(*args, **kwargs)
Overloaded function.
NoneType
detach_from(rosetta.core.pose.PDBInfo)
Detaches the Conformation and stops observation
unicode
empty_record()
Returns the chain id character specifying "empty record",...
int
get_num_unrecognized_atoms(rosetta.core.pose.PDBInfo)
int
get_num_unrecognized_res(rosetta.core.pose.PDBInfo)
 
get_reslabels(...)
get_reslabels(self : rosetta.core.pose.PDBInfo, res : int) -> rosetta.utility.vector1_std_string
rosetta.utility.vector1_core_pose_UnrecognizedAtomRecord
get_unrecognized_atoms(rosetta.core.pose.PDBInfo)
remembers info about atoms not read into the pose
 
get_unrecognized_res_name(...)
get_unrecognized_res_name(self : rosetta.core.pose.PDBInfo, i : int) -> unicode
 
get_unrecognized_res_size(...)
get_unrecognized_res_size(self : rosetta.core.pose.PDBInfo, i : int) -> int
 
header_information(*args, **kwargs)
Overloaded function.
 
icode(*args, **kwargs)
Overloaded function.
 
is_het(*args, **kwargs)
Overloaded function.
rosetta.std.weak_ptr_const_core_conformation_Conformation_t
is_observing(rosetta.core.pose.PDBInfo)
Returns the Conformation if this PDBInfo is currently observing a conformation, otherwise return NULL
 
modeltag(*args, **kwargs)
Overloaded function.
 
name(*args, **kwargs)
Overloaded function.
 
natoms(...)
natoms(self : rosetta.core.pose.PDBInfo, res : int) -> int
int
nres(rosetta.core.pose.PDBInfo)
Returns the number of residues represented in PDBInfo
 
number(*args, **kwargs)
Overloaded function.
 
obsolete(*args, **kwargs)
Overloaded function.
 
occupancy(*args, **kwargs)
Overloaded function.
 
on_connection_change(...)
on_connection_change(self : rosetta.core.pose.PDBInfo, event : rosetta.core.conformation.signals.ConnectionEvent) -> NoneType
 
on_identity_change(...)
on_identity_change(self : rosetta.core.pose.PDBInfo, event : rosetta.core.conformation.signals.IdentityEvent) -> NoneType
 
on_length_change(...)
on_length_change(self : rosetta.core.pose.PDBInfo, event : rosetta.core.conformation.signals.LengthEvent) -> NoneType
 
pdb2pose(*args, **kwargs)
Overloaded function.
 
pose2pdb(...)
pose2pdb(self : rosetta.core.pose.PDBInfo, res : int) -> unicode
 
prepend_res(*args, **kwargs)
Overloaded function.
NoneType
rebuild_pdb2pose(rosetta.core.pose.PDBInfo)
rebuilds PDBPoseMap from scratch
 
remarks(*args, **kwargs)
Overloaded function.
 
replace_res(...)
replace_res(self : rosetta.core.pose.PDBInfo, res : int, natoms : int) -> NoneType
 
replace_res_remap_bfactors(...)
replace_res_remap_bfactors(self : rosetta.core.pose.PDBInfo, res : int, tgt : rosetta.core.conformation.Residue) -> NoneType
 
res_haslabel(...)
res_haslabel(self : rosetta.core.pose.PDBInfo, res : int, target_label : unicode) -> bool
 
resize_atom_records(*args, **kwargs)
Overloaded function.
 
resize_residue_records(...)
resize_residue_records(self : rosetta.core.pose.PDBInfo, n : int) -> NoneType
 
segmentID(*args, **kwargs)
Overloaded function.
 
set_chains(...)
set_chains(self : rosetta.core.pose.PDBInfo, id : unicode) -> NoneType
 
set_crystinfo(...)
set_crystinfo(self : rosetta.core.pose.PDBInfo, crystinfoin : rosetta.core.io.CrystInfo) -> NoneType
 
set_resinfo(*args, **kwargs)
Overloaded function.
 
temperature(*args, **kwargs)
Overloaded function.
NoneType
tighten_memory(rosetta.core.pose.PDBInfo)
Tightens memory usage

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __subclasshook__

Properties [hide private]

Inherited from object: __class__

Method Details [hide private]

__init__(*args, **kwargs)
(Constructor)

  
Overloaded function.

1. __init__(rosetta.core.pose.PDBInfo) -> NoneType

2. __init__(self : rosetta.core.pose.PDBInfo, n : int) -> NoneType

3. __init__(rosetta.core.pose.PDBInfo, rosetta.core.pose.Pose) -> NoneType

doc

4. __init__(self : rosetta.core.pose.PDBInfo, pose : rosetta.core.pose.Pose, init : bool) -> NoneType

5. __init__(self : rosetta.core.pose.PDBInfo, info : rosetta.core.pose.PDBInfo) -> NoneType
Overrides: object.__init__

__new__(T, S, ...)

 
Returns: a new object with type S, a subtype of T
Overrides: object.__new__

__str__(rosetta.core.pose.PDBInfo)
(Informal representation operator)

 

str(x)

Returns: unicode
Overrides: object.__str__

add_reslabel(...)

  
add_reslabel(self : rosetta.core.pose.PDBInfo, res : int, label : unicode) -> NoneType

adds a label associated to a pose resid.
 

  residue in pose numbering
 

  string that is the "label"

add_unrecognized_atoms(...)

 

add_unrecognized_atoms(self : rosetta.core.pose.PDBInfo, UAs : rosetta.utility.vector1_core_pose_UnrecognizedAtomRecord) -> NoneType

remembers info about atoms not read into the pose

alt_loc(*args, **kwargs)

  
Overloaded function.

1. alt_loc(self : rosetta.core.pose.PDBInfo, res : int, atom_index : int) -> unicode

Returns the alternate location for the  <atom_index>  atom of pose
 residue  <res>

 example(s):
     pose.pdb_info().alt_loc(1,1)
 See also:
     Pose
     PDBInfo
     PDBInfo.pdb2pose
     PDBInfo.pose2pdb

2. alt_loc(self : rosetta.core.pose.PDBInfo, res : int, atom_index : int, loc : unicode) -> NoneType

Sets the alternate location of the  <atom_index>  atom of pose
 residue  <res>  to   <loc>
 

:  <loc> is an alternate location character

append_res(*args, **kwargs)

  
Overloaded function.

1. append_res(self : rosetta.core.pose.PDBInfo, res : int, natoms : int) -> NoneType

Appends residue records given a pose residue number  <res>
 

  residue to append after (in internal/pose numbering)
 

  number of atoms in type of appended residue
 

    number of residue records to append

2. append_res(self : rosetta.core.pose.PDBInfo, res : int, natoms : int, n : int) -> NoneType

Appends residue records given a pose residue number  <res>
 

  residue to append after (in internal/pose numbering)
 

  number of atoms in type of appended residue
 

    number of residue records to append

assign(...)

 

assign(self : rosetta.core.pose.PDBInfo, info : rosetta.core.pose.PDBInfo) -> rosetta.core.pose.PDBInfo

copy assignment

attach_to(...)

  
attach_to(self : rosetta.core.pose.PDBInfo, conf : rosetta.core.conformation.Conformation) -> NoneType

Attaches the Conformation  <conf>  and begins observation

 example(s):

 See also:
     Pose
     PDBInfo

bfactor(*args, **kwargs)

  
Overloaded function.

1. bfactor(self : rosetta.core.pose.PDBInfo, res : int, atom_index : int) -> float

Returns the temperature for the  <atom_index>  atom of pose residue  <res>

 example(s):
     pose.pdb_info().temperature(1,1)
 See also:
     Pose
     PDBInfo
     PDBInfo.pdb2pose
     PDBInfo.pose2pdb

2. bfactor(self : rosetta.core.pose.PDBInfo, res : int, atom_index : int, t : float) -> NoneType

Sets the temperature of the  <atom_index>  atom of pose residue
 <res>  to  <t>

chain(*args, **kwargs)

  
Overloaded function.

1. chain(self : rosetta.core.pose.PDBInfo, res : int) -> unicode

Returns the chain id for pose residue  <res>

 example(s):
     pose.pdb_info().chain(3)
 See also:
     Pose
     PDBInfo
     PDBInfo.pdb2pose
     PDBInfo.pose2pdb

2. chain(self : rosetta.core.pose.PDBInfo, res : int, chain_id : unicode) -> NoneType

Sets the chain id of pose residue  <res>  to  <chain_id>
 

 chain id should not be the empty record character, currently '^'
 

 Returns the pdb insertion code of residue  <res>

 example(s):
     pose.pdb_info().chain(3,"R")
 See also:
     Pose
     PDBInfo
     PDBInfo.pdb2pose
     PDBInfo.pose2pdb

clear_reslabel(...)

  
clear_reslabel(self : rosetta.core.pose.PDBInfo, res : int) -> NoneType

clean all the label(s) associated to a pose resid.
 

  residue in pose numbering

copy(...)

  
copy(self : rosetta.core.pose.PDBInfo, input_info : rosetta.core.pose.PDBInfo, copy_from : int, copy_to : int, start_from : int) -> NoneType

Copyies a section from PDBInfo  <input_info>
 

 the PDBInfo to copy from
 

 the first residue position in input_info to copy
 

 the final residue position in input_info to copy
 

 the first residue position in this PDBInfo to
  copy into

delete_res(*args, **kwargs)

  
Overloaded function.

1. delete_res(self : rosetta.core.pose.PDBInfo, res : int) -> NoneType

Deletes  <n>  residue records starting from pose residue  <res>
 

  residue to start deleting from (in internal/pose numbering)
 

    number of residue records to delete

2. delete_res(self : rosetta.core.pose.PDBInfo, res : int, n : int) -> NoneType

Deletes  <n>  residue records starting from pose residue  <res>
 

  residue to start deleting from (in internal/pose numbering)
 

    number of residue records to delete

detach_from(rosetta.core.pose.PDBInfo)

  
Detaches the Conformation and stops observation
 

 takes no arguments because PDBInfo can only observe one
 Conformation at a time

 example(s):
     pose.pdb_info().detach_from()
 See also:
     Pose
     PDBInfo
Returns: NoneType

empty_record()

  
Returns the chain id character specifying "empty record",
 currently '^'
Returns: unicode

get_reslabels(...)

  
get_reslabels(self : rosetta.core.pose.PDBInfo, res : int) -> rosetta.utility.vector1_std_string

returns the pose(number) labels associated to the residue
 

  residue in pose numbering

header_information(*args, **kwargs)

  
Overloaded function.

1. header_information(self : rosetta.core.pose.PDBInfo, header_information : rosetta.core.io.HeaderInformation) -> NoneType

Note: The header information is only initialized if it is needed.
 Generally this requires using the -run:preserve_header options flag.

2. header_information(rosetta.core.pose.PDBInfo) -> rosetta.core.io.HeaderInformation

3. header_information(rosetta.core.pose.PDBInfo) -> rosetta.core.io.HeaderInformation

icode(*args, **kwargs)

  
Overloaded function.

1. icode(self : rosetta.core.pose.PDBInfo, res : int) -> unicode

Returns the pdb insertion code of residue  <res>

 example(s):
     pose.pdb_info().icode(3)
 See also:
     Pose
     PDBInfo
     PDBInfo.pdb2pose
     PDBInfo.pose2pdb

2. icode(self : rosetta.core.pose.PDBInfo, res : int, ins_code : unicode) -> NoneType

Sets the insertion code of pose residue  <res>  to  _code>
 

 Returns the pdb insertion code of residue  <res>

 example(s):

 See also:
     Pose
     PDBInfo
     PDBInfo.pdb2pose
     PDBInfo.pose2pdb

is_het(*args, **kwargs)

  
Overloaded function.

1. is_het(self : rosetta.core.pose.PDBInfo, res : int, atom_index : int) -> bool

Returns true if the  <atom_index>  atom of pose residue  <res>
 is a heteratom
 

: atom index within instance of core::conformation::Residue,
 currently Rosetta's pdb file output treats the value of .is_het() as an
 override -- if this is set to true, the record will be hetatm, otherwise it
 will decide by Residue type (the usual default)

2. is_het(self : rosetta.core.pose.PDBInfo, res : int, atom_index : int, flag : bool) -> NoneType

Sets the heteroatom flag of the  <atom_index>  atom of pose
 residue  <res>  to  <flag>
 

 currently Rosetta's pdb file output treats the value of .is_het() as an
 override -- if this is set to true, the record will be hetatm, otherwise it
 will decide by Residue type (the usual default)

is_observing(rosetta.core.pose.PDBInfo)

  
Returns the Conformation if this PDBInfo is currently observing
 a conformation, otherwise return NULL

 example(s):
     pose.pdb_info().is_observing()
 See also:
     Pose
     PDBInfo
Returns: rosetta.std.weak_ptr_const_core_conformation_Conformation_t

modeltag(*args, **kwargs)

  
Overloaded function.

1. modeltag(rosetta.core.pose.PDBInfo) -> unicode

Returns the model tag for a multi-model pdb

 example(s):
     pose.pdb_info().modeltag()
 See also:
     Pose
     PDBInfo

2. modeltag(self : rosetta.core.pose.PDBInfo, tag : unicode) -> NoneType

Sets the model tag for a multi-model pdb to  <tag>

 example(s):
     pose.pdb_info().modeltag('Number1')
 See also:
     Pose
     PDBInfo

name(*args, **kwargs)

  
Overloaded function.

1. name(rosetta.core.pose.PDBInfo) -> unicode

Returns the pdb name

 example(s):
     pose.pdb_info().name()
 See also:
     Pose
     PDBInfo

2. name(self : rosetta.core.pose.PDBInfo, s : unicode) -> NoneType

Sets the pdb name

 example(s):
     pose.pdb_info().name('MyPDB')
 See also:
     Pose
     PDBInfo

natoms(...)

  
natoms(self : rosetta.core.pose.PDBInfo, res : int) -> int

Returns the number of atoms represented for the residue  <res>
 

: residue  <res>  must be in pose numbering

 example(s):
     pose.pdb_info().natoms(3)
 See also:
     Pose
     PDBInfo

nres(rosetta.core.pose.PDBInfo)

  
Returns the number of residues represented in PDBInfo

 example(s):
     pose.pdb_info().nres()
 See also:
     Pose
     PDBInfo
Returns: int

number(*args, **kwargs)

  
Overloaded function.

1. number(self : rosetta.core.pose.PDBInfo, res : int) -> int

Returns the pdb sequence number of pose residue  <res>

 example(s):
     pose.pdb_info().number(3)
 See also:
     Pose
     PDBInfo
     PDBInfo.pdb2pose
     PDBInfo.pose2pdb

2. number(self : rosetta.core.pose.PDBInfo, res : int, pdb_res : int) -> NoneType

Sets the pdb sequence residue number of pose residue  <res>  to  <pdb_res>
 

 Returns the pdb insertion code of residue  <res>

 example(s):
     pose.pdb_info().number(3,81)
 See also:
     Pose
     PDBInfo
     PDBInfo.pdb2pose
     PDBInfo.pose2pdb

obsolete(*args, **kwargs)

  
Overloaded function.

1. obsolete(rosetta.core.pose.PDBInfo) -> bool

Returns true if PDBInfo is obsolete and needs updating
 

 This flag is currently not used within the class and
 is provided for user convenience.  Setting this will
 forcibly turn off pdb numbering when dumping pdbs.

 example(s):
     pose.pdb_info().obsolete()
 See also:
     Pose
     PDBInfo

2. obsolete(self : rosetta.core.pose.PDBInfo, flag : bool) -> NoneType

Sets the obsolete state to  <flag>
 

 this flag is currently not used within the class and
 is provided for user convenience.  Setting this will
 forcibly turn off pdb numbering when dumping pdbs.

occupancy(*args, **kwargs)

  
Overloaded function.

1. occupancy(self : rosetta.core.pose.PDBInfo, res : int, atom_index : int) -> float

Returns the occupancy for the  <atom_index>  atom  of pose residue  <res>

 example(s):
     pose.pdb_info().occupancy(1,1)
 See also:
     Pose
     PDBInfo
     PDBInfo.pdb2pose
     PDBInfo.pose2pdb

2. occupancy(self : rosetta.core.pose.PDBInfo, res : int, atom_index : int, occ : float) -> NoneType

Sets the occupancy of the  <atom_index>  atom of pose residue
 <res>  to  <occ>

on_connection_change(...)

 

on_connection_change(self : rosetta.core.pose.PDBInfo, event : rosetta.core.conformation.signals.ConnectionEvent) -> NoneType

Updates when connection to Conformation is changed

on_identity_change(...)

 

on_identity_change(self : rosetta.core.pose.PDBInfo, event : rosetta.core.conformation.signals.IdentityEvent) -> NoneType

Updates atom records when residue identity changes in Conformation

on_length_change(...)

  
on_length_change(self : rosetta.core.pose.PDBInfo, event : rosetta.core.conformation.signals.LengthEvent) -> NoneType

Updates residue and atom records when length changes in Conformation,
 obsoletes PDBInfo

pdb2pose(*args, **kwargs)

  
Overloaded function.

1. pdb2pose(self : rosetta.core.pose.PDBInfo, chain : unicode, res : int) -> int

Returns the pose numbering of the pdb residue with chain  <chain>,
 pdb residue  <res>, and insertion code  <icode>
 

:  <icode>  is not required, returns 0 if not found,
 pose numbering is sequential ie. starts at 1 and goes up
 pdb numbering can be anything

 example(s):
     pose.pdb_info().pdb2pose("B",5)
 See also:
     Pose
     PDBInfo
     PDBInfo.pose2pdb

2. pdb2pose(self : rosetta.core.pose.PDBInfo, chain : unicode, res : int, icode : unicode) -> int

Returns the pose numbering of the pdb residue with chain  <chain>,
 pdb residue  <res>, and insertion code  <icode>
 

:  <icode>  is not required, returns 0 if not found,
 pose numbering is sequential ie. starts at 1 and goes up
 pdb numbering can be anything

 example(s):
     pose.pdb_info().pdb2pose("B",5)
 See also:
     Pose
     PDBInfo
     PDBInfo.pose2pdb

3. pdb2pose(rosetta.core.pose.PDBInfo) -> rosetta.core.pose.PDBPoseMap

Returns the internally maintained PDBPoseMap

 example(s):

 See also:
     Pose
     PDBInfo
     PDBInfo.pdb2pose
     PDBInfo.pose2pdb

pose2pdb(...)

  
pose2pdb(self : rosetta.core.pose.PDBInfo, res : int) -> unicode

Returns the pdb numbering string of pose residue  <res>
 

: pdb string contains the chainID and number
 pose numbering is sequential ie. starts at 1 and goes up
 pdb numbering can be anything

 example(s):
     pose.pdb_info().pose2pdb(25)
 See also:
     Pose
     PDBInfo
     PDBInfo.pdb2pose

prepend_res(*args, **kwargs)

  
Overloaded function.

1. prepend_res(self : rosetta.core.pose.PDBInfo, res : int, natoms : int) -> NoneType

Prepends residue records before given pose residue number  <res>
 

  residue to prepend before (in internal/pose numbering)
 

  number of atoms in type of appended residue
 

    number of residue records to prepend

2. prepend_res(self : rosetta.core.pose.PDBInfo, res : int, natoms : int, n : int) -> NoneType

Prepends residue records before given pose residue number  <res>
 

  residue to prepend before (in internal/pose numbering)
 

  number of atoms in type of appended residue
 

    number of residue records to prepend

remarks(*args, **kwargs)

  
Overloaded function.

1. remarks(rosetta.core.pose.PDBInfo) -> rosetta.core.io.Remarks

Returns the pdb remarks (const)

 example(s):
     pose.pdb_info().remarks()
 See also:
     Pose
     PDBInfo

2. remarks(rosetta.core.pose.PDBInfo) -> rosetta.core.io.Remarks

Returns the pdb remarks (mutable)
 

 we allow direct access to the remarks vector because its
 state is independent of the rest of PDBInfo and it's much more
 convenient for the user

 example(s):
     pose.pdb_info().remarks()
 See also:
     Pose
     PDBInfo

3. remarks(self : rosetta.core.pose.PDBInfo, in : rosetta.core.io.Remarks) -> NoneType

Sets the pdb remarks to  <in>

 example(s):

 See also:
     Pose
     PDBInfo

replace_res(...)

  
replace_res(self : rosetta.core.pose.PDBInfo, res : int, natoms : int) -> NoneType

"Replaces" residue record for pose residue  <res>
 

 Leaves information in residue record untouched, but resizes
 and zeroes atom records for the residue.
 

 residue to replace
 

 number of atoms in type of residue

replace_res_remap_bfactors(...)

 

replace_res_remap_bfactors(self : rosetta.core.pose.PDBInfo, res : int, tgt : rosetta.core.conformation.Residue) -> NoneType

same as replace_res BUT remaps B factors from src to tgt

res_haslabel(...)

  
res_haslabel(self : rosetta.core.pose.PDBInfo, res : int, target_label : unicode) -> bool

uses std iterators to check if a residue has a label associated to it
 

  residue in pose numbering
 

 string to look for inside the labes associated to the residue

resize_atom_records(*args, **kwargs)

  
Overloaded function.

1. resize_atom_records(self : rosetta.core.pose.PDBInfo, res : int, n : int) -> NoneType

Ensures  <n>  atom records for residue  <res>  are available
 

: if  <zero>  is true, zero the atom records for this residue

2. resize_atom_records(self : rosetta.core.pose.PDBInfo, res : int, n : int, zero : bool) -> NoneType

Ensures  <n>  atom records for residue  <res>  are available
 

: if  <zero>  is true, zero the atom records for this residue

3. resize_atom_records(self : rosetta.core.pose.PDBInfo, n : int) -> NoneType

Ensures  <n>  atom records for residue  <res>  are available
 

: if  <zero>  is true, zero the atom records for this residue

4. resize_atom_records(self : rosetta.core.pose.PDBInfo, n : int, zero : bool) -> NoneType

Ensures  <n>  atom records for residue  <res>  are available
 

: if  <zero>  is true, zero the atom records for this residue

5. resize_atom_records(self : rosetta.core.pose.PDBInfo, pose : rosetta.core.pose.Pose) -> NoneType

Updates the number of atom records with respect to atoms in  <pose>
 

 Number of internally available atom records will be adjusted
 to match number of atoms within each residue in Pose.  Only newly
 created records will be zeroed, any existing records are untouched.

resize_residue_records(...)

  
resize_residue_records(self : rosetta.core.pose.PDBInfo, n : int) -> NoneType

Resizes for  <n>  residue records
 

 Leaves atom record state inconsistent.  Atom records for
 remaining residues are untouched while new residues have no atom
 records, so make sure and call one of resize_atom_records()
 afterwards if necessary.
 

 Do not use this method for ins/del of residues, as it leaves
 the data state inconsistent.  See append_res/prepend_res/delete_res
 for that type of functionality.

segmentID(*args, **kwargs)

  
Overloaded function.

1. segmentID(self : rosetta.core.pose.PDBInfo, res : int) -> unicode

2. segmentID(self : rosetta.core.pose.PDBInfo, res : int, segmentID : unicode) -> NoneType

Sets the insertion code of pose residue  <res>  to  _code>
 

 Returns the pdb insertion code of residue  <res>

 example(s):

 See also:
     Pose
     PDBInfo
     PDBInfo.pdb2pose
     PDBInfo.pose2pdb

set_chains(...)

 

set_chains(self : rosetta.core.pose.PDBInfo, id : unicode) -> NoneType

Sets all residue chain ids to the character <id>

set_crystinfo(...)

 

set_crystinfo(self : rosetta.core.pose.PDBInfo, crystinfoin : rosetta.core.io.CrystInfo) -> NoneType

Sets the pdb crystinfo

set_resinfo(*args, **kwargs)

  
Overloaded function.

1. set_resinfo(self : rosetta.core.pose.PDBInfo, res : int, chain_id : unicode, pdb_res : int) -> NoneType

Sets the chain id, pdb sequence residue numbering, and insertion
 code for pose residue  <res>  to  <chain_id>  ,  <pdb_res>  , and
 _code>  respectfully
 

: convenience method; more efficient than doing each individually
 due to map updates
 

 Returns the pdb insertion code of residue  <res>

 example(s):
     pose.pdb_info().icode(3)
 See also:
     Pose
     PDBInfo
     PDBInfo.chain
     PDBInfo.icode
     PDBInfo.number
     PDBInfo.pdb2pose
     PDBInfo.pose2pdb

2. set_resinfo(self : rosetta.core.pose.PDBInfo, res : int, chain_id : unicode, pdb_res : int, ins_code : unicode) -> NoneType

Sets the chain id, pdb sequence residue numbering, and insertion
 code for pose residue  <res>  to  <chain_id>  ,  <pdb_res>  , and
 _code>  respectfully
 

: convenience method; more efficient than doing each individually
 due to map updates
 

 Returns the pdb insertion code of residue  <res>

 example(s):
     pose.pdb_info().icode(3)
 See also:
     Pose
     PDBInfo
     PDBInfo.chain
     PDBInfo.icode
     PDBInfo.number
     PDBInfo.pdb2pose
     PDBInfo.pose2pdb

temperature(*args, **kwargs)

  
Overloaded function.

1. temperature(self : rosetta.core.pose.PDBInfo, res : int, atom_index : int) -> float

Returns the temperature for the  <atom_index>  atom of pose residue  <res>

 example(s):
     pose.pdb_info().temperature(1,1)
 See also:
     Pose
     PDBInfo
     PDBInfo.pdb2pose
     PDBInfo.pose2pdb

2. temperature(self : rosetta.core.pose.PDBInfo, res : int, atom_index : int, t : float) -> NoneType

Sets the temperature of the  <atom_index>  atom of pose residue
 <res>  to  <t>

   Home       Trees       Indices       Help   
Generated by Epydoc 3.0.1 on Fri Jul 29 19:29:07 2016 http://epydoc.sourceforge.net