Source code for schrodinger.application.prime.input

"""
A class for reading and writing Prime simplified input files.

Copyright Schrodinger, LLC. All rights reserved.

"""
#Contributors: Matvey Adzhigirey

# Ev:67675

from schrodinger.application.inputconfig import InputConfig

spec_str = """
PRIME_TYPE           = option('SIDE_PRED', 'LOOP_BLD', 'REAL_MIN', 'SITE_OPT', 'ENERGY')
THREADS              = integer()
MAX_JOBS             = integer()
NUM_OUTPUT_STRUCT    = integer()
ECUTOFF              = float()
STRUCT_FILE          = string()
USE_RANDOM_SEED      = boolean()
SEED                 = integer()
USE_CRYSTAL_SYMMETRY = boolean()
INT_DIEL             = float()
EXT_DIEL             = float()
USE_MAE_CHARGES      = boolean()
USE_MEMBRANE         = boolean()
SELECT               = option('all', 'pick')
RESIDUE_FILE         = string()
LIGAND               = string()
NPASSES              = integer()
LOOP_i_RES_j         = string()
RES_SPHERE           = string()
MAX_CA_MOVEMENT      = float()
MIN_OVERLAP          = float()
RESIDUE_i            = string()
BUILD_TAIL           = boolean()
"""
prime_specs = []
for line in spec_str.split('\n'):
    prime_specs.append(line)


class Prime(InputConfig):
    """
    Class for reading and writing simplified Prime input files.

    Example 1::
        config = Prime(keyword_dict)
        config.write("path.inp")

    Example 2::
        config = Prime("path.inp")
        inpath = config['STRUCT_FILE']

    Example 3::
        config = Prime()
        config['STRUCT_FILE'] = "path.mae"
        config.write("path.inp")

    """

    def __init__(self, kw=None):
        """
        Accepts one argument which is either a path or a keyword dictionary.

        """

        InputConfig.__init__(self, kw, prime_specs)
        if kw:
            # Validate the InputConfig to specs (will convert to correct types)
            self.validateValues(preserve_errors=False, copy=False)

    def write(self, filename):
        """
        Writes a simplified input file to filename.

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

        """

        if not filename.endswith('.inp'):
            raise ValueError("Prime input file should end with *.inp")
        self.writeInputFile(filename,
                            ignore_none=True,
                            yesno=True,
                            smartsort=True)
        # smartsort is enabled as part of PYTHON-1815

        return filename