schrodinger.application.matsci.buildcomplex2d module¶

Utilities for the 2D-to-3D *sdf to *mae file conversion for a metal complex.

class schrodinger.application.matsci.buildcomplex2d.DummiesToHydrogens(st)¶

Bases: object

Context manager to temporarily convert dummy atoms to hydrogens.

__init__(st)¶

class schrodinger.application.matsci.buildcomplex2d.RemoveMetalBonds(st)¶

Bases: object

Context manager to temporarily remove bonds to the metal atom in a complex.

__init__(st)¶

exception schrodinger.application.matsci.buildcomplex2d.ComplexSdfToMaeException¶

Bases: Exception

__init__(*args, **kwargs)¶

args¶

with_traceback()¶: Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

class schrodinger.application.matsci.buildcomplex2d.ComplexSdfToMae(sdf_file, logger=None)¶

Bases: object

Manage the 2D-to-3D *sdf to *mae file conversion for a metal complex.

SD_PROP_PATTERN = re.compile('><(.*)>')¶

SD_PROP_STARTER = 's_sd_'¶

DUMMY_ATOMIC_NUMBER = -2¶

BIND_PROP = 'b_user_metal_neighbor'¶

HAPTIC_ATOM_PROP = 'b_user_haptic_atom'¶

__init__(sdf_file, logger=None)¶

Create an instance.

Parameters

sdf_file (str) – the 2D *sdf file
logger (logging.Logger or None) – output logger or None if there isn’t one

static read_sdf(sdf_file)¶

Wrapper to read an *sdf file.

Parameters: sdf_file (str) – the *sdf file
Raises: ComplexSdfToMaeException – if there is an issue
Return type: schrodinger.structure.Structure
Returns: the structure

getCenterIdx()¶

Return the atom index that serves as the complex center, typically a metal atom.

Raises: ComplexSdfToMaeException – if there is an issue
Return type: int
Returns: the atom index that serves as the complex center

prepare()¶: Prepare the structure.

addHydrogens(st)¶

Add hydrogens to the given structure.

Parameters: st (schrodinger.structure.Structure) – the structure

build()¶

Build the complex.

Raises: ComplexSdfToMaeException – if there is an issue
Return type: schrodinger.structure.Structure
Returns: the complex

fixRingSpears(st)¶

Fix ring-spears.

Parameters: st (schrodinger.structure.Structure) – the structure

updateProperties(st)¶

Update properties on the given structure.

Parameters: st (schrodinger.structure.Structure) – the structure

run()¶

Run.

Return type: schrodinger.structure.Structure
Returns: the structure

write(mae_file=None)¶

Write.

Parameters: mae_file (str) – the 3D *mae file
Return type: str
Returns: the 3D *mae file

sculptComplexBuild(sites=None, geometry=None, optimize=True)¶

Build the complex using sculpt complex.

Parameters

sites (list or None) – contains atom index pair tuples, the first index is for the atom that binds to the metal and is negated for eta-coordinated ligands, the second index is for the atom that represents the metal positioning relative to the ligand and is 0 for eta-coordinated ligands, the order of sites in this list determines the coordination geometry of the complex, if None an arbitrarily ordered list of sites will be determined from the structure
geometry (str or None) – the VSEPR geometry from the buildcomplex geometry constants, if None uses the sculpt complex convention of using the last geometry for a given number of slots coming from the order in buildcomplex.IDEAL_SLOTS
optimize (bool) – whether to perform a standard geometry optimization on the final sculpted complex

Raises

ComplexSdfToMaeException – if there is an issue

Return type

schrodinger.structure.Structure

Returns

the complex

buildComplexBuild()¶

Build the complex using build complex.

Raises: ComplexSdfToMaeException – if there is an issue
Return type: schrodinger.structure.Structure
Returns: the complex

static type_cast_sdf_file(sdf_file)¶

Type cast the 2D *sdf file.

Parameters: sdf_file (str) – the 2D *sdf file
Raises: argparse.ArgumentTypeError – is there is an issue
Return type: str
Returns: the 2D *sdf file

getAvailableGeometries(geometry=None)¶

Return the available geometries.

Parameters: geometry (str or None) – the specific coordination geometry to use, if not specified all available geometries will be considered
Raises: ComplexSdfToMaeException – if there is an issue
Return type: list[str]
Returns: contains available geometries

get3DIsomers(geometry=None, out_rep=None, epsilon=2)¶

Return 3D isomers.

Parameters

geometry (str or None) – the specific coordination geometry to use, if not specified all available geometries will be considered
out_rep (str or None) – if None then the conversion is to the opposite of the given representation, eta to centroid or centroid to eta, if a string then must be either module constant parserutils.CENTROID or parserutils.ETA in which case the conversion will always provide an output representation of the given type
epsilon (float) – the energy window in kcal/mol for binning isomers

Raises

ComplexSdfToMaeException – if there is an issue

Return type

list[schrodinger.structure.Structure]

Returns

contains 3D isomers

class schrodinger.application.matsci.buildcomplex2d.ComplexSdfToRxnWF(sdf_file, reference_rxnwf_file=None, handle_rotamers=True, logger=None)¶

Bases: schrodinger.application.matsci.buildcomplex2d.ComplexSdfToMae

Manage the 2D-to-3D *sdf to *_rxnwf_mae file conversion for a metal complex.

R_GROUP_SD_KEY_PATTERN = re.compile('R(\\d+)(.*)')¶

SITE_ATOM_KEY = 'i_matsci_Reaction_Workflow_Enumeration_Atom'¶

REPLACE_ATOM_SD_KEY = 'Replace Indices'¶

SUPERPOSITION_ATOM_SD_KEY = 'Superimpose Indices'¶

__init__(sdf_file, reference_rxnwf_file=None, handle_rotamers=True, logger=None)¶

Create an instance.

Parameters

sdf_file (str) – the 2D *sdf file
reference_rxnwf_file (str) – the reaction workflow file containing the reference structures, used for finding an optimal 3D geometry
handle_rotamers (bool) – whether to rotate mono-dentate haptic ligands containing superposition atoms such that they maximally overlap with the reference reaction workflow
logger (logging.Logger or None) – output logger or None if there isn’t one

static parse_novel_sdf_file(sdf_file)¶

Parse the novel 2D *sdf file.

Parameters: sdf_file (str) – the novel 2D *sdf file
Returns: list, list, list, list
Returns: (1) contains R-group file data as [R-group file, R-group index] pairs, (2) contains site data as [site “to” index, R-group index] pairs, (3) contains replace indicies, (4) contains superposition indices

static type_cast_novel_sdf_file(sdf_file)¶

Type cast the novel 2D *sdf file.

Parameters: sdf_file (str) – the novel 2D *sdf file
Raises: argparse.ArgumentTypeError – is there is an issue
Return type: str
Returns: the novel 2D *sdf file

updateProperties(st)¶

Update properties on the given structure.

Parameters: st (schrodinger.structure.Structure) – the structure

buildBestRotamer(nov_st)¶

Build the best rotamer:

Parameters: nov_st (schrodinger.structure.Structure) – the novel structure
Raises: ComplexSdfToMaeException – if there is an issue

run()¶

Run.

Return type: schrodinger.structure.Structure
Returns: the structure

write(rxnwf_file=None)¶

Write.

Parameters: rxnwf_file (str) – the 3D *_rxnwf.mae file
Return type: str, list
Returns: the 3D *_rxnwf.mae file, contains for each site a list of data [from_idx, to_idx, rgroup_idx]

BIND_PROP = 'b_user_metal_neighbor'¶

DUMMY_ATOMIC_NUMBER = -2¶

HAPTIC_ATOM_PROP = 'b_user_haptic_atom'¶

SD_PROP_PATTERN = re.compile('><(.*)>')¶

SD_PROP_STARTER = 's_sd_'¶

addHydrogens(st)¶

Add hydrogens to the given structure.

Parameters: st (schrodinger.structure.Structure) – the structure

build()¶

Build the complex.

Raises: ComplexSdfToMaeException – if there is an issue
Return type: schrodinger.structure.Structure
Returns: the complex

buildComplexBuild()¶

Build the complex using build complex.

Raises: ComplexSdfToMaeException – if there is an issue
Return type: schrodinger.structure.Structure
Returns: the complex

fixRingSpears(st)¶

Fix ring-spears.

Parameters: st (schrodinger.structure.Structure) – the structure

get3DIsomers(geometry=None, out_rep=None, epsilon=2)¶

Return 3D isomers.

Parameters

geometry (str or None) – the specific coordination geometry to use, if not specified all available geometries will be considered
out_rep (str or None) – if None then the conversion is to the opposite of the given representation, eta to centroid or centroid to eta, if a string then must be either module constant parserutils.CENTROID or parserutils.ETA in which case the conversion will always provide an output representation of the given type
epsilon (float) – the energy window in kcal/mol for binning isomers

Raises

ComplexSdfToMaeException – if there is an issue

Return type

list[schrodinger.structure.Structure]

Returns

contains 3D isomers

getAvailableGeometries(geometry=None)¶

Return the available geometries.

Parameters: geometry (str or None) – the specific coordination geometry to use, if not specified all available geometries will be considered
Raises: ComplexSdfToMaeException – if there is an issue
Return type: list[str]
Returns: contains available geometries

getCenterIdx()¶

Return the atom index that serves as the complex center, typically a metal atom.

Raises: ComplexSdfToMaeException – if there is an issue
Return type: int
Returns: the atom index that serves as the complex center

prepare()¶: Prepare the structure.

static read_sdf(sdf_file)¶

Wrapper to read an *sdf file.

Parameters: sdf_file (str) – the *sdf file
Raises: ComplexSdfToMaeException – if there is an issue
Return type: schrodinger.structure.Structure
Returns: the structure

sculptComplexBuild(sites=None, geometry=None, optimize=True)¶

Build the complex using sculpt complex.

Parameters

sites (list or None) – contains atom index pair tuples, the first index is for the atom that binds to the metal and is negated for eta-coordinated ligands, the second index is for the atom that represents the metal positioning relative to the ligand and is 0 for eta-coordinated ligands, the order of sites in this list determines the coordination geometry of the complex, if None an arbitrarily ordered list of sites will be determined from the structure
geometry (str or None) – the VSEPR geometry from the buildcomplex geometry constants, if None uses the sculpt complex convention of using the last geometry for a given number of slots coming from the order in buildcomplex.IDEAL_SLOTS
optimize (bool) – whether to perform a standard geometry optimization on the final sculpted complex

Raises

ComplexSdfToMaeException – if there is an issue

Return type

schrodinger.structure.Structure

Returns

the complex

static type_cast_sdf_file(sdf_file)¶

Type cast the 2D *sdf file.

Parameters: sdf_file (str) – the 2D *sdf file
Raises: argparse.ArgumentTypeError – is there is an issue
Return type: str
Returns: the 2D *sdf file

schrodinger.application.matsci.buildcomplex2d.convert_sdf_to_rxnwf(sdf_file, reference_rxnwf_file, handle_rotamers=True, output_rxnwf_file_name=None, logger=None)¶

Convert the given single structure 2D *sdf file to a 3D *_rxnwf.mae file.

Parameters

sdf_file (str) – the *sdf file
reference_rxnwf_file (str) – the reaction workflow file containing the reference structures, used for finding an optimal 3D geometry
handle_rotamers (bool) – whether to rotate mono-dentate haptic ligands containing superposition atoms such that they maximally overlap with the reference reaction workflow
output_rxnwf_file_name (str) – the output reaction workflow file name
logger (logging.Logger or None) – output logger or None if there isn’t one

Return type

str, list, list

Returns

(1) the 3D *_rxnwf.mae file, (2) contains R-group file data as [R-group file, R-group index] pairs, (3) contains for each site a list of data [from_idx, to_idx, rgroup_idx]

schrodinger.application.matsci.buildcomplex2d.get_3d_isomers(sdf_file, geometry=None, out_rep=None, epsilon=2, logger=None)¶

Return 3D isomers for the given 2D *sdf file of a transition metal complex.

Parameters

sdf_file (str) – the *sdf file
geometry (str or None) – the specific coordination geometry to use, if not specified all available geometries will be considered
out_rep (str or None) – if None then the conversion is to the opposite of the given representation, eta to centroid or centroid to eta, if a string then must be either module constant parserutils.CENTROID or parserutils.ETA in which case the conversion will always provide an output representation of the given type
epsilon (float) – the energy window in kcal/mol for binning isomers
logger (logging.Logger or None) – output logger or None if there isn’t one

Return type

list[schrodinger.structure.Structure]

Returns

contains 3D isomers