prometry.pdbgeometry.GeometryMaker

class documentation

class GeometryMaker:

Constructor: GeometryMaker(pobjs, log, exc_hetatm)

View In Hierarchy

Undocumented

Method __init__ Initialises a GeoDataFrame with the list of biopython structures
Method calculateData Creates the geoemtry from the structures in the class
Method calculateGeometry Creates the geoemtry from the structures in the class
Method calculateOneGeometry Creates the geoemtry from the structure in the class for 1 geo
Method filterDataFrame Undocumented
Method geoToAtoms Converts a single geo to the residue and atoms reuired
Method getMatchingAtoms Undocumented
Method getMatchingStartAtoms Undocumented
Method getNearestAtom Undocumented
Method getNearestAtomMatch Undocumented
Method infoAtoms Undocumented
Instance Variable exc_hetatm Undocumented
Instance Variable log Undocumented
Instance Variable pobjs Undocumented
def __init__(self, pobjs, log=0, exc_hetatm=True):

Initialises a GeoDataFrame with the list of biopython structures

:param biopython_structures: A list of structures that has been created from biopython

def calculateData(self, hues=['pdb_code', 'resolution', 'chain', 'aa', 'rid', 'ridx', 'atom_no', 'atom_name', 'element', 'bfactor', 'occupancy', 'x', 'y', 'z'], log=0):

Creates the geoemtry from the structures in the class

def calculateGeometry(self, geos, log=0):

Creates the geoemtry from the structures in the class

def calculateOneGeometry(self, pobj, chain, resno, geo_atoms, geo_type, log=0):

Creates the geoemtry from the structure in the class for 1 geo

:param chain: The chain id :param rid: The residue number :param geo_atoms: A list of tuples that is the atom, the displacement

:returns: [bool,float,bfactor, occupancy, atoms, GeoAtom] a bool for if it could be calculated, and the value, and the reference atom

def filterDataFrame(self, data, inclusions={}, exclusions={}):

Undocumented

def geoToAtoms(self, geo):

Converts a single geo to the residue and atoms reuired

def getMatchingAtoms(self, pobj, resno, chain, res, atom, geo_atom):

Undocumented

def getMatchingStartAtoms(self, pobj, chain, resno, geo_atom):

Undocumented

def getNearestAtom(self, pobj, refatm, ref_rid, ref_chain, atmtypes, resmax, nearest, log=0, elements=False):

Undocumented

def getNearestAtomMatch(self, pobj, atom, candidate_atoms, nearest, criteria):

Undocumented

def infoAtoms(self, atoms):

Undocumented

exc_hetatm =

Undocumented

log =

Undocumented

pobjs =

Undocumented