schrodinger.infra.mm module¶

Python-level wrappers for the SWIG-wrapped C and C++ functions.

This module exists to make use of pymmlibs a bit easier and provides access to all functions and constants present in that module.

It adds a layer of automatic error checking to the SWIG wrapped mmlib functions. Instead of returning function return values to the user, the values are checked for indication of failure. If a failure occurs, an MmException is raised. (The underlying return code can be accessed as the ‘rc’ attribute of an MmException.) If a failure does not occur, the caller will not see the mmlib function return value at all.

To access the mmlibs functions in their “pure” form (i.e. the basic SWIG wrapped functions without automatic error checking) use the pymmlibs module, which can be imported with ‘import pymmlibs’.

To call mmlibs functions from python, use input arguments of the appropriate type. Output arguments will be returned as function return values. In the event that there are multiple output arguments, a tuple of these values will be returned. (If you are using functions from the pymmlibs module, the first value in your return tuple will always be the return value of the C function.)

Some mmlibs debugging and profiling niceties are provided through this module. For debugging python calls to mmlibs, you can set SCHRODINGER_PYTHON_MMLIBS_TRACE to any non-null value to get a debug-level logger that prints every call to a wrapped mmlibs function. For assistance in profiling, set SCHRODINGER_PYTHON_CPROFILE to a non-null value. This will set up an additional wrapper with a unique name for each mmlib function so they can be attributed in profiles run via the cProfile module. Without SCHRODINGER_PYTHON_CPROFILE, all mmlibs calls will be attributed to the _Wrapper.__call__ method.

NOTE: If a unittest.mock.MagicMock object is passed to a wrapped C++ api, the mock object’s magic methods (e.g., __int__, __bool__, __float__, and __complex__) could provide valid inputs to the C++ api, which would result in undefined behavior.

class schrodinger.infra.mm.CaptureMMErr¶

property messages¶

class schrodinger.infra.mm.Cartesian¶

__init__(*args, **kwargs)¶

static angle(a, b, c, norm_threshold=0.0) → double¶

apply(self, func) → Cartesian¶

as_unit_vector(self) → Cartesian¶

cross(self, c) → Cartesian¶

static dihedral(a, b, c, d) → double¶

static distance(c1, c2) → double¶

magnitude(self) → double¶

map(self, func) → Cartesian¶

scale_to_unit_magnitude(self) → Cartesian¶

sq(self) → double¶

static square_distance(c1, c2) → double¶

to_array(self) → std::array< double,3 >¶

to_vector(self) → std::vector< double,std::allocator< double > >¶

x¶

y¶

z¶

zero(self) → Cartesian¶

schrodinger.infra.mm.Cartesian_angle(a, b, c, norm_threshold=0.0) → double¶

schrodinger.infra.mm.Cartesian_dihedral(a, b, c, d) → double¶

schrodinger.infra.mm.Cartesian_distance(c1, c2) → double¶

schrodinger.infra.mm.Cartesian_square_distance(c1, c2) → double¶

class schrodinger.infra.mm.FFBundleVersionData¶

schrodinger::forcefield::FFBundleVersionData

__init__(*args, **kwargs)¶

archive_filename¶

opls_version¶

spff_version¶

class schrodinger.infra.mm.FFVersionData¶

schrodinger::forcefield::FFVersionData

__init__(*args, **kwargs)¶

display_name¶

version_major¶

version_minor¶

version_patch¶

class schrodinger.infra.mm.FfldSpec¶

schrodinger::forcefield::FfldSpec

__init__(*args, **kwargs)¶

custom_path¶

installation_path¶

version¶

class schrodinger.infra.mm.FitParamInfo¶

schrodinger::forcefield::FitParamInfo

__init__(*args, **kwargs)¶

opls¶

types¶

vs¶

class schrodinger.infra.mm.LigandParameters¶

::LigandParameters

__init__(*args, **kwargs)¶

allow_amino_acid_only_molecules¶

allow_ion_only_molecules¶

allow_nucleic_acid_only_molecules¶

excluded_residue_names¶

included_residue_names¶

max_atom_count¶

min_heavy_atom_count¶

class schrodinger.infra.mm.LigandScoreStructure¶

::LigandScoreStructure

__init__(*args, **kwargs)¶

getGradient(self, wm_st) → double¶

getNumLigandAtom(self) → int¶

getNumSite(self) → int¶

getOverlapSite(self)¶

getScore(self) → double¶

getTdSLigandAtom(self)¶

getTdSSite(self)¶

getdGLigandAtom(self)¶

getdGSite(self)¶

getdHLigandAtom(self)¶

getdHSite(self)¶

schrodinger.infra.mm.MMCOUNTBITS32(n) → unsigned int¶

schrodinger.infra.mm.MMCOUNTBITS64(n) → unsigned int¶

class schrodinger.infra.mm.MMFfldAssign¶

schrodinger::forcefield::MMFfldAssign

__init__(*args, **kwargs)¶

class schrodinger.infra.mm.MMFfldEsp¶

schrodinger::forcefield::MMFfldEsp

__init__(*args, **kwargs)¶

addRmsdPropToCT(self, rmse, ffld_version, ct, ct_with_virt)¶

fillWeightedDiffList(self, weighted_diff_list, atomic_charges)¶

getMmVsQmRmse(self, atomic_charges) → double¶

m_esp_data¶

m_xyz¶

overwriteQmEspFromCharges(self, charge_list)¶

class schrodinger.infra.mm.MMFfldEspData¶

schrodinger::forcefield::MMFfldEspData

__init__(*args, **kwargs)¶

grid¶

qm_potential¶

weights¶

class schrodinger.infra.mm.MMFfldHandle¶

schrodinger::forcefield::MMFfldHandle

__init__(*args, **kwargs)¶

getHandle(self) → int¶

setOption(self, option, value)¶

class schrodinger.infra.mm.MMFfldInitializer¶

schrodinger::forcefield::MMFfldInitializer

__init__(*args, **kwargs)¶

class schrodinger.infra.mm.MMFileContext¶

::MMFileContext

__init__(*args, **kwargs)¶

class schrodinger.infra.mm.MMFragHandle¶

__init__(*args, **kwargs)¶

getHandle(self) → MMFrag_Handle¶

getStructure(self) → schrodinger::Structure¶

releaseOwnership(self)¶

setFragment(self, frag_name)¶

class schrodinger.infra.mm.MMPREF¶

::MMPREF

__init__(*args, **kwargs)¶

beginGroup(self, suffix) → MMpref_Err¶

beginOsAttribute(self, iplat=MMPREF_NONE)¶

clearSettings(self)¶

endGroup(self)¶

endOsAttribute(self)¶

get(self, key, i) → MMpref_Err¶
get(self, key, d) → MMpref_Err
get(self, key, s) → MMpref_Err
get(self, key, b) → MMpref_Err

getBool(self, key, bval) → MMpref_Err¶
getBool(self, key, bval, bdefval) → MMpref_Err

getBoolList(self, groupname, bkeyvalue) → MMpref_Err¶

getDouble(self, key) → MMpref_Err¶
getDouble(self, key, ddefval) → MMpref_Err

getDoubleList(self, groupname, dkeyvalue) → MMpref_Err¶

getGroup(self) → std::string¶

getInt(self, key, val) → MMpref_Err¶
getInt(self, key, idefval) → MMpref_Err

getIntList(self, groupname, ikeyvalue) → MMpref_Err¶

getKeySource(self, key) → MMPrefSource¶

getSettingsFile(self, sfallbackfile)¶

getString(self, key, sval) → MMpref_Err¶
getString(self, key, sval, sdefval) → MMpref_Err

getStringList(self, groupname, skeyvalue) → MMpref_Err¶

getSubgroups(self, subgroups, level=0) → int¶

getType(self, key) → MMPREF_TYPE¶

hasKey(self, key, type) → MMpref_Err¶
hasKey(self, key) → MMpref_Err

removeKey(self, key, type=MMPREF_TYPE_NONE) → int¶

set(self, key, val, comment='') → MMpref_Err¶

syncSettings(self) → MMpref_Err¶

class schrodinger.infra.mm.MetadataCompatibility¶

FULL = 0¶

MAJOR_ONLY = 1¶

MAJOR_MISMATCH = 2¶

class schrodinger.infra.mm.MetalSupportStatus¶

schrodinger::forcefield::MetalSupportStatus

__init__(*args, **kwargs)¶

is_supported¶

unsupported_atoms¶

class schrodinger.infra.mm.MinimizeResults¶

schrodinger::forcefield::MinimizeResults

__init__(*args, **kwargs)¶

converged¶

potential_energy¶

rms_derivative¶

exception schrodinger.infra.mm.MmException(wrapped_function, args, rc)¶

An exception class that specifically indicates the failure of an mmlibs call. The underlying value of the error code returned by the mmlib function can be retrieved through the ‘rc’ attribute of the exception. The name of the return code can be retrieved through the ‘rc_name’ attribute of the exception.

__init__(wrapped_function, args, rc)¶: Initialize with the wrapped function, arguments used, and the return code.

class schrodinger.infra.mm.OPLSArchive¶

schrodinger::forcefield::OPLSArchive

__init__(*args, **kwargs)¶

add(self, datafile_path)¶
add(self, parameter_data, datafile) → None

contains(self, datafile) → bool¶

static create(archive_path) → OPLSArchive¶

empty(self) → bool¶

extractOPLS2005Files(self, output_dir)¶

getFilename(self) → boost::filesystem::path¶

static isCompatible(archive_path) → bool¶

merge(self, datafile_path)¶

merge_archive(self, src_archive_path)¶

remove(self, datafile)¶

static upgrade(archive_path)¶

static validate(archive_path)¶

class schrodinger.infra.mm.OPLSArchiveError¶

schrodinger::forcefield::OPLSArchiveError

__init__(*args, **kwargs)¶

schrodinger.infra.mm.OPLSArchive_create(archive_path) → OPLSArchive¶

schrodinger.infra.mm.OPLSArchive_isCompatible(archive_path) → bool¶

schrodinger.infra.mm.OPLSArchive_upgrade(archive_path)¶

schrodinger.infra.mm.OPLSArchive_validate(archive_path)¶

class schrodinger.infra.mm.OPLSDatafile¶

schrodinger::forcefield::OPLSDatafile

__init__(*args, **kwargs)¶

type(self) → schrodinger::forcefield::OPLSDatafileType¶

version(self) → std::optional< schrodinger::forcefield::OPLSVersion >¶

class schrodinger.infra.mm.OPLSDatafileType¶

METAFILE_JSON = 0¶

ASSIGN_METAL_PROPERTIES_TYPE = 1¶

CONFGEN_TORSION_TYPE = 2¶

CONF_CLEANUP_TORSION_TYPE = 3¶

DEFAULTS = 4¶

STRETCH_DEFAULT_DATA = 5¶

STRUCTURE_PREP_GEOMETRIC_RULES = 6¶

BCC_OVERWRITE_TYPE = 7¶

BEND_DAT = 8¶

BEND_INDEX_DAT = 9¶

CMAP_DAT = 10¶

CMAP_TYPE = 11¶

CONSOLV_TYPE = 12¶

DEFAULTS_DAT = 13¶

EXPONENTIAL_REP_DAT = 14¶

IMPROPER_TORSIONS_DAT = 15¶

METAL_COMPLEX_SETUP = 16¶

OPLSAA_BCC = 17¶

OPLSAA_BCI = 18¶

OPLSAA_NOSORT_TYPE = 19¶

OPLSAA_SIMIL_TBL = 20¶

OPLSAA_TYPE = 21¶

OPLSAA_VDW = 22¶

SGBNP_PARAM = 23¶

SPECIAL_SYMBOL_TYPE = 24¶

SPREAD_FORMAL_CHARGE_DAT = 25¶

SPREAD_ZOB_FORMAL_CHARGE_DAT = 26¶

STRETCH_DAT = 27¶

STRETCH_INDEX_DAT = 28¶

SYMBOL_COMPRESSION_DAT = 29¶

TORSION_DAT = 30¶

TORSION_INDEX_DAT = 31¶

UTT_BOND_INDEX_TYPE = 32¶

UTT_DAT = 33¶

VIRTUAL_SITE_TYPE = 34¶

POLARIZABILITY = 35¶

OPLS_M = 36¶

class schrodinger.infra.mm.OPLSVersion¶

F14 = 14¶

F16 = 16¶

F17 = 17¶

class schrodinger.infra.mm.OPLSVersionHash¶

schrodinger::forcefield::OPLSVersionHash

__init__(*args, **kwargs)¶

class schrodinger.infra.mm.Preferences¶

__init__(*args, **kwargs)¶

clear(self)¶

hasKey(self, key) → bool¶

removeKey(self, key)¶

class schrodinger.infra.mm.RedirectMmerrToPythonStderr¶

schrodinger::mmlibs::RedirectMmerrToPythonStderr

__init__(*args, **kwargs)¶

close(self)¶

class schrodinger.infra.mm.ScoreAtom¶

::ScoreAtom

__init__(*args, **kwargs)¶

is_hydrogen¶

vdw_radius¶

x¶

y¶

z¶

class schrodinger.infra.mm.UTT¶

::UTT

__init__(*args, **kwargs)¶

addParam(self, spec)¶

atom1¶

atom2¶

canonicalize(self)¶

central_bt¶

comment¶

end_atoms1¶

end_atoms2¶

getDefinitionString(self) → std::string¶

info¶

matched¶

opt¶

quality¶

regular_torsion¶

reverseOrder(self)¶

scl14type¶

updateSymbolNumbers(self, fcn)¶

utt_par¶

utt_reverse_order¶

class schrodinger.infra.mm.UTTAtom¶

::UTTAtom

__init__(*args, **kwargs)¶

atom_idx¶

symbol¶

symbol_num¶

updateSymbolNumber(self, fcn)¶

class schrodinger.infra.mm.UTTDefSpec¶

::UTTDefSpec

__init__(*args, **kwargs)¶

comment¶

def_str¶

info¶

opt¶

quality¶

scl14type¶

class schrodinger.infra.mm.UTTEndAtom¶

::UTTEndAtom

__init__(*args, **kwargs)¶

bt¶

invariant(self) → bond_index_t¶

class schrodinger.infra.mm.UTTParamSpec¶

::UTTParamSpec

__init__(*args, **kwargs)¶

bt0¶

bt3¶

comment¶

sym0¶

sym3¶

v¶

class schrodinger.infra.mm.UTTParameter¶

::UTTParameter

__init__(*args, **kwargs)¶

comment¶

end_atom0¶

end_atom3¶

v¶

class schrodinger.infra.mm.UTTPolicy¶

ALL = 0¶

FROM_TORS_ATOMS_ONLY = 1¶

class schrodinger.infra.mm.UnpairedElectronsReplacementMode¶

LeaveUnspecified = 0¶

ExplicitHydrogens = 1¶

SetAsCharge = 2¶

class schrodinger.infra.mm.WaterMapAtom¶

::WaterMapAtom

__init__(*args, **kwargs)¶

energy¶

entropy¶

free_energy¶

occupancy¶

vdw_radius¶

x¶

y¶

z¶

class schrodinger.infra.mm.WaterMapAtomList¶

std::vector< WaterMapAtom >

__init__(*args, **kwargs)¶

__len__()¶: Return len(self).

append(self, x)¶

assign(self, n, x)¶

back(self) → WaterMapAtom¶

begin(self) → std::vector< WaterMapAtom >::iterator¶

capacity(self) → std::vector< WaterMapAtom >::size_type¶

clear(self)¶

empty(self) → bool¶

end(self) → std::vector< WaterMapAtom >::iterator¶

erase(self, pos) → std::vector< WaterMapAtom >::iterator¶
erase(self, first, last) → std::vector< WaterMapAtom >::iterator

front(self) → WaterMapAtom¶

get_allocator(self) → std::vector< WaterMapAtom >::allocator_type¶

insert(self, pos, x) → std::vector< WaterMapAtom >::iterator¶
insert(self, pos, n, x) → None

iterator(self) → SwigPyIterator¶

pop(self) → WaterMapAtom¶

pop_back(self)¶

push_back(self, x)¶

rbegin(self) → std::vector< WaterMapAtom >::reverse_iterator¶

rend(self) → std::vector< WaterMapAtom >::reverse_iterator¶

reserve(self, n)¶

resize(self, new_size)¶
resize(self, new_size, x) → None

size(self) → std::vector< WaterMapAtom >::size_type¶

swap(self, v)¶

class schrodinger.infra.mm.WaterMapStructure¶

::WaterMapStructure

__init__(*args, **kwargs)¶

atom¶

continuous(self) → bool¶

schrodinger.infra.mm.assert_development_license_exists()¶

schrodinger.infra.mm.changeParameterValuesByIndex(mmffld_id, paramtype, index, parameter_list) → MMFfldStatus¶

schrodinger.infra.mm.current_opls_metadata() → std::string¶

schrodinger.infra.mm.development_license_exists() → bool¶

schrodinger.infra.mm.ffld_main_licenses_exist(version) → bool¶

schrodinger.infra.mm.ffld_spec_to_string(ffld_spec) → std::string¶

schrodinger.infra.mm.find_ligand_atoms(ct, params) → MM_Bitset¶

schrodinger.infra.mm.find_ligand_molecules(ct, params) → std::vector< std::vector< int,std::allocator< int > >,std::allocator< std::vector< int,std::allocator< int > > > >¶

schrodinger.infra.mm.get_OPLS_data_filename(opls_dir, version, data_file_basename='utt.dat') → std::string¶

schrodinger.infra.mm.get_OPLS_data_subdirectory(opls_dir, version) → std::string¶

schrodinger.infra.mm.get_angle_between_two_vectors(vector1, vector2) → double¶

schrodinger.infra.mm.get_archive_path(oplsdir) → boost::filesystem::path¶

schrodinger.infra.mm.get_compatible_archive_path(oplsdir) → boost::filesystem::path¶

schrodinger.infra.mm.get_current_OPLS_data_filename(opls_dir, data_file_basename='utt.dat') → std::string¶

schrodinger.infra.mm.get_current_OPLS_data_subdirectory(opls_dir) → std::string¶

schrodinger.infra.mm.get_dihedral(bond2_1, bond2_3, bond2_4) → double¶

schrodinger.infra.mm.get_ffld_spec(version, archive_path='') → FfldSpec¶

schrodinger.infra.mm.get_ligand_parameters() → LigandParameters¶

schrodinger.infra.mm.get_localhost_temp_dir() → std::string¶

schrodinger.infra.mm.get_mmshare_data_directory() → std::string¶

schrodinger.infra.mm.get_normal_vector_to_three_points(point1, point2, point3) → Cartesian¶

schrodinger.infra.mm.get_opls_metadata_compatibility(metadata, version) → schrodinger::forcefield::MetadataCompatibility¶

schrodinger.infra.mm.get_preference_custom_opls_path() → std::string¶

schrodinger.infra.mm.get_preference_most_recent_custom_opls_paths() → std::vector< std::string,std::allocator< std::string > >¶

schrodinger.infra.mm.get_preference_opls_version(allow_opls5=False) → schrodinger::forcefield::OPLSVersion¶

schrodinger.infra.mm.get_preference_use_custom_opls() → bool¶

schrodinger.infra.mm.get_schrodinger_temp_dir() → std::string¶

schrodinger.infra.mm.get_structure_UTTs(mmffld_handle, st, policy=ALL) → std::vector< UTT,std::allocator< UTT > >¶

schrodinger.infra.mm.get_torsion_fit_info(mmffld_id, ct) → FitParamInfo¶

schrodinger.infra.mm.installation_archive_path() → boost::filesystem::path¶

schrodinger.infra.mm.int_to_opls_version(version) → schrodinger::forcefield::OPLSVersion¶

schrodinger.infra.mm.is_valid_opls_directory(oplsdir) → bool¶

schrodinger.infra.mm.ligprep3_refcount() → int¶

schrodinger.infra.mm.make_metal_force_field_manager(ffld_version, archive_path) → schrodinger::energy::MetalForceFieldManager¶

schrodinger.infra.mm.make_metal_force_field_manager_from_ffld_spec(ffld_spec) → schrodinger::energy::MetalForceFieldManager¶

schrodinger.infra.mm.make_metal_force_field_manager_from_mmffld_handle(mmffld_handle) → schrodinger::energy::MetalForceFieldManager¶

schrodinger.infra.mm.minimization_license_exists() → bool¶

schrodinger.infra.mm.mmalign_get_aligned_sequence(alignment, nth_aligned_seq) → MMsequence¶

schrodinger.infra.mm.mmalign_get_end_position(alignment, nth_aligned_seq) → int¶

schrodinger.infra.mm.mmalign_get_evalue(alignment, nth_aligned_seq) → double¶

schrodinger.infra.mm.mmalign_get_num_aligned_sequences(alignment) → int¶

schrodinger.infra.mm.mmalign_get_percent_gaps(alignment, nth_aligned_seq) → int¶

schrodinger.infra.mm.mmalign_get_percent_identity(alignment, nth_aligned_seq) → int¶

schrodinger.infra.mm.mmalign_get_percent_positive(alignment, nth_aligned_seq) → int¶

schrodinger.infra.mm.mmalign_get_query_sequence(alignment) → MMsequence¶

schrodinger.infra.mm.mmalign_get_score(alignment, nth_aligned_seq) → double¶

schrodinger.infra.mm.mmalign_get_start_position(alignment, nth_aligned_seq) → int¶

schrodinger.infra.mm.mmalign_in_use(alignment) → MMbool¶

schrodinger.infra.mm.mmat_get_atom_type(arg1) → int¶

schrodinger.infra.mm.mmat_get_central_geometry(arg1) → int¶

schrodinger.infra.mm.mmat_get_color(arg1) → int¶

schrodinger.infra.mm.mmat_get_element_by_atomic_number(atomic_number) → char *¶

schrodinger.infra.mm.mmat_get_formal_charge(arg1) → int¶

schrodinger.infra.mm.mmat_get_largest_vdw_radius() → double¶

schrodinger.infra.mm.mmat_get_mmod_name(arg1) → char *¶

schrodinger.infra.mm.mmat_get_nhua(arg1) → int¶

schrodinger.infra.mm.mmat_get_valence(arg1) → int¶

schrodinger.infra.mm.mmat_get_vdw_radius(arg1) → double¶

schrodinger.infra.mm.mmat_get_wildcard(arg1) → int¶

schrodinger.infra.mm.mmat_is_wildcard(arg1) → int¶

schrodinger.infra.mm.mmbs_get_next(ibs, pos) → int¶

schrodinger.infra.mm.mmbs_in_use(ibs) → MMbool¶
schrodinger.infra.mm.mmbs_in_use(bs) → MMbool

schrodinger.infra.mm.mmbs_is_on(ibs, pos) → MMbool¶

schrodinger.infra.mm.mmcolor_vector_to_index(color_vector_in)¶

schrodinger.infra.mm.mmcolor_vector_to_string(color_vector_in)¶

schrodinger.infra.mm.mmcommon_display_ffbuilder() → MMbool¶

schrodinger.infra.mm.mmcommon_display_opls2() → MMbool¶

schrodinger.infra.mm.mmcommon_display_scisol() → MMbool¶

schrodinger.infra.mm.mmcommon_display_watermap() → MMbool¶

schrodinger.infra.mm.mmcommon_get_license_feature_version(feature) → int¶

schrodinger.infra.mm.mmcommon_get_scratch_project_regular_expression() → std::string¶

schrodinger.infra.mm.mmct_atom_get_atom_entry(ict, iatom) → int¶

schrodinger.infra.mm.mmct_atom_get_atom_mol(cthandle, iatom) → int¶

schrodinger.infra.mm.mmct_atom_get_bond_angle(ct1, ct1atom, ct2, ct2atom, ct3, ct3atom) → MM_Angle¶

schrodinger.infra.mm.mmct_atom_get_charge1(cthandle, iatom) → MM_Charge¶

schrodinger.infra.mm.mmct_atom_get_charge2(cthandle, iatom) → MM_Charge¶

schrodinger.infra.mm.mmct_atom_get_chargef(cthandle, iatom) → int¶

schrodinger.infra.mm.mmct_atom_get_color(cthandle, iatom) → int¶

schrodinger.infra.mm.mmct_atom_get_dihedral_angle(ct1, ct1atom, ct2, ct2atom, ct3, ct3atom, ct4, ct4atom) → MM_Angle¶

schrodinger.infra.mm.mmct_atom_get_distance(ct1, ct1atom, ct2, ct2atom) → MM_Coord¶

schrodinger.infra.mm.mmct_atom_get_distance_pbc(ct1, ct1atom, ct2, ct2atom) → MM_Coord¶

schrodinger.infra.mm.mmct_atom_get_entry_mol_num(ict, iatom) → int¶

schrodinger.infra.mm.mmct_atom_get_secondary_struct(cthandle, iatom) → int¶

schrodinger.infra.mm.mmct_atom_get_x(cthandle, iatom) → MM_Coord¶

schrodinger.infra.mm.mmct_atom_get_y(cthandle, iatom) → MM_Coord¶

schrodinger.infra.mm.mmct_atom_get_z(cthandle, iatom) → MM_Coord¶

schrodinger.infra.mm.mmct_atom_has_alt_position(cthandle, iatom) → MMbool¶

schrodinger.infra.mm.mmct_atom_is_selected(cthandle, iatom) → MMbool¶

schrodinger.infra.mm.mmct_ct_get_all_xyz_copy(cthandle)¶

schrodinger.infra.mm.mmct_ct_get_all_xyz_live(cthandle)¶

schrodinger.infra.mm.mmct_ct_get_first_entry_atom(ct, entry_name) → MM_Index¶

schrodinger.infra.mm.mmct_ct_in_use(cthandle) → int¶

schrodinger.infra.mm.mmct_id_map_in_use(imap) → MMbool¶

schrodinger.infra.mm.mmct_is_enabled(option) → int¶

schrodinger.infra.mm.mmct_is_standard_biopolymer(res_name) → MMbool¶

schrodinger.infra.mm.mmct_is_standard_nucleotide(res_name) → MMbool¶

schrodinger.infra.mm.mmct_is_standard_residue(res_name) → MMbool¶

schrodinger.infra.mm.mmct_res_connected(ct, res1_atom, res2_atom) → MMbool¶

schrodinger.infra.mm.mmct_valid_atom(atom_index) → MMbool¶

schrodinger.infra.mm.mmelement_get_atomic_number_by_symbol(symbol) → int¶

schrodinger.infra.mm.mmelement_get_atomic_weight_by_atomic_number(atnum) → double¶

schrodinger.infra.mm.mmelement_get_atomic_weight_by_symbol(symbol) → double¶

schrodinger.infra.mm.mmelement_get_max_valence(atomic_number) → size_t¶

schrodinger.infra.mm.mmelement_get_period(atomic_number) → size_t¶

schrodinger.infra.mm.mmelement_get_symbol_by_atomic_number(atnum) → char const *¶

schrodinger.infra.mm.mmelement_get_valence_count(atomic_number) → size_t¶

schrodinger.infra.mm.mmffld_checkMetalSupport(mmffld_handle, st, adapt_in_place=False, component=schrodinger::energy::MetalForceFieldComponent::LIGAND_FIELD) → MetalSupportStatus¶

schrodinger.infra.mm.mmffld_compute_esp_rmse(qm_potential, mm_potential, weights) → double¶

schrodinger.infra.mm.mmffld_compute_mm_esp(atomic_charges, grid, xyz) → Eigen::VectorXd¶

schrodinger.infra.mm.mmffld_getAtomicCharges(mmffld_handle, include_charge_transfers=False) → std::vector< double,std::allocator< double > >¶

schrodinger.infra.mm.mmffld_getCoordinates(mmffld_handle, relax_drudes=False) → std::vector< double,std::allocator< double > >¶

schrodinger.infra.mm.mmffld_getEnergyForce(mmffld_id) → std::pair< std::vector< double,std::allocator< double > >,std::vector< double,std::allocator< double > > >¶

schrodinger.infra.mm.mmffld_getEnvEnergyForce(mmffld_id, center_atom_list, env_atom_list={}) → std::pair< double,std::vector< double,std::allocator< double > > >¶

schrodinger.infra.mm.mmffld_getExcludedAtoms(mmffld_handle, i) → std::unordered_set< unsigned int,std::hash< unsigned int >,std::equal_to< unsigned int >,std::allocator< unsigned int > >¶

schrodinger.infra.mm.mmffld_getMetalComplexParameters(mmffld_handle, component) → MetalSystemsParams¶

schrodinger.infra.mm.mmffld_getOplsmLigandTypes(mmffld_handle, component) → MetalSystemsTypeMap¶

schrodinger.infra.mm.mmffld_getOplsmMetalTypes(mmffld_handle) → MetalSystemsTypeMap¶

schrodinger.infra.mm.mmffld_get_LJ_type_from_symbol(mmffld_id, vdw_type) → int¶

schrodinger.infra.mm.mmffld_get_error_handler() → int¶

schrodinger.infra.mm.mmffld_get_loaded_UTTs(mmffld_handle) → std::map< std::string,UTT,std::less< std::string >,std::allocator< std::pair< std::string const,UTT > > >¶

schrodinger.infra.mm.mmffld_hasMetalComplexLewisUnadaptInfo(ct_handle) → bool¶

schrodinger.infra.mm.mmffld_minimize()¶: mmffld_minimize_lic(mmffld_id) -> MinimizeResults

schrodinger.infra.mm.mmffld_minimize_lic(mmffld_id) → MinimizeResults¶

schrodinger.infra.mm.mmffld_overwrite_vdw_interaction_parameter_IAC(mmffld_id, iac_i, iac_j, value_a, value_b)¶

schrodinger.infra.mm.mmffld_refcount() → int¶

schrodinger.infra.mm.mmffld_setElectricField(mmffld_handle, electric_field)¶

schrodinger.infra.mm.mmffld_setMetalComplexParameters(mmffld_handle, params, component)¶

schrodinger.infra.mm.mmffld_solveFlucCTPlusDrudes(mmffld_handle) → std::pair< std::vector< double,std::allocator< double > >,std::vector< double,std::allocator< double > > >¶

schrodinger.infra.mm.mmffld_unadaptMetalComplexLewis(ct_handle)¶

schrodinger.infra.mm.mmfile_get_config_dir() → std::string¶

schrodinger.infra.mm.mmfile_get_directory_path(which_directory) → std::string¶

schrodinger.infra.mm.mmfile_get_maestro_scripts_path(path_type) → std::string¶

schrodinger.infra.mm.mmfile_get_product_dir_path(product_name) → std::string¶

schrodinger.infra.mm.mmfile_get_product_directory_names() → std::vector< std::string,std::allocator< std::string > >¶

schrodinger.infra.mm.mmjag_basis_count() → int¶

schrodinger.infra.mm.mmjag_key_nondef_count(h) → int¶

schrodinger.infra.mm.mmjag_scan_adjust(h, ct, coord_type, i, j, k, l, value, allow_linear, ct_ref) → int¶

schrodinger.infra.mm.mmjag_scan_useable(scan_code) → MMjag_bool¶

schrodinger.infra.mm.mmjag_terminate()¶

schrodinger.infra.mm.mmlewis_get_error_handler() → int¶

schrodinger.infra.mm.mmlewis_refcount() → int¶

schrodinger.infra.mm.mmlist_get(list_id, list_index) → int¶

schrodinger.infra.mm.mmlist_get_size(list_id) → int¶

schrodinger.infra.mm.mmlist_in_list(list_id, val) → int¶

schrodinger.infra.mm.mmmdl_escape_property_name(name) → std::string¶

schrodinger.infra.mm.mmneut_get_errhandle() → int¶

schrodinger.infra.mm.mmneut_set_errhandle(arg1) → int¶

schrodinger.infra.mm.mmpatty_get_error_handler() → int¶

schrodinger.infra.mm.mmpdb_get_three_to_one_letter_residue_map() → std::unordered_map< resname_t,char > const &¶

schrodinger.infra.mm.mmpipeline_initialize() → char *¶

schrodinger.infra.mm.mmseq_get_accession_number(sequence) → char const *¶

schrodinger.infra.mm.mmseq_get_all_codes(sequence) → char const *¶

schrodinger.infra.mm.mmseq_get_chainstr(sequence) → std::string¶

schrodinger.infra.mm.mmseq_get_description(sequence) → char const *¶

schrodinger.infra.mm.mmseq_get_length(sequence) → int¶

schrodinger.infra.mm.mmseq_get_name(sequence) → char const *¶

schrodinger.infra.mm.mmtable_table_is_valid(table) → MMbool¶

schrodinger.infra.mm.mmtable_terminate()¶

schrodinger.infra.mm.mmzip_file_name(handle, index) → char const *¶

schrodinger.infra.mm.opls_name_to_version(name) → schrodinger::forcefield::OPLSVersion¶

schrodinger.infra.mm.opls_names(name_type=COMMON) → std::vector< std::string,std::allocator< std::string > >¶

schrodinger.infra.mm.opls_version_to_name(version, name_type=COMMON) → std::string¶

schrodinger.infra.mm.opls_versions() → std::vector< int,std::allocator< int > >¶

schrodinger.infra.mm.read_utts(archive, version) → std::vector< UTT,std::allocator< UTT > >¶

schrodinger.infra.mm.resolve_archive_path(archive_path='') → std::string¶

schrodinger.infra.mm.set_globals()¶

schrodinger.infra.mm.set_ligand_parameters(params)¶

schrodinger.infra.mm.set_preference_custom_opls_path(custom_opls_path)¶

schrodinger.infra.mm.set_preference_most_recent_custom_opls_paths(most_recent_custom_opls_paths)¶

schrodinger.infra.mm.set_preference_opls_version(opls_version)¶

schrodinger.infra.mm.set_preference_use_custom_opls(use_custom_opls)¶

schrodinger.infra.mm.validate_opls_directory(oplsdir)¶

schrodinger.infra.mm.validate_opls_metadata(metadata)¶