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.

class schrodinger.infra.mm.CaptureMMErr[source]
property messages
__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

addMessagesAsDetails(base_message) → std::string
append()

appends another ‘this’ object

getMessages() → std::string
getMessagesOrDefault(arg2) → std::string
next()

returns the next ‘this’ object

restore()
class schrodinger.infra.mm.Cartesian
__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

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

angle(a, b, c) -> double

append()

appends another ‘this’ object

apply(func) → Cartesian
as_unit_vector() → Cartesian
cross(c) → Cartesian
static dihedral(a, b, c, d) → double
static distance(c1, c2) → double
magnitude() → double
map(func) → Cartesian
next()

returns the next ‘this’ object

scale_to_unit_magnitude() → Cartesian
sq() → double
static square_distance(c1, c2) → double
to_array() → std::array< double,3 >
to_vector() → std::vector< double,std::allocator< double > >
x
y
z
zero() → Cartesian
schrodinger.infra.mm.Cartesian_angle(a, b, c) → 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.FitParamInfo

schrodinger::forcefield::FitParamInfo

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

next()

returns the next ‘this’ object

opls

schrodinger::forcefield::FitParamInfo.opls

types

schrodinger::forcefield::FitParamInfo.types

vs

schrodinger::forcefield::FitParamInfo.vs

class schrodinger.infra.mm.LigandParameters

::LigandParameters

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

allow_amino_acid_only_molecules
allow_ion_only_molecules
append()

appends another ‘this’ object

excluded_residue_names
included_residue_names
max_atom_count
min_heavy_atom_count
next()

returns the next ‘this’ object

class schrodinger.infra.mm.LigandScoreStructure

::LigandScoreStructure

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

getGradient(wm_st) → double
getNumLigandAtom() → int
getNumSite() → int
getOverlapSite()
getScore() → double
getTdSLigandAtom()
getTdSSite()
getdGLigandAtom()
getdGSite()
getdHLigandAtom()
getdHSite()
next()

returns the next ‘this’ object

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)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

next()

returns the next ‘this’ object

class schrodinger.infra.mm.MMFfldHandle

schrodinger::forcefield::MMFfldHandle

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

getHandle() → int
next()

returns the next ‘this’ object

setOption(option, value)
class schrodinger.infra.mm.MMFfldInitializer

schrodinger::forcefield::MMFfldInitializer

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

next()

returns the next ‘this’ object

class schrodinger.infra.mm.MMFileContext

::MMFileContext

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

next()

returns the next ‘this’ object

class schrodinger.infra.mm.MMPREF

::MMPREF

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

beginGroup(suffix) → MMpref_Err
beginOsAttribute(iplat=MMPREF_NONE)

beginOsAttribute()

clearSettings()
endGroup()
endOsAttribute()
get(key, i) → MMpref_Err

get(key, d) -> MMpref_Err get(key, s) -> MMpref_Err get(key, b) -> MMpref_Err

getBool(key, bval) → MMpref_Err

getBool(key, bval, bdefval) -> MMpref_Err

getBoolList(groupname, bkeyvalue) → MMpref_Err
getDouble(key) → MMpref_Err

getDouble(key, ddefval) -> MMpref_Err

getDoubleList(groupname, dkeyvalue) → MMpref_Err
getGroup() → std::string
getInt(key, val) → MMpref_Err

getInt(key, idefval) -> MMpref_Err

getIntList(groupname, ikeyvalue) → MMpref_Err
getSettingsFile(sfallbackfile)
getString(key, sval) → MMpref_Err

getString(key, sval, sdefval) -> MMpref_Err

getStringList(groupname, skeyvalue) → MMpref_Err
getSubgroups(subgroups, level=0) → int

getSubgroups(subgroups) -> int

getType(key) → MMPREF_TYPE
hasKey(key, type) → MMpref_Err

hasKey(key) -> MMpref_Err

next()

returns the next ‘this’ object

removeKey(key, type=MMPREF_TYPE_NONE) → int

removeKey(key) -> int

set(key, val, comment) → MMpref_Err

set(key, val) -> MMpref_Err

syncSettings() → MMpref_Err
exception schrodinger.infra.mm.MmException(wrapped_function, args, rc)[source]

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)[source]

Initialize with the wrapped function, arguments used, and the return code.

args
with_traceback()

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

class schrodinger.infra.mm.MmPdbContext
__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

next()

returns the next ‘this’ object

class schrodinger.infra.mm.OPLSArchive

schrodinger::forcefield::OPLSArchive

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

add(datafile_path)

add(parameter_data, datafile)

append()

appends another ‘this’ object

contains(datafile) → bool
static create(archive_path) → OPLSArchive
empty() → bool
getFilename() → boost::filesystem::path
static isCompatible(archive_path) → bool
merge(datafile_path)
merge_archive(src_archive_path)
next()

returns the next ‘this’ object

remove(datafile)
static upgrade(archive_path)
static validate(archive_path)
class schrodinger.infra.mm.OPLSArchiveError

schrodinger::forcefield::OPLSArchiveError

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

next()

returns the next ‘this’ object

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)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

next()

returns the next ‘this’ object

class schrodinger.infra.mm.OPLSDatafileHash

schrodinger::forcefield::OPLSDatafileHash

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

next()

returns the next ‘this’ object

class schrodinger.infra.mm.OPLSVersion[source]
F14 = 14
F16 = 16
class schrodinger.infra.mm.OPLSVersionData

schrodinger::forcefield::OPLSVersionData

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

archive_filename

schrodinger::forcefield::OPLSVersionData.archive_filename

display_name

schrodinger::forcefield::OPLSVersionData.display_name

next()

returns the next ‘this’ object

version_major

schrodinger::forcefield::OPLSVersionData.version_major

version_minor

schrodinger::forcefield::OPLSVersionData.version_minor

version_patch

schrodinger::forcefield::OPLSVersionData.version_patch

class schrodinger.infra.mm.OPLSVersionHash

schrodinger::forcefield::OPLSVersionHash

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

next()

returns the next ‘this’ object

class schrodinger.infra.mm.Preferences
__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

clear()
hasKey(key) → bool
next()

returns the next ‘this’ object

removeKey(key)
class schrodinger.infra.mm.ScoreAtom

::ScoreAtom

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

is_hydrogen
next()

returns the next ‘this’ object

vdw_radius
x
y
z
class schrodinger.infra.mm.UTT

::UTT

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

addParam(spec)
append()

appends another ‘this’ object

atom1
atom2
canonicalize()
central_bt
comment
end_atoms1
end_atoms2
getDefinitionString() → std::string
info
matched
next()

returns the next ‘this’ object

opt
quality
regular_torsion
reverseOrder()
scl14type
updateSymbolNumbers(fcn)
utt_par
utt_reverse_order
class schrodinger.infra.mm.UTTAtom

::UTTAtom

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

atom_idx
next()

returns the next ‘this’ object

symbol
symbol_num
updateSymbolNumber(fcn)
class schrodinger.infra.mm.UTTDefSpec

::UTTDefSpec

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

comment
def_str
info
next()

returns the next ‘this’ object

opt
quality
scl14type
class schrodinger.infra.mm.UTTEndAtom

::UTTEndAtom

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

atom_idx
bt
invariant() → bond_index_t
next()

returns the next ‘this’ object

symbol
symbol_num
updateSymbolNumber(fcn)
class schrodinger.infra.mm.UTTParamSpec

::UTTParamSpec

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

bt0
bt3
comment
next()

returns the next ‘this’ object

sym0
sym3
v
class schrodinger.infra.mm.UTTParameter

::UTTParameter

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

comment
end_atom0
end_atom3
next()

returns the next ‘this’ object

v
class schrodinger.infra.mm.UnpairedElectronsReplacementMode[source]
LeaveUnspecified = 0
ExplicitHydrogens = 1
SetAsCharge = 2
class schrodinger.infra.mm.WaterMapAtom

::WaterMapAtom

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

energy
entropy
free_energy
next()

returns the next ‘this’ object

occupancy
vdw_radius
x
y
z
class schrodinger.infra.mm.WaterMapStructure

::WaterMapStructure

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

atom
continuous() → bool
next()

returns the next ‘this’ object

class schrodinger.infra.mm.WithMMFileSearchPath

::WithMMFileSearchPath

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

next()

returns the next ‘this’ object

schrodinger.infra.mm.aacg_vdw_parameters(site_types, parameter_files, enhancement_files, enhancement_level=0.0, encrypt=False) → std::pair< std::string,std::string >

aacg_vdw_parameters(site_types, parameter_files, enhancement_files, enhancement_level=0.0) -> std::pair< std::string,std::string > aacg_vdw_parameters(site_types, parameter_files, enhancement_files) -> std::pair< std::string,std::string >

schrodinger.infra.mm.assert_development_license_exists()
schrodinger.infra.mm.assert_opls_main_license_exists(version)
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.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) → std::string

get_OPLS_data_filename(opls_dir, version) -> 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) → std::string

get_current_OPLS_data_filename(opls_dir) -> 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_knime_workflows_url()
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_schrodinger_temp_dir() → std::string
schrodinger.infra.mm.get_torsion_fit_info(mmffld_id, ct) → FitParamInfo
schrodinger.infra.mm.installation_archive_path() → boost::filesystem::path
schrodinger.infra.mm.is_compatible_opls_metadata(metadata) → bool
schrodinger.infra.mm.is_valid_opls_directory(oplsdir) → bool
schrodinger.infra.mm.ligprep3_refcount() → int
schrodinger.infra.mm.m2io_refcount() → int
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.mmasl_refcount() → int
schrodinger.infra.mm.mmat_get_anyatom() → int
schrodinger.infra.mm.mmat_get_atom_type(arg1) → int
schrodinger.infra.mm.mmat_get_atomic_num(arg1) → int
schrodinger.infra.mm.mmat_get_atomic_number_by_element(arg1) → int
schrodinger.infra.mm.mmat_get_atomic_weight(arg1) → double
schrodinger.infra.mm.mmat_get_central_geometry(arg1) → int
schrodinger.infra.mm.mmat_get_color(arg1) → int
schrodinger.infra.mm.mmat_get_description(atom_type) → char *
schrodinger.infra.mm.mmat_get_element(arg1) → char *
schrodinger.infra.mm.mmat_get_element_by_atomic_number(atomic_number) → char *
schrodinger.infra.mm.mmat_get_eneg(arg1) → double
schrodinger.infra.mm.mmat_get_eqat13(arg1) → char *
schrodinger.infra.mm.mmat_get_formal_charge(arg1) → int
schrodinger.infra.mm.mmat_get_generalized_type(atom_type) → int
schrodinger.infra.mm.mmat_get_hadded(arg1) → char *
schrodinger.infra.mm.mmat_get_largest_atype() → int
schrodinger.infra.mm.mmat_get_largest_vdw_radius() → double
schrodinger.infra.mm.mmat_get_mmod_name(arg1) → char *
schrodinger.infra.mm.mmat_get_natype() → int
schrodinger.infra.mm.mmat_get_next(atom_type) → int
schrodinger.infra.mm.mmat_get_nhua(arg1) → int
schrodinger.infra.mm.mmat_get_pdb_name(arg1) → char *
schrodinger.infra.mm.mmat_get_solv_eqat13(arg1) → char *
schrodinger.infra.mm.mmat_get_uaroot(arg1) → char *
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_initialize(arg1, arg2, arg3) → int
schrodinger.infra.mm.mmat_is_catdel(arg1) → int
schrodinger.infra.mm.mmat_is_deloc(arg1) → int
schrodinger.infra.mm.mmat_is_generalized_type(atom_type) → int
schrodinger.infra.mm.mmat_is_valid(atom_type) → int
schrodinger.infra.mm.mmat_is_wildcard(arg1) → int
schrodinger.infra.mm.mmat_terminate()
schrodinger.infra.mm.mmbs_get_next(ibs, pos) → int
schrodinger.infra.mm.mmbs_get_previous(ibs, pos) → int
schrodinger.infra.mm.mmbs_in_use(ibs) → MMbool

mmbs_in_use(bs) -> MMbool

schrodinger.infra.mm.mmbs_is_off(ibs, pos) → MMbool
schrodinger.infra.mm.mmbs_is_on(ibs, pos) → MMbool
schrodinger.infra.mm.mmcolor_rgb_to_vector(color_rgb_in)
schrodinger.infra.mm.mmcolor_vector_set(r, g, b)
schrodinger.infra.mm.mmcolor_vector_to_index(color_vector_in)
schrodinger.infra.mm.mmcolor_vector_to_rgb(color_vector_in)
schrodinger.infra.mm.mmcolor_vector_to_string(color_vector_in)
schrodinger.infra.mm.mmcolor_vectors_equal(color1, color2) → MMbool
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.mmcommon_web_access_allowed() → MMbool
schrodinger.infra.mm.mmcrystal_tag_ok(crystal_tag) → MMbool
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_bond_angle_pbc(ct1, ct1atom, ct2, ct2atom, ct3, ct3atom) → MM_Coord
schrodinger.infra.mm.mmct_atom_get_chain_char(cthandle, iatom) → char
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_dihedral_angle_pbc(ct1, ct1atom, ct2, ct2atom, ct4, ct4atom, ct3, ct3atom) → MM_Coord
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_mol_num(cthandle, iatom) → int
schrodinger.infra.mm.mmct_atom_get_res(cthandle, iatom) → char
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_bond_get_order(cthandle, iatom, conn_atom) → int
schrodinger.infra.mm.mmct_ct_compare_jaguar_geometry(ict1, ict2) → int
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_property_dependency(cthandle, idependency, property, dependency_type) → ErrLevel
schrodinger.infra.mm.mmct_ct_get_xmax(cthandle) → MM_Coord
schrodinger.infra.mm.mmct_ct_get_xmin(cthandle) → MM_Coord
schrodinger.infra.mm.mmct_ct_get_ymax(cthandle) → MM_Coord
schrodinger.infra.mm.mmct_ct_get_ymin(cthandle) → MM_Coord
schrodinger.infra.mm.mmct_ct_get_zmax(cthandle) → MM_Coord
schrodinger.infra.mm.mmct_ct_get_zmin(cthandle) → MM_Coord
schrodinger.infra.mm.mmct_ct_in_use(cthandle) → int
schrodinger.infra.mm.mmct_current_errhandler() → int
schrodinger.infra.mm.mmct_id_map_get(imap, iatom) → MM_Index
schrodinger.infra.mm.mmct_id_map_get_size(imap) → 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_refcount() → int
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_clear()
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_default_color(atomic_number) → int
schrodinger.infra.mm.mmelement_get_electronegativity_by_atomic_number(atnum) → double
schrodinger.infra.mm.mmelement_get_full_valence(atomic_number) → size_t
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.mmerr_return_code(level) → char *
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_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_overwrite_vdw_interaction_parameter_IAC(mmffld_id, iac_i, iac_j, value_a, value_b)
schrodinger.infra.mm.mmffld_refcount() → int
schrodinger.infra.mm.mmfile_get_appdata_release_dir_path() → std::string
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.mmfrag_refcount() → size_t
schrodinger.infra.mm.mmim_is_dihedral(ct, i, j, k, l) → MMim_bool
schrodinger.infra.mm.mmim_is_ringbond(ct, j, k) → MMim_bool
schrodinger.infra.mm.mmjag_atomic_number(lbl) → int
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.mmjag_zmat_count(h) → int
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.mmlist_in_range(list_id, min, max) → int
schrodinger.infra.mm.mmmdl_refcount() → int
schrodinger.infra.mm.mmmol2_refcount() → int
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.mmpatty_refcount() → int
schrodinger.infra.mm.mmpdb_get_three_to_one_letter_residue_map() → std::unordered_map< std::string,char > const &
schrodinger.infra.mm.mmpdb_refcount() → int
schrodinger.infra.mm.mmpipeline_initialize() → char *
schrodinger.infra.mm.mmseq_create_sequence_name(prefix, ename, chain_name) → 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_ca_index(sequence, position) → MM_Index
schrodinger.infra.mm.mmseq_get_chain(sequence) → char
schrodinger.infra.mm.mmseq_get_chainstr(sequence) → std::string
schrodinger.infra.mm.mmseq_get_code(sequence, position) → char
schrodinger.infra.mm.mmseq_get_code_ids(sequence) → char const **
schrodinger.infra.mm.mmseq_get_code_ids_range(sequence, start_pos, num_c) → char **
schrodinger.infra.mm.mmseq_get_code_range(sequence, start_pos, num_c) → char *
schrodinger.infra.mm.mmseq_get_description(sequence) → char const *
schrodinger.infra.mm.mmseq_get_entry_name(sequence) → char const *
schrodinger.infra.mm.mmseq_get_id(sequence, position) → char const *
schrodinger.infra.mm.mmseq_get_length(sequence) → int
schrodinger.infra.mm.mmseq_get_name(sequence) → char const *
schrodinger.infra.mm.mmseq_get_subsequence(sequence, start, end, name) → MMsequence
schrodinger.infra.mm.mmseq_get_type(sequence) → MMseq_sequence_type
schrodinger.infra.mm.mmseq_in_use(sequence) → MMbool
schrodinger.infra.mm.mmseqio_get_seq_type(seq, seq_len) → MMseq_sequence_type
schrodinger.infra.mm.mmseqio_in_use(seqio) → MMbool
schrodinger.infra.mm.mmsys_get_short_host() → std::string
schrodinger.infra.mm.mmsys_is_localhost(name) → bool
schrodinger.infra.mm.mmsys_version_to_string(version) → char *
schrodinger.infra.mm.mmtable_is_enabled(option) → MMbool
schrodinger.infra.mm.mmtable_refcount() → int
schrodinger.infra.mm.mmtable_table_is_valid(table) → MMbool
schrodinger.infra.mm.mmtable_terminate()
schrodinger.infra.mm.mmtaut_get_error_handler() → int
schrodinger.infra.mm.mmzip_contains_file(handle, filename) → MMbool
schrodinger.infra.mm.mmzip_file_name(handle, index) → char const *
schrodinger.infra.mm.opls_main_license_exists(version) → bool
schrodinger.infra.mm.opls_name_to_version(name) → schrodinger::forcefield::OPLSVersion
schrodinger.infra.mm.opls_names() → std::vector< std::string,std::allocator< std::string > >
schrodinger.infra.mm.opls_version_to_name(version, name_type) → std::string

opls_version_to_name(version) -> std::string

schrodinger.infra.mm.read_utts(archive) → std::vector< UTT,std::allocator< UTT > >
schrodinger.infra.mm.set_globals()[source]
schrodinger.infra.mm.set_ligand_parameters(params)
schrodinger.infra.mm.validate_opls_directory(oplsdir)
schrodinger.infra.mm.validate_opls_metadata(metadata)
schrodinger.infra.mm.weakref_proxy()

proxy(object[, callback]) – create a proxy object that weakly references ‘object’. ‘callback’, if given, is called with a reference to the proxy when ‘object’ is about to be finalized.