schrodinger.application.prime.wrapper module

Classes to assist in preparing prime input files

class schrodinger.application.prime.wrapper.PrimeConfig(kw=None)

Bases: InputConfig

Class for reading and writing simplified Prime homology modeling input files.

specs = ["JOB_TYPE                   = string(default='MODEL')", "DIR_NAME                   = string(default='.')", 'QUERY_OFFSET               = integer(default=0)', 'TAILS                      = integer(default=0)', "SIDE_OPT                   = string(default='false')", "MINIMIZE                   = string(default='true')", "BUILD_INSERTIONS           = string(default='true')", 'MAX_INSERTION_SIZE         = integer(default=20)', "BUILD_TRANSITIONS          = string(default='true')", "BUILD_DELETIONS            = string(default='true')", "KEEP_ROTAMERS              = string(default='true')", "KNOWLEDGE_BASED            = string(default='true')", 'NUM_OUTPUT_STRUCT          = integer(default=1)', "TEMPLATE_RESIDUE_NUMBERS   = string(default='false')"]

__init__(kw=None)

Accepts one argument which is either a path or a keyword dictionary.

setAlignment(alignment, ligands=('all',), include_water=False, template_number=1)

Parameters:

• alignment (BasePrimeAlignment) – Alignment.

• ligands (tuple of str) – Names of ligands to be included in the model.

• include_water (bool) – Whether to include water molecules in the built model.

• template_number (int) – Template number

writeConfig(filename)

Writes a simplified input file to filename.

This input file needs to be run via $SCHRODINGER/prime.

Parameters:

filename (str) – Name of output file.

class schrodinger.application.prime.wrapper.ConsensusConfig(kw=None)

Bases: InputConfig

Class for reading and writing simplified Prime consensus modeling input files.

specs = ["ALIGN_FILE                 = string()SC_OPT                     = string(default='yes')"]

__init__(kw=None)

Accepts one argument which is either a path or a keyword dictionary.

setAlignment(alignment)

writeConfig(filename)

Writes a simplified input file to filename.

This input file needs to be run via $SCHRODINGER/consensus_homology.

Parameters:

filename (str) – Name of output file.

class schrodinger.application.prime.wrapper.PrimeTemplate(pdb_id='')

Bases: _WorkingDirectoryMixin

This class encapsulates Prime template structure. A template includes a single chain.

WATER_NAMES = {'HOH', 'WAT'}

FIND_LIGANDS_KWARGS = {'allow_ion_only_molecules': True, 'excluded_residue_names': {'HOH', 'WAT'}, 'min_heavy_atom_count': 1}

__init__(pdb_id='')

property file_name

property st

property ligands

Returns a list of ligands found in the template structure.

Return type:

list of schrodinger.structuils.analyze.Ligand objects

Returns:

List of ligands in current template structure.

property waters

writePDB()

Writes template structure to PDB file.

Return type:

bool

Returns:

True on successful write.

class schrodinger.application.prime.wrapper.BasePrimeAlignment(name, query_seq)

Bases: _WorkingDirectoryMixin

Encapsulates pairwise query-template alignment. Allows writing alignment files in Prime format.

__init__(name, query_seq)

Parameters:

• name (str) – Alignment name.

• query_seq (str) – Text of prealigned query sequence.

property name

property query_sequence

property template

property template_sequence

setTemplate(template, sequence=None)

Adds a pre-aligned template sequence to the alignment.

Parameters:

• template (PrimeTemplate) – Template.

• sequence (str) – Template sequence aligned to query (i.e. including gaps).

setWorkingDirectory(wd)

Propagate change in working directory to template

getAlnFilename()

Get the filename of the aln written by writeInputForPrime.

writeInputForPrime()

Writes Prime alignment to external file.

writeInputForConsensus(file_name, append=False)

Writes out FASTA alignment for consensus homology modeling. The alignment needs to include chain name and secondary structure definition for each template sequence.

Parameters:

• append (bool) – Whether to append to existing file.

• file_name (str) – Name of output file.

getSSA(st, chain_id='')

Gets a secondary structure annotation string for structure st chain chain_id.

Parameters:

• st (schrodinger.structure.Structure) – Input structure.

• chain_id (str) – Chain ID to extract SSA from.

schrodinger.application.prime.wrapper.basename_no_ext(file_name)

Returns file basename without extension.

schrodinger.application.prime.wrapper.convert_gaps_to_dots(sequence)

Replaces gap symbols with dots to make a sequence compatible with Prime.

Parameters:

sequence (str) – Input gapped sequence.

Return type:

str

Returns:

Converted sequence.

schrodinger.application.prime.wrapper.convert_gaps_to_tildes(sequence)

Replaces gap symbols with tildes to make a sequence compatible with consensus modeling.

Parameters:

sequence (str) – Input gapped sequence.

Return type:

str

Returns:

Converted sequence.