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samirelanduk committed May 12, 2019
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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

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