schrodinger.application.prepwizard module

Shared functionality between PrepWizard GUI and command-line PrepWizard.

Copyright Schrodinger, LLC. All rights reserved.

schrodinger.application.prepwizard.count_clashes_of_het_state(complex_st, het_atoms)

Return the number of atoms with wich hydrogens of the current state for het defined by het_atoms are clashing with - including other atoms in the same het.

schrodinger.application.prepwizard.find_het_atoms(complex_st, hetnum)

Return a list of het heavy atoms in the given complex structure.

class schrodinger.application.prepwizard.HetType

Bases: Enum

METAL_OR_ION = 1
DETECTED_LIGAND = 2
NON_WATER_SOLVENT = 3
OTHER = 4
schrodinger.application.prepwizard.get_atoms_by_orig_anum(st)

Return a dict where keys are atom indices in the original structure (prior to preparation) and values are atom indices in the given st.

schrodinger.application.prepwizard.retrieve_and_read_pdb(pdbid)

Retrieve the given PDB and return the Structure object. On error, raises RuntimeError.

schrodinger.application.prepwizard.find_metals_in_structure(st)
class schrodinger.application.prepwizard.JsonableHetStates(states_by_het=None)

Bases: JsonableClassMixin

JSON serializable class that represents the hets(ligands) table, as well all information about all states of all hets, as generated by Epik and the post-processing. Currently only information that is saved here is stored in self.states_by_het, which has het numbers as keys and lists of HetStates objects for each het as values.

__init__(states_by_het=None)
classmethod fromJsonImplementation(serialized_states)

Return an instance of JsonableHetStates from a serialized JSON dict. NOTE to future dev: If format of this JSON is changed in the future, please implement a new fromJsonImplementation() method, and add a json.adapter method for converting this older format into the new format.

toJsonImplementation()

Return a dict that can be serialized to JSON, which represents all het states for all hets.

schrodinger.application.prepwizard.serialize_het_states(states_by_het, complex_st)

Set JSON string for all given states as a CT-level property.

schrodinger.application.prepwizard.deserialize_het_states(complex_st)

Attempt to read the het states from the CT using the s_ppw_het_states property, if present.

class schrodinger.application.prepwizard.HetState(hetnum)

Bases: object

Class representing an ionization/tautomeric state of a het (e.g. ligand).

__init__(hetnum)
classmethod initFromEpikOutput(hetnum, state_st)

Return a HetState instance for the given Epik output structure.

extractStateChargesAndOrders(state_st)
applyState(st, is_original=False)

Apply this het state to the specified complex structure: modify the bond orders and formal charges to apply the currently selected het state. Used by PPW2 GUI.

Also calculates the score and info_str properties, even if they are already present, as user may have modified the structure since.

Raises RuntimeError if any of the het atoms are no longer in the structure, or are not numbered correctly.

applyStateToComplex(st)

Adjust charges and bond order in the given structure. Used by the PPW2 GUI.

calcStateScore(complex_st, het_atoms, all_recep_metals=None)

Calculate the score for the current het state (must already been applied to the complex structure). The following facctors contribute to the score:

  1. The Epik state penalty (r_epik_Sate_Penalty) is subtracted from the score. If all other factors are the same, states are sorted by Epik state penalty.

  2. Clashes betwen het hydrogens and non het atoms - including clashes between a hydrogen and another atom in the het - penalize the score (e.g. 8qze, 7s25)

  3. Tertiary amides interacting with metals penalize the score (e.g. 1ft7)

  4. H-bonds between the het and other atoms in the structure (usually receptor) are rewarded (e.g. 7s25)

  5. States with Epik’s r_epik_Metal_State_Penalty get penalized - the smallest penalty available in any atom of the het is used, but only from atoms that are within 3A of a metal (e.g. 2bnu, 3ld6)

Complex_st:

Structure containing the het and receptor atoms.

Het_atoms:

List of atoms (complex indexed) that are part of the het.

findHetAtoms(complex_st)

Return a list of het heavy atoms in the given complex structure.

schrodinger.application.prepwizard.fix_common_structure_mistakes(st)

Fixes common problems in structures and returns a list of correction strings that are to be reported to the user.

schrodinger.application.prepwizard.atomsasl(atoms)

Generates an ASL expression for the specified atoms.

schrodinger.application.prepwizard.create_glycosylation_bonds(st, dist=1.8, verbose=True)

Create glycosylation bonds for N-linked or O-linked glycosilation events Identfies neutral O or N with implicit or explicit hydrogens and forms bonds to sugars ( ring with 5 aliphatic carbons and one oxygen ) at locations adjacent to the oxygen. :param st: Structure to modify. :type st: Schrodinger.structure

Parameters:

  • dist (float) – Atoms must be at least this close to consider for for glycosilation

  • verbose (boolean) – Whether to print formed bonds to stdout

Rparam:

Pairs of atom ( in the output structure ) where bonds were added

Return type:

list of schrodinger atom objects

schrodinger.application.prepwizard.create_palmitoylation_bonds(st, dist=1.8, verbose=True)

Create palmitoylation bonds. Identfies neutral cysteine S with implicit or explicit hydrogens and palmitoyl groups or palmitoyl groups with the OH of the acid replace by a hydrogen :param st: Structure to modify. :type st: Schrodinger.structure

Parameters:

  • dist (float) – Atoms must be at least this close to consider for for pamitoylation

  • verbose (boolean) – Whether to print formed bonds to stdout

Rparam:

Pairs of atom ( in the output structure ) where bonds were added

Return type:

list of schrodinger atom objects

schrodinger.application.prepwizard.create_disulfide_bonds(st, dist=3.2, verbose=False)

Create bonds between proximal Sulfurs, deleting any hydrogens on them. If verbose is True, prints log info to the termnal. Returns a list of (atom1, atom2) for ever added bond.

schrodinger.application.prepwizard.convert_selenomethionines(st)

Convert MSE residues to METs. Returns a list of residue strings that were converted.

schrodinger.application.prepwizard.does_res_have_missing_side_chains(residue)

Given a _Residue object, returns True if the residue is missing side-chain atoms. If at least one backbone atom is (also) missing, False is returned.

Basically only residues for which Prime missing-side-chains job can be run will return True.

schrodinger.application.prepwizard.do_any_residues_have_missing_side_chains(st)

Returns True if at least one of the residue in the given structure has missing side-chain atoms (backbone atoms are ignored).

schrodinger.application.prepwizard.find_missing_res_atoms(st)

Seaches the specified structure for missing residue atoms, and returns a list of: (atomnum, num_heavy, expected_heavy, missing_only_sidechains)

This list DOES include residues with only backbone atoms missing.

schrodinger.application.prepwizard.fix_sulfur_charges(st)

Post process by fixing the charge on zero-order-bonded Sulfurs Gives -1 or -2 charge to Sulfurs as appropriate. Deletes a hydrogen from Sulfurs coordinating with metals (Ev:61622)

schrodinger.application.prepwizard.extract_het_from_complex(complex_st, het_atoms)

Extract the het defined by the given ASL from the complex structure, and include receptor atoms withing 2 bonds (for covalently bound ligands).

Parameters:

  • complex_st (structure.Structure) – Receptor-ligand complex structure

  • het_atoms (list(int)) – List of atom indices for the het

Returns:

Het structure, Het structure plus some receptor atoms (covalent ligands only), and het type.

Return type:

(structure.Structure, structure.Structure, HetType)

schrodinger.application.prepwizard.extract_hets_from_complex(complex_st, het_atoms_lists)

Detect hets in the given complex structure, and extract them into separate substructures. For covalent ligands, receptor atoms within 2 bonds are also retained, so that Epik can account for them.

Parameters:

  • complex_st (structure.Structure) – Receptor-ligand complex structure

  • het_atoms_lists (list(list(int))) – List of atoms for all hets

Returns:

Yields tuples of: Het structure, Het structure plus some receptor atoms (covalent ligands only), and het type.

Return type:

generator(structure.Structure, structure.Structure, HetType)

schrodinger.application.prepwizard.prepare_for_epik(complex_st, types_to_process)

Extract hets from the given complex structure, (except het types that user requested to skip), and separate retained hets into 2 lists: Those that Epik should be run on, those that Epik doesn’t produce any states for. Atoms in the original structure will be marked with i_ppw_anum property, for matching Epik output to atoms in the input structure.

Parameters:

  • complex_st (structure.Structure) – Receptor-ligand complex structure

  • types_to_process ([HetType]) – List of het types should be processed

Returns:

List of structures to run Epik on, and list of structures that should be processed, but without Epik.

Return type:

[structure.Structure], [structure.Structure]

schrodinger.application.prepwizard.filter_undesired_states(orig_st, state_sts)

Returns a subset of state structures, which excludes metal-binding states for hets that are not within 5A of a metal.

Parameters:

  • orig_st (structure.Structure) – Original complex structure (receptor, ligands, metals)

  • state_st (Iterable of structure.Structure) – Epik output states to filter.

Returns:

List of filtered structures.

Return type:

List of structure.Structure

schrodinger.application.prepwizard.get_asl_for_ppw_atoms(atoms)

Return an ASL that would match the given atom numbers from input structure (prior to preparation).

schrodinger.application.prepwizard.find_ppw_atom(st, anum)

Find the atom in the given structure whose i_ppw_anum property is set to the given value. ValueError exception is raised if such atom is not found. Used by PPW1 only. PPW2 uses an optimization instead.

schrodinger.application.prepwizard.detect_symmetry_in_het(st, het_atom_indices)

Find all symmetry-equivalent matches (using the molecule as both query and target); ignore hydrogens (they generate a ton of symmetries).

Return a list of mappings for all possible symmetry operations, where each atom is mapped to the symmetrical atom from the original structure.

First symmetrical mapping is a match to itself, so that the first state can be scored as well. If the structure has additional symmetrical groups, those mappings will be included in the output list. Each mapping is a dict of original atom indices, keys represent the original atoms and values represent the equivalent atom in the symmetrical group.

# Example: # C1 - C2 # / ＼ # N1 N2 # ＼ / # C3 - C4

# output: # [ # {C1:C1, C2:C2, N2:N2, C4:C4, C3:C4, N1:N1}, # first state # {C1:C2, N1:N2, C3:C4, C4:C3, N2:N1, C2:C1}, # symmetry around vertical axis # {C1:C3, C2:C4, N2:N2, C4:C2, C3:C1, N1:N1}, # symmetry around horizontal axis # and additional symmetries # ]

schrodinger.application.prepwizard.map_orders_and_charges(orders, charges, _map)
schrodinger.application.prepwizard.get_state_penalties(state_st)

Return the Epik state penalty for this Epik output structure, as well as metal penalties for each atom that has the r_epik_Metal_State_Penalty property set.

schrodinger.application.prepwizard.get_smallest_metal_penalty(metal_penalties, all_recep_metals)

Return the lowest metal penalty of all het atoms, considering only atoms that are within 3A of a receptor metal.

schrodinger.application.prepwizard.calc_hbond_energy(hydrogen, acceptor)

Calculate H-bond energy. Overly simple, to address PLDB-3337 and similar.

schrodinger.application.prepwizard.generate_metal_and_ion_states(sts)
schrodinger.application.prepwizard.get_bridging_waters(st, min_hbonds=3)

Return a list of all waters in the specified structure that make at least <min_hbonds> number of H-bonds (H-bonds to other waters excluded). The list contains both oxygen and hydrogen atoms (if present).

schrodinger.application.prepwizard.hydrogen_neighbors(st, atoms)

Returns the list of neighbor (bonded) atoms that are hydrogens.

Parameters:

  • st (structure.Structure) – Structure where atoms are from.

  • atoms (list of ints) – List of atom indices for the heavy atoms.

Returns:

List of hydrogen atom indices

Return type:

list of ints.

schrodinger.application.prepwizard.get_num_clashes_with_metals(st, het_anums)

Returns the number of times there is a hydrogen on a tertiary amide is clashing with a metal. For now, only hydrogens on aliphatic nitrogens that are zero- order bonded to metals are considered. Geometry is not considered, because amides are rotatable groups. Clashes can not be used to detect these, as the hydrogens are too far from the metal. Example case: 1ft7 (-NH2 is preferred over -NH3)

Parameters:

st (structure.Structure) – Structure where atoms are from.

:param het_anumst of atom indices for the heavy atoms. :type het_anumst of ints

Returns:

List of nitrogen atoms.

Return type:

list(structure._StructureAtom)

schrodinger.application.prepwizard.get_pdb_id(st)

Returns the PDB ID of the given structure. If the property does not exist, returns the string “unknown”.

schrodinger.application.prepwizard.get_het_name(st, het_atoms, include_chain=False)

Return the het “name” to display for the user for the given het. Assumes all residues have the same chain name.

Example outputs:

“HEM 123a” “HEM A:123a” “HEM 154 Fe” “GLY-VAL-PRO 110-111-112” “GLY-VAL-PRO A:110-111-112”

Parameters:

  • st (structure.Structure) – Structure containing the het

  • het_atoms (list of ints) – Atoms from this het.

  • include_chain (bool) – Whether the chain name should be included.

schrodinger.application.prepwizard.add_prepared_props(st)

Adds “prepared” and “prepared with version” properties to the given structure.

schrodinger.application.prepwizard.delete_far_waters(st, angstroms=5)
schrodinger.application.prepwizard.delete_non_bridging_waters(st, delwater_hbond_cutoff)

Delete waters that do not make at least this number of hydrogen bonds to non-waters.

schrodinger.application.prepwizard.idealize_hydrogen_temp_factor(st)

Set temperature factor for hydrogens without temperature factors to that of the bonded heavy atom (if available). This is important for X-ray refinement to prevent R-factor collapse.

Parameters:

st (Schrodinger.structure) – Input Structure

Returns:

None, but alters hydrogen temperature factors in place.

schrodinger.application.prepwizard.get_het_atom_numbers(st)

Get the list of het groups in a structure

Parameters:

st (schrodinger.structure.Structure) – Input Structure

Returns:

atom numbers in hetero atom fields. Each list is the atoms within a given hetero group

Return type:

list of list of integers

class schrodinger.application.prepwizard.PrepWizardSettings(*args, _param_type=<object object>, **kwargs)

Bases: CompoundParam

Used for storing settings in prepwizard_driver.py, which is then passed to update_task_from_settings() to convert settings to PreprocessInput for use in PPW2 tasks. Also used as input for the prepare_structure() API. Also see tasks.PreprocessInput which has many similarities

jobname: str

A parameter of the class.

force_field: str

A parameter of the class.

preprocess: bool

A parameter of the class.

assign_bond_orders: bool

A parameter of the class.

use_ccd: bool

A parameter of the class.

skip_assigned_residues: bool

A parameter of the class.

add_missing_inter_residue_bonds: bool

A parameter of the class.

add_hydrogens: bool

A parameter of the class.

readd_hydrogens: bool

A parameter of the class.

idealize_hydrogen_tf: bool

A parameter of the class.

add_terminal_oxygens: bool

A parameter of the class.

cap_termini: bool

A parameter of the class.

cap_termini_min_atoms: int

A parameter of the class.

preprocess_delete_far_waters: bool

A parameter of the class.

preprocess_watdist: float

A parameter of the class.

delete_far_waters: bool

A parameter of the class.

watdist: float

A parameter of the class.

treat_metals: bool

A parameter of the class.

treat_disulfides: bool

A parameter of the class.

treat_glycosylation: bool

A parameter of the class.

treat_palmitoylation: bool

A parameter of the class.

selenomethionines: bool

A parameter of the class.

antibody_cdr_scheme: AntibodyCDRScheme

A parameter of the class.

renumber_ab_residues: bool

A parameter of the class.

tcr_cdr_scheme: AntibodyCDRScheme

A parameter of the class.

renumber_tcr_residues: bool

A parameter of the class.

fillsidechains: bool

A parameter of the class.

fillloops: bool

A parameter of the class.

custom_fasta_file: bool

A parameter of the class.

run_epik: bool

A parameter of the class.

use_epikx: bool

A parameter of the class.

max_states: int

A parameter of the class.

run_protassign: bool

A parameter of the class.

samplewater: bool

A parameter of the class.

include_epik_states: bool

A parameter of the class.

xtal: bool

A parameter of the class.

pH: float

A parameter of the class.

epik_pH: float

A parameter of the class.

epik_pHt: float

A parameter of the class.

use_propka: bool

A parameter of the class.

propka_pH: float

A parameter of the class.

label_pkas: bool

A parameter of the class.

force_list: list

A parameter of the class.

minimize_adj_h: bool

A parameter of the class.

protassign_number_sequential_cycles: int

A parameter of the class.

protassign_max_cluster_size: int

A parameter of the class.

delwater_hbond_cutoff: int

A parameter of the class.

delete_nonbridging_waters: bool

A parameter of the class.

run_impref: bool

A parameter of the class.

rmsd: float

A parameter of the class.

fixheavy: bool

A parameter of the class.

reference_struct: Structure

A parameter of the class.

use_PDB_pH: bool

A parameter of the class.

preserve_st_titles: bool

A parameter of the class.

add_hydrogensChanged

A pyqtSignal emitted by instances of the class.

add_hydrogensReplaced

A pyqtSignal emitted by instances of the class.

add_missing_inter_residue_bondsChanged

A pyqtSignal emitted by instances of the class.

add_missing_inter_residue_bondsReplaced

A pyqtSignal emitted by instances of the class.

add_terminal_oxygensChanged

A pyqtSignal emitted by instances of the class.

add_terminal_oxygensReplaced

A pyqtSignal emitted by instances of the class.

antibody_cdr_schemeChanged

A pyqtSignal emitted by instances of the class.

antibody_cdr_schemeReplaced

A pyqtSignal emitted by instances of the class.

assign_bond_ordersChanged

A pyqtSignal emitted by instances of the class.

assign_bond_ordersReplaced

A pyqtSignal emitted by instances of the class.

cap_terminiChanged

A pyqtSignal emitted by instances of the class.

cap_terminiReplaced

A pyqtSignal emitted by instances of the class.

cap_termini_min_atomsChanged

A pyqtSignal emitted by instances of the class.

cap_termini_min_atomsReplaced

A pyqtSignal emitted by instances of the class.

custom_fasta_fileChanged

A pyqtSignal emitted by instances of the class.

custom_fasta_fileReplaced

A pyqtSignal emitted by instances of the class.

delete_far_watersChanged

A pyqtSignal emitted by instances of the class.

delete_far_watersReplaced

A pyqtSignal emitted by instances of the class.

delete_nonbridging_watersChanged

A pyqtSignal emitted by instances of the class.

delete_nonbridging_watersReplaced

A pyqtSignal emitted by instances of the class.

delwater_hbond_cutoffChanged

A pyqtSignal emitted by instances of the class.

delwater_hbond_cutoffReplaced

A pyqtSignal emitted by instances of the class.

epik_pHChanged

A pyqtSignal emitted by instances of the class.

epik_pHReplaced

A pyqtSignal emitted by instances of the class.

epik_pHtChanged

A pyqtSignal emitted by instances of the class.

epik_pHtReplaced

A pyqtSignal emitted by instances of the class.

fillloopsChanged

A pyqtSignal emitted by instances of the class.

fillloopsReplaced

A pyqtSignal emitted by instances of the class.

fillsidechainsChanged

A pyqtSignal emitted by instances of the class.

fillsidechainsReplaced

A pyqtSignal emitted by instances of the class.

fixheavyChanged

A pyqtSignal emitted by instances of the class.

fixheavyReplaced

A pyqtSignal emitted by instances of the class.

force_fieldChanged

A pyqtSignal emitted by instances of the class.

force_fieldReplaced

A pyqtSignal emitted by instances of the class.

force_listChanged

A pyqtSignal emitted by instances of the class.

force_listReplaced

A pyqtSignal emitted by instances of the class.

idealize_hydrogen_tfChanged

A pyqtSignal emitted by instances of the class.

idealize_hydrogen_tfReplaced

A pyqtSignal emitted by instances of the class.

include_epik_statesChanged

A pyqtSignal emitted by instances of the class.

include_epik_statesReplaced

A pyqtSignal emitted by instances of the class.

jobnameChanged

A pyqtSignal emitted by instances of the class.

jobnameReplaced

A pyqtSignal emitted by instances of the class.

label_pkasChanged

A pyqtSignal emitted by instances of the class.

label_pkasReplaced

A pyqtSignal emitted by instances of the class.

max_statesChanged

A pyqtSignal emitted by instances of the class.

max_statesReplaced

A pyqtSignal emitted by instances of the class.

minimize_adj_hChanged

A pyqtSignal emitted by instances of the class.

minimize_adj_hReplaced

A pyqtSignal emitted by instances of the class.

pHChanged

A pyqtSignal emitted by instances of the class.

pHReplaced

A pyqtSignal emitted by instances of the class.

preprocessChanged

A pyqtSignal emitted by instances of the class.

preprocessReplaced

A pyqtSignal emitted by instances of the class.

preprocess_delete_far_watersChanged

A pyqtSignal emitted by instances of the class.

preprocess_delete_far_watersReplaced

A pyqtSignal emitted by instances of the class.

preprocess_watdistChanged

A pyqtSignal emitted by instances of the class.

preprocess_watdistReplaced

A pyqtSignal emitted by instances of the class.

preserve_st_titlesChanged

A pyqtSignal emitted by instances of the class.

preserve_st_titlesReplaced

A pyqtSignal emitted by instances of the class.

propka_pHChanged

A pyqtSignal emitted by instances of the class.

propka_pHReplaced

A pyqtSignal emitted by instances of the class.

protassign_max_cluster_sizeChanged

A pyqtSignal emitted by instances of the class.

protassign_max_cluster_sizeReplaced

A pyqtSignal emitted by instances of the class.

protassign_number_sequential_cyclesChanged

A pyqtSignal emitted by instances of the class.

protassign_number_sequential_cyclesReplaced

A pyqtSignal emitted by instances of the class.

readd_hydrogensChanged

A pyqtSignal emitted by instances of the class.

readd_hydrogensReplaced

A pyqtSignal emitted by instances of the class.

reference_structChanged

A pyqtSignal emitted by instances of the class.

reference_structReplaced

A pyqtSignal emitted by instances of the class.

renumber_ab_residuesChanged

A pyqtSignal emitted by instances of the class.

renumber_ab_residuesReplaced

A pyqtSignal emitted by instances of the class.

renumber_tcr_residuesChanged

A pyqtSignal emitted by instances of the class.

renumber_tcr_residuesReplaced

A pyqtSignal emitted by instances of the class.

rmsdChanged

A pyqtSignal emitted by instances of the class.

rmsdReplaced

A pyqtSignal emitted by instances of the class.

run_epikChanged

A pyqtSignal emitted by instances of the class.

run_epikReplaced

A pyqtSignal emitted by instances of the class.

run_imprefChanged

A pyqtSignal emitted by instances of the class.

run_imprefReplaced

A pyqtSignal emitted by instances of the class.

run_protassignChanged

A pyqtSignal emitted by instances of the class.

run_protassignReplaced

A pyqtSignal emitted by instances of the class.

samplewaterChanged

A pyqtSignal emitted by instances of the class.

samplewaterReplaced

A pyqtSignal emitted by instances of the class.

selenomethioninesChanged

A pyqtSignal emitted by instances of the class.

selenomethioninesReplaced

A pyqtSignal emitted by instances of the class.

skip_assigned_residuesChanged

A pyqtSignal emitted by instances of the class.

skip_assigned_residuesReplaced

A pyqtSignal emitted by instances of the class.

tcr_cdr_schemeChanged

A pyqtSignal emitted by instances of the class.

tcr_cdr_schemeReplaced

A pyqtSignal emitted by instances of the class.

treat_disulfidesChanged

A pyqtSignal emitted by instances of the class.

treat_disulfidesReplaced

A pyqtSignal emitted by instances of the class.

treat_glycosylationChanged

A pyqtSignal emitted by instances of the class.

treat_glycosylationReplaced

A pyqtSignal emitted by instances of the class.

treat_metalsChanged

A pyqtSignal emitted by instances of the class.

treat_metalsReplaced

A pyqtSignal emitted by instances of the class.

treat_palmitoylationChanged

A pyqtSignal emitted by instances of the class.

treat_palmitoylationReplaced

A pyqtSignal emitted by instances of the class.

use_PDB_pHChanged

A pyqtSignal emitted by instances of the class.

use_PDB_pHReplaced

A pyqtSignal emitted by instances of the class.

use_ccdChanged

A pyqtSignal emitted by instances of the class.

use_ccdReplaced

A pyqtSignal emitted by instances of the class.

use_epikxChanged

A pyqtSignal emitted by instances of the class.

use_epikxReplaced

A pyqtSignal emitted by instances of the class.

use_propkaChanged

A pyqtSignal emitted by instances of the class.

use_propkaReplaced

A pyqtSignal emitted by instances of the class.

watdistChanged

A pyqtSignal emitted by instances of the class.

watdistReplaced

A pyqtSignal emitted by instances of the class.

xtalChanged

A pyqtSignal emitted by instances of the class.

xtalReplaced

A pyqtSignal emitted by instances of the class.

schrodinger.application.prepwizard.update_task_from_settings(task, settings)

Update the given PPWorkflowTask with these given PrepWizardSettings.

schrodinger.application.prepwizard.prepare_structure(st, options, logger=None)

Prepare the given protein structure using PrepWizard.

Parameters:
Raises:

RuntimeError – When preparation fails for any reason.

Returns:

Prepared structures. Depending on the number of hets in the protein, up to options.max_states number of structures will be produced; by default 1.

Return type:

List[structure.Structure]

schrodinger.application.prepwizard.tag_st_het_num_prop(sts)

Set the hetero atom number property to the sequence number in sts on the structures :param sts: the structures to tag :type sts: List[structure.Structure]

schrodinger.application.prepwizard.extract_state_charges_and_orders(hetnum, state_st, het_atom_indices)

Return list of charges and list of bond orders representing the current het state for the given het in the state_st structure.

@param hetnum: PPW-assigned het number identifying the het in the structure. @type hetnum: int

@param state_st: Structure containing the het @type state_st: structure.Structure

@param het_atom_indices: Atom indicies for atoms that are part of the het. @type het_atom_indices: list(int)

@return: (charges, orders)

charges - list of (original atom number, formal charge) orders - list of (original atom num 1, original atom num 2, bond order)

schrodinger.application.prepwizard.find_missing_loops(st)

Seaches the specified structure for missing loops and returns a list of: (begin residue, end residue, sequence)

Each residue in the sequence is represented as a 3-letter code.