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
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 from
Returns: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
receptor_residue_sequence_tags

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

get_protein_residues_sequence_tags()
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 and

ligand2
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
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
wt_residue_sequence_tags

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
mut_residue_sequence_tags

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

get_protein_residues_sequence_tags()
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 and

ligand2
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 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.

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
receptor_residue_sequence_tags

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
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 and

ligand2
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_protein_residues_sequence_tags()
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 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.

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
receptor_residue_sequence_tags

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
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 and

ligand2
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()
get_protein_residues_sequence_tags()
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 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.

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
receptor_residue_sequence_tags

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]