Model¶

The Model class stores the structural data of your system, and as such it contains all Chain, Molecule, and Atom instances of your system. It is possibly the most useful class for a user in practice, as the function that generates hybrid systems to be used in alchemical calculations (pmx.alchemy.mutate()) acts on this object.

API Reference¶

class pmx.model.Model(filename=None, pdbline=None, renumber_atoms=True, renumber_residues=True, rename_atoms=False, scale_coords=None, bPDBTER=True, bNoNewID=True, bPDBGAP=False, **kwargs)¶

Model Class.

Parameters

filename (str) – filename of input structure
pdbline (bool(?)) – what is pdbline?
renumber_atoms (bool, optional) – renumber all atoms from 1. Default is True.
renumber_residues (bool, optional) – renumber all residues from 1. In this way, each residue will have a unique ID, also across chains. Default is True.
rename_atoms (bool, optional) – rename atoms so to conform to Gromacs format. Default is False.
scale_coords (A|nm, optional) – whether to enforce the units of the coordinates to be in A or in nm. By default, PDB coordinates are assumed to be in Angstrom (A) and GRO coordinates in nanometers (nm). If you read a PDB file but would like operate on nm coordinates, then select “nm”. Viceversa, if you read a GRO file but would like to work on A coordinates, select “A”. Note that if you read a PDB file in A coordinates and select “A”, nothing happens (same for GRO and “nm” selection).
bPDBTER (bool) – whether to recognize TER lines and other chain breaks, e.g. discontinuous residue indices(?). Default is True.
bNoNewID (bool) – whether to assign new chain IDs? If True, new chain IDs starting with ‘pmx’ will be assigned(?). Only relevant if bPDBTER is True. Default is True.
bPDBGAP (bool) – whether search for gaps in the chain to assign new chain IDs.

title¶

title of model. Default is ‘PMX MODEL’.

Type: str

filename¶

filename from which the Model was imported, otherwise None.

Type: str

chains¶

list of Chain instances

Type: list

chdic¶

dict with chain IDs as keys and Chain instances as values

Type: dict

residues¶

list of molecules/residues

Type: list

unity¶

coordinates unit, either ‘A’ or ‘nm’.

Type: str

box¶

3x3 array containing the box vectors. See Gromacs manual, Table 3.1

Type: 2d array

moltype¶

Type of system: protein, dna, rna, or unknown if organic molecule or a mix of molecules are in the system.

Type: str

Methods

`read`(filename[, bPDBTER, bNoNewID, bPDBGAP])	PDB/GRO file reader.
`write`(fn[, title, nr, bPDBTER, bAssignChainIDs])	Writes Model to file.
`renumber_residues`()	Renumbers all residues from 1.
`renumber_atoms`([start])	Renumber all atoms starting from a chosen number (default is 1).
`insert_residue`(pos, res, chain_id)	Inserts a residue in Model.
`insert_chain`(pos, new_chain)	Inserts a Chain in Model.
`remove_atom`(atom)	Removes an Atom instance.
`remove_residue`(residue[, renumber_atoms, …])	Removes a Molecule/residue instance.
`remove_chain`(key)	Removes a Chain instance given the chain ID.
`replace_residue`(residue, new[, bKeepResNum])	Replaces a residue.
`fetch_residue`(idx[, chain])	Get a residue based on its index, or index and chain.
`fetch_residues`(key[, inv])	Gets residues using a list of residue names.