Adding bcifreader

uibcdf · Dec 16, 2024 · b9204c5 · b9204c5
1 parent 902c65a
commit b9204c5
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Showing 10 changed files with 13 additions and 15 deletions.
diff --git a/devtools/conda-build/meta.yaml b/devtools/conda-build/meta.yaml
@@ -33,8 +33,7 @@ requirements:
   - biopython
   - ipywidgets
   - tqdm
-  - pip:
-    - mmcif
+  - bcifreader
 about:
   home: https://uibcdf.org
   license: MIT License

diff --git a/devtools/conda-envs/development_env.yaml b/devtools/conda-envs/development_env.yaml
@@ -25,8 +25,7 @@ dependencies:
 - biopython
 - ipywidgets
 - tqdm
-- pip:
-  - mmcif
+- bcifreader
 - pytest
 - pytest-cov
 - codecov

diff --git a/devtools/conda-envs/docs_env.yaml b/devtools/conda-envs/docs_env.yaml
@@ -25,8 +25,7 @@ dependencies:
 - biopython
 - ipywidgets
 - tqdm
-- pip:
-  - mmcif
+- bcifreader
 - jupyterlab
 - sphinx
 - pydata-sphinx-theme

diff --git a/devtools/conda-envs/production_env.yaml b/devtools/conda-envs/production_env.yaml
@@ -25,5 +25,4 @@ dependencies:
 - biopython
 - ipywidgets
 - tqdm
-- pip:
-  - mmcif
+- bcifreader
diff --git a/devtools/conda-envs/test_env.yaml b/devtools/conda-envs/test_env.yaml
@@ -25,8 +25,7 @@ dependencies:
 - biopython
 - ipywidgets
 - tqdm
-- pip:
-  - mmcif
+- bcifreader
 - pytest
 - pytest-cov
 - codecov

diff --git a/devtools/requirements.yaml b/devtools/requirements.yaml
@@ -32,8 +32,7 @@ production:
     - biopython
     - ipywidgets
     - tqdm
-    - pip:
-      - mmcif
+    - bcifreader
 
 test:
   channels: &test_channels

diff --git a/molsysmt/form/file_bcif/to_mmcif_PdbxContainers_DataContainer.py b/molsysmt/form/file_bcif/to_mmcif_PdbxContainers_DataContainer.py
@@ -3,7 +3,8 @@
 @digest(form='file:cif')
 def to_mmcif_PdbxContainers_DataContainer(item, atom_indices='all', skip_digestion=False):
 
-    from mmcif.io.BinaryCifReader import BinaryCifReader
+    #from mmcif.io.BinaryCifReader import BinaryCifReader
+    from bcifreader import BinaryCifReader
 
     binary_cif_reader = BinaryCifReader()
     containers = binary_cif_reader.deserialize(item)

diff --git a/molsysmt/form/file_bcif_gz/to_mmcif_PdbxContainers_DataContainer.py b/molsysmt/form/file_bcif_gz/to_mmcif_PdbxContainers_DataContainer.py
@@ -3,7 +3,8 @@
 @digest(form='file:cif.gz')
 def to_mmcif_PdbxContainers_DataContainer(item, atom_indices='all', skip_digestion=False):
 
-    from mmcif.io.BinaryCifReader import BinaryCifReader
+    #from mmcif.io.BinaryCifReader import BinaryCifReader
+    from bcifreader import BinaryCifReader
 
     binary_cif_reader = BinaryCifReader()
     containers = binary_cif_reader.deserialize(item)

diff --git a/molsysmt/form/string_pdb_id/to_mmcif_PdbxContainers_DataContainer.py b/molsysmt/form/string_pdb_id/to_mmcif_PdbxContainers_DataContainer.py
@@ -3,7 +3,8 @@
 @digest(form='string:pdb_id')
 def to_mmcif_PdbxContainers_DataContainer(item, atom_indices='all', structure_indices='all', skip_digestion=False):
 
-    from mmcif.io.BinaryCifReader import BinaryCifReader
+    #from mmcif.io.BinaryCifReader import BinaryCifReader
+    from bcifreader import BinaryCifReader
 
 
     tmp_item = item.split(':')[-1]

diff --git a/pyproject.toml b/pyproject.toml
@@ -37,6 +37,7 @@ dependencies = [
     "biopython",
     "tqdm",
     "ipywidgets",
+    "bcifreader"
 ]
 
 # Update the urls once the hosting is set up.