Some utilities for topological analysis

Module contents for quippy.topology:

Functions

delete_metal_connects(at) Remove bonds for metal ions - everything but H, C, N, O, Si, P, S, Cl Uses remove_bond in atoms_module.
find_motif_backbone(motif,is_proline)
Parameters:
write_brookhaven_pdb_file(…) Writes Brookhaven PDB format charges are printed into the PSF file, too use CHARGE_EXTENDED keyword i.e.
calc_mean_pos(at,indices)
Parameters:
find_a2_monomer(…)
Parameters:
write_cp2k_pdb_file(…) Writes modified PDB format for accurate coordinates and charges, for CP2K Use CHARGE_EXTENDED keyword i.e.
find_ab_monomer(…)
Parameters:
find_water_monomer(…)
Parameters:
create_residue_labels_arb_pos(…) Topology calculation using arbitrary (usually avgpos) coordinates, as a wrapper to find_residue_labels if EVB is being used, must pass exact connectivity object and set evb_nneighb_only to false
write_psf_file_arb_pos(…)
Parameters:
write_psf_file(…) Writes PSF topology file, to be used with the PDB coordinate file.

Attributes

Name Value
NONE_RUN -100
QS_RUN -1
MM_RUN 0
QMMM_RUN_EXTENDED 2
QMMM_RUN_CORE 1
quippy.topology.delete_metal_connects(at)

Remove bonds for metal ions - everything but H, C, N, O, Si, P, S, Cl Uses remove_bond in atoms_module.

Parameters:
at : Atoms object

References

Routine is wrapper around Fortran routine delete_metal_connects defined in file src/libAtoms/Topology.f95.

quippy.topology.find_motif_backbone(motif, is_proline)
Parameters:
motif : input rank-2 array(‘i’) with bounds (qp_n0,qp_n1)
is_proline : input int
Returns:
ret_backbone : rank-2 array(‘i’) with bounds (5,3)

References

Routine is wrapper around Fortran routine find_motif_backbone defined in file src/libAtoms/Topology.f95.

quippy.topology.write_brookhaven_pdb_file(at, pdb_file[, run_type_string])

Writes Brookhaven PDB format charges are printed into the PSF file, too use CHARGE_EXTENDED keyword i.e. reads charges from the last column of PDB file Sample line: ATOM 1 CT3 ALA A 1 0.767 0.801 13.311 0.00 0.00 ALA C -0.2700 ATOM 2 HA ALA A 1 0.074 -0.060 13.188 0.00 0.00 ALA H 0.0900 ATOM 3 HA ALA A 1 0.176 1.741 13.298 0.00 0.00 ALA H 0.0900

Parameters:
at : Atoms object
pdb_file : input string(len=-1)
run_type_string : input string(len=-1), optional

References

Routine is wrapper around Fortran routine write_brookhaven_pdb_file defined in file src/libAtoms/Topology.f95.

quippy.topology.calc_mean_pos(at, indices)
Parameters:
at : Atoms object
indices : input rank-1 array(‘i’) with bounds (qp_n0)
Returns:
ret_pos : rank-1 array(‘d’) with bounds (3)

References

Routine is wrapper around Fortran routine calc_mean_pos defined in file src/libAtoms/Topology.f95.

quippy.topology.find_a2_monomer(at, atomic_number, monomer_cutoff, n0[, error])
Parameters:
at : Atoms object
atomic_number : input int
monomer_cutoff : input float
n0 : input int

shape(qp_A2_index,0)

error : in/output rank-0 array(int,’i’), optional
Returns:
a2_index : rank-1 array(‘i’) with bounds (qp_n0)

References

Routine is wrapper around Fortran routine find_a2_monomer defined in file src/libAtoms/Topology.f95.

quippy.topology.write_cp2k_pdb_file(at, pdb_file[, run_type_string])

Writes modified PDB format for accurate coordinates and charges, for CP2K Use CHARGE_EXTENDED keyword i.e. reads charges from the last column of PDB file Sample line: ATOM 1 CT3 ALA A 1 0.76700000 0.80100000 13.31100000 0.00 0.00 ALA C -0.27 ATOM 2 HA ALA A 1 0.07400000 -0.06000000 13.18800000 0.00 0.00 ALA H 0.09 ATOM 3 HA ALA A 1 0.17600000 1.74100000 13.29800000 0.00 0.00 ALA H 0.09

Parameters:
at : Atoms object
pdb_file : input string(len=-1)
run_type_string : input string(len=-1), optional

References

Routine is wrapper around Fortran routine write_cp2k_pdb_file defined in file src/libAtoms/Topology.f95.

quippy.topology.find_ab_monomer(at, atomic_number, monomer_cutoff, n0, n1[, error])
Parameters:
at : Atoms object
atomic_number : input rank-1 array(‘i’) with bounds (2)
monomer_cutoff : input float
n0 : input int

shape(qp_AB_index,0)

n1 : input int

shape(qp_AB_index,1)

error : in/output rank-0 array(int,’i’), optional
Returns:
ab_index : rank-2 array(‘i’) with bounds (qp_n0,qp_n1)

References

Routine is wrapper around Fortran routine find_ab_monomer defined in file src/libAtoms/Topology.f95.

quippy.topology.find_water_monomer(at, n0[, ohh_ordercheck, monomer_cutoff, error])
Parameters:
at : Atoms object
n0 : input int

shape(qp_water_index,0)

ohh_ordercheck : input int, optional
monomer_cutoff : input float, optional
error : in/output rank-0 array(int,’i’), optional
Returns:
water_index : rank-2 array(‘i’) with bounds (3,qp_n0)

References

Routine is wrapper around Fortran routine find_water_monomer defined in file src/libAtoms/Topology.f95.

quippy.topology.create_residue_labels_arb_pos(at[, do_charmm, intrares_impropers, find_silica_residue, pos_field_for_connectivity, form_bond, break_bond, silica_pos_dep_charges, silica_charge_transfer, have_titania_potential, find_molecules, evb_nneighb_only, remove_si_h_silica_bonds, remove_ti_h_titania_bonds, error])

Topology calculation using arbitrary (usually avgpos) coordinates, as a wrapper to find_residue_labels if EVB is being used, must pass exact connectivity object and set evb_nneighb_only to false

Parameters:
at : Atoms object
do_charmm : input int, optional
intrares_impropers : Table object, optional
find_silica_residue : input int, optional
pos_field_for_connectivity : input string(len=-1), optional
form_bond : input rank-1 array(‘i’) with bounds (2), optional
break_bond : input rank-1 array(‘i’) with bounds (2), optional
silica_pos_dep_charges : input int, optional
silica_charge_transfer : input float, optional
have_titania_potential : input int, optional
find_molecules : input int, optional
evb_nneighb_only : input int, optional
remove_si_h_silica_bonds : input int, optional
remove_ti_h_titania_bonds : input int, optional
error : in/output rank-0 array(int,’i’), optional

References

Routine is wrapper around Fortran routine create_residue_labels_arb_pos defined in file src/libAtoms/Topology.f95.

quippy.topology.write_psf_file_arb_pos(at, psf_file[, run_type_string, intrares_impropers, imp_filename, add_silica_23body, pos_field_for_connectivity, form_bond, break_bond, remove_qmmm_link_bonds, run_suffix, error])
Parameters:
at : Atoms object
psf_file : input string(len=-1)
run_type_string : input string(len=-1), optional
intrares_impropers : Table object, optional
imp_filename : input string(len=80), optional
add_silica_23body : input int, optional
pos_field_for_connectivity : input string(len=-1), optional
form_bond : input rank-1 array(‘i’) with bounds (2), optional
break_bond : input rank-1 array(‘i’) with bounds (2), optional
remove_qmmm_link_bonds : input int, optional
run_suffix : input string(len=-1), optional
error : in/output rank-0 array(int,’i’), optional

References

Routine is wrapper around Fortran routine write_psf_file_arb_pos defined in file src/libAtoms/Topology.f95.

quippy.topology.write_psf_file(at, psf_file[, run_type_string, intrares_impropers, imp_filename, add_silica_23body, heuristics_nneighb_only, alt_connect, remove_qmmm_link_bonds, run_suffix, error])

Writes PSF topology file, to be used with the PDB coordinate file. PSF contains the list of atoms, bonds, angles, impropers, dihedrals.

Parameters:
at : Atoms object
psf_file : input string(len=-1)
run_type_string : input string(len=-1), optional
intrares_impropers : Table object, optional
imp_filename : input string(len=80), optional
add_silica_23body : input int, optional
heuristics_nneighb_only : input int, optional
alt_connect : Connection object, optional
remove_qmmm_link_bonds : input int, optional
run_suffix : input string(len=-1), optional
error : in/output rank-0 array(int,’i’), optional

References

Routine is wrapper around Fortran routine write_psf_file defined in file src/libAtoms/Topology.f95.