schrodinger.application.desmond.fep_edge_data module¶
-
schrodinger.application.desmond.fep_edge_data.
water_mol
(respdb: str) → schrodinger.structure.structure.Structure¶ Return a water molecule CT.
-
schrodinger.application.desmond.fep_edge_data.
tag_protein
(proteinA, proteinB)¶ - 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]¶
-
class
schrodinger.application.desmond.fep_edge_data.
ResData
¶ Bases:
schrodinger.application.desmond.fep_edge_data.ResData
A class to store the molecule number, chain, name, and number of a residue
-
fullName
()¶ Return a string of the residue data formatted as chain:resname_resnum
Returns: The formatted residue data Return type: str
-
nameNum
()¶ Return the residue name and number formatted as resname_resnum
Returns: The formatted residue data Return type: str
-
__contains__
¶ Return key in self.
-
__init__
¶ Initialize self. See help(type(self)) for accurate signature.
-
__len__
¶ Return len(self).
-
chain
¶ Alias for field number 1
-
count
(value) → integer -- return number of occurrences of value¶
-
index
(value[, start[, stop]]) → integer -- 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)¶ 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)¶ Initialize self. See help(type(self)) for accurate signature.
-
sol_result
¶
-
cpx_result
¶
-
max_potential_energy
¶
-
potential_energy
¶ Returns potential energy that’s offset to zero
-
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
-
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
-
plot
(ax, color='gray', for_print=False, pot_tick_pos='right', hist_tick_pos='Bottom')¶
-
-
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')¶ 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')¶ Initialize self. See help(type(self)) for accurate signature.
-
matched_tors
¶
-
unmatched_tors
¶
-
all_tors
¶
-
matched_total
¶
-
unmatched_total
¶
-
tors_total
¶
-
-
class
schrodinger.application.desmond.fep_edge_data.
FEPEdgeData
(complex_sea, solvent_sea, pv_st=None, atom_mapping=None, perturbation_type='small_molecule', corrected_sol_dg=None)¶ 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', corrected_sol_dg=None)¶ Parameters: - complex_sea (
sea
) – SEA object with results pertaining to the complex leg of the FEP calculation - solvent_sea (
sea
) – SEA object with results pertaining to the solvent leg of the FEP calculation - pv_st (
schrodinger.Structure
) – PoseViewer file must contain 3 structures.. [receptor, lig1, lig2]; otherwise it’s None - atom_mapping (tuple(int, int)) – mapping of ligand2 to ligand1 atoms
- complex_sea (
-
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.
-
fep_simulation_details
¶
-
static
get_smiles
(st)¶ rtype: str return: Generate SMILES from a given ligand structure.
-
atom_mapping
¶
-
ligand1_fragments
(offset_by_receptor_natoms=True)¶
-
ligand2_fragments
(offset_by_receptor_natoms=True)¶
-
ligand1_sol_sid_rb_strain
(stats=True)¶
-
ligand2_sol_sid_rb_strain
(stats=True)¶
-
ligand1_cpx_sid_rb_strain
(stats=True)¶
-
ligand2_cpx_sid_rb_strain
(stats=True)¶
-
ligand_torsions
¶ Return type: ( FEPTorsionsContainer
object,FEPTorsionsContainer
object)Returns: FEPTorsionsContainer
objects for lambda0 and lambda1.
-
ligand1_cpx_sid_waters
(stats=True)¶
-
ligand2_cpx_sid_waters
(stats=True)¶
-
ligand1_sol_sid_lighb
(stats=True)¶
-
ligand2_sol_sid_lighb
(stats=True)¶
-
ligand1_cpx_sid_lighb
(stats=True)¶
-
ligand2_cpx_sid_lighb
(stats=True)¶
-
ligand1_sol_sid_sasa
(stats=True)¶
-
ligand2_sol_sid_sasa
(stats=True)¶
-
ligand1_cpx_sid_sasa
(stats=True)¶
-
ligand2_cpx_sid_sasa
(stats=True)¶
-
ligand1_sol_sid_molsa
(stats=True)¶
-
ligand2_sol_sid_molsa
(stats=True)¶
-
ligand1_cpx_sid_molsa
(stats=True)¶
-
ligand2_cpx_sid_molsa
(stats=True)¶
-
ligand1_sol_sid_psa
(stats=True)¶
-
ligand2_sol_sid_psa
(stats=True)¶
-
ligand1_cpx_sid_psa
(stats=True)¶
-
ligand2_cpx_sid_psa
(stats=True)¶
-
ligand1_sol_sid_rgyr
(stats=True)¶
-
ligand2_sol_sid_rgyr
(stats=True)¶
-
ligand1_cpx_sid_rgyr
(stats=True)¶
-
ligand2_cpx_sid_rgyr
(stats=True)¶
-
ligand1_sol_sid_rmsd
(stats=True)¶
-
ligand2_sol_sid_rmsd
(stats=True)¶
-
ligand1_cpx_sid_rmsd
(stats=True)¶
-
ligand2_cpx_sid_rmsd
(stats=True)¶
-
get_ligand1_atom_dict
()¶
-
get_ligand2_atom_dict
()¶
-
sse_limits_lambda0
¶
-
sse_limits_lambda1
¶
-
receptor_sid_rmsd_ligand_lambda0
¶ ligand1 RMSD wrt the protein
-
receptor_sid_rmsd_ligand_lambda1
¶ ligand2 RMSD wrt the protein
-
static
protein_residue
(res)¶ Get data about the specified residue
Parameters: res ( schrodinger.structure._Residue
) – The residue object to get data fromReturns: A namedtuple containing the molecule number, chain, residue name, and residue number :rtype:
ResData
-
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: ResData
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
-
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.
-
receptor_sid_rmsd_backbone_lambda0
¶
-
receptor_sid_rmsd_backbone_lambda1
¶
-
receptor_sid_rmsf_backbone_lambda0
¶
-
receptor_sid_rmsf_backbone_lambda1
¶
-
cpx_sid_lp_results
¶
-
pl_contact_data0
¶ A dictionary containing PL interactions for lambda=0
-
pl_contact_data1
¶ A dictionary containing PL interactions for lambda=1
-
pl_interaction_similarity_matrix0
¶ Protein-ligand interactions similarity matrix for lambda=0 sys for all available frames.
-
pl_interaction_similarity_matrix1
¶ Protein-ligand interactions similarity matrix for lambda=1 sys for all available frames.
-
fullsystem_ct
¶
-
cpx_sid_pl_results
¶
-
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
-
receptor_residues_interaction_ligand1
¶ A list of preotein residues that interact just with ligand1 :rtype: list :return: list of protein residue tags
-
receptor_residues_interaction_ligand2
¶ A list of preotein residues that interact just with ligand2 :rtype: list :return: list of protein residue tags
-
cpx_sid_trajectory_interval_ns
¶
-
sol_sid_trajectory_interval_ns
¶
-
cpx_sid_snashot_times_ps
¶
-
cpx_sid_snapshot_times_ps
¶
-
sol_sid_snapshot_times_ps
¶
-
cpx_sid_number_of_frames
¶
-
sol_sid_number_of_frames
¶
-
leg1_name
¶
-
leg2_name
¶
-
sol_timestep_list
¶
-
cpx_timestep_list
¶
-
sol_timestep_interval
¶
-
cpx_timestep_interval
¶
-
sol_delta_g_sliding_err
¶
-
cpx_delta_g_sliding_err
¶
-
sol_delta_g_sliding
¶
-
cpx_delta_g_sliding
¶
-
sol_delta_g_reverse_err
¶
-
cpx_delta_g_reverse_err
¶
-
sol_delta_g_reverse
¶
-
cpx_delta_g_reverse
¶
-
sol_delta_g_forward_err
¶
-
cpx_delta_g_forward_err
¶
-
sol_delta_g_forward_dg
¶
-
cpx_delta_g_forward_dg
¶
-
sol_delta_g_forward_bootstrap_std
¶
-
cpx_delta_g_forward_bootstrap_std
¶
-
sol_delta_g_forward_analytical_std
¶
-
cpx_delta_g_forward_analytical_std
¶
-
sol_delta_g_forward_df_per_replica
¶
-
cpx_delta_g_forward_df_per_replica
¶
-
sol_delta_g_forward
¶
-
cpx_delta_g_forward
¶
-
sol_end_time_ns
¶
-
cpx_end_time_ns
¶
-
sol_start_time_ns
¶
-
cpx_start_time_ns
¶
-
receptor_charge
¶
-
receptor_total_heavy
¶
-
receptor_total_atom
¶
-
receptor_title
¶
-
receptor_total_residues_in_chains
¶
-
receptor_chain_names
¶
-
receptor_total_residues
¶
-
ligand1_total_rot_bonds
¶
-
ligand2_total_rot_bonds
¶
-
ligand1_total_fragments
¶
-
ligand2_total_fragments
¶
-
ligand1_mol_formula
¶
-
ligand2_mol_formula
¶
-
ligand1_charge
¶
-
ligand2_charge
¶
-
ligand1_alchemical_mols
¶
-
ligand2_alchemical_mols
¶
-
ligand1_alchemical_atom_total
¶
-
ligand2_alchemical_atom_total
¶
-
ligand1_atomic_mass
¶
-
ligand2_atomic_mass
¶
-
ligand1_rot_bonds
¶
-
ligand2_rot_bonds
¶
-
ligand1_total_hot
¶
-
ligand2_total_hot
¶
-
ligand1_total_heavy
¶
-
ligand2_total_heavy
¶
-
ligand1_total_atoms
¶
-
ligand2_total_atoms
¶
-
ligand1_cpx_asl
¶
-
ligand2_cpx_asl
¶
-
ligand1_sol_asl
¶
-
ligand2_sol_asl
¶
-
ligand1_pdb_name
¶
-
ligand2_pdb_name
¶
-
ligand1_smiles
¶
-
ligand2_smiles
¶
-
static
ligand_name
(st)¶
-
ligand1_name
¶
-
ligand2_name
¶
-
short_hash
¶
-
ligand1_hash
¶
-
ligand2_hash
¶
-
jobname
¶
-
delta_delta_g
¶
-
sol_delta_g
¶ Returns: dG and its standard deviation Return type: float, float
-
sol_correction
¶
-
is_sol_dg_corrected
¶
-
cpx_delta_g
¶ Returns: dG and its standard deviation Return type: float, float
-
sol_total_replicas
¶
-
cpx_total_replicas
¶
-
sol_total_waters
¶
-
cpx_total_waters
¶
-
sol_total_atoms
¶
-
cpx_total_atoms
¶
-
sol_sim_time
¶ Values returned in Ns (nanoseconds)
-
cpx_sim_time
¶ Values returned in Ns (nanoseconds)
-
sol_temperature
¶
-
cpx_temperature
¶
-
sol_ff
¶
-
cpx_ff
¶
-
sol_ensemble
¶
-
cpx_ensemble
¶
-
sol_charge
¶
-
cpx_charge
¶
-
sol_salt_molecules
¶
-
cpx_salt_molecules
¶
-
sol_salt_info
¶
-
cpx_salt_info
¶
-
receptor_st
¶ Returns receptor structure
-
ligand1_st
¶ Returns ligand_1 structure
-
ligand2_st
¶ Returns ligand_2 structure
-
sol_rest_exchanges
¶
-
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)¶ 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)¶ Parameters: - complex_sea (
sea
) – SEA object with results pertaining to the complex leg of the FEP calculation - solvent_sea (
sea
) – SEA object with results pertaining to the solvent leg of the FEP calculation - pv_st (
schrodinger.Structure
) – PoseViewer file must contain 2 or 3 structures. [receptor, lig1, lig2]; otherwise it’s None - atom_mapping (
int
,int
) – mapping of ligand2 to ligand1 atoms - frag_atom_mapping (
int
,int
) – mapping of frag1 and frag2 atoms
- complex_sea (
-
wt_st
¶ Returns full structure of a WT protein
-
mut_st
¶ Returns full structure of a mutated protein
-
ligand1_st
¶ Returns ligand_1 structure
-
ligand2_st
¶ Returns ligand_2 structure
-
receptor_st
¶ Returns receptor structure
-
wt_frag_st
¶
-
mut_frag_st
¶
-
solvent_fullsystem_ct
¶
-
ligand_st_mol_formula
¶
-
prm_name
¶
-
receptor_sid_rmsf_backbone_lambda0
¶
-
receptor_sid_rmsf_backbone_lambda1
¶
-
ligand_torsions
¶ Return type: ( FEPTorsionsContainer
object,FEPTorsionsContainer
object)Returns: FEPTorsionsContainer
objects for lambda0 and lambda1.
-
static
peptide_name
(st)¶
-
wt_name
¶
-
mut_name
¶
-
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: ResData
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
-
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: ResData
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
-
cpx_sid_lp_results
¶
-
atom_mapping
¶
-
cpx_charge
¶
-
cpx_delta_g
¶ Returns: dG and its standard deviation Return type: float, float
-
cpx_delta_g_forward
¶
-
cpx_delta_g_forward_analytical_std
¶
-
cpx_delta_g_forward_bootstrap_std
¶
-
cpx_delta_g_forward_df_per_replica
¶
-
cpx_delta_g_forward_dg
¶
-
cpx_delta_g_forward_err
¶
-
cpx_delta_g_reverse
¶
-
cpx_delta_g_reverse_err
¶
-
cpx_delta_g_sliding
¶
-
cpx_delta_g_sliding_err
¶
-
cpx_end_time_ns
¶
-
cpx_ensemble
¶
-
cpx_ff
¶
-
cpx_rest_exchanges
¶
-
cpx_salt_info
¶
-
cpx_salt_molecules
¶
-
cpx_sid_number_of_frames
¶
-
cpx_sid_pl_results
¶
-
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
-
cpx_sid_snapshot_times_ps
¶
-
cpx_sid_snashot_times_ps
¶
-
cpx_sid_trajectory_interval_ns
¶
-
cpx_sim_time
¶ Values returned in Ns (nanoseconds)
-
cpx_start_time_ns
¶
-
cpx_temperature
¶
-
cpx_timestep_interval
¶
-
cpx_timestep_list
¶
-
cpx_total_atoms
¶
-
cpx_total_replicas
¶
-
cpx_total_waters
¶
-
delta_delta_g
¶
-
fep_simulation_details
¶
-
fullsystem_ct
¶
-
get_ligand1_atom_dict
()¶
-
get_ligand2_atom_dict
()¶
-
static
get_smiles
(st)¶ rtype: str return: Generate SMILES from a given ligand structure.
-
is_sol_dg_corrected
¶
-
jobname
¶
-
leg1_name
¶
-
leg2_name
¶
-
ligand1_alchemical_atom_total
¶
-
ligand1_alchemical_mols
¶
-
ligand1_atomic_mass
¶
-
ligand1_charge
¶
-
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)¶
-
ligand1_hash
¶
-
ligand1_mol_formula
¶
-
ligand1_name
¶
-
ligand1_pdb_name
¶
-
ligand1_rot_bonds
¶
-
ligand1_smiles
¶
-
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)¶
-
ligand1_total_atoms
¶
-
ligand1_total_fragments
¶
-
ligand1_total_heavy
¶
-
ligand1_total_hot
¶
-
ligand1_total_rot_bonds
¶
-
ligand2_alchemical_atom_total
¶
-
ligand2_alchemical_mols
¶
-
ligand2_atomic_mass
¶
-
ligand2_charge
¶
-
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)¶
-
ligand2_hash
¶
-
ligand2_mol_formula
¶
-
ligand2_name
¶
-
ligand2_pdb_name
¶
-
ligand2_rot_bonds
¶
-
ligand2_smiles
¶
-
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)¶
-
ligand2_total_atoms
¶
-
ligand2_total_fragments
¶
-
ligand2_total_heavy
¶
-
ligand2_total_hot
¶
-
ligand2_total_rot_bonds
¶
-
static
ligand_name
(st)¶
-
pl_contact_data0
¶ A dictionary containing PL interactions for lambda=0
-
pl_contact_data1
¶ A dictionary containing PL interactions for lambda=1
-
pl_interaction_similarity_matrix0
¶ Protein-ligand interactions similarity matrix for lambda=0 sys for all available frames.
-
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 fromReturns: 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.
-
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.
-
receptor_chain_names
¶
-
receptor_charge
¶
-
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: ResData
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
-
receptor_residues_interaction_ligand1
¶ A list of preotein residues that interact just with ligand1 :rtype: list :return: list of protein residue tags
-
receptor_residues_interaction_ligand2
¶ A list of preotein residues that interact just with ligand2 :rtype: list :return: list of protein residue tags
-
receptor_sid_rmsd_backbone_lambda0
¶
-
receptor_sid_rmsd_backbone_lambda1
¶
-
receptor_sid_rmsd_ligand_lambda0
¶ ligand1 RMSD wrt the protein
-
receptor_sid_rmsd_ligand_lambda1
¶ ligand2 RMSD wrt the protein
-
receptor_title
¶
-
receptor_total_atom
¶
-
receptor_total_heavy
¶
-
receptor_total_residues
¶
-
receptor_total_residues_in_chains
¶
-
short_hash
¶
-
sol_charge
¶
-
sol_correction
¶
-
sol_delta_g
¶ Returns: dG and its standard deviation Return type: float, float
-
sol_delta_g_forward
¶
-
sol_delta_g_forward_analytical_std
¶
-
sol_delta_g_forward_bootstrap_std
¶
-
sol_delta_g_forward_df_per_replica
¶
-
sol_delta_g_forward_dg
¶
-
sol_delta_g_forward_err
¶
-
sol_delta_g_reverse
¶
-
sol_delta_g_reverse_err
¶
-
sol_delta_g_sliding
¶
-
sol_delta_g_sliding_err
¶
-
sol_end_time_ns
¶
-
sol_ensemble
¶
-
sol_ff
¶
-
sol_rest_exchanges
¶
-
sol_salt_info
¶
-
sol_salt_molecules
¶
-
sol_sid_number_of_frames
¶
-
sol_sid_snapshot_times_ps
¶
-
sol_sid_trajectory_interval_ns
¶
-
sol_sim_time
¶ Values returned in Ns (nanoseconds)
-
sol_start_time_ns
¶
-
sol_temperature
¶
-
sol_timestep_interval
¶
-
sol_timestep_list
¶
-
sol_total_atoms
¶
-
sol_total_replicas
¶
-
sol_total_waters
¶
-
sse_limits_lambda0
¶
-
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)¶ 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)¶ Parameters: - complex_sea (
sea
) – SEA object with results pertaining to the complex leg of the FEP calculation - solvent_sea (
sea
) – SEA object with results pertaining to the solvent leg of the FEP calculation - pv_st (
schrodinger.Structure
) – PoseViewer file must contain 2 structures. [complex1, complex2]; otherwise it’s None - sol_st (solvent fragments tuple) – (
schrodinger.Structure
,schrodinger.Structure
) - atom_mapping (
int
,int
) – mapping of ligand2 to ligand1 atoms - frag_atom_mapping (
int
,int
) – mapping of frag1 and frag2 atoms
- complex_sea (
-
wt_st
¶ Returns full structure of a WT protein
-
mut_st
¶ Returns full structure of a mutated protein
-
receptor_st
¶ Returns receptor structure
-
ligand1_cpx_st
¶
-
ligand2_cpx_st
¶
-
ligand1_st
¶ Returns ligand_1 structure
-
ligand2_st
¶ Returns ligand_2 structure
-
solvent_fullsystem_ct
¶
-
receptor_sid_rmsf_backbone_lambda0
¶
-
receptor_sid_rmsf_backbone_lambda1
¶
-
ligand_torsions
¶ Return type: ( FEPTorsionsContainer
object,FEPTorsionsContainer
object)Returns: FEPTorsionsContainer
objects for lambda0 and lambda1.
-
receptor_title
¶
-
cpx_sid_lp_results
¶
-
get_ligand1_atom_dict
()¶
-
get_ligand2_atom_dict
()¶
-
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
)
-
cpx_charge
¶
-
cpx_delta_g
¶ Returns: dG and its standard deviation Return type: float, float
-
cpx_delta_g_forward
¶
-
cpx_delta_g_forward_analytical_std
¶
-
cpx_delta_g_forward_bootstrap_std
¶
-
cpx_delta_g_forward_df_per_replica
¶
-
cpx_delta_g_forward_dg
¶
-
cpx_delta_g_forward_err
¶
-
cpx_delta_g_reverse
¶
-
cpx_delta_g_reverse_err
¶
-
cpx_delta_g_sliding
¶
-
cpx_delta_g_sliding_err
¶
-
cpx_end_time_ns
¶
-
cpx_ensemble
¶
-
cpx_ff
¶
-
cpx_rest_exchanges
¶
-
cpx_salt_info
¶
-
cpx_salt_molecules
¶
-
cpx_sid_number_of_frames
¶
-
cpx_sid_pl_results
¶
-
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
-
cpx_sid_snapshot_times_ps
¶
-
cpx_sid_snashot_times_ps
¶
-
cpx_sid_trajectory_interval_ns
¶
-
cpx_sim_time
¶ Values returned in Ns (nanoseconds)
-
cpx_start_time_ns
¶
-
cpx_temperature
¶
-
cpx_timestep_interval
¶
-
cpx_timestep_list
¶
-
cpx_total_atoms
¶
-
cpx_total_replicas
¶
-
cpx_total_waters
¶
-
delta_delta_g
¶
-
fep_simulation_details
¶
-
fullsystem_ct
¶
-
static
get_smiles
(st)¶ rtype: str return: Generate SMILES from a given ligand structure.
-
is_sol_dg_corrected
¶
-
jobname
¶
-
leg1_name
¶
-
leg2_name
¶
-
ligand1_alchemical_atom_total
¶
-
ligand1_alchemical_mols
¶
-
ligand1_atomic_mass
¶
-
ligand1_charge
¶
-
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)¶
-
ligand1_hash
¶
-
ligand1_mol_formula
¶
-
ligand1_name
¶
-
ligand1_pdb_name
¶
-
ligand1_rot_bonds
¶
-
ligand1_smiles
¶
-
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)¶
-
ligand1_total_atoms
¶
-
ligand1_total_fragments
¶
-
ligand1_total_heavy
¶
-
ligand1_total_hot
¶
-
ligand1_total_rot_bonds
¶
-
ligand2_alchemical_atom_total
¶
-
ligand2_alchemical_mols
¶
-
ligand2_atomic_mass
¶
-
ligand2_charge
¶
-
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)¶
-
ligand2_hash
¶
-
ligand2_mol_formula
¶
-
ligand2_name
¶
-
ligand2_pdb_name
¶
-
ligand2_rot_bonds
¶
-
ligand2_smiles
¶
-
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)¶
-
ligand2_total_atoms
¶
-
ligand2_total_fragments
¶
-
ligand2_total_heavy
¶
-
ligand2_total_hot
¶
-
ligand2_total_rot_bonds
¶
-
static
ligand_name
(st)¶
-
pl_contact_data0
¶ A dictionary containing PL interactions for lambda=0
-
pl_contact_data1
¶ A dictionary containing PL interactions for lambda=1
-
pl_interaction_similarity_matrix0
¶ Protein-ligand interactions similarity matrix for lambda=0 sys for all available frames.
-
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 fromReturns: 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.
-
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.
-
receptor_chain_names
¶
-
receptor_charge
¶
-
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: ResData
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
-
receptor_residues_interaction_ligand1
¶ A list of preotein residues that interact just with ligand1 :rtype: list :return: list of protein residue tags
-
receptor_residues_interaction_ligand2
¶ A list of preotein residues that interact just with ligand2 :rtype: list :return: list of protein residue tags
-
receptor_sid_rmsd_backbone_lambda0
¶
-
receptor_sid_rmsd_backbone_lambda1
¶
-
receptor_sid_rmsd_ligand_lambda0
¶ ligand1 RMSD wrt the protein
-
receptor_sid_rmsd_ligand_lambda1
¶ ligand2 RMSD wrt the protein
-
receptor_total_atom
¶
-
receptor_total_heavy
¶
-
receptor_total_residues
¶
-
receptor_total_residues_in_chains
¶
-
short_hash
¶
-
sol_charge
¶
-
sol_correction
¶
-
sol_delta_g
¶ Returns: dG and its standard deviation Return type: float, float
-
sol_delta_g_forward
¶
-
sol_delta_g_forward_analytical_std
¶
-
sol_delta_g_forward_bootstrap_std
¶
-
sol_delta_g_forward_df_per_replica
¶
-
sol_delta_g_forward_dg
¶
-
sol_delta_g_forward_err
¶
-
sol_delta_g_reverse
¶
-
sol_delta_g_reverse_err
¶
-
sol_delta_g_sliding
¶
-
sol_delta_g_sliding_err
¶
-
sol_end_time_ns
¶
-
sol_ensemble
¶
-
sol_ff
¶
-
sol_rest_exchanges
¶
-
sol_salt_info
¶
-
sol_salt_molecules
¶
-
sol_sid_number_of_frames
¶
-
sol_sid_snapshot_times_ps
¶
-
sol_sid_trajectory_interval_ns
¶
-
sol_sim_time
¶ Values returned in Ns (nanoseconds)
-
sol_start_time_ns
¶
-
sol_temperature
¶
-
sol_timestep_interval
¶
-
sol_timestep_list
¶
-
sol_total_atoms
¶
-
sol_total_replicas
¶
-
sol_total_waters
¶
-
sse_limits_lambda0
¶
-
sse_limits_lambda1
¶
-
-
class
schrodinger.application.desmond.fep_edge_data.
MetalloproteinEdgeData
(complex_sea, solvent_sea, pv_st=None, atom_mapping=None, perturbation_type='metalloprotein')¶ 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')¶ Parameters: - complex_sea (
sea
) – SEA object with results pertaining to the complex leg of the FEP calculation - solvent_sea (
sea
) – SEA object with results pertaining to the solvent leg of the FEP calculation - pv_st (
schrodinger.Structure
) – PoseViewer file must contain 3 structures.. [receptor, lig1, lig2]; otherwise it’s None - atom_mapping (Dict[int, int]) – mapping of ligand2 to ligand1 atoms
- complex_sea (
-
fullsystem_ct
¶ Return type: schrodinger.structure.Structure
Returns: The full system structure.
-
receptor_st
¶ Return type: schrodinger.structure.Structure
Returns: The receptor structure.
-
ligand1_st
¶ Return type: schrodinger.structure.Structure
Returns: The ligand1 structure.
-
ligand2_st
¶ Return type: schrodinger.structure.Structure
Returns: The ligand2 structure.
-
ligand_torsions
¶ Return type: ( FEPTorsionsContainer
object,FEPTorsionsContainer
object)Returns: FEPTorsionsContainer
objects for lambda0 and lambda1.
-
receptor_sid_rmsf_backbone_lambda0
¶ Return type: List[float] Returns: The RMSF for each receptor residue in lambda0.
-
receptor_sid_rmsf_backbone_lambda1
¶ Return type: List[float] Returns: The RMSF for each receptor residue in lambda1.
-
atom_mapping
¶
-
cpx_charge
¶
-
cpx_delta_g
¶ Returns: dG and its standard deviation Return type: float, float
-
cpx_delta_g_forward
¶
-
cpx_delta_g_forward_analytical_std
¶
-
cpx_delta_g_forward_bootstrap_std
¶
-
cpx_delta_g_forward_df_per_replica
¶
-
cpx_delta_g_forward_dg
¶
-
cpx_delta_g_forward_err
¶
-
cpx_delta_g_reverse
¶
-
cpx_delta_g_reverse_err
¶
-
cpx_delta_g_sliding
¶
-
cpx_delta_g_sliding_err
¶
-
cpx_end_time_ns
¶
-
cpx_ensemble
¶
-
cpx_ff
¶
-
cpx_rest_exchanges
¶
-
cpx_salt_info
¶
-
cpx_salt_molecules
¶
-
cpx_sid_lp_results
¶
-
cpx_sid_number_of_frames
¶
-
cpx_sid_pl_results
¶
-
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
-
cpx_sid_snapshot_times_ps
¶
-
cpx_sid_snashot_times_ps
¶
-
cpx_sid_trajectory_interval_ns
¶
-
cpx_sim_time
¶ Values returned in Ns (nanoseconds)
-
cpx_start_time_ns
¶
-
cpx_temperature
¶
-
cpx_timestep_interval
¶
-
cpx_timestep_list
¶
-
cpx_total_atoms
¶
-
cpx_total_replicas
¶
-
cpx_total_waters
¶
-
delta_delta_g
¶
-
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.
-
is_sol_dg_corrected
¶
-
jobname
¶
-
leg1_name
¶
-
leg2_name
¶
-
ligand1_alchemical_atom_total
¶
-
ligand1_alchemical_mols
¶
-
ligand1_atomic_mass
¶
-
ligand1_charge
¶
-
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)¶
-
ligand1_hash
¶
-
ligand1_mol_formula
¶
-
ligand1_name
¶
-
ligand1_pdb_name
¶
-
ligand1_rot_bonds
¶
-
ligand1_smiles
¶
-
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)¶
-
ligand1_total_atoms
¶
-
ligand1_total_fragments
¶
-
ligand1_total_heavy
¶
-
ligand1_total_hot
¶
-
ligand1_total_rot_bonds
¶
-
ligand2_alchemical_atom_total
¶
-
ligand2_alchemical_mols
¶
-
ligand2_atomic_mass
¶
-
ligand2_charge
¶
-
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)¶
-
ligand2_hash
¶
-
ligand2_mol_formula
¶
-
ligand2_name
¶
-
ligand2_pdb_name
¶
-
ligand2_rot_bonds
¶
-
ligand2_smiles
¶
-
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)¶
-
ligand2_total_atoms
¶
-
ligand2_total_fragments
¶
-
ligand2_total_heavy
¶
-
ligand2_total_hot
¶
-
ligand2_total_rot_bonds
¶
-
static
ligand_name
(st)¶
-
pl_contact_data0
¶ A dictionary containing PL interactions for lambda=0
-
pl_contact_data1
¶ A dictionary containing PL interactions for lambda=1
-
pl_interaction_similarity_matrix0
¶ Protein-ligand interactions similarity matrix for lambda=0 sys for all available frames.
-
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 fromReturns: 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.
-
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.
-
receptor_chain_names
¶
-
receptor_charge
¶
-
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: ResData
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
-
receptor_residues_interaction_ligand1
¶ A list of preotein residues that interact just with ligand1 :rtype: list :return: list of protein residue tags
-
receptor_residues_interaction_ligand2
¶ A list of preotein residues that interact just with ligand2 :rtype: list :return: list of protein residue tags
-
receptor_sid_rmsd_backbone_lambda0
¶
-
receptor_sid_rmsd_backbone_lambda1
¶
-
receptor_sid_rmsd_ligand_lambda0
¶ ligand1 RMSD wrt the protein
-
receptor_sid_rmsd_ligand_lambda1
¶ ligand2 RMSD wrt the protein
-
receptor_title
¶
-
receptor_total_atom
¶
-
receptor_total_heavy
¶
-
receptor_total_residues
¶
-
receptor_total_residues_in_chains
¶
-
short_hash
¶
-
sol_charge
¶
-
sol_correction
¶
-
sol_delta_g
¶ Returns: dG and its standard deviation Return type: float, float
-
sol_delta_g_forward
¶
-
sol_delta_g_forward_analytical_std
¶
-
sol_delta_g_forward_bootstrap_std
¶
-
sol_delta_g_forward_df_per_replica
¶
-
sol_delta_g_forward_dg
¶
-
sol_delta_g_forward_err
¶
-
sol_delta_g_reverse
¶
-
sol_delta_g_reverse_err
¶
-
sol_delta_g_sliding
¶
-
sol_delta_g_sliding_err
¶
-
sol_end_time_ns
¶
-
sol_ensemble
¶
-
sol_ff
¶
-
sol_rest_exchanges
¶
-
sol_salt_info
¶
-
sol_salt_molecules
¶
-
sol_sid_number_of_frames
¶
-
sol_sid_snapshot_times_ps
¶
-
sol_sid_trajectory_interval_ns
¶
-
sol_sim_time
¶ Values returned in Ns (nanoseconds)
-
sol_start_time_ns
¶
-
sol_temperature
¶
-
sol_timestep_interval
¶
-
sol_timestep_list
¶
-
sol_total_atoms
¶
-
sol_total_replicas
¶
-
sol_total_waters
¶
-
sse_limits_lambda0
¶
-
sse_limits_lambda1
¶
-
-
schrodinger.application.desmond.fep_edge_data.
parse_sid
(obj_sea)¶
-
schrodinger.application.desmond.fep_edge_data.
parse_sea
(sea_obj)¶ Given an ark object, parse the data
-
schrodinger.application.desmond.fep_edge_data.
get_ticks
(min_val, max_val, num_ticks)¶ 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]