Merge pull request #70 from 3dem/mmcifio-fix

Mmcifio fix

install_script.sh

@@ -42,7 +42,7 @@ then
   exit 1;
 fi
 
-conda install pytorch torchvision torchaudio pytorch-cuda=11.7 -c pytorch -c nvidia
+conda install pytorch torchvision torchaudio pytorch-cuda=11.7 -c pytorch -c nvidia -y
 
 if [ "${torch_home_path}" ]
 then
@@ -51,7 +51,6 @@ fi
 
 python_exc="${CONDA_PREFIX}/bin/python"
 
-$python_exc -mpip install -r requirements.txt
 $python_exc setup.py install
 
 if [[ "${DOWNLOAD_WEIGHTS}" ]]; then

model_angelo/__init__.py

@@ -5,4 +5,4 @@
 """
 
 
-__version__ = "1.0.1"
+__version__ = "1.0.2"

model_angelo/utils/save_pdb_utils.py

@@ -2,14 +2,15 @@
 import os
 import pickle
 from typing import List, Union
+from copy import deepcopy
 
 import numpy as np
 import pandas as pd
 from Bio.PDB.mmcifio import MMCIFIO
 from Bio.PDB.StructureBuilder import StructureBuilder
 
 from model_angelo.utils.misc_utils import assertion_check
-from model_angelo.utils.protein import Protein, frames_and_literature_positions_to_atomc_pos, \
+from model_angelo.utils.protein import Protein, \
     frames_and_literature_positions_to_atom3_pos
 from model_angelo.utils.residue_constants import (
     index_to_restype_3,
@@ -24,6 +25,16 @@
 SEQUENCE_BASED_CHAIN_IDS = "abcdefghijklmnopqrstuvwxyz0123456789"
 
 
+
+class ModelAngeloMMCIFIO(MMCIFIO):
+    def _save_dict(self, out_file):
+        auth_seq_id = deepcopy(self.dic["_atom_site.label_seq_id"])
+        label_seq_id = deepcopy(self.dic["_atom_site.auth_seq_id"])
+        self.dic["_atom_site.label_seq_id"] = label_seq_id
+        self.dic["_atom_site.auth_seq_id"] = auth_seq_id
+        return super()._save_dict(out_file)
+
+
 def number_to_base(n, b):
     """
     From https://stackoverflow.com/questions/2267362/how-to-convert-an-integer-to-a-string-in-any-base
@@ -69,6 +80,12 @@ def points_to_xyz(path_to_save, points, zyx_order=False):
                 f.write(f"C {point[2]} {point[1]} {point[0]}\n")
 
 
+def save_structure_to_cif(structure, path_to_save: str):
+    io = ModelAngeloMMCIFIO()
+    io.set_structure(structure)
+    io.save(path_to_save)
+
+
 def points_to_pdb(path_to_save, points):
     struct = StructureBuilder()
     struct.init_structure("1")
@@ -80,9 +97,7 @@ def points_to_pdb(path_to_save, points):
         struct.init_residue(f"ALA", " ", i, " ")
         struct.init_atom("CA", point, 0, 1, " ", "CA", "C")
     struct = struct.get_structure()
-    io = MMCIFIO()
-    io.set_structure(struct)
-    io.save(path_to_save)
+    save_structure_to_cif(struct, path_to_save)
 
 
 def ca_ps_to_pdb(path_to_save, ca_points, p_points):
@@ -118,9 +133,7 @@ def ca_ps_to_pdb(path_to_save, ca_points, p_points):
             element="P",
         )
     struct = struct.get_structure()
-    io = MMCIFIO()
-    io.set_structure(struct)
-    io.save(path_to_save)
+    save_structure_to_cif(struct, path_to_save)
 
 
 def chains_to_pdb(path_to_save, chains):
@@ -135,9 +148,7 @@ def chains_to_pdb(path_to_save, chains):
             struct.init_residue(f"ALA", " ", j, " ")
             struct.init_atom("CA", point, 0, 1, " ", "CA", "C")
     struct = struct.get_structure()
-    io = MMCIFIO()
-    io.set_structure(struct)
-    io.save(path_to_save)
+    save_structure_to_cif(struct, path_to_save)
 
 
 def to_xyz(directory):
@@ -208,9 +219,7 @@ def atom14_to_cif(
             )
             res_counter += 1
     struct = struct.get_structure()
-    io = MMCIFIO()
-    io.set_structure(struct)
-    io.save(path_to_save)
+    save_structure_to_cif(struct, path_to_save)
 
 
 def protein_to_cif(
@@ -280,9 +289,7 @@ def protein_to_cif(
             )
             res_counter += 1
     struct = struct.get_structure()
-    io = MMCIFIO()
-    io.set_structure(struct)
-    io.save(path_to_save)
+    save_structure_to_cif(struct, path_to_save)
 
 
 def chain_atom14_to_cif(
@@ -363,9 +370,7 @@ def chain_atom14_to_cif(
                 res_counter += 1
 
     struct = struct.get_structure()
-    io = MMCIFIO()
-    io.set_structure(struct)
-    io.save(path_to_save)
+    save_structure_to_cif(struct, path_to_save)
 
 
 def write_chain_report(

setup.py

@@ -24,4 +24,16 @@
     },
     package_data={'': ['utils/stereo_chemical_props.txt']},
     version=model_angelo.__version__,
+    install_requires=[
+        "tqdm",
+        "scipy",
+        "biopython>=1.81",
+        "einops",
+        "matplotlib",
+        "mrcfile",
+        "pandas",
+        "fair-esm",
+        "pyhmmer>=0.10.1",
+        "loguru",
+    ],
 )

test/bc3-new.fasta

@@ -0,0 +1,2 @@
+>5UDE_1|Chain A[auth F]|Fusion glycoprotein F0|Human Respiratory syncytial virus 9320 (253182)
+MKCLLYLAFLFIGVNCQNITEEFYQSTCSAVSRGYFSALRTGWYTSVITIELSNIKEPKCNGTDTKVKLIKQELDKYKNAVTELQLLMQSGGPGSGGGGSGGGGSRFPPFPLGVGSAIASGIAVSKVLHLPGEVNKIKNALLSTNKAVVSLSNGVSVLTSKVLDLKNYINNQLLPIVNQQSCRISNIETVIEFQQKNSRLLEITREFSVNAGVTTPLSTYMLTNSELLSLINDMPITNDQKKLMSSNVPIVRQQSYSIMSIIKEEVLAYVVQLPIYGVIDTPCWKLHTSPLCTTNIKEGSNICLTRTDRGWYCDNAGSVSFFPQADTCKVQSNRVFCDTMNSLTLPPEVSLCNTDIFNSKYDCKIMTSKTDISSSVITSLGAIVSCYGKTKCTASNKNRGIIKTFSNGCDYVSNKGVDTVSVGNTLYYVNKLEGKNLYVKGEPIINYYDPLVFPSDEFDASISQVNEKINQSLAFIRRSDELLGSGYIPEAPRDGQAYVRKDGEWVLLSTFLG