[WIP] Very rough initial draft of mmcif parser

README.md

@@ -75,7 +75,7 @@ RMSD: 2.6444 Angstrom
 
 #### Requirements
 
-- [Python](https://www.python.org) 2.7, 3.5, or 3.6
+- [Python](https://www.python.org) >=3.7
 - [NumPy](http://www.numpy.org) >= 1.11.2
 - [SciPy](https://www.scipy.org/scipylib/index.html) >= 0.18.1
 - [Pandas](http://pandas.pydata.org) >= 0.19.1

biopandas/mmcif/__init__.py

@@ -0,0 +1,15 @@
+# BioPandas
+# Authors: Sebastian Raschka <mail@sebastianraschka.com>
+# Authors: Arian Jamasb <arian@jamasb.io>
+# License: BSD 3 clause
+# Project Website: http://rasbt.github.io/biopandas/
+# Code Repository: https://github.com/rasbt/biopandas
+
+"""
+BioPandas module for working with mmCIF
+files in pandas DataFrames.
+"""
+
+from .pandas_mmcif import PandasMmcif
+
+__all__ = ["PandasMmcif"]

biopandas/mmcif/engines.py

@@ -0,0 +1,46 @@
+from typing import Any, Dict
+
+mmcif_col_types: Dict[str, Any] = {
+    "B_iso_or_equiv": float,
+    "Cartn_x": float,
+    "Cartn_y": float,
+    "Cartn_z": float,
+    "auth_asym_id": str,
+    "auth_atom_id": str,
+    "auth_comp_id": str,
+    "auth_seq_id": int,
+    "group_PDB": str,
+    "id": int,
+    "label_alt_id": int,
+    "label_asym_id": str,
+    "label_atom_id": str,
+    "label_comp_id": str,
+    "label_entity_id": int,
+    "label_seq_id": int,
+    "occupancy": float,
+    "pdbx_PDB_ins_code": str,
+    "pdbx_PDB_model_num": int,
+    "pdbx_formal_charge": int,
+    "type_symbol": str,
+}
+
+ANISOU_DF_COLUMNS = [
+    "id",
+    "type_symbol",
+    "pdbx_label_atom_id",
+    "pdbx_label_alt_id",
+    "pdbx_label_comp_id",
+    "pdbx_label_asym_id",
+    "pdbx_label_seq_id",
+    "pdbx_PDB_ins_code",
+    "U[1][1]",
+    "U[2][2]",
+    "U[3][3]",
+    "U[1][2]",
+    "U[1][3]",
+    "U[2][3]",
+    "pdbx_auth_seq_id",
+    "pdbx_auth_comp_id",
+    "pdbx_auth_asym_id",
+    "pdbx_auth_atom_id",
+]