Create specification

specification/spec.txt

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+* = methods which return queryable sets of structures
+
+AtomStructure
+	id --> unique ID
+	name --> structure's name
+	internal_id --> how the structure is referred to internally, if applicable
+
+	mass --> sum of all atom masses
+	charge --> sum of all atom charges
+	formula --> count of all atoms
+	center_of_mass --> centre of mass
+	radius_of_gyration --> radius of gyration
+	*pairwise_atoms --> all combinations of two atoms
+
+	pairing_with() --> mapping of atoms to atoms in other structure
+	rmsd_with() --> RMSD with other structure
+	create_grid() --> creates grid of coordinates
+	*nearby_atoms() --> atoms within certain distance of structure
+	check_ids() --> checks all IDs are unique
+	save() --> saves to file
+
+	translate() --> move structure
+	transform() --> transform structure coordinates with matrix
+	rotate() --> rotate structure around axis
+	trim() --> trim coordinates to lower precision
+
+
+Molecule
+	model --> The model above
+
+	(AtomStructure attributes)
+
+
+Het
+
+	*container*
+
+	chain --> chain above
+	model --> model above
+
+	full_name --> full English name
+
+	*nearby_structures() --> structures within a given cutoff distance
+
+	(AtomStructure attributes)
+
+
+Model
+	file --> the file the model is part of
+	*chains --> contains the polymers
+	*ligands --> contains the small molecules
+	*waters --> contains the water molecules
+
+	*container*
+
+	*molecules --> contains all the above
+	*residues --> contains the residues in the chains
+	*atoms --> contains all atoms
+
+	copy() --> creates a deep copy of the model
+	dehydrated() --> creates copy without waters
+
+	(AtomStructure attributes)
+
+
+Chain
+	*residues --> contains the residues in sequence
+	sequence --> the single letter codes of the residues
+
+	*iterable*
+	*indexable*
+	*container*
+
+	length --> the number of residues
+	*ligands --> the ligands associated with the chain
+	*atoms --> the atoms in the chain
+	present_sequence --> the actual sequence contained here
+	helices --> alpha helixes
+	strands --> beta strands
+
+	copy() --> creates a deep copy of the chain
+
+	(Molecule attributes)
+
+
+Ligand
+	*atoms --> ligand's atoms
+
+	is_water --> true if ligand is water
+
+
+	copy() --> creates a deep copy of the residue
+
+	(Het attributes)
+
+
+Residue
+	*atoms --> residue's atoms
+	next --> next residue in sequence
+	previous --> previous residue in sequence
+
+	code --> single letter code
+	secondary_structure --> secondary structure contribution
+
+	copy() --> creates a deep copy of the residue
+
+	(Het attributes)
+
+
+Atom
+	element --> periodic table element
+	location --> cartesian coordinates
+	id --> unique ID
+	name --> atom's name
+	charge --> electronic charge
+	bvalue --> positional uncertainty
+	anisotropy --> Directional uncertainty
+	het --> het atom is part of
+	bonded_atoms --> atoms bound to this one
+
+	*equality*
+	*iterable*
+
+	mass --> mass based on element
+	is_metal --> true if metal based on element
+	chain --> chain above
+	model --> model above
+
+	distance_to() --> distance to atom or vector
+	angle() --> angle with two other atoms
+	*nearby_atoms() --> atoms within distance cutoff
+	*nearby_structures() --> structures within distance cutoff
+
+	translate() --> translates atom with vector
+	transform() --> transforms atom using matrix
+	rotate() --> rotates atom around axis
+	trim() --> trims atom coordinates
+	copy() --> creates copy of atom
+
+
+
+File
+	code
+	title
+	deposition_date
+	classification
+	keywords
+	authors
+
+	technique
+	source_organisms
+	expression_systems
+
+	assembly_matrices
+	unit_cell
+	space_group
+
+	models
+	model