classMolecule

The major class of MolecularComponents is classMolecule, which classPolymer, classWater, and classLigand all inherit from.

Attributes

x.atoms

list of atoms

x.atom_dict

dictionary of atoms; indexed by atom_number

x.features

features dictionary

x.centroid

centroid point object

x.chain_name

chain name

x.res_type

res_type -- if polymer, the first monomer's res_type is used

x.selected

selected boolean ()

x.visible

'is currently visible' bool (described in class MolecularViewer)

x.vtk_arg_list

a list of visualization args (described in MolecularViewer)

Functions

x.add_atom(atom)

adds an atom to both .atoms and .atom_dict

x.get_bounds()

uses atoms to determine x, y, and z bounds

x.len()

returns the number of atoms

x.pdb_print()

calls pdb_print on every atom in x.atoms

x.get_pdb_lines()

returns pdb lines as a list of strings

x.select()

selects all atoms

x.deselect()

deselects all atoms

x.get_bonds_list(atom)

used during initialization; locates the .atoms index of the argument atom for x.get_bonds_list_from_int()

x.get_bonds_list_from_int(index)

uses the index to access self.atoms[index]. Returns a set of coordinates denoting the half-way point to all of the covalently bonded atoms. This is only used for graphics, but can be modified to give the covalently bonded atoms themselves.

x.min_bonded_distance(atom1, atom2)

returns the minimum distance for two atoms to be bonded, given their atom types.

x.get_central_pt()

only works for classes AminoAcid and Nucleotide. Returns the alpha carbon atom coordinates for amino acids, or the 'C3' atom from nucleotides. Returns a Point object.

x.update_cfs(coor_list)

updates the coordinates (ie. transition to the next conformer). This accepts a list of stings as input, where the format is - res_type res_number chain_name float float float ... The float float float triples should be in the same order as the atoms in the pdb file for that residue

x.build_futamura_intersection_table(solvent_radius)

adds x.x_table to the molecule's features. The x_table is a dictionary, indexed by the atom_number of all atoms in the molecule. Each element of the dictionary contains a list of various info on atoms that are distanced from each other by less than the solvent_radius argument given.

x.fill_densities(distance_cutoff)

Calculates atomic densities for all atoms. This is the number of atoms within a sphere of radius distance_cutoff from each query atom. The number over the max seen over the molecule is added to the atom's .features dictionary under the index 'atomic_density'.