PyPI - stjames - Versions diffs - 0.0.52__tar.gz → 0.0.53__tar.gz - Mend

stjames 0.0.52tar.gz → 0.0.53tar.gz

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

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Files changed (76) hide show

{stjames-0.0.52/stjames.egg-info → stjames-0.0.53}/PKG-INFO RENAMED Viewed

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: stjames
-Version: 0.0.52
+Version: 0.0.53
 Summary: standardized JSON atom/molecule encoding scheme
 Author-email: Corin Wagen <corin@rowansci.com>
 Project-URL: Homepage, https://github.com/rowansci/stjames
@@ -12,6 +12,7 @@ Requires-Dist: atomium<2,>=1
 Requires-Dist: pydantic>=2.4
 Requires-Dist: numpy
 Requires-Dist: atomium<2.0,>=1.0
+Requires-Dist: requests
 # stjames

{stjames-0.0.52 → stjames-0.0.53}/pyproject.toml RENAMED Viewed

@@ -1,6 +1,6 @@
 [project]
 name = "stjames"
-version = "0.0.52"
+version = "0.0.53"
 description = "standardized JSON atom/molecule encoding scheme"
 readme = "README.md"
 requires-python = ">=3.11"
@@ -13,6 +13,7 @@ dependencies = [
     "pydantic>=2.4",
     "numpy",
     "atomium>=1.0,<2.0",
+    "requests"
 ]
 [build-system]

stjames-0.0.53/stjames/atomium_stjames/__init__.py ADDED Viewed

@@ -0,0 +1,5 @@
+from .mmcif import mmcif_dict_to_data_dict, mmcif_string_to_mmcif_dict
+from .pdb import pdb_dict_to_data_dict, pdb_string_to_pdb_dict
+from .utilities import fetch, open
+__all__ = ["open", "fetch", "pdb_dict_to_data_dict", "pdb_string_to_pdb_dict", "mmcif_dict_to_data_dict", "mmcif_string_to_mmcif_dict"]

stjames-0.0.53/stjames/atomium_stjames/data.py ADDED Viewed

@@ -0,0 +1,377 @@
+"""Contains logic for turning data dictionaies into a parsed Python objects."""
+PERIODIC_TABLE = {
+    "H": 1.0079,
+    "HE": 4.0026,
+    "LI": 6.941,
+    "BE": 9.0122,
+    "B": 10.811,
+    "C": 12.0107,
+    "N": 14.0067,
+    "O": 15.9994,
+    "F": 18.9984,
+    "NE": 20.1797,
+    "NA": 22.9897,
+    "MG": 24.305,
+    "AL": 26.9815,
+    "SI": 28.0855,
+    "P": 30.9738,
+    "S": 32.065,
+    "CL": 35.453,
+    "K": 39.0983,
+    "AR": 39.948,
+    "CA": 40.078,
+    "SC": 44.9559,
+    "TI": 47.867,
+    "V": 50.9415,
+    "CR": 51.9961,
+    "MN": 54.938,
+    "FE": 55.845,
+    "NI": 58.6934,
+    "CO": 58.9332,
+    "CU": 63.546,
+    "ZN": 65.39,
+    "GA": 69.723,
+    "GE": 72.64,
+    "AS": 74.9216,
+    "SE": 78.96,
+    "BR": 79.904,
+    "KR": 83.8,
+    "RB": 85.4678,
+    "SR": 87.62,
+    "Y": 88.9059,
+    "ZR": 91.224,
+    "NB": 92.9064,
+    "MO": 95.94,
+    "TC": 98,
+    "RU": 101.07,
+    "RH": 102.9055,
+    "PD": 106.42,
+    "AG": 107.8682,
+    "CD": 112.411,
+    "IN": 114.818,
+    "SN": 118.71,
+    "SB": 121.76,
+    "I": 126.9045,
+    "TE": 127.6,
+    "XE": 131.293,
+    "CS": 132.9055,
+    "BA": 137.327,
+    "LA": 138.9055,
+    "CE": 140.116,
+    "PR": 140.9077,
+    "ND": 144.24,
+    "PM": 145,
+    "SM": 150.36,
+    "EU": 151.964,
+    "GD": 157.25,
+    "TB": 158.9253,
+    "DY": 162.5,
+    "HO": 164.9303,
+    "ER": 167.259,
+    "TM": 168.9342,
+    "YB": 173.04,
+    "LU": 174.967,
+    "HF": 178.49,
+    "TA": 180.9479,
+    "W": 183.84,
+    "RE": 186.207,
+    "OS": 190.23,
+    "IR": 192.217,
+    "PT": 195.078,
+    "AU": 196.9665,
+    "HG": 200.59,
+    "TL": 204.3833,
+    "PB": 207.2,
+    "BI": 208.9804,
+    "PO": 209,
+    "AT": 210,
+    "RN": 222,
+    "FR": 223,
+    "RA": 226,
+    "AC": 227,
+    "PA": 231.0359,
+    "TH": 232.0381,
+    "NP": 237,
+    "U": 238.0289,
+    "AM": 243,
+    "PU": 244,
+    "CM": 247,
+    "BK": 247,
+    "CF": 251,
+    "ES": 252,
+    "FM": 257,
+    "MD": 258,
+    "NO": 259,
+    "RF": 261,
+    "LR": 262,
+    "DB": 262,
+    "BH": 264,
+    "SG": 266,
+    "MT": 268,
+    "RG": 272,
+    "HS": 277,
+}
+COVALENT_RADII = {
+    "H": 0.31,
+    "HE": 0.28,
+    "LI": 1.28,
+    "BE": 0.96,
+    "B": 0.85,
+    "C": 0.76,
+    "N": 0.71,
+    "O": 0.66,
+    "F": 0.57,
+    "NE": 0.58,
+    "NA": 1.66,
+    "MG": 1.41,
+    "AL": 1.21,
+    "SI": 1.11,
+    "P": 1.07,
+    "S": 1.05,
+    "CL": 1.02,
+    "AR": 1.06,
+    "K": 2.03,
+    "CA": 1.76,
+    "SC": 1.7,
+    "TI": 1.6,
+    "V": 1.53,
+    "CR": 1.39,
+    "MN": 1.39,
+    "FE": 1.32,
+    "CO": 1.26,
+    "NI": 1.24,
+    "CU": 1.32,
+    "ZN": 1.22,
+    "GA": 1.22,
+    "GE": 1.2,
+    "AS": 1.19,
+    "SE": 1.2,
+    "BR": 1.2,
+    "KR": 1.16,
+    "RB": 2.2,
+    "SR": 1.95,
+    "Y": 1.9,
+    "ZR": 1.75,
+    "NB": 1.64,
+    "MO": 1.54,
+    "TC": 1.47,
+    "RU": 1.46,
+    "RH": 1.42,
+    "PD": 1.39,
+    "AG": 1.45,
+    "CD": 1.44,
+    "IN": 1.42,
+    "SN": 1.39,
+    "SB": 1.39,
+    "TE": 1.38,
+    "I": 1.39,
+    "XE": 1.4,
+    "CS": 2.44,
+    "BA": 2.15,
+    "LA": 2.07,
+    "CE": 2.04,
+    "PR": 2.03,
+    "ND": 2.01,
+    "PM": 1.99,
+    "SM": 1.98,
+    "EU": 1.98,
+    "GD": 1.96,
+    "TB": 1.94,
+    "DY": 1.92,
+    "HO": 1.92,
+    "ER": 1.89,
+    "TM": 1.9,
+    "YB": 1.87,
+    "LU": 1.87,
+    "HF": 1.75,
+    "TA": 1.7,
+    "W": 1.62,
+    "RE": 1.51,
+    "OS": 1.44,
+    "IR": 1.41,
+    "PT": 1.36,
+    "AU": 1.36,
+    "HG": 1.32,
+    "TL": 1.45,
+    "PB": 1.46,
+    "BI": 1.48,
+    "PO": 1.4,
+    "AT": 1.5,
+    "RN": 1.5,
+    "FR": 2.6,
+    "RA": 2.21,
+    "AC": 2.15,
+    "TH": 2.06,
+    "PA": 2.0,
+    "U": 1.96,
+    "NP": 1.9,
+    "PU": 1.87,
+    "AM": 1.8,
+    "CM": 1.69,
+}
+METALS = [
+    "LI",
+    "BE",
+    "NA",
+    "MG",
+    "AL",
+    "K",
+    "CA",
+    "SC",
+    "TI",
+    "V",
+    "CR",
+    "MN",
+    "FE",
+    "CO",
+    "NI",
+    "CU",
+    "ZN",
+    "HA",
+    "RB",
+    "SR",
+    "Y",
+    "ZR",
+    "NB",
+    "MO",
+    "TC",
+    "RU",
+    "RH",
+    "PD",
+    "AG",
+    "CD",
+    "IN",
+    "SN",
+    "CS",
+    "BA",
+    "LA",
+    "CE",
+    "PR",
+    "ND",
+    "PM",
+    "SM",
+    "EU",
+    "GD",
+    "TB",
+    "DY",
+    "HO",
+    "ER",
+    "TM",
+    "YB",
+    "LU",
+    "HF",
+    "TA",
+    "W",
+    "RE",
+    "OS",
+    "IR",
+    "PT",
+    "AU",
+    "HG",
+    "TL",
+    "PB",
+    "BI",
+    "PO",
+    "FR",
+    "RA",
+    "AC",
+    "TH",
+    "PA",
+    "U",
+    "NP",
+    "PU",
+    "AM",
+    "CM",
+    "BK",
+    "CF",
+    "ES",
+    "FM",
+    "MD",
+    "NO",
+    "LR",
+    "RF",
+    "DB",
+    "SG",
+    "BH",
+    "HS",
+    "MT",
+    "DS",
+    "RG",
+    "CN",
+    "UUT",
+    "FL",
+    "LV",
+]
+FULL_NAMES = {
+    "GLY": "glycine",
+    "ALA": "alanine",
+    "VAL": "valine",
+    "LEU": "leucine",
+    "ILE": "isoleucine",
+    "MET": "methionine",
+    "PHE": "phenylalanine",
+    "TRP": "tryptophan",
+    "PRO": "proline",
+    "SER": "serine",
+    "THR": "threonine",
+    "CYS": "cysteine",
+    "TYR": "tyrosine",
+    "ASN": "asparagine",
+    "GLN": "glutamine",
+    "ASP": "aspartic acid",
+    "GLU": "glutamic acid",
+    "LYS": "lysine",
+    "ARG": "arginine",
+    "HIS": "histidine",
+    "HOH": "water",
+}
+CODES = {
+    "VAL": "V",
+    "ILE": "I",
+    "LEU": "L",
+    "GLU": "E",
+    "GLN": "Q",
+    "ASP": "D",
+    "ASN": "N",
+    "HIS": "H",
+    "TRP": "W",
+    "PHE": "F",
+    "TYR": "Y",
+    "ARG": "R",
+    "LYS": "K",
+    "SER": "S",
+    "THR": "T",
+    "MET": "M",
+    "ALA": "A",
+    "GLY": "G",
+    "PRO": "P",
+    "CYS": "C",
+}
+REVERSE_CODES = {
+    "V": "VAL",
+    "I": "ILE",
+    "L": "LEU",
+    "E": "GLU",
+    "Q": "GLN",
+    "D": "ASP",
+    "N": "ASN",
+    "H": "HIS",
+    "W": "TRP",
+    "F": "PHE",
+    "Y": "TYR",
+    "R": "ARG",
+    "K": "LYS",
+    "S": "SER",
+    "T": "THR",
+    "M": "MET",
+    "A": "ALA",
+    "G": "GLY",
+    "P": "PRO",
+    "C": "CYS",
+}

stjames 0.0.52__tar.gz → 0.0.53__tar.gz

Potentially problematic release.

stjames 0.0.52tar.gz → 0.0.53tar.gz