Module bioiain.base.ligand

Classes

class Ligand (atoms, parent=None, relevance_threshold=15, **kwargs)

Expand source code

class Ligand(object):
        child_class = BIAtom
        type = "ligand"
        def __init__(self, atoms, parent=None, relevance_threshold=15, **kwargs):
                self.atoms = atoms

                self.name = self.atoms[0].resname
                self.chain = self.atoms[0].chain
                self.complex = self.atoms[0].complex
                self.entity = self.atoms[0].entity
                self.model = self.atoms[0].model

                self.id = (self.name, self.complex)
                self.id2 = (self.name, self.chain)

                self.relevant = True

                self._com = None

                if parent is not None:
                        self._determine_relevance(entity=parent, relevance_threshold=relevance_threshold)


        def _determine_relevance(self, entity=None, relevance_threshold=15):
                self.relevant = False
                if entity is None:
                        self.relevant = True
                else:
                        sa = self._calculate_sasa(entity=entity)
                        if sa < relevance_threshold:
                                self.relevant = True
                        #print("SASA", sa, "LIGAND:", self)


                return self.relevant

        def _calculate_sasa(self, entity=None):
                from ..tools.SASA import SASA
                sasa = SASA()
                sasas = sasa.compute(entity=entity, targets=self.atoms, quiet=True)
                assert len(sasas) == len(self.atoms)

                av_sasa = sum(sasas) / len(sasas)
                self.sasa = av_sasa
                return self.sasa



        def com(self, force=False):
                if self._com is None or force:
                        from ..utilities.maths import find_com
                        self._com = find_com(self.atoms)
                return self._com

        def __repr__(self):
                return f"<bi.{self.__class__.__name__} id={self.id2}({self.complex})>"

Class variables

var child_class

The type of the None singleton.

var type

The type of the None singleton.

Methods

def com(self, force=False)

Expand source code

def com(self, force=False):
        if self._com is None or force:
                from ..utilities.maths import find_com
                self._com = find_com(self.atoms)
        return self._com

class Water (atoms, **kwargs)

Expand source code

class Water(object):
        child_class = BIAtom
        type = "water"
        def __init__(self, atoms, **kwargs):
                self.atoms = atoms

                for a in self.atoms:
                        if a.name == "O":
                                self.o = a
                self.resseq = self.o.resseq
                self.id = self.resseq
                self.relevant = False

        def __repr__(self):
                return f"<bi.{self.__class__.__name__} id={self.id}>"

Class variables

var child_class

The type of the None singleton.

var type

The type of the None singleton.