psiresp
v0.2
Contents:
Installation
Usage
Examples
Molecules
Charge constraints
Using PsiRESP on HPC
API
References
psiresp
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Index
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Index
A
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B
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C
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D
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E
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F
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G
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I
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K
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M
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N
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O
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P
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Q
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R
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S
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T
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U
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V
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W
A
a (psiresp.constraint.ESPSurfaceConstraintMatrix property)
(psiresp.constraint.SparseGlobalConstraintMatrix attribute)
add_charge_sum_constraint_from_indices() (psiresp.charge.MoleculeChargeConstraints method)
add_compute() (psiresp.qm.QMGeometryOptimizationOptions method)
add_conformer() (psiresp.molecule.Molecule method)
add_conformer_with_coordinates() (psiresp.molecule.Molecule method)
add_constraints_from_charges() (psiresp.charge.MoleculeChargeConstraints method)
add_orientation_with_coordinates() (psiresp.conformer.Conformer method)
add_sp3_equivalences() (psiresp.charge.MoleculeChargeConstraints method)
all_vdw_radii (psiresp.grid.GridOptions property)
atomic_number (psiresp.molecule.Atom property)
atoms (psiresp.charge.ChargeEquivalenceConstraint attribute)
B
b (psiresp.constraint.ESPSurfaceConstraintMatrix property)
(psiresp.constraint.SparseGlobalConstraintMatrix attribute)
basis (psiresp.qcutils.QCWaveFunction attribute)
(psiresp.qm.QMEnergyOptions attribute)
C
cavity_area (psiresp.qm.PCMOptions attribute)
cavity_mode (psiresp.qm.PCMOptions attribute)
cavity_radii_set (psiresp.qm.PCMOptions attribute)
cavity_scaling (psiresp.qm.PCMOptions attribute)
cavity_type (psiresp.qm.PCMOptions attribute)
charge (psiresp.charge.ChargeEquivalenceConstraint property)
(psiresp.charge.ChargeSumConstraint attribute)
(psiresp.molecule.Molecule attribute)
charge_constraints (psiresp.configs.Resp2 attribute)
(psiresp.job.Job attribute)
(psiresp.resp.RespCharges attribute)
charge_difference (psiresp.constraint.SparseGlobalConstraintMatrix property)
charges (psiresp.configs.Resp2 property)
(psiresp.constraint.SparseGlobalConstraintMatrix property)
(psiresp.job.Job property)
(psiresp.resp.RespCharges property)
compute_charges() (psiresp.job.Job method)
compute_esp() (psiresp.orientation.Orientation method)
compute_esp_from_record() (psiresp.orientation.Orientation method)
compute_esps() (psiresp.job.Job method)
compute_esps_and_charges() (psiresp.job.Job method)
compute_grid() (psiresp.orientation.Orientation method)
compute_orientation_energies() (psiresp.job.Job method)
conformer_generation_options (psiresp.molecule.Molecule attribute)
conformers (psiresp.molecule.Molecule attribute)
constraint_matrix (psiresp.orientation.Orientation property)
construct_constraint_matrix() (psiresp.orientation.Orientation method)
construct_surface_constraint_matrix() (psiresp.job.Job method)
coordinates (psiresp.moleculebase.BaseMolecule property)
D
defer_errors (psiresp.configs.Resp2 attribute)
(psiresp.job.Job attribute)
driver (psiresp.qm.QMEnergyOptions attribute)
(psiresp.qm.QMGeometryOptimizationOptions attribute)
E
effective_rmax (psiresp.grid.GridOptions property)
energy (psiresp.orientation.Orientation property)
(psiresp.qcutils.QCWaveFunction attribute)
energy_window (psiresp.conformer.ConformerGenerationOptions attribute)
esp (psiresp.orientation.Orientation attribute)
F
from_a_and_b() (psiresp.constraint.ESPSurfaceConstraintMatrix class method)
from_atomicresult() (psiresp.qcutils.QCWaveFunction class method)
from_charge_constraints() (psiresp.charge.MoleculeChargeConstraints class method)
from_constraints() (psiresp.constraint.SparseGlobalConstraintMatrix class method)
from_molecule() (psiresp.molecule.Atom class method)
from_orientations() (psiresp.constraint.ESPSurfaceConstraintMatrix class method)
from_qcrecord() (psiresp.qcutils.QCWaveFunction class method)
from_rdkit() (psiresp.molecule.Molecule class method)
from_smiles() (psiresp.molecule.Molecule class method)
full_hess_every (psiresp.qm.QMGeometryOptimizationOptions attribute)
G
g_convergence (psiresp.qm.QMGeometryOptimizationOptions attribute)
generate_atom_combinations() (psiresp.moleculebase.BaseMolecule method)
generate_conformers() (psiresp.job.Job method)
(psiresp.molecule.Molecule method)
generate_connolly_spheres() (psiresp.grid.GridOptions method)
generate_coordinates() (psiresp.conformer.ConformerGenerationOptions method)
generate_grid() (psiresp.grid.GridOptions method)
generate_keywords() (psiresp.qm.PCMOptions method)
(psiresp.qm.QMGeometryOptimizationOptions method)
generate_molecule_charge_constraints() (psiresp.job.Job method)
generate_orientation_coordinates() (psiresp.molecule.Molecule method)
generate_orientations() (psiresp.job.Job method)
(psiresp.molecule.Molecule method)
generate_transformations() (psiresp.molecule.Molecule method)
generate_unit_sphere() (psiresp.grid.GridOptions static method)
get_atoms_from_smarts() (psiresp.molecule.Molecule method)
get_boltzmann_weight() (psiresp.orientation.Orientation method)
get_charges() (psiresp.configs.Resp2 method)
get_density_ordering() (psiresp.qcutils.QCWaveFunction method)
get_hash() (psiresp.base.Model method)
get_shell_within_bounds() (psiresp.grid.GridOptions method)
get_smarts_matches() (psiresp.moleculebase.BaseMolecule method)
get_vdwradii_for_elements() (psiresp.grid.GridOptions method)
get_weight() (psiresp.orientation.Orientation method)
get_weighted_matrix() (psiresp.orientation.Orientation method)
grid (psiresp.orientation.Orientation attribute)
grid_options (psiresp.configs.Resp2 attribute)
(psiresp.job.Job attribute)
grid_rmax (psiresp.grid.GridOptions attribute)
grid_rmin (psiresp.grid.GridOptions attribute)
I
index (psiresp.molecule.Atom attribute)
is_optimized (psiresp.conformer.Conformer attribute)
iter_conformers() (psiresp.job.Job method)
iter_orientations() (psiresp.job.Job method)
K
keep_original_conformer (psiresp.conformer.ConformerGenerationOptions attribute)
keep_original_orientation (psiresp.molecule.Molecule attribute)
M
mask (psiresp.constraint.SparseGlobalConstraintMatrix attribute)
matrix (psiresp.constraint.ESPSurfaceConstraintMatrix attribute)
max_iter (psiresp.qm.QMGeometryOptimizationOptions attribute)
medium_solvent (psiresp.qm.PCMOptions attribute)
medium_solver_type (psiresp.qm.PCMOptions attribute)
method (psiresp.qm.QMEnergyOptions attribute)
molecule (psiresp.molecule.Atom attribute)
molecules (psiresp.charge.MoleculeChargeConstraints attribute)
(psiresp.configs.Resp2 attribute)
(psiresp.job.Job attribute)
multiplicity (psiresp.molecule.Molecule attribute)
N
n_alpha (psiresp.qcutils.QCWaveFunction attribute)
n_atoms (psiresp.charge.MoleculeChargeConstraints property)
(psiresp.moleculebase.BaseMolecule property)
n_conformer_pool (psiresp.conformer.ConformerGenerationOptions attribute)
n_conformers (psiresp.job.Job property)
(psiresp.molecule.Molecule property)
n_dim (psiresp.constraint.ESPSurfaceConstraintMatrix property)
n_max_conformers (psiresp.conformer.ConformerGenerationOptions attribute)
n_orientations (psiresp.conformer.Conformer property)
(psiresp.job.Job property)
(psiresp.molecule.Molecule property)
n_processes (psiresp.configs.Resp2 attribute)
(psiresp.job.Job attribute)
n_structure_array (psiresp.constraint.SparseGlobalConstraintMatrix attribute)
n_transformations (psiresp.molecule.Molecule property)
O
optimize_geometries() (psiresp.job.Job method)
optimize_geometry (psiresp.molecule.Molecule attribute)
orientations (psiresp.conformer.Conformer attribute)
P
pcm_options (psiresp.qm.QMEnergyOptions attribute)
position (psiresp.molecule.Atom property)
protocols (psiresp.qm.QMEnergyOptions attribute)
Q
qc_wavefunction (psiresp.orientation.Orientation attribute)
(psiresp.qcutils.QCWaveFunction attribute)
qcmol (psiresp.moleculebase.BaseMolecule attribute)
qcmol_with_coordinates() (psiresp.moleculebase.BaseMolecule method)
qm_esp_options (psiresp.job.Job attribute)
qm_optimization_options (psiresp.job.Job attribute)
query_interval (psiresp.qm.QMEnergyOptions attribute)
R
reconstruct_density() (psiresp.qcutils.QCWaveFunction method)
reorientations (psiresp.molecule.Molecule attribute)
resp_a (psiresp.resp.RespCharges attribute)
resp_a1 (psiresp.resp.RespOptions attribute)
resp_a2 (psiresp.resp.RespOptions attribute)
resp_options (psiresp.configs.Resp2 attribute)
(psiresp.job.Job attribute)
restrained_charges (psiresp.resp.RespCharges property)
rms_tolerance (psiresp.conformer.ConformerGenerationOptions attribute)
rotations (psiresp.molecule.Molecule attribute)
run() (psiresp.configs.Resp2 method)
(psiresp.job.Job method)
S
set_optimized_geometry() (psiresp.conformer.Conformer method)
solvated (psiresp.configs.Resp2 attribute)
solve() (psiresp.resp.RespCharges method)
solvent_qm_esp_options (psiresp.configs.Resp2 attribute)
solvent_qm_optimization_options (psiresp.configs.Resp2 attribute)
stage_1_charges (psiresp.job.Job attribute)
stage_1_restrained_charges (psiresp.molecule.Molecule attribute)
stage_1_unrestrained_charges (psiresp.molecule.Molecule attribute)
stage_2 (psiresp.resp.RespOptions attribute)
stage_2_charges (psiresp.job.Job attribute)
stage_2_restrained_charges (psiresp.molecule.Molecule attribute)
stage_2_unrestrained_charges (psiresp.molecule.Molecule attribute)
surface_constraints (psiresp.resp.RespCharges attribute)
symbol (psiresp.molecule.Atom property)
symmetric_methylenes (psiresp.charge.ChargeConstraintOptions attribute)
symmetric_methyls (psiresp.charge.ChargeConstraintOptions attribute)
T
temperature (psiresp.configs.Resp2 attribute)
(psiresp.job.Job attribute)
to_a_col_constraints() (psiresp.charge.MoleculeChargeConstraints method)
to_b_constraints() (psiresp.charge.MoleculeChargeConstraints method)
to_psi4_string() (psiresp.qm.PCMOptions method)
to_row_constraint() (psiresp.charge.ChargeEquivalenceConstraint method)
(psiresp.charge.ChargeSumConstraint method)
to_smiles() (psiresp.moleculebase.BaseMolecule method)
transformations (psiresp.molecule.Molecule property)
translations (psiresp.molecule.Molecule attribute)
U
unconstrained_atoms (psiresp.charge.MoleculeChargeConstraints attribute)
unrestrained_charges (psiresp.resp.RespCharges property)
update_molecule_charges() (psiresp.job.Job method)
use_radii (psiresp.grid.GridOptions attribute)
V
vacuum (psiresp.configs.Resp2 attribute)
validate_array() (psiresp.constraint.ESPSurfaceConstraintMatrix method)
vdw_point_density (psiresp.grid.GridOptions attribute)
vdw_radii (psiresp.grid.GridOptions attribute)
vdw_scale_factors (psiresp.grid.GridOptions attribute)
W
wait_for_results() (psiresp.qm.QMEnergyOptions method)
(psiresp.qm.QMGeometryOptimizationOptions method)
weight (psiresp.orientation.Orientation attribute)
with_n_dim() (psiresp.constraint.ESPSurfaceConstraintMatrix class method)
working_directory (psiresp.configs.Resp2 attribute)
(psiresp.job.Job attribute)
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