schrodinger.application.prime.wrapper module¶
Classes to assist in preparing prime input files
- class schrodinger.application.prime.wrapper.PrimeConfig(kw=None)¶
Bases:
schrodinger.application.inputconfig.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:
schrodinger.application.inputconfig.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:
schrodinger.application.prime.wrapper._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:
schrodinger.application.prime.wrapper._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.