Molecular system

System

Aqua defines a moleculer system with the class msystem. This python class is the parent object where all info about the molecular system (topology, attributes, coordinates) as well as functions for its analysis is found.

class msystem(input_file=None, download=None, coors=False, with_bonds=True, missing_atoms=True, verbose=False)

Supra class containing the whole data related with the system (topology, trajectory,...) A file containing the description of the system must be provided to initialize this object, either a pdb, gro or psf file as input_file, either a pdb code to be downloaded from the Protein Data Bank.

Parameters:

• input_file (String) – Input file in the following formats: pdb, gro, psf.
• download (String) – PDB code to be downloaded.
• coors (Bool) – Loading coordinates from the topology file (if there exist).
• with_bonds (Bool) – Automatic covalent bonds detection.
• missing_atoms (Bool) – Printing out missing atoms.
• verbose (Bool) – Printing out information about the loaded system.

msystem.file_topol

Name of the input file with the topology. (String)

msystem.file_topol_type

Extension of the topology file: pdb, gro or psf. (String)

msystem.atom

List of atoms. Each atom is an object of unit class. (List)

msystem.resid

List of residues. Each residue is an object of residue class. (List)

msystem.chain

List of chains. Each chain is an object of xx class. (List)

msystem.chains

List of chain names. (List)

msystem.ion

List of ions. Each ion is an object of xx class. (List)

msystem.water

List of waters. Each water is an object of xx class.

msystem.water_model

Water model found in the system. (String)

msystem.acceptors

List of indexes of acceptor atoms. (List)

msystem.donors

List of pairs: [index of donor atom, index of H atom bond to donor]. (list of lists)

msystem.num_atoms

Total number of atoms. (int)

msystem.dimensionality

Dimensionality of the molecular system: 3*num_atoms (int)

msystem.name

Name of the system. Taken from file_topol. (String)

msystem.num_residues

Total number of residues. (int)

msystem.num_waters

Total number of water molecules. (int)

msystem.num_chains

Total number of chains in the system. (int)

msystem.num_ions

Total number of ions in the system. (int)

msystem.list_atoms

List of atom indexes. If msystem was created from a file: range(msystem.num_atoms). (List)

msystem.traj

List of trajectories. Each trajectory is an object of xx class. (List)

msystem.pdb_header

Header of the a pdb file. (String)

msystem.pdb_ss

Secondary structure description from the pdb file. (String)

Atom

Atoms are represented by objects of class atom with the common attributes:

class atom

atom.name

Name of atom as in msystem.input_file. (String)

atom.type

Type of atom. (String)

atom.index

Index of atom in msystem.atom[]. (int)

atom.pdb_index

Index of atom in msystem.input_file. (int)

atom.resid

Residue to which the atom belongs. (class residue)

atom.chain

Chain to which the atom belongs. (class chain)

atom.covalent_bonds

List of atom indexes with a covalent bond. (List)

atom.acceptor

The atom is acceptor for hydrogen bonds. (Bool)

atom.donor

The atom is donor for hydrogen bonds. (Bool)

atom.mass

Mass of atom. (Float)

atom.charge

Charge of atom. (Float)

atom.vdw

Van der Waals radius of atom. (Float)

atom.occup

Occupancy of atom in a PDB. (Float)

atom.bfactor

B-factor of atom in a PDB. (Float)

atom.alt_log

Alternate location in a PDB.

atom.code_ins_res

Code of insertion of residues in a PDB.

atom.seg_ident

Index of segment in a PDB. (String)

atom.elem_symb

Element symbol in a PDB. (String)

atom.type_pdb

Type of atom for the PDB: ATOM, HETATM,... (String)

Residue

Residues are represented by objects of class atom with the common attributes:

class resid

resid.name

Name of residue as it comes from msystem.input_file. (String)

resid.type

Type of residue. (String)

resid.index

Index of residue in msystem.resid[]. (int)

resid.pdb_index

Index of residue in msystem.input_file. (int)

resid.num_atoms

Number of atoms in residue. (int)

resid.list_atoms

List of atom indexes in the residue. (List)

resid.chain

Chain to which the residue belongs. (class chain)

Chain

Chains are represented by objects of class chain with the common attributes:

class chain

chain.name

Name of chain as it comes from msystem.input_file. (String)

chain.index

Index of chain in msystem.chain[]. (int)

chain.list_atoms

List of atom indexes in the chain. (List)

Water

Water molecules are represented as residues in msystem.resid. In addition there is an special class to include other common attributes of these molecules.

class water

water.index

Index of water molecule in msystem.resid list. (int)

water.name

Name of water molecule. Equal than resid.name. (String)

water.model

Name of water model. (String)

water.list_atoms

List of atom indexes in the water molecule. (List)

water.O.index

Index of atom Oxygen in msystem.atom list. (int)

water.O.name

Name of atom. Equal than atom.name (String)

water.H1.index

Index of atom Hydrogen 1 in msystem.atom list. (int)

water.H1.name

Name of atom. Equal than atom.name (String)

water.H2.index

Index of atom Hydrogen 2 in msystem.atom list. (int)

water.H2.name

Name of atom. Equal than atom.name (String)

water.uvect_norm

Perpendicular normal vector OH1xOH2. (Numpy array)