AmberResidueType¶
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class
biskit.
AmberResidueType
(name=None, code=None, letter=None, source=None)[source]¶ Bases:
biskit.pdbModel.PDBModel
Standard description of a certain class of residues.
In addition to the normal PDBModel things, this class defines three additional fields:
- name … the full long residue name (str), e.g. ‘Alanine’
- code … the three-letter name used in PDB files (str), e.g. ‘ALA’
- letter … the single-letter residue code (str), e.g. ‘A’
The order and names of atoms are supposed to serve as a reference to check and normalize actual residues parsed from PDB files.
Currently, AmberResidueTypes can only be created from Amber prep library files.
An alternative method would be to create AmberResidueTypes from some standard PDB file:
>>> m = PDBModel('standard_aa.pdb') >>> standard_res = [ AmberResidueType( res ) for res in m.resModels() ]
See also
Methods Overview
__init__
param name: full residue name (converted to lower letters) :type name: str :param code: three-letter residue code (converted to upper letters) :type code: str :param letter: single-letter residue code (converted to upper letter) :type letter: str :param source: pdb file, model or structure of residue from which to extract all the other data :type source: PDBModel or str addChainFromSegid
Takes the last letter of the segment ID and adds it as chain ID. addChainId
Assign consecutive chain identifiers A - Z to all atoms. argsort
Prepare sorting atoms within residues according to comparison function. atom2chainIndices
Convert atom indices to chain indices. atom2chainMask
Mask (set to 0) chains for which all atoms are masked (0) in atomMask. atom2resIndices
Get list of indices of residues for which any atom is in indices. atom2resMask
Mask (set 0) residues for which all atoms are masked (0) in atomMask. atom2resProfile
Get a residue profile where each residue has the value that its first atom has in the atom profile. atomNames
Return a list of atom names from start to stop RESIDUE index atomRange
>>> m.atomRange() == range( m.lenAtoms() )
atomkey
Create a string key encoding the atom content of this model independent of the order in which atoms appear within residues. biomodel
Return the ‘biologically relevant assembly’ of this model according to the information in the PDB’s BIOMT record (captured in info[‘BIOMT’]). center
Geometric centar of model. centerOfMass
Center of mass of PDBModel. centered
Get model with centered coordinates. chain2atomIndices
Convert chain indices into atom indices. chain2atomMask
Convert chain mask to atom mask. chainBreaks
Identify discontinuities in the molecule’s backbone. chainEndIndex
Get the position of the each residue’s last atom. chainIndex
Get indices of first atom of each chain. chainMap
Get chain index of each atom. clone
Clone PDBModel. compareAtoms
Get list of atom indices for this and reference model that converts both into 2 models with identical residue and atom content. compareChains
Get list of corresponding chain indices for this and reference model. compress
Compress PDBmodel using mask. concat
Concatenate atoms, coordinates and profiles. disconnect
Disconnect this model from its source (if any). equals
Compares the residue and atom sequence in the given range. extendIndex
Translate a list of positions that is defined, e.g., on residues (/chains) to a list of atom positions AND also return the starting position of each residue (/chain) in the new sub-list of atoms. extendMask
Translate a mask that is defined,e.g., on residues(/chains) to a mask that is defined on atoms. filter
Extract atoms that match a combination of key=values. filterIndex
Get atom positions that match a combination of key=values. fit
Least-square fit this model onto refMode getAtoms
Get atom CrossViews that can be used like dictionaries. getPdbCode
Return pdb code of model. getXyz
Get coordinates, fetch from source PDB or pickled PDBModel, if necessary. index2map
Create a map of len_i length, giving the residue(/chain) numer of each atom, from list of residue(/chain) starting positions. indices
Get atom indices conforming condition. indicesFrom
Get atom indices conforming condition applied to an atom profile. keep
Replace atoms,coordinates,profiles of this(!) model with sub-set. lenAtoms
Number of atoms in model. lenBiounits
Number of biological assemblies defined in PDB BIOMT record, if any. lenChains
Number of chains in model. lenResidues
Number of residues in model. magicFit
Superimpose this model onto a ref. map2index
Identify the starting positions of each residue(/chain) from a map giving the residue(/chain) number of each atom. mask
Get atom mask. maskBB
Short cut for mask of all backbone atoms. maskCA
Short cut for mask of all CA atoms. maskCB
Short cut for mask of all CB I{and} CA of GLY. maskDNA
Short cut for mask of all atoms in DNA (based on residue name). maskF
Create list whith result of atomFunction( atom ) for each atom. maskFrom
Create an atom mask from the values of a specific profile. maskH
Short cut for mask of hydrogens. maskH2O
Short cut for mask of all atoms in residues named TIP3, HOH and WAT maskHeavy
Short cut for mask of all heavy atoms. maskHetatm
Short cut for mask of all HETATM maskNA
Short cut for mask of all atoms in DNA or RNA (based on residue name). maskProtein
Short cut for mask containing all atoms of amino acids. maskRNA
Short cut for mask of all atoms in RNA (based on residue name). maskSolvent
Short cut for mask of all atoms in residues named TIP3, HOH, WAT, Na+, Cl-, CA, ZN mass
Molecular weight of PDBModel. masses
Collect the molecular weight of all atoms in PDBModel. mergeChains
Merge two adjacent chains. mergeResidues
Merge two adjacent residues. plot
Get a quick & dirty overview over the content of a PDBModel. profile
Use:: profile( name, updateMissing=0) -> atom or residue profile profile2atomMask
Same as profile2mask
, but converts residue mask to atom mask.profile2mask
param cutoff_min: low value cutoff (all values >= cutoff_min) :type cutoff_min: float :param cutoff_max: high value cutoff (all values < cutoff_max) :type cutoff_max: float profile2resList
Group the profile values of each residue’s atoms into a separate list. profileChangedFromDisc
Check if profile has changed compared to source. profileInfo
Use: remove
Convenience access to the 3 different remove methods. removeProfile
Remove residue or atom profile(s) removeRes
Remove all atoms with a certain residue name. renameAmberRes
Rename special residue names from Amber back into standard names (i.e CYX S{->} CYS ) renumberResidues
Make all residue numbers consecutive and remove any insertion code letters. report
Print (or return) a brief description of this model. reportAtoms
param i: optional list of atom positions to report (default: all) :type i: [ int ] :return: formatted string with atom and residue names similar to PDB :rtype: str res2atomIndices
Convert residue indices to atom indices. res2atomMask
Convert residue mask to atom mask. res2atomProfile
Get an atom profile where each atom has the value its residue has in the residue profile. resEndIndex
Get the position of the each residue’s last atom. resIndex
Get the position of the each residue’s first atom. resList
Return list of lists of atom pseudo dictionaries per residue, which allows to iterate over residues and atoms of residues. resMap
Get list to map from any atom to a continuous residue numbering (starting with 0). resMapOriginal
Generate list to map from any atom to its ORIGINAL(!) PDB residue number. resModels
Creates one new PDBModel for each residue in the parent PDBModel. residusMaximus
Take list of value per atom, return list where all atoms of any residue are set to the highest value of any atom in that residue. rms
Rmsd between two PDBModels. saveAs
Pickle this PDBModel to a file, set the ‘source’ field to this file name and mark atoms, xyz, and profiles as unchanged. sequence
Amino acid sequence in one letter code. setPdbCode
Set model pdb code. setSource
param source: LocalPath OR PDBModel OR str setXyz
Replace coordinates. slim
Remove xyz array and profiles if they haven’t been changed and could hence be loaded from the source file (only if there is a source file…). sort
Apply a given sort list to the atoms of this model. sourceFile
Name of pickled source or PDB file. structureFit
Structure-align this model onto a reference model using the external TM-Align program (which needs to be installed). take
Overriding PDBModel.take to rescue and copy additional fields takeChains
Get copy of this model with only the given chains. takeResidues
Copy the given residues into a new model. transform
Transform coordinates of PDBModel. transformation
Get the transformation matrix which least-square fits this model onto the other model. unequalAtoms
Identify atoms that are not matching between two models. unsort
Undo a previous sorting on the model itself (no copy). update
Read coordinates, atoms, fileName, etc. validSource
Check for a valid source on disk. version
writePdb
Save model as PDB file. xplor2amber
Rename atoms so that tleap from Amber can read the PDB. xyzChangedFromDisc
Tell whether xyz can currently be reconstructed from a source on disc. xyzIsChanged
Tell if xyz or atoms have been changed compared to source file or source object (which can be still in memory). Attributes Overview
PDB_KEYS
AmberResidueType Method & Attribute Details
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__init__
(name=None, code=None, letter=None, source=None)[source]¶ Parameters: - name (str) – full residue name (converted to lower letters)
- code (str) – three-letter residue code (converted to upper letters)
- letter (str) – single-letter residue code (converted to upper letter)
- source (PDBModel or str) – pdb file, model or structure of residue from which to extract all the other data