schrodinger.application.desmond.fep_edge_data module¶
-
schrodinger.application.desmond.fep_edge_data.
water_mol
(respdb: str) → schrodinger.structure._structure.Structure[source]¶ Return a water molecule CT.
-
schrodinger.application.desmond.fep_edge_data.
tag_protein
(proteinA, proteinB)[source]¶ - This is function was adopted from:
scisol.leadoptmap.protein_fep_mapper.tag_protein
This proceeds in several steps for mutation of protein A -> protein B Loop over all other atoms in the two full length proteins and assign 1:1 atom mapping. For the mutated residue, it might put some wrong numbers in, but it is fine as the correct value will later overwrite them.
:param proteinA : protein A :type proteinA : structure :param proteinB : protein B :type proteinB : structure
-
schrodinger.application.desmond.fep_edge_data.
get_fep_simulation_details
(*, complex_sid: Dict[str, object], solvent_sid: Dict[str, object]) → Dict[str, object][source]¶
-
class
schrodinger.application.desmond.fep_edge_data.
ResData
(molnum, chain, name, number)[source]¶ Bases:
schrodinger.application.desmond.fep_edge_data.ResData
A class to store the molecule number, chain, name, and number of a residue
-
fullName
()[source]¶ Return a string of the residue data formatted as chain:resname_resnum
- Returns
The formatted residue data
- Return type
str
-
nameNum
()[source]¶ Return the residue name and number formatted as resname_resnum
- Returns
The formatted residue data
- Return type
str
-
__contains__
(key, /)¶ Return key in self.
-
__len__
()¶ Return len(self).
-
chain
¶ Alias for field number 1
-
count
(value, /)¶ Return number of occurrences of value.
-
index
(value, start=0, stop=9223372036854775807, /)¶ Return first index of value.
Raises ValueError if the value is not present.
-
molnum
¶ Alias for field number 0
-
name
¶ Alias for field number 2
-
number
¶ Alias for field number 3
-
-
class
schrodinger.application.desmond.fep_edge_data.
FEPTorsions
(ark_sol=None, ark_cpx=None, sol_idx_offset=0, cpx_idx_offset=0)[source]¶ Bases:
object
- Variables
NULL_Y_LIM – The default y min and max for plots which don’t contain torsion data
- Vartype
tuple(int, int)
-
POT_NTICKS
= 3¶
-
NULL_Y_LIM
= (-1, 1)¶
-
Y_AXIS_SCALE
= 1.05¶
-
__init__
(ark_sol=None, ark_cpx=None, sol_idx_offset=0, cpx_idx_offset=0)[source]¶ Initialize self. See help(type(self)) for accurate signature.
-
property
sol_result
¶
-
property
cpx_result
¶
-
property
max_potential_energy
¶
-
property
potential_energy
¶ Returns potential energy that’s offset to zero
-
property
starting_conformation
¶ - Returns
the starting conformation’s torsion value, with a preference for the value in the complex. None if not found.
- Return type
float or NoneType
-
property
strain
¶ - Returns
the value (float) and standard deviation (float) tuples for torsion strain in the complex and solvent, i.e., ((cpx_val, cpx_std_dev), (sol_val, sol_st_dev)). If the complex or solution didn’t have torsion values None will be returned for the tuple in question
- Return type
tuple
-
class
schrodinger.application.desmond.fep_edge_data.
FEPTorsionsContainer
(sol_torsions_sea_list, cpx_torsions_sea_list, sol_idx_offset=0, cpx_idx_offset=0, perturbation_type='small_molecule')[source]¶ Bases:
object
Class that stores torsions for a single ligand. These torsions are from both solvent and complex legs of the simulations, corresponding to a single lambda value.
-
__init__
(sol_torsions_sea_list, cpx_torsions_sea_list, sol_idx_offset=0, cpx_idx_offset=0, perturbation_type='small_molecule')[source]¶ Initialize self. See help(type(self)) for accurate signature.
-
property
matched_tors
¶
-
property
unmatched_tors
¶
-
property
all_tors
¶
-
property
matched_total
¶
-
property
unmatched_total
¶
-
property
tors_total
¶
-
-
class
schrodinger.application.desmond.fep_edge_data.
FEPEdgeData
(complex_sea, solvent_sea, pv_st=None, atom_mapping=None, perturbation_type='small_molecule', ddg_corrections_map=None)[source]¶ Bases:
object
FEPEdgeData contains all the data related to an FEP perturbation. This includes both solvent and complex legs of the simulations as well as analysis results produced by SID.
-
__init__
(complex_sea, solvent_sea, pv_st=None, atom_mapping=None, perturbation_type='small_molecule', ddg_corrections_map=None)[source]¶ - Parameters
complex_sea (
sea
) – SEA object with results pertaining to the complex leg of the FEP calculationsolvent_sea (
sea
) – SEA object with results pertaining to the solvent leg of the FEP calculationpv_st (
schrodinger.Structure
) – PoseViewer file must contain 3 structures.. [receptor, lig1, lig2]; otherwise it’s Noneatom_mapping (tuple(int, int)) – mapping of ligand2 to ligand1 atoms
-
rate
(name: str) → schrodinger.application.desmond.fep_edge_data_classifier.Rating[source]¶ Return rating for the FEP edge data with the given
name
. The valid names can be found in fep_edge_data_classifiers.py.
-
property
fep_simulation_details
¶
-
property
atom_mapping
¶
-
property
ligand_torsions
¶ - Return type
(
FEPTorsionsContainer
object,FEPTorsionsContainer
object)- Returns
FEPTorsionsContainer
objects for lambda0 and lambda1.
-
property
sse_limits_lambda0
¶
-
property
sse_limits_lambda1
¶
-
property
receptor_sid_rmsd_ligand_lambda0
¶ ligand1 RMSD wrt the protein
-
property
receptor_sid_rmsd_ligand_lambda1
¶ ligand2 RMSD wrt the protein
-
static
protein_residue
(res)[source]¶ Get data about the specified residue
- Parameters
res (
schrodinger.structure._Residue
) – The residue object to get data from- Returns
A namedtuple containing the molecule number, chain, residue name,
and residue number :rtype:
ResData
-
property
receptor_residue_sequence_list
¶ Return a list of residue objects (ResData) in amino-to-carboxy order. :return: a list of residue objects, ordered N->C (amino to carboxy
tails).
- Return type
A residue tag looks like this: A:THR_124 (Chain:resname_resnum) if chain is not defined, use ‘_’ (underscore) :return: a list of residue tags :rtype:
residue_tag
-
property
receptor_b_factor
¶ Return B factors grouped by residues using PDB tfactor values stored in the structure. If the PDB tfactor values are not present, return zeros.
-
property
receptor_sid_rmsd_backbone_lambda0
¶
-
property
receptor_sid_rmsd_backbone_lambda1
¶
-
receptor_sid_rmsf_backbone_lambda0
¶ Decorator that converts a method with a single self argument into a property cached on the instance.
Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.
This class is based on code that is Copyright (c) Django Software Foundation
-
receptor_sid_rmsf_backbone_lambda1
¶ Decorator that converts a method with a single self argument into a property cached on the instance.
Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.
This class is based on code that is Copyright (c) Django Software Foundation
-
property
cpx_sid_lp_results
¶
-
property
pl_contact_data0
¶ A dictionary containing PL interactions for lambda=0
-
property
pl_contact_data1
¶ A dictionary containing PL interactions for lambda=1
-
property
pl_interaction_similarity_matrix0
¶ Protein-ligand interactions similarity matrix for lambda=0 sys for all available frames.
-
property
pl_interaction_similarity_matrix1
¶ Protein-ligand interactions similarity matrix for lambda=1 sys for all available frames.
-
property
fullsystem_ct
¶
-
property
cpx_sid_pl_results
¶
-
property
cpx_sid_protein_residues
¶ A list of protein residues that interact with both ligand1 and ligand2 throughout the simulation :rtype:
str
:return: a list of protein tags that interact with both ligand1 andligand2
-
property
receptor_residues_interaction_ligand1
¶ A list of preotein residues that interact just with ligand1 :rtype: list :return: list of protein residue tags
-
property
receptor_residues_interaction_ligand2
¶ A list of preotein residues that interact just with ligand2 :rtype: list :return: list of protein residue tags
-
property
cpx_sid_trajectory_interval_ns
¶
-
property
sol_sid_trajectory_interval_ns
¶
-
property
cpx_sid_snashot_times_ps
¶
-
property
cpx_sid_snapshot_times_ps
¶
-
property
sol_sid_snapshot_times_ps
¶
-
property
cpx_sid_number_of_frames
¶
-
property
sol_sid_number_of_frames
¶
-
property
leg1_name
¶
-
property
leg2_name
¶
-
property
sol_timestep_list
¶
-
property
cpx_timestep_list
¶
-
property
sol_timestep_interval
¶
-
property
cpx_timestep_interval
¶
-
property
sol_delta_g_sliding_err
¶
-
property
cpx_delta_g_sliding_err
¶
-
property
sol_delta_g_sliding
¶
-
property
cpx_delta_g_sliding
¶
-
property
sol_delta_g_reverse_err
¶
-
property
cpx_delta_g_reverse_err
¶
-
property
sol_delta_g_reverse
¶
-
property
cpx_delta_g_reverse
¶
-
property
sol_delta_g_forward_err
¶
-
property
cpx_delta_g_forward_err
¶
-
property
sol_delta_g_forward_dg
¶
-
property
cpx_delta_g_forward_dg
¶
-
property
sol_delta_g_forward_bootstrap_std
¶
-
property
cpx_delta_g_forward_bootstrap_std
¶
-
property
sol_delta_g_forward_analytical_std
¶
-
property
cpx_delta_g_forward_analytical_std
¶
-
property
sol_delta_g_forward_df_per_replica
¶
-
property
cpx_delta_g_forward_df_per_replica
¶
-
property
sol_delta_g_forward
¶
-
property
cpx_delta_g_forward
¶
-
property
sol_end_time_ns
¶
-
property
cpx_end_time_ns
¶
-
property
sol_start_time_ns
¶
-
property
cpx_start_time_ns
¶
-
property
receptor_charge
¶
-
property
receptor_total_heavy
¶
-
property
receptor_total_atom
¶
-
property
receptor_title
¶
-
property
receptor_total_residues_in_chains
¶
-
property
receptor_chain_names
¶
-
property
receptor_total_residues
¶
-
property
ligand1_total_rot_bonds
¶
-
property
ligand2_total_rot_bonds
¶
-
property
ligand1_total_fragments
¶
-
property
ligand2_total_fragments
¶
-
property
ligand1_mol_formula
¶
-
property
ligand2_mol_formula
¶
-
property
ligand1_charge
¶
-
property
ligand2_charge
¶
-
property
ligand1_alchemical_mols
¶
-
property
ligand2_alchemical_mols
¶
-
property
ligand1_alchemical_atom_total
¶
-
property
ligand2_alchemical_atom_total
¶
-
property
ligand1_atomic_mass
¶
-
property
ligand2_atomic_mass
¶
-
property
ligand1_rot_bonds
¶
-
property
ligand2_rot_bonds
¶
-
property
ligand1_total_hot
¶
-
property
ligand2_total_hot
¶
-
property
ligand1_total_heavy
¶
-
property
ligand2_total_heavy
¶
-
property
ligand1_total_atoms
¶
-
property
ligand2_total_atoms
¶
-
property
ligand1_cpx_asl
¶
-
property
ligand2_cpx_asl
¶
-
property
ligand1_sol_asl
¶
-
property
ligand2_sol_asl
¶
-
property
ligand1_pdb_name
¶
-
property
ligand2_pdb_name
¶
-
property
ligand1_smiles
¶
-
property
ligand2_smiles
¶
-
property
ligand1_name
¶
-
property
ligand2_name
¶
-
property
short_hash
¶
-
property
ligand1_hash
¶
-
property
ligand2_hash
¶
-
property
jobname
¶
-
property
delta_delta_g
¶
-
property
sol_delta_g
¶ - Returns
dG and its standard deviation
- Return type
float, float
-
property
ddg_corrections_map
¶
-
property
ddg_corrections_sum
¶
-
property
cpx_delta_g
¶ - Returns
dG and its standard deviation
- Return type
float, float
-
property
sol_total_replicas
¶
-
property
cpx_total_replicas
¶
-
property
sol_total_waters
¶
-
property
cpx_total_waters
¶
-
property
sol_total_atoms
¶
-
property
cpx_total_atoms
¶
-
property
sol_sim_time
¶ Values returned in Ns (nanoseconds)
-
property
cpx_sim_time
¶ Values returned in Ns (nanoseconds)
-
property
sol_temperature
¶
-
property
cpx_temperature
¶
-
property
sol_ff
¶
-
property
cpx_ff
¶
-
property
sol_ensemble
¶
-
property
cpx_ensemble
¶
-
property
sol_charge
¶
-
property
cpx_charge
¶
-
property
sol_salt_molecules
¶
-
property
cpx_salt_molecules
¶
-
property
sol_salt_info
¶
-
property
cpx_salt_info
¶
-
property
receptor_st
¶ Returns receptor structure
-
property
ligand1_st
¶ Returns ligand_1 structure
-
property
ligand2_st
¶ Returns ligand_2 structure
-
property
sol_rest_exchanges
¶
-
property
cpx_rest_exchanges
¶
-
-
class
schrodinger.application.desmond.fep_edge_data.
PRMEdgeData
(complex_sea, solvent_sea, pv_st=None, atom_mapping=None, perturbation_type='small_molecule', frag_atom_mapping=None)[source]¶ Bases:
schrodinger.application.desmond.fep_edge_data.FEPEdgeData
PRMEdgeData is an object that stores Protein Residue Mutation related data. And inherits from FEPEdgeData.
-
__init__
(complex_sea, solvent_sea, pv_st=None, atom_mapping=None, perturbation_type='small_molecule', frag_atom_mapping=None)[source]¶ - Parameters
complex_sea (
sea
) – SEA object with results pertaining to the complex leg of the FEP calculationsolvent_sea (
sea
) – SEA object with results pertaining to the solvent leg of the FEP calculationpv_st (
schrodinger.Structure
) – PoseViewer file must contain 2 or 3 structures. [receptor, lig1, lig2]; otherwise it’s Noneatom_mapping (
int
,int
) – mapping of ligand2 to ligand1 atomsfrag_atom_mapping (
int
,int
) – mapping of frag1 and frag2 atoms
-
property
wt_st
¶ Returns full structure of a WT protein
-
property
mut_st
¶ Returns full structure of a mutated protein
-
property
ligand1_st
¶ Returns ligand_1 structure
-
property
ligand2_st
¶ Returns ligand_2 structure
-
property
receptor_st
¶ Returns receptor structure
-
property
wt_frag_st
¶
-
property
mut_frag_st
¶
-
property
solvent_fullsystem_ct
¶
-
property
ligand_st_mol_formula
¶
-
property
prm_name
¶
-
receptor_sid_rmsf_backbone_lambda0
¶ Decorator that converts a method with a single self argument into a property cached on the instance.
Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.
This class is based on code that is Copyright (c) Django Software Foundation
-
receptor_sid_rmsf_backbone_lambda1
¶ Decorator that converts a method with a single self argument into a property cached on the instance.
Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.
This class is based on code that is Copyright (c) Django Software Foundation
-
property
ligand_torsions
¶ - Return type
(
FEPTorsionsContainer
object,FEPTorsionsContainer
object)- Returns
FEPTorsionsContainer
objects for lambda0 and lambda1.
-
property
wt_name
¶
-
property
mut_name
¶
-
property
wt_residue_sequence_list
¶ Return a list of residue objects (ResData) in amino-to-carboxy order. :return: a list of residue objects, ordered N->C (amino to carboxy
tails).
- Return type
A residue tag looks like this: A:THR_124 (Chain:resname_resnum) if chain is not defined, use ‘_’ (underscore) :return: a list of residue tags :rtype:
residue_tag
-
property
mut_residue_sequence_list
¶ Return a list of residue objects (ResData) in amino-to-carboxy order. :return: a list of residue objects, ordered N->C (amino to carboxy
tails).
- Return type
A residue tag looks like this: A:THR_124 (Chain:resname_resnum) if chain is not defined, use ‘_’ (underscore) :return: a list of residue tags :rtype:
residue_tag
-
property
cpx_sid_lp_results
¶
-
property
atom_mapping
¶
-
property
cpx_charge
¶
-
property
cpx_delta_g
¶ - Returns
dG and its standard deviation
- Return type
float, float
-
property
cpx_delta_g_forward
¶
-
property
cpx_delta_g_forward_analytical_std
¶
-
property
cpx_delta_g_forward_bootstrap_std
¶
-
property
cpx_delta_g_forward_df_per_replica
¶
-
property
cpx_delta_g_forward_dg
¶
-
property
cpx_delta_g_forward_err
¶
-
property
cpx_delta_g_reverse
¶
-
property
cpx_delta_g_reverse_err
¶
-
property
cpx_delta_g_sliding
¶
-
property
cpx_delta_g_sliding_err
¶
-
property
cpx_end_time_ns
¶
-
property
cpx_ensemble
¶
-
property
cpx_ff
¶
-
property
cpx_rest_exchanges
¶
-
property
cpx_salt_info
¶
-
property
cpx_salt_molecules
¶
-
property
cpx_sid_number_of_frames
¶
-
property
cpx_sid_pl_results
¶
-
property
cpx_sid_protein_residues
¶ A list of protein residues that interact with both ligand1 and ligand2 throughout the simulation :rtype:
str
:return: a list of protein tags that interact with both ligand1 andligand2
-
property
cpx_sid_snapshot_times_ps
¶
-
property
cpx_sid_snashot_times_ps
¶
-
property
cpx_sid_trajectory_interval_ns
¶
-
property
cpx_sim_time
¶ Values returned in Ns (nanoseconds)
-
property
cpx_start_time_ns
¶
-
property
cpx_temperature
¶
-
property
cpx_timestep_interval
¶
-
property
cpx_timestep_list
¶
-
property
cpx_total_atoms
¶
-
property
cpx_total_replicas
¶
-
property
cpx_total_waters
¶
-
property
ddg_corrections_map
¶
-
property
ddg_corrections_sum
¶
-
property
delta_delta_g
¶
-
property
fep_simulation_details
¶
-
property
fullsystem_ct
¶
-
get_ligand1_atom_dict
()¶
-
get_ligand2_atom_dict
()¶
-
static
get_smiles
(st)¶ rtype: str return: Generate SMILES from a given ligand structure.
-
property
jobname
¶
-
property
leg1_name
¶
-
property
leg2_name
¶
-
property
ligand1_alchemical_atom_total
¶
-
property
ligand1_alchemical_mols
¶
-
property
ligand1_atomic_mass
¶
-
property
ligand1_charge
¶
-
property
ligand1_cpx_asl
¶
-
ligand1_cpx_sid_lighb
(stats=True)¶
-
ligand1_cpx_sid_molsa
(stats=True)¶
-
ligand1_cpx_sid_psa
(stats=True)¶
-
ligand1_cpx_sid_rb_strain
(stats=True)¶
-
ligand1_cpx_sid_rgyr
(stats=True)¶
-
ligand1_cpx_sid_rmsd
(stats=True)¶
-
ligand1_cpx_sid_sasa
(stats=True)¶
-
ligand1_cpx_sid_waters
(stats=True)¶
-
ligand1_fragments
(offset_by_receptor_natoms=True)¶
-
property
ligand1_hash
¶
-
property
ligand1_mol_formula
¶
-
property
ligand1_name
¶
-
property
ligand1_pdb_name
¶
-
property
ligand1_rot_bonds
¶
-
property
ligand1_smiles
¶
-
property
ligand1_sol_asl
¶
-
ligand1_sol_sid_lighb
(stats=True)¶
-
ligand1_sol_sid_molsa
(stats=True)¶
-
ligand1_sol_sid_psa
(stats=True)¶
-
ligand1_sol_sid_rb_strain
(stats=True)¶
-
ligand1_sol_sid_rgyr
(stats=True)¶
-
ligand1_sol_sid_rmsd
(stats=True)¶
-
ligand1_sol_sid_sasa
(stats=True)¶
-
property
ligand1_total_atoms
¶
-
property
ligand1_total_fragments
¶
-
property
ligand1_total_heavy
¶
-
property
ligand1_total_hot
¶
-
property
ligand1_total_rot_bonds
¶
-
property
ligand2_alchemical_atom_total
¶
-
property
ligand2_alchemical_mols
¶
-
property
ligand2_atomic_mass
¶
-
property
ligand2_charge
¶
-
property
ligand2_cpx_asl
¶
-
ligand2_cpx_sid_lighb
(stats=True)¶
-
ligand2_cpx_sid_molsa
(stats=True)¶
-
ligand2_cpx_sid_psa
(stats=True)¶
-
ligand2_cpx_sid_rb_strain
(stats=True)¶
-
ligand2_cpx_sid_rgyr
(stats=True)¶
-
ligand2_cpx_sid_rmsd
(stats=True)¶
-
ligand2_cpx_sid_sasa
(stats=True)¶
-
ligand2_cpx_sid_waters
(stats=True)¶
-
ligand2_fragments
(offset_by_receptor_natoms=True)¶
-
property
ligand2_hash
¶
-
property
ligand2_mol_formula
¶
-
property
ligand2_name
¶
-
property
ligand2_pdb_name
¶
-
property
ligand2_rot_bonds
¶
-
property
ligand2_smiles
¶
-
property
ligand2_sol_asl
¶
-
ligand2_sol_sid_lighb
(stats=True)¶
-
ligand2_sol_sid_molsa
(stats=True)¶
-
ligand2_sol_sid_psa
(stats=True)¶
-
ligand2_sol_sid_rb_strain
(stats=True)¶
-
ligand2_sol_sid_rgyr
(stats=True)¶
-
ligand2_sol_sid_rmsd
(stats=True)¶
-
ligand2_sol_sid_sasa
(stats=True)¶
-
property
ligand2_total_atoms
¶
-
property
ligand2_total_fragments
¶
-
property
ligand2_total_heavy
¶
-
property
ligand2_total_hot
¶
-
property
ligand2_total_rot_bonds
¶
-
static
ligand_name
(st)¶
-
property
pl_contact_data0
¶ A dictionary containing PL interactions for lambda=0
-
property
pl_contact_data1
¶ A dictionary containing PL interactions for lambda=1
-
property
pl_interaction_similarity_matrix0
¶ Protein-ligand interactions similarity matrix for lambda=0 sys for all available frames.
-
property
pl_interaction_similarity_matrix1
¶ Protein-ligand interactions similarity matrix for lambda=1 sys for all available frames.
-
static
protein_residue
(res)¶ Get data about the specified residue
- Parameters
res (
schrodinger.structure._Residue
) – The residue object to get data from- Returns
A namedtuple containing the molecule number, chain, residue name,
and residue number :rtype:
ResData
-
rate
(name: str) → schrodinger.application.desmond.fep_edge_data_classifier.Rating¶ Return rating for the FEP edge data with the given
name
. The valid names can be found in fep_edge_data_classifiers.py.
-
property
receptor_b_factor
¶ Return B factors grouped by residues using PDB tfactor values stored in the structure. If the PDB tfactor values are not present, return zeros.
-
property
receptor_chain_names
¶
-
property
receptor_charge
¶
-
property
receptor_residue_sequence_list
¶ Return a list of residue objects (ResData) in amino-to-carboxy order. :return: a list of residue objects, ordered N->C (amino to carboxy
tails).
- Return type
A residue tag looks like this: A:THR_124 (Chain:resname_resnum) if chain is not defined, use ‘_’ (underscore) :return: a list of residue tags :rtype:
residue_tag
-
property
receptor_residues_interaction_ligand1
¶ A list of preotein residues that interact just with ligand1 :rtype: list :return: list of protein residue tags
-
property
receptor_residues_interaction_ligand2
¶ A list of preotein residues that interact just with ligand2 :rtype: list :return: list of protein residue tags
-
property
receptor_sid_rmsd_backbone_lambda0
¶
-
property
receptor_sid_rmsd_backbone_lambda1
¶
-
property
receptor_sid_rmsd_ligand_lambda0
¶ ligand1 RMSD wrt the protein
-
property
receptor_sid_rmsd_ligand_lambda1
¶ ligand2 RMSD wrt the protein
-
property
receptor_title
¶
-
property
receptor_total_atom
¶
-
property
receptor_total_heavy
¶
-
property
receptor_total_residues
¶
-
property
receptor_total_residues_in_chains
¶
-
property
short_hash
¶
-
property
sol_charge
¶
-
property
sol_delta_g
¶ - Returns
dG and its standard deviation
- Return type
float, float
-
property
sol_delta_g_forward
¶
-
property
sol_delta_g_forward_analytical_std
¶
-
property
sol_delta_g_forward_bootstrap_std
¶
-
property
sol_delta_g_forward_df_per_replica
¶
-
property
sol_delta_g_forward_dg
¶
-
property
sol_delta_g_forward_err
¶
-
property
sol_delta_g_reverse
¶
-
property
sol_delta_g_reverse_err
¶
-
property
sol_delta_g_sliding
¶
-
property
sol_delta_g_sliding_err
¶
-
property
sol_end_time_ns
¶
-
property
sol_ensemble
¶
-
property
sol_ff
¶
-
property
sol_rest_exchanges
¶
-
property
sol_salt_info
¶
-
property
sol_salt_molecules
¶
-
property
sol_sid_number_of_frames
¶
-
property
sol_sid_snapshot_times_ps
¶
-
property
sol_sid_trajectory_interval_ns
¶
-
property
sol_sim_time
¶ Values returned in Ns (nanoseconds)
-
property
sol_start_time_ns
¶
-
property
sol_temperature
¶
-
property
sol_timestep_interval
¶
-
property
sol_timestep_list
¶
-
property
sol_total_atoms
¶
-
property
sol_total_replicas
¶
-
property
sol_total_waters
¶
-
property
sse_limits_lambda0
¶
-
property
sse_limits_lambda1
¶
-
-
class
schrodinger.application.desmond.fep_edge_data.
CovalentFEPEdgeData
(complex_sea, solvent_sea, pv_st=None, sol_st=None, atom_mapping=None, perturbation_type='small_molecule', frag_atom_mapping=None)[source]¶ Bases:
schrodinger.application.desmond.fep_edge_data.FEPEdgeData
This object stores covalent FEP related data.
-
__init__
(complex_sea, solvent_sea, pv_st=None, sol_st=None, atom_mapping=None, perturbation_type='small_molecule', frag_atom_mapping=None)[source]¶ - Parameters
complex_sea (
sea
) – SEA object with results pertaining to the complex leg of the FEP calculationsolvent_sea (
sea
) – SEA object with results pertaining to the solvent leg of the FEP calculationpv_st (
schrodinger.Structure
) – PoseViewer file must contain 2 structures. [complex1, complex2]; otherwise it’s Nonesol_st (solvent fragments tuple) – (
schrodinger.Structure
,schrodinger.Structure
)atom_mapping (
int
,int
) – mapping of ligand2 to ligand1 atomsfrag_atom_mapping (
int
,int
) – mapping of frag1 and frag2 atoms
-
property
wt_st
¶ Returns full structure of a WT protein
-
property
mut_st
¶ Returns full structure of a mutated protein
-
property
receptor_st
¶ Returns receptor structure
-
property
ligand1_cpx_st
¶
-
property
ligand2_cpx_st
¶
-
property
ligand1_st
¶ Returns ligand_1 structure
-
property
ligand2_st
¶ Returns ligand_2 structure
-
property
solvent_fullsystem_ct
¶
-
receptor_sid_rmsf_backbone_lambda0
¶ Decorator that converts a method with a single self argument into a property cached on the instance.
Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.
This class is based on code that is Copyright (c) Django Software Foundation
-
receptor_sid_rmsf_backbone_lambda1
¶ Decorator that converts a method with a single self argument into a property cached on the instance.
Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.
This class is based on code that is Copyright (c) Django Software Foundation
-
property
ligand_torsions
¶ - Return type
(
FEPTorsionsContainer
object,FEPTorsionsContainer
object)- Returns
FEPTorsionsContainer
objects for lambda0 and lambda1.
-
property
receptor_title
¶
-
property
cpx_sid_lp_results
¶
-
property
atom_mapping
¶ Return atom mapping for both ligand fragment that is used in the SID calculation. Ligands used in the solvent leg are different than those used in the complex leg. The difference is:
- Complex leg – we use the side chain of the attached residue plus
the ligand.
Solvent leg – we use the peptide plus the ligand.
- Returns
atom mapping for ligand1 and ligand2. The values should
- Return type
(
list
,list
)
-
property
cpx_charge
¶
-
property
cpx_delta_g
¶ - Returns
dG and its standard deviation
- Return type
float, float
-
property
cpx_delta_g_forward
¶
-
property
cpx_delta_g_forward_analytical_std
¶
-
property
cpx_delta_g_forward_bootstrap_std
¶
-
property
cpx_delta_g_forward_df_per_replica
¶
-
property
cpx_delta_g_forward_dg
¶
-
property
cpx_delta_g_forward_err
¶
-
property
cpx_delta_g_reverse
¶
-
property
cpx_delta_g_reverse_err
¶
-
property
cpx_delta_g_sliding
¶
-
property
cpx_delta_g_sliding_err
¶
-
property
cpx_end_time_ns
¶
-
property
cpx_ensemble
¶
-
property
cpx_ff
¶
-
property
cpx_rest_exchanges
¶
-
property
cpx_salt_info
¶
-
property
cpx_salt_molecules
¶
-
property
cpx_sid_number_of_frames
¶
-
property
cpx_sid_pl_results
¶
-
property
cpx_sid_protein_residues
¶ A list of protein residues that interact with both ligand1 and ligand2 throughout the simulation :rtype:
str
:return: a list of protein tags that interact with both ligand1 andligand2
-
property
cpx_sid_snapshot_times_ps
¶
-
property
cpx_sid_snashot_times_ps
¶
-
property
cpx_sid_trajectory_interval_ns
¶
-
property
cpx_sim_time
¶ Values returned in Ns (nanoseconds)
-
property
cpx_start_time_ns
¶
-
property
cpx_temperature
¶
-
property
cpx_timestep_interval
¶
-
property
cpx_timestep_list
¶
-
property
cpx_total_atoms
¶
-
property
cpx_total_replicas
¶
-
property
cpx_total_waters
¶
-
property
ddg_corrections_map
¶
-
property
ddg_corrections_sum
¶
-
property
delta_delta_g
¶
-
property
fep_simulation_details
¶
-
property
fullsystem_ct
¶
-
static
get_smiles
(st)¶ rtype: str return: Generate SMILES from a given ligand structure.
-
property
jobname
¶
-
property
leg1_name
¶
-
property
leg2_name
¶
-
property
ligand1_alchemical_atom_total
¶
-
property
ligand1_alchemical_mols
¶
-
property
ligand1_atomic_mass
¶
-
property
ligand1_charge
¶
-
property
ligand1_cpx_asl
¶
-
ligand1_cpx_sid_lighb
(stats=True)¶
-
ligand1_cpx_sid_molsa
(stats=True)¶
-
ligand1_cpx_sid_psa
(stats=True)¶
-
ligand1_cpx_sid_rb_strain
(stats=True)¶
-
ligand1_cpx_sid_rgyr
(stats=True)¶
-
ligand1_cpx_sid_rmsd
(stats=True)¶
-
ligand1_cpx_sid_sasa
(stats=True)¶
-
ligand1_cpx_sid_waters
(stats=True)¶
-
ligand1_fragments
(offset_by_receptor_natoms=True)¶
-
property
ligand1_hash
¶
-
property
ligand1_mol_formula
¶
-
property
ligand1_name
¶
-
property
ligand1_pdb_name
¶
-
property
ligand1_rot_bonds
¶
-
property
ligand1_smiles
¶
-
property
ligand1_sol_asl
¶
-
ligand1_sol_sid_lighb
(stats=True)¶
-
ligand1_sol_sid_molsa
(stats=True)¶
-
ligand1_sol_sid_psa
(stats=True)¶
-
ligand1_sol_sid_rb_strain
(stats=True)¶
-
ligand1_sol_sid_rgyr
(stats=True)¶
-
ligand1_sol_sid_rmsd
(stats=True)¶
-
ligand1_sol_sid_sasa
(stats=True)¶
-
property
ligand1_total_atoms
¶
-
property
ligand1_total_fragments
¶
-
property
ligand1_total_heavy
¶
-
property
ligand1_total_hot
¶
-
property
ligand1_total_rot_bonds
¶
-
property
ligand2_alchemical_atom_total
¶
-
property
ligand2_alchemical_mols
¶
-
property
ligand2_atomic_mass
¶
-
property
ligand2_charge
¶
-
property
ligand2_cpx_asl
¶
-
ligand2_cpx_sid_lighb
(stats=True)¶
-
ligand2_cpx_sid_molsa
(stats=True)¶
-
ligand2_cpx_sid_psa
(stats=True)¶
-
ligand2_cpx_sid_rb_strain
(stats=True)¶
-
ligand2_cpx_sid_rgyr
(stats=True)¶
-
ligand2_cpx_sid_rmsd
(stats=True)¶
-
ligand2_cpx_sid_sasa
(stats=True)¶
-
ligand2_cpx_sid_waters
(stats=True)¶
-
ligand2_fragments
(offset_by_receptor_natoms=True)¶
-
property
ligand2_hash
¶
-
property
ligand2_mol_formula
¶
-
property
ligand2_name
¶
-
property
ligand2_pdb_name
¶
-
property
ligand2_rot_bonds
¶
-
property
ligand2_smiles
¶
-
property
ligand2_sol_asl
¶
-
ligand2_sol_sid_lighb
(stats=True)¶
-
ligand2_sol_sid_molsa
(stats=True)¶
-
ligand2_sol_sid_psa
(stats=True)¶
-
ligand2_sol_sid_rb_strain
(stats=True)¶
-
ligand2_sol_sid_rgyr
(stats=True)¶
-
ligand2_sol_sid_rmsd
(stats=True)¶
-
ligand2_sol_sid_sasa
(stats=True)¶
-
property
ligand2_total_atoms
¶
-
property
ligand2_total_fragments
¶
-
property
ligand2_total_heavy
¶
-
property
ligand2_total_hot
¶
-
property
ligand2_total_rot_bonds
¶
-
static
ligand_name
(st)¶
-
property
pl_contact_data0
¶ A dictionary containing PL interactions for lambda=0
-
property
pl_contact_data1
¶ A dictionary containing PL interactions for lambda=1
-
property
pl_interaction_similarity_matrix0
¶ Protein-ligand interactions similarity matrix for lambda=0 sys for all available frames.
-
property
pl_interaction_similarity_matrix1
¶ Protein-ligand interactions similarity matrix for lambda=1 sys for all available frames.
-
static
protein_residue
(res)¶ Get data about the specified residue
- Parameters
res (
schrodinger.structure._Residue
) – The residue object to get data from- Returns
A namedtuple containing the molecule number, chain, residue name,
and residue number :rtype:
ResData
-
rate
(name: str) → schrodinger.application.desmond.fep_edge_data_classifier.Rating¶ Return rating for the FEP edge data with the given
name
. The valid names can be found in fep_edge_data_classifiers.py.
-
property
receptor_b_factor
¶ Return B factors grouped by residues using PDB tfactor values stored in the structure. If the PDB tfactor values are not present, return zeros.
-
property
receptor_chain_names
¶
-
property
receptor_charge
¶
-
property
receptor_residue_sequence_list
¶ Return a list of residue objects (ResData) in amino-to-carboxy order. :return: a list of residue objects, ordered N->C (amino to carboxy
tails).
- Return type
A residue tag looks like this: A:THR_124 (Chain:resname_resnum) if chain is not defined, use ‘_’ (underscore) :return: a list of residue tags :rtype:
residue_tag
-
property
receptor_residues_interaction_ligand1
¶ A list of preotein residues that interact just with ligand1 :rtype: list :return: list of protein residue tags
-
property
receptor_residues_interaction_ligand2
¶ A list of preotein residues that interact just with ligand2 :rtype: list :return: list of protein residue tags
-
property
receptor_sid_rmsd_backbone_lambda0
¶
-
property
receptor_sid_rmsd_backbone_lambda1
¶
-
property
receptor_sid_rmsd_ligand_lambda0
¶ ligand1 RMSD wrt the protein
-
property
receptor_sid_rmsd_ligand_lambda1
¶ ligand2 RMSD wrt the protein
-
property
receptor_total_atom
¶
-
property
receptor_total_heavy
¶
-
property
receptor_total_residues
¶
-
property
receptor_total_residues_in_chains
¶
-
property
short_hash
¶
-
property
sol_charge
¶
-
property
sol_delta_g
¶ - Returns
dG and its standard deviation
- Return type
float, float
-
property
sol_delta_g_forward
¶
-
property
sol_delta_g_forward_analytical_std
¶
-
property
sol_delta_g_forward_bootstrap_std
¶
-
property
sol_delta_g_forward_df_per_replica
¶
-
property
sol_delta_g_forward_dg
¶
-
property
sol_delta_g_forward_err
¶
-
property
sol_delta_g_reverse
¶
-
property
sol_delta_g_reverse_err
¶
-
property
sol_delta_g_sliding
¶
-
property
sol_delta_g_sliding_err
¶
-
property
sol_end_time_ns
¶
-
property
sol_ensemble
¶
-
property
sol_ff
¶
-
property
sol_rest_exchanges
¶
-
property
sol_salt_info
¶
-
property
sol_salt_molecules
¶
-
property
sol_sid_number_of_frames
¶
-
property
sol_sid_snapshot_times_ps
¶
-
property
sol_sid_trajectory_interval_ns
¶
-
property
sol_sim_time
¶ Values returned in Ns (nanoseconds)
-
property
sol_start_time_ns
¶
-
property
sol_temperature
¶
-
property
sol_timestep_interval
¶
-
property
sol_timestep_list
¶
-
property
sol_total_atoms
¶
-
property
sol_total_replicas
¶
-
property
sol_total_waters
¶
-
property
sse_limits_lambda0
¶
-
property
sse_limits_lambda1
¶
-
-
class
schrodinger.application.desmond.fep_edge_data.
MetalloproteinEdgeData
(complex_sea, solvent_sea, pv_st=None, atom_mapping=None, perturbation_type='metalloprotein')[source]¶ Bases:
schrodinger.application.desmond.fep_edge_data.FEPEdgeData
This object stores Metalloprotein FEP related data.
-
__init__
(complex_sea, solvent_sea, pv_st=None, atom_mapping=None, perturbation_type='metalloprotein')[source]¶ - Parameters
complex_sea (
sea
) – SEA object with results pertaining to the complex leg of the FEP calculationsolvent_sea (
sea
) – SEA object with results pertaining to the solvent leg of the FEP calculationpv_st (
schrodinger.Structure
) – PoseViewer file must contain 3 structures.. [receptor, lig1, lig2]; otherwise it’s Noneatom_mapping (Dict[int, int]) – mapping of ligand2 to ligand1 atoms
-
property
fullsystem_ct
¶ - Return type
- Returns
The full system structure.
-
property
receptor_st
¶ - Return type
- Returns
The receptor structure.
-
property
ligand1_st
¶ - Return type
- Returns
The ligand1 structure.
-
property
ligand2_st
¶ - Return type
- Returns
The ligand2 structure.
-
property
ligand_torsions
¶ - Return type
(
FEPTorsionsContainer
object,FEPTorsionsContainer
object)- Returns
FEPTorsionsContainer
objects for lambda0 and lambda1.
-
receptor_sid_rmsf_backbone_lambda0
¶ Decorator that converts a method with a single self argument into a property cached on the instance.
Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.
This class is based on code that is Copyright (c) Django Software Foundation
-
receptor_sid_rmsf_backbone_lambda1
¶ Decorator that converts a method with a single self argument into a property cached on the instance.
Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.
This class is based on code that is Copyright (c) Django Software Foundation
-
property
atom_mapping
¶
-
property
cpx_charge
¶
-
property
cpx_delta_g
¶ - Returns
dG and its standard deviation
- Return type
float, float
-
property
cpx_delta_g_forward
¶
-
property
cpx_delta_g_forward_analytical_std
¶
-
property
cpx_delta_g_forward_bootstrap_std
¶
-
property
cpx_delta_g_forward_df_per_replica
¶
-
property
cpx_delta_g_forward_dg
¶
-
property
cpx_delta_g_forward_err
¶
-
property
cpx_delta_g_reverse
¶
-
property
cpx_delta_g_reverse_err
¶
-
property
cpx_delta_g_sliding
¶
-
property
cpx_delta_g_sliding_err
¶
-
property
cpx_end_time_ns
¶
-
property
cpx_ensemble
¶
-
property
cpx_ff
¶
-
property
cpx_rest_exchanges
¶
-
property
cpx_salt_info
¶
-
property
cpx_salt_molecules
¶
-
property
cpx_sid_lp_results
¶
-
property
cpx_sid_number_of_frames
¶
-
property
cpx_sid_pl_results
¶
-
property
cpx_sid_protein_residues
¶ A list of protein residues that interact with both ligand1 and ligand2 throughout the simulation :rtype:
str
:return: a list of protein tags that interact with both ligand1 andligand2
-
property
cpx_sid_snapshot_times_ps
¶
-
property
cpx_sid_snashot_times_ps
¶
-
property
cpx_sid_trajectory_interval_ns
¶
-
property
cpx_sim_time
¶ Values returned in Ns (nanoseconds)
-
property
cpx_start_time_ns
¶
-
property
cpx_temperature
¶
-
property
cpx_timestep_interval
¶
-
property
cpx_timestep_list
¶
-
property
cpx_total_atoms
¶
-
property
cpx_total_replicas
¶
-
property
cpx_total_waters
¶
-
property
ddg_corrections_map
¶
-
property
ddg_corrections_sum
¶
-
property
delta_delta_g
¶
-
property
fep_simulation_details
¶
-
get_ligand1_atom_dict
()¶
-
get_ligand2_atom_dict
()¶
-
static
get_smiles
(st)¶ rtype: str return: Generate SMILES from a given ligand structure.
-
property
jobname
¶
-
property
leg1_name
¶
-
property
leg2_name
¶
-
property
ligand1_alchemical_atom_total
¶
-
property
ligand1_alchemical_mols
¶
-
property
ligand1_atomic_mass
¶
-
property
ligand1_charge
¶
-
property
ligand1_cpx_asl
¶
-
ligand1_cpx_sid_lighb
(stats=True)¶
-
ligand1_cpx_sid_molsa
(stats=True)¶
-
ligand1_cpx_sid_psa
(stats=True)¶
-
ligand1_cpx_sid_rb_strain
(stats=True)¶
-
ligand1_cpx_sid_rgyr
(stats=True)¶
-
ligand1_cpx_sid_rmsd
(stats=True)¶
-
ligand1_cpx_sid_sasa
(stats=True)¶
-
ligand1_cpx_sid_waters
(stats=True)¶
-
ligand1_fragments
(offset_by_receptor_natoms=True)¶
-
property
ligand1_hash
¶
-
property
ligand1_mol_formula
¶
-
property
ligand1_name
¶
-
property
ligand1_pdb_name
¶
-
property
ligand1_rot_bonds
¶
-
property
ligand1_smiles
¶
-
property
ligand1_sol_asl
¶
-
ligand1_sol_sid_lighb
(stats=True)¶
-
ligand1_sol_sid_molsa
(stats=True)¶
-
ligand1_sol_sid_psa
(stats=True)¶
-
ligand1_sol_sid_rb_strain
(stats=True)¶
-
ligand1_sol_sid_rgyr
(stats=True)¶
-
ligand1_sol_sid_rmsd
(stats=True)¶
-
ligand1_sol_sid_sasa
(stats=True)¶
-
property
ligand1_total_atoms
¶
-
property
ligand1_total_fragments
¶
-
property
ligand1_total_heavy
¶
-
property
ligand1_total_hot
¶
-
property
ligand1_total_rot_bonds
¶
-
property
ligand2_alchemical_atom_total
¶
-
property
ligand2_alchemical_mols
¶
-
property
ligand2_atomic_mass
¶
-
property
ligand2_charge
¶
-
property
ligand2_cpx_asl
¶
-
ligand2_cpx_sid_lighb
(stats=True)¶
-
ligand2_cpx_sid_molsa
(stats=True)¶
-
ligand2_cpx_sid_psa
(stats=True)¶
-
ligand2_cpx_sid_rb_strain
(stats=True)¶
-
ligand2_cpx_sid_rgyr
(stats=True)¶
-
ligand2_cpx_sid_rmsd
(stats=True)¶
-
ligand2_cpx_sid_sasa
(stats=True)¶
-
ligand2_cpx_sid_waters
(stats=True)¶
-
ligand2_fragments
(offset_by_receptor_natoms=True)¶
-
property
ligand2_hash
¶
-
property
ligand2_mol_formula
¶
-
property
ligand2_name
¶
-
property
ligand2_pdb_name
¶
-
property
ligand2_rot_bonds
¶
-
property
ligand2_smiles
¶
-
property
ligand2_sol_asl
¶
-
ligand2_sol_sid_lighb
(stats=True)¶
-
ligand2_sol_sid_molsa
(stats=True)¶
-
ligand2_sol_sid_psa
(stats=True)¶
-
ligand2_sol_sid_rb_strain
(stats=True)¶
-
ligand2_sol_sid_rgyr
(stats=True)¶
-
ligand2_sol_sid_rmsd
(stats=True)¶
-
ligand2_sol_sid_sasa
(stats=True)¶
-
property
ligand2_total_atoms
¶
-
property
ligand2_total_fragments
¶
-
property
ligand2_total_heavy
¶
-
property
ligand2_total_hot
¶
-
property
ligand2_total_rot_bonds
¶
-
static
ligand_name
(st)¶
-
property
pl_contact_data0
¶ A dictionary containing PL interactions for lambda=0
-
property
pl_contact_data1
¶ A dictionary containing PL interactions for lambda=1
-
property
pl_interaction_similarity_matrix0
¶ Protein-ligand interactions similarity matrix for lambda=0 sys for all available frames.
-
property
pl_interaction_similarity_matrix1
¶ Protein-ligand interactions similarity matrix for lambda=1 sys for all available frames.
-
static
protein_residue
(res)¶ Get data about the specified residue
- Parameters
res (
schrodinger.structure._Residue
) – The residue object to get data from- Returns
A namedtuple containing the molecule number, chain, residue name,
and residue number :rtype:
ResData
-
rate
(name: str) → schrodinger.application.desmond.fep_edge_data_classifier.Rating¶ Return rating for the FEP edge data with the given
name
. The valid names can be found in fep_edge_data_classifiers.py.
-
property
receptor_b_factor
¶ Return B factors grouped by residues using PDB tfactor values stored in the structure. If the PDB tfactor values are not present, return zeros.
-
property
receptor_chain_names
¶
-
property
receptor_charge
¶
-
property
receptor_residue_sequence_list
¶ Return a list of residue objects (ResData) in amino-to-carboxy order. :return: a list of residue objects, ordered N->C (amino to carboxy
tails).
- Return type
A residue tag looks like this: A:THR_124 (Chain:resname_resnum) if chain is not defined, use ‘_’ (underscore) :return: a list of residue tags :rtype:
residue_tag
-
property
receptor_residues_interaction_ligand1
¶ A list of preotein residues that interact just with ligand1 :rtype: list :return: list of protein residue tags
-
property
receptor_residues_interaction_ligand2
¶ A list of preotein residues that interact just with ligand2 :rtype: list :return: list of protein residue tags
-
property
receptor_sid_rmsd_backbone_lambda0
¶
-
property
receptor_sid_rmsd_backbone_lambda1
¶
-
property
receptor_sid_rmsd_ligand_lambda0
¶ ligand1 RMSD wrt the protein
-
property
receptor_sid_rmsd_ligand_lambda1
¶ ligand2 RMSD wrt the protein
-
property
receptor_title
¶
-
property
receptor_total_atom
¶
-
property
receptor_total_heavy
¶
-
property
receptor_total_residues
¶
-
property
receptor_total_residues_in_chains
¶
-
property
short_hash
¶
-
property
sol_charge
¶
-
property
sol_delta_g
¶ - Returns
dG and its standard deviation
- Return type
float, float
-
property
sol_delta_g_forward
¶
-
property
sol_delta_g_forward_analytical_std
¶
-
property
sol_delta_g_forward_bootstrap_std
¶
-
property
sol_delta_g_forward_df_per_replica
¶
-
property
sol_delta_g_forward_dg
¶
-
property
sol_delta_g_forward_err
¶
-
property
sol_delta_g_reverse
¶
-
property
sol_delta_g_reverse_err
¶
-
property
sol_delta_g_sliding
¶
-
property
sol_delta_g_sliding_err
¶
-
property
sol_end_time_ns
¶
-
property
sol_ensemble
¶
-
property
sol_ff
¶
-
property
sol_rest_exchanges
¶
-
property
sol_salt_info
¶
-
property
sol_salt_molecules
¶
-
property
sol_sid_number_of_frames
¶
-
property
sol_sid_snapshot_times_ps
¶
-
property
sol_sid_trajectory_interval_ns
¶
-
property
sol_sim_time
¶ Values returned in Ns (nanoseconds)
-
property
sol_start_time_ns
¶
-
property
sol_temperature
¶
-
property
sol_timestep_interval
¶
-
property
sol_timestep_list
¶
-
property
sol_total_atoms
¶
-
property
sol_total_replicas
¶
-
property
sol_total_waters
¶
-
property
sse_limits_lambda0
¶
-
property
sse_limits_lambda1
¶
-
-
class
schrodinger.application.desmond.fep_edge_data.
AbFEPEdgeData
(complex_sea, solvent_sea, pv_st=None, atom_mapping=None, perturbation_type='absolute_binding', ddg_corrections_map=None)[source]¶ Bases:
schrodinger.application.desmond.fep_edge_data.FEPEdgeData
This object stores Absolute Binding FEP related data.
-
__init__
(complex_sea, solvent_sea, pv_st=None, atom_mapping=None, perturbation_type='absolute_binding', ddg_corrections_map=None)[source]¶ - Parameters
complex_sea (
sea
) – SEA object with results pertaining to the complex leg of the FEP calculationsolvent_sea (
sea
) – SEA object with results pertaining to the solvent leg of the FEP calculationpv_st (
schrodinger.Structure
) – PoseViewer file must contain 3 structures, [receptor, lig1, lig2]atom_mapping (Dict[int, int]) – mapping of ligand2 to ligand1 atoms
See
FEPEdgeData
for definitions of other parameters.
-
property
fullsystem_ct
¶ - Return type
- Returns
The full system structure.
-
property
receptor_st
¶ - Return type
- Returns
The receptor structure.
-
property
ligand1_st
¶ - Return type
- Returns
The ligand1 structure.
-
property
ligand2_st
¶ - Return type
- Returns
The ligand2 structure.
-
property
ligand_torsions
¶ - Return type
(
FEPTorsionsContainer
object,FEPTorsionsContainer
object)- Returns
FEPTorsionsContainer
objects for lambda0 and lambda1.
-
property
ligand1_hash
¶
-
property
delta_delta_g
¶
-
property
cpx_sid_protein_residues
¶ A list of protein residues that interact with both ligand1 throughout the simulation :rtype:
str
:return: a list of protein tags that interact with ligand1
-
property
atom_mapping
¶
-
property
cpx_charge
¶
-
property
cpx_delta_g
¶ - Returns
dG and its standard deviation
- Return type
float, float
-
property
cpx_delta_g_forward
¶
-
property
cpx_delta_g_forward_analytical_std
¶
-
property
cpx_delta_g_forward_bootstrap_std
¶
-
property
cpx_delta_g_forward_df_per_replica
¶
-
property
cpx_delta_g_forward_dg
¶
-
property
cpx_delta_g_forward_err
¶
-
property
cpx_delta_g_reverse
¶
-
property
cpx_delta_g_reverse_err
¶
-
property
cpx_delta_g_sliding
¶
-
property
cpx_delta_g_sliding_err
¶
-
property
cpx_end_time_ns
¶
-
property
cpx_ensemble
¶
-
property
cpx_ff
¶
-
property
cpx_rest_exchanges
¶
-
property
cpx_salt_info
¶
-
property
cpx_salt_molecules
¶
-
property
cpx_sid_lp_results
¶
-
property
cpx_sid_number_of_frames
¶
-
property
cpx_sid_pl_results
¶
-
property
cpx_sid_snapshot_times_ps
¶
-
property
cpx_sid_snashot_times_ps
¶
-
property
cpx_sid_trajectory_interval_ns
¶
-
property
cpx_sim_time
¶ Values returned in Ns (nanoseconds)
-
property
cpx_start_time_ns
¶
-
property
cpx_temperature
¶
-
property
cpx_timestep_interval
¶
-
property
cpx_timestep_list
¶
-
property
cpx_total_atoms
¶
-
property
cpx_total_replicas
¶
-
property
cpx_total_waters
¶
-
property
ddg_corrections_map
¶
-
property
ddg_corrections_sum
¶
-
property
fep_simulation_details
¶
-
get_ligand1_atom_dict
()¶
-
get_ligand2_atom_dict
()¶
-
static
get_smiles
(st)¶ rtype: str return: Generate SMILES from a given ligand structure.
-
property
jobname
¶
-
property
leg1_name
¶
-
property
leg2_name
¶
-
property
ligand1_alchemical_atom_total
¶
-
property
ligand1_alchemical_mols
¶
-
property
ligand1_atomic_mass
¶
-
property
ligand1_charge
¶
-
property
ligand1_cpx_asl
¶
-
ligand1_cpx_sid_lighb
(stats=True)¶
-
ligand1_cpx_sid_molsa
(stats=True)¶
-
ligand1_cpx_sid_psa
(stats=True)¶
-
ligand1_cpx_sid_rb_strain
(stats=True)¶
-
ligand1_cpx_sid_rgyr
(stats=True)¶
-
ligand1_cpx_sid_rmsd
(stats=True)¶
-
ligand1_cpx_sid_sasa
(stats=True)¶
-
ligand1_cpx_sid_waters
(stats=True)¶
-
ligand1_fragments
(offset_by_receptor_natoms=True)¶
-
property
ligand1_mol_formula
¶
-
property
ligand1_name
¶
-
property
ligand1_pdb_name
¶
-
property
ligand1_rot_bonds
¶
-
property
ligand1_smiles
¶
-
property
ligand1_sol_asl
¶
-
ligand1_sol_sid_lighb
(stats=True)¶
-
ligand1_sol_sid_molsa
(stats=True)¶
-
ligand1_sol_sid_psa
(stats=True)¶
-
ligand1_sol_sid_rb_strain
(stats=True)¶
-
ligand1_sol_sid_rgyr
(stats=True)¶
-
ligand1_sol_sid_rmsd
(stats=True)¶
-
ligand1_sol_sid_sasa
(stats=True)¶
-
property
ligand1_total_atoms
¶
-
property
ligand1_total_fragments
¶
-
property
ligand1_total_heavy
¶
-
property
ligand1_total_hot
¶
-
property
ligand1_total_rot_bonds
¶
-
property
ligand2_alchemical_atom_total
¶
-
property
ligand2_alchemical_mols
¶
-
property
ligand2_atomic_mass
¶
-
property
ligand2_charge
¶
-
property
ligand2_cpx_asl
¶
-
ligand2_cpx_sid_lighb
(stats=True)¶
-
ligand2_cpx_sid_molsa
(stats=True)¶
-
ligand2_cpx_sid_psa
(stats=True)¶
-
ligand2_cpx_sid_rb_strain
(stats=True)¶
-
ligand2_cpx_sid_rgyr
(stats=True)¶
-
ligand2_cpx_sid_rmsd
(stats=True)¶
-
ligand2_cpx_sid_sasa
(stats=True)¶
-
ligand2_cpx_sid_waters
(stats=True)¶
-
ligand2_fragments
(offset_by_receptor_natoms=True)¶
-
property
ligand2_hash
¶
-
property
ligand2_mol_formula
¶
-
property
ligand2_name
¶
-
property
ligand2_pdb_name
¶
-
property
ligand2_rot_bonds
¶
-
property
ligand2_smiles
¶
-
property
ligand2_sol_asl
¶
-
ligand2_sol_sid_lighb
(stats=True)¶
-
ligand2_sol_sid_molsa
(stats=True)¶
-
ligand2_sol_sid_psa
(stats=True)¶
-
ligand2_sol_sid_rb_strain
(stats=True)¶
-
ligand2_sol_sid_rgyr
(stats=True)¶
-
ligand2_sol_sid_rmsd
(stats=True)¶
-
ligand2_sol_sid_sasa
(stats=True)¶
-
property
ligand2_total_atoms
¶
-
property
ligand2_total_fragments
¶
-
property
ligand2_total_heavy
¶
-
property
ligand2_total_hot
¶
-
property
ligand2_total_rot_bonds
¶
-
static
ligand_name
(st)¶
-
property
pl_contact_data0
¶ A dictionary containing PL interactions for lambda=0
-
property
pl_contact_data1
¶ A dictionary containing PL interactions for lambda=1
-
property
pl_interaction_similarity_matrix0
¶ Protein-ligand interactions similarity matrix for lambda=0 sys for all available frames.
-
property
pl_interaction_similarity_matrix1
¶ Protein-ligand interactions similarity matrix for lambda=1 sys for all available frames.
-
static
protein_residue
(res)¶ Get data about the specified residue
- Parameters
res (
schrodinger.structure._Residue
) – The residue object to get data from- Returns
A namedtuple containing the molecule number, chain, residue name,
and residue number :rtype:
ResData
-
rate
(name: str) → schrodinger.application.desmond.fep_edge_data_classifier.Rating¶ Return rating for the FEP edge data with the given
name
. The valid names can be found in fep_edge_data_classifiers.py.
-
property
receptor_b_factor
¶ Return B factors grouped by residues using PDB tfactor values stored in the structure. If the PDB tfactor values are not present, return zeros.
-
property
receptor_chain_names
¶
-
property
receptor_charge
¶
-
property
receptor_residue_sequence_list
¶ Return a list of residue objects (ResData) in amino-to-carboxy order. :return: a list of residue objects, ordered N->C (amino to carboxy
tails).
- Return type
A residue tag looks like this: A:THR_124 (Chain:resname_resnum) if chain is not defined, use ‘_’ (underscore) :return: a list of residue tags :rtype:
residue_tag
-
property
receptor_residues_interaction_ligand1
¶ A list of preotein residues that interact just with ligand1 :rtype: list :return: list of protein residue tags
-
property
receptor_residues_interaction_ligand2
¶ A list of preotein residues that interact just with ligand2 :rtype: list :return: list of protein residue tags
-
property
receptor_sid_rmsd_backbone_lambda0
¶
-
property
receptor_sid_rmsd_backbone_lambda1
¶
-
property
receptor_sid_rmsd_ligand_lambda0
¶ ligand1 RMSD wrt the protein
-
property
receptor_sid_rmsd_ligand_lambda1
¶ ligand2 RMSD wrt the protein
-
receptor_sid_rmsf_backbone_lambda0
¶ Decorator that converts a method with a single self argument into a property cached on the instance.
Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.
This class is based on code that is Copyright (c) Django Software Foundation
-
receptor_sid_rmsf_backbone_lambda1
¶ Decorator that converts a method with a single self argument into a property cached on the instance.
Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.
This class is based on code that is Copyright (c) Django Software Foundation
-
property
receptor_title
¶
-
property
receptor_total_atom
¶
-
property
receptor_total_heavy
¶
-
property
receptor_total_residues
¶
-
property
receptor_total_residues_in_chains
¶
-
property
short_hash
¶
-
property
sol_charge
¶
-
property
sol_delta_g
¶ - Returns
dG and its standard deviation
- Return type
float, float
-
property
sol_delta_g_forward
¶
-
property
sol_delta_g_forward_analytical_std
¶
-
property
sol_delta_g_forward_bootstrap_std
¶
-
property
sol_delta_g_forward_df_per_replica
¶
-
property
sol_delta_g_forward_dg
¶
-
property
sol_delta_g_forward_err
¶
-
property
sol_delta_g_reverse
¶
-
property
sol_delta_g_reverse_err
¶
-
property
sol_delta_g_sliding
¶
-
property
sol_delta_g_sliding_err
¶
-
property
sol_end_time_ns
¶
-
property
sol_ensemble
¶
-
property
sol_ff
¶
-
property
sol_rest_exchanges
¶
-
property
sol_salt_info
¶
-
property
sol_salt_molecules
¶
-
property
sol_sid_number_of_frames
¶
-
property
sol_sid_snapshot_times_ps
¶
-
property
sol_sid_trajectory_interval_ns
¶
-
property
sol_sim_time
¶ Values returned in Ns (nanoseconds)
-
property
sol_start_time_ns
¶
-
property
sol_temperature
¶
-
property
sol_timestep_interval
¶
-
property
sol_timestep_list
¶
-
property
sol_total_atoms
¶
-
property
sol_total_replicas
¶
-
property
sol_total_waters
¶
-
property
sse_limits_lambda0
¶
-
property
sse_limits_lambda1
¶
-
-
schrodinger.application.desmond.fep_edge_data.
parse_sea
(sea_obj)[source]¶ Given an ark object, parse the data
-
schrodinger.application.desmond.fep_edge_data.
get_ticks
(min_val, max_val, num_ticks)[source]¶ Return tick values and labels for an axis with the given min and max
- Parameters
min_val (float) – The minimum value on the axis
max_val (float) – The maximum value on the axis
num_ticks (int) – How many ticks to use on the axis
- Returns
tick values and tick labels
- Return type
list[float], list[str]