qmmmrebind.parameterize.PrepareQMMM

class qmmmrebind.parameterize.PrepareQMMM(init_pdb, distance, num_residues, guest_resname, cleaned_pdb='system.pdb', guest_init_pdb='guest_init.pdb', host_pdb='host.pdb', guest_pdb='guest_init_II.pdb', guest_xyz='guest_coord.txt', residue_list='residue_list.txt', host_qm_atoms='host_qm.txt', host_mm_atoms='host_mm.txt', host_qm_pdb='host_qm.pdb', host_mm_pdb='host_mm.pdb', qm_pdb='qm.pdb', mm_pdb='mm.pdb', host_mm_region_I_atoms='host_mm_region_I.txt', host_mm_region_II_atoms='host_mm_region_II.txt', host_mm_region_I_pdb='host_mm_region_I.pdb', host_mm_region_II_pdb='host_mm_region_II.pdb')[source]

A class used to segregate the QM and MM regions.

This class contain methods to remove the solvent, ions and all entities that are exclusive of receptor and the ligand. It also defines the Quantum Mechanical (QM) region and the Molecular Mechanical (MM) region based upon the distance of the ligand from the receptor and the chosen number of receptor residues. It is also assumed that the initial PDB file will have the receptor followed by the ligand.

…

Variables

  • init_pdb (str) – Initial PDB file containing the receptor-ligand complex with solvent, ions, etc.

  • cleaned_pdb (str) – Formatted PDB file containing only the receptor and the ligand.

  • guest_init_pdb (str) – A separate ligand PDB file with atom numbers not beginning from 1.

  • host_pdb (str) – A separate receptor PDB file with atom numbers beginning from 1.

  • guest_resname (str) – Three letter residue ID for the ligand.

  • guest_pdb (str, optional) – Ligand PDB file with atom numbers beginning from 1.

  • guest_xyz (str, optional) – A text file of the XYZ coordinates of the ligand.

  • distance (float, optional) – The distance required to define the QM region of the receptor. This is the distance between the atoms of the ligand and the atoms of the receptor.

  • residue_list (str, optional) – A text file of the residue numbers of the receptor within the proximity (as defined by the distance) from the ligand.

  • host_qm_atoms (str, optional) – A text file of the atom numbers of the receptors in the QM region.

  • host_mm_atoms (str, optional) – A text file of the atom numbers of the receptors in the MM region (all atoms except atoms in the QM region)

  • host_qm_pdb (str, optional) – PDB file for the receptor’s QM region.

  • host_mm_pdb (str, optional) – PDB file for the receptor’s MM region.

  • qm_pdb (str, optional) – PDB file for the QM region (receptor’s QM region and the ligand).

  • mm_pdb (str, optional) – PDB file for the MM region.

  • host_mm_region_I_atoms (str, optional) – A text file of the atom numbers of the receptors in the MM region preceeding the QM region.

  • host_mm_region_II_atoms (str, optional) – A text file of the atom numbers of the receptors in the MM region following the QM region.

  • host_mm_region_I_pdb (str, optional) – PDB file of the receptor in the MM region preceeding the QM region.

  • host_mm_region_II_pdb (str, optional) – PDB file of the receptor in the MM region following the QM region.

  • num_residues (int, optional) – Number of residues required in the QM region of the receptor.

__init__(init_pdb, distance, num_residues, guest_resname, cleaned_pdb='system.pdb', guest_init_pdb='guest_init.pdb', host_pdb='host.pdb', guest_pdb='guest_init_II.pdb', guest_xyz='guest_coord.txt', residue_list='residue_list.txt', host_qm_atoms='host_qm.txt', host_mm_atoms='host_mm.txt', host_qm_pdb='host_qm.pdb', host_mm_pdb='host_mm.pdb', qm_pdb='qm.pdb', mm_pdb='mm.pdb', host_mm_region_I_atoms='host_mm_region_I.txt', host_mm_region_II_atoms='host_mm_region_II.txt', host_mm_region_I_pdb='host_mm_region_I.pdb', host_mm_region_II_pdb='host_mm_region_II.pdb')[source]

Methods

__init__(init_pdb, distance, num_residues, ...)

clean_up()

Reads the given PDB file, removes all entities except the receptor and ligand and saves a new pdb file.

create_host_guest()

Saves separate receptor and ligand PDB files.

get_guest_coord()

Saves a text file of the XYZ coordinates of the ligand.

get_host_mm_region_atoms()

Saves a text file for the atoms of the receptor's MM region preceding the QM region and saves another text file for the atoms of the receptor's MM region folllowing the QM region.

get_host_qm_mm_atoms()

Saves a text file of the atom numbers of the receptors in the QM region and MM region separately.

get_qm_mm_regions()

Saves separate PDB files for the QM and MM regions.

get_qm_resids()

Saves a text file of the residue numbers of the receptor within the proximity (as defined by the distance) from the ligand.

realign_guest()

Saves a ligand PDB file with atom numbers beginning from 1.

save_host_mm_regions_pdbs()

Saves a PDB file for the receptor's MM region preceding the QM region and saves another PDB file for the receptor's MM region folllowing the QM region.

save_host_pdbs()

Saves a PDB file for the receptor's QM region and MM region separately.