PyPI - stjames - Versions diffs - 0.0.52__tar.gz → 0.0.54__tar.gz - Mend

stjames 0.0.52tar.gz → 0.0.54tar.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.

Potentially problematic release.

This version of stjames might be problematic. Click here for more details.

Files changed (76) hide show

{stjames-0.0.52/stjames.egg-info → stjames-0.0.54}/PKG-INFO RENAMED Viewed

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: stjames
-Version: 0.0.52
+Version: 0.0.54
 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-0.0.54}/pyproject.toml RENAMED Viewed

@@ -1,6 +1,6 @@
 [project]
 name = "stjames"
-version = "0.0.52"
+version = "0.0.54"
 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-0.0.54/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-0.0.54/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 → 0.0.54__tar.gz

Potentially problematic release.

stjames 0.0.52tar.gz → 0.0.54tar.gz