Module protein

Creates an ASL based on a residue's chain, residue number and inscode. The ASL can optionally only include the alpha carbon of the residue.

Parameters:

• residue (schrodinger.structure._Residue) - The residue to create an ASL for

Returns: str

ASL expression for residue

Raises:

• RuntimeError - If the passed in residue is incorrect type

Creates an ASL based on a list of residue's chains, residue numbers and inscodes. The ASL can optionally only include the alpha carbon of the residue.

Parameters:

• residue (list or tuple of schrodinger.structure._Residues) - The residues to create an ASL for

Returns: str

ASL expression for all residues

Raises:

• RuntimeError - If residues are not a list or tuple
• RuntimeError - If any passed in residues are incorrect type

Run a script using schrodinger.utils.subprocess.Popen. An interpreter is not needed for these and any executable found in $SCHRODINGER or $SCHRODINGER/utilities does not need the full path. Also any executable found by $SCHRODINGER/run will be found so these do not need the full path either.

Parameters:

• commands - List fo commands fed into subprocess.Popen

Returns:

(STDOUT, STDERR)

Returns a list of residues for st that are within within angstroms of each residue. If the ca keyword is True the within calculation will only look for alpha carbon in residues. This means that if within is set to 5.5 angstroms and there is only a single atom that belongs to a residue at that cutoff, the residue that the atom belongs to will be refined.

Parameters:

• st (schrodinger.structure.Structure) - Structure to evaluate and which all residues correspond
• residues (list or tuple of schrodinger.structure._Residues) - All residues targeted for refinement
• within (float) - Distance (angstroms) of residues to include in refinement
• ca (bool) - Use only alpha carbons to find residues within

Returns: list

List of schrodinger.structure._Residue objects

Tests whether a residue is polar

Parameters:

• residue (structure._Residue) - Residue to test

Returns: bool

Tests whether a residue is nonpolar

Parameters:

• residue (structure._Residue) - Residue to test

Returns: bool

Returns true if the atom is considered non-polar. Here are the rules for non-polar atoms:

• The atom's element is a C or S
• The atom's element is a H and one bonded atom's element is C or S

Parameters:

• atom (schrodinger.structure._StructureAtom)

AA_1_LETTER_MAP

Value:

{"A": "ALA", "R": "ARG", "N": "ASN", "D": "ASP", "C": "CYS", "Q": "GLN ", "E": "GLU", "G": "GLY", "H": "HIS", "I": "ILE", "L": "LEU", "K": "L YS", "M": "MET", "F": "PHE", "P": "PRO", "S": "SER", "T": "THR", "W": "TRP", "Y": "TYR", "V": "VAL"}

AA_3_LETTER_MAP

Value:

{"ALA": "A", "ARG": "R", "ARN": "R", "ASN": "N", "ASP": "D", "ASH": "D ", "CYS": "C", "GLN": "Q", "GLU": "E", "GLH": "E", "GLY": "G", "HIS": "H", "HIE": "H", "HIP": "H", "HID": "H", "ILE": "I", "LEU": "L", "LYS" : "K", "LYN": "K", "MET": "M", "PHE": "F", "PRO": "P", "SER": "S", "TH R": "T", "TRP": "W", "TYR": "Y", "VAL": "V"}

ALL_RESIDUES

Value:

['ALA', 'ARG', 'ASN', 'ASP', 'CYS', 'GLN', 'GLU', 'GLY', 'HIS', 'HIP', 'HIE', 'ILE', 'LEU', 'LYS', 'MET', 'PHE', 'PRO', 'SER', 'THR', 'TRP', 'TYR', 'VAL']

POLAR_RESIDUES

Value:

['ARG', 'ASP', 'GLU', 'HIS', 'ASN', 'GLN', 'LYS', 'SER', 'THR', 'HID', 'HIE']

NONPOLAR_RESIDUES

Value:

['PHE', 'LEU', 'ILE', 'TYR', 'TRP', 'VAL', 'MET', 'PRO', 'CYS', 'ALA']

NEUTRAL_RESIDUES

Value:

['ALA', 'ASN', 'CYS', 'GLN', 'GLY', 'HIE', 'ILE', 'LEU', 'MET', 'PHE', 'PRO', 'SER', 'THR', 'TRP', 'TYR', 'VAL']

RESIDUE_ROTOR_COUNT

Value:

{'ALA': 0, 'ARG': 4, 'ARN': 4, 'ASN': 2, 'ASH': 2, 'ASP': 2, 'CYS': 2, 'GLN': 3, 'GLU': 3, 'GLH': 3, 'GLY': 0, 'HIS': 2, 'HID': 2, 'HIP': 2, 'HIE': 2, 'ILE': 2, 'LEU': 2, 'LYN': 4, 'LYS': 4, 'MET': 3, 'PHE': 2, 'PRO': 0, 'SER': 2, 'THR': 2, 'TRP': 2, 'TYR': 3, 'VAL': 1,}

HYDROPATHY_SCALE

Value:

{'ALA': 1.8, 'ARG':-4.5, 'ARN':-4.5, 'ASH':-3.5, 'ASN':-3.5, 'ASP':-3. 5, 'CYS': 2.5, 'CYX': 2.5, 'CYT': 2.5, 'GLH':-3.5, 'GLN':-3.5, 'GLU':- 3.5, 'GLY':-0.4, 'HIS':-3.2, 'HID':-3.2, 'HIE':-3.2, 'HIP':-3.2, 'ILE' : 4.5, 'LEU': 3.8, 'LYN':-3.9, 'LYS':-3.9, 'MET': 1.9, 'PHE': 2.8, 'PR O':-1.6, 'SER':-0.8, 'SRO':-0.8, 'SEP':-0.8, 'THR':-0.7, 'THO':-0.7, ' TPO':-0.7, 'TRP':-0.9, 'TYR':-1.3, 'TYO':-1.3, 'PTR':-1.3, 'VAL': 4.2, }

MUTATION_1_LETTER_RE

Value:

re.compile(r""" (?P<chain>[a-zA-Z_]{1}) : (?P<resnum>\d+) (?P<inscode>[a-zA-Z]{1})? # optional \s? # optional (?P<mutations>[%s]+)? # optional """ % ''.join(AA_1_LETTER_MAP.keys()), re.VERBOSE)

MUTATION_3_LETTER_RE

Value:

re.compile(r""" (?P<chain>[a-zA-Z_]{1}) : (?P<resnum>\d+) (?P<inscode>[a-zA-Z]{1})? # optional \s? # optional (?P<mutations>(%s)(,%s)*)? # optional """ %('|'.join(AA_3_LETTER_MAP.keys()), '|,'.join(AA_3_LETTER_MAP. ...

MUTATION_RE

Value:

re.compile(r""" (?P<chain>[a-zA-Z_]{1}) : (?P<resnum>\d+) (?P<inscode>[a-zA-Z]{1})? # optional -> (?P<new_resname>(%s)) """ %('|'.join(AA_3_LETTER_MAP.keys())), re.VERBOSE)

PROP_CONVERSIONS

Value:

{'e_pot': 'Potential_energy', 'e_internal': 'Internal_energy', 'e_inte raction': 'Interaction_energy', 'prime_energy': 'Prime_Energy', 'prime _coulomb': 'Prime_Coulomb', 'prime_cov': 'Prime_Covalent', 'prime_vdw' : 'Prime_vdW', 'prime_gb': 'Prime_Solv_GB', 'prime_sa': 'Prime_Solv_SA ', 'prime_lipo': 'Prime_Lipo', 'prime_hbond': 'Prime_Hbond', 'prime_pa cking': 'Prime_Packing', 'prime_selfcont': 'Prime_SelfCont', 'affinity _coulomb': 'Affinity_Coulomb', 'affinity_cov': 'Affinity_Covalent', 'a ffinity_vdw': 'Affinity_vdW', 'affinity_gb': 'Affinity_Solv_GB', 'affi ...