fix default options

app.py

@@ -240,11 +240,12 @@ def predict(
     order = int(order)
 
     max_extra_msa = max_msa * 8
+    print("sequence", sequence)
     sequence = re.sub("[^A-Z:]", "", sequence.replace("/", ":").upper())
     sequence = re.sub(":+", ":", sequence)
     sequence = re.sub("^[:]+", "", sequence)
     sequence = re.sub("[:]+$", "", sequence)
-
+    print("sequence", sequence)
     if sym in ["X", "C"]:
         copies = int(order)
     elif sym in ["D"]:
@@ -270,7 +271,7 @@ def predict(
 
     print(f"jobname: {jobname}")
     print(f"lengths: {lengths}")
-
+    print("final_sequence", u_sequences)
     os.makedirs(jobname, exist_ok=True)
     if msa_method == "mmseqs2":
         get_msa(u_sequences, jobname, mode=pair_mode, max_msa=max_extra_msa)
@@ -279,19 +280,17 @@ def predict(
         u_sequence = "/".join(u_sequences)
         with open(f"{jobname}/msa.a3m", "w") as a3m:
             a3m.write(f">{jobname}\n{u_sequence}\n")
-
-    elif msa_method == "custom_a3m":
-        print("upload custom a3m")
-        # msa_dict = files.upload()
-        lines = msa_dict[list(msa_dict.keys())[0]].decode().splitlines()
-        a3m_lines = []
-        for line in lines:
-            line = line.replace("\x00", "")
-            if len(line) > 0 and not line.startswith("#"):
-                a3m_lines.append(line)
-
-        with open(f"{jobname}/msa.a3m", "w") as a3m:
-            a3m.write("\n".join(a3m_lines))
+    # elif msa_method == "custom_a3m":
+    #     print("upload custom a3m")
+    #     # msa_dict = files.upload()
+    #     lines = msa_dict[list(msa_dict.keys())[0]].decode().splitlines()
+    #     a3m_lines = []
+    #     for line in lines:
+    #         line = line.replace("\x00", "")
+    #         if len(line) > 0 and not line.startswith("#"):
+    #             a3m_lines.append(line)
+    #     with open(f"{jobname}/msa.a3m", "w") as a3m:
+    #         a3m.write("\n".join(a3m_lines))
 
     best_plddt = None
     best_seed = None
@@ -300,13 +299,15 @@ def predict(
         random.seed(seed)
         np.random.seed(seed)
         npz = f"{jobname}/rf2_seed{seed}_00.npz"
+        mlm = 0.15 if use_mlm else 0
+        print("MLM", mlm, use_mlm)
         pred.predict(
             inputs=[f"{jobname}/msa.a3m"],
             out_prefix=f"{jobname}/rf2_seed{seed}",
             symm=symm,
             ffdb=None,  # TODO (templates),
             n_recycles=num_recycles,
-            msa_mask=0.15 if use_mlm else 0.0,
+            msa_mask=0.15 if use_mlm else 0,
             msa_concat_mode=msa_concat_mode,
             nseqs=max_msa,
             nseqs_full=max_extra_msa,

rosettafold_pymol.py

@@ -1,6 +1,7 @@
 from pymol import cmd
 import requests
 
+import os
 
 # from gradio_client import Client
 
@@ -68,13 +69,13 @@ def query_rosettafold2(
     msa_concat_mode: str = "diag",
     msa_method: str = "single_sequence",
     pair_mode: str = "unpaired_paired",
-    collapse_identical: bool = True,
-    num_recycles: int = 0,
-    use_mlm: bool = True,
-    use_dropout: bool = True,
+    collapse_identical: bool = False,
+    num_recycles: int = 1,
+    use_mlm: bool = False,
+    use_dropout: bool = False,
     max_msa: int = 16,
     random_seed: int = 0,
-    num_models: int = 0,
+    num_models: int = 1,
 ):
     """
     AUTHOR
@@ -115,13 +116,13 @@ def query_rosettafold2(
     Collapse identical sequences Default:True
 
     num_recycles:
-    Number of recycles Default:0 Options: 0, 1, 3, 6, 12, 24
+    Number of recycles Default:6 Options: 0, 1, 3, 6, 12, 24
 
     use_mlm:
-    Use MLM Default:True
+    Use MLM Default:False
 
     use_dropout:
-    Use dropout Default:True
+    Use dropout Default:False
 
     max_msa:
     Max MSA Default:16
@@ -132,8 +133,13 @@ def query_rosettafold2(
     num_models:
     Number of models Default:0
     """
+    if os.path.exists("/home/user/app/"):
+        url = "https://simonduerr-rosettafold2.hf.space"
+    else:
+        url = "http://localhost:7860"
+
     response = requests.post(
-        "https://simonduerr-rosettafold2.hf.space/run/rosettafold2/",
+        url + "/run/rosettafold2/",
         json={
             "data": [
                 sequence,  # str  in 'sequence' Textbox component
@@ -143,10 +149,10 @@ def query_rosettafold2(
                 "diag",  # str (Option from: ['diag', 'repeat', 'default']) in 'msa_concat_mode' Dropdown component
                 "single_sequence",  # str (Option from: ['mmseqs2', 'single_sequence', 'custom_a3m']) in 'msa_method' Dropdown component
                 "unpaired_paired",  # str (Option from: ['unpaired_paired', 'paired', 'unpaired']) in 'pair_mode' Dropdown component
-                True,  # bool  in 'collapse_identical' Checkbox component
-                0,  # int (Option from: ['0', '1', '3', '6', '12', '24']) in 'num_recycles' Dropdown component
-                True,  # bool  in 'use_mlm' Checkbox component
-                True,  # bool  in 'use_dropout' Checkbox component
+                False,  # bool  in 'collapse_identical' Checkbox component
+                6,  # int (Option from: ['0', '1', '3', '6', '12', '24']) in 'num_recycles' Dropdown component
+                False,  # bool  in 'use_mlm' Checkbox component
+                False,  # bool  in 'use_dropout' Checkbox component
                 16,  # int (Option from: ['16', '32', '64', '128', '256', '512']) in 'max_msa' Dropdown component
                 0,  # int  in 'random_seed' Textbox component
                 1,  # int (Option from: ['1', '2', '4', '8', '16', '32']) in 'num_models' Dropdown component