update

keisuke-yanagisawa · Nov 4, 2023 · e19d9c6 · e19d9c6
1 parent bc72911
commit e19d9c6
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Showing 5 changed files with 30 additions and 7 deletions.
diff --git a/script/utilities/Bio/PDB.py b/script/utilities/Bio/PDB.py
@@ -23,6 +23,7 @@
 from Bio.PDB.Structure import Structure
 import numpy.typing as npt
 from ..scipy.spatial_func import estimate_volume
+from ..util import expandpath
 
 
 class AtomSelector(PDB.Select):
@@ -137,7 +138,7 @@ class PDBIOhelper():
     """
 
     def __init__(self, path: str):
-        self.path = path
+        self.path = expandpath(path)
         self.open()
 
     def __enter__(self):
@@ -197,6 +198,7 @@ def get_structure(filepath: str, structname="") -> Structure:
     Bio.PDB.Structure
         Structure object of the PDB file
     """
+    filepath = expandpath(filepath)
     if filepath.endswith(".gz"):
         fileobj = gzip.open(filepath, "rt")
     else:
@@ -414,6 +416,7 @@ def save(structs, path) -> None:
     structs : Bio.PDB.Struct or list of Bio.PDB.Struct
     path : str
     """
+    path = expandpath(path)
 
     if not isinstance(structs, Iterable):
         structs = [structs]

diff --git a/script/utilities/executable/cpptraj.py b/script/utilities/executable/cpptraj.py
@@ -43,7 +43,7 @@ def run(self, basedir, prefix, box_center=[0., 0., 0.], box_size=80, interval=1,
         self._gen_parm7()
 
         _, self.inp = tempfile.mkstemp(prefix=const.TMP_PREFIX, suffix=const.EXT_INP)
-        _, tmp_rmsdfile = tempfile.mkstemp(suffix=".dat")
+        rmsdfile = "rmsd.dat"
         _, tmp_volumefile = tempfile.mkstemp(suffix=".dat")
 
         data = {
@@ -56,7 +56,7 @@ def run(self, basedir, prefix, box_center=[0., 0., 0.], box_size=80, interval=1,
             "map_voxel": " ".join([str(n) for n in self.voxel]) + " gridcenter " + " ".join([str(x) for x in box_center]),
             "prefix": self.prefix,
             "maps": maps,
-            "tmp_rmsdfile": tmp_rmsdfile,
+            "rmsdfile": rmsdfile,
             "tmp_volumefile": tmp_volumefile,
         }
 
@@ -67,13 +67,16 @@ def run(self, basedir, prefix, box_center=[0., 0., 0.], box_size=80, interval=1,
             logger.info(template.render(data))
         command = Command(f"{self.exe} < {self.inp}")
         logger.debug(command)
-        logger.info(command.run())
+        try:
+            logger.info(command.run())
+        except e:
+            Command(f"cat {self.inp}")
+            raise e
 
         for i in range(len(maps)):
             maps[i]["grid"] = f"{self.basedir}/{self.prefix}_{maps[i]['suffix']}.dx"
 
-        self.frames = len(open(tmp_rmsdfile).readlines()) - 1  # -1 for header line
-        os.system(f"rm {tmp_rmsdfile}")
+        self.frames = len(open(rmsdfile).readlines()) - 1  # -1 for header line
         self.last_volume = float(open(tmp_volumefile).readlines()[-1].split()[1])
         os.system(f"rm {tmp_volumefile}")
         for i in range(len(maps)):

diff --git a/script/utilities/executable/parmchk.py b/script/utilities/executable/parmchk.py
@@ -3,6 +3,7 @@
 from .execute import Command
 from .. import const
 from ..logger import logger
+from ..util import expandpath
 
 
 class Parmchk(object):
@@ -12,6 +13,7 @@ def __init__(self, debug=False):
         self.debug = debug
 
     def set(self, mol2, at):
+        mol2 = expandpath(mol2)
         if at not in self.at_indices:
             raise ValueError(f"atomtype {at} is not supported")
         if not os.path.exists(mol2):

diff --git a/script/utilities/executable/template/cpptraj_pmap.in b/script/utilities/executable/template/cpptraj_pmap.in
@@ -10,7 +10,7 @@ center @CA&(!:CA)&(!:{{ cid }})
 fiximagedbonds
 autoimage
 
-rms ToREF ref [REF] @CA&(!:CA)&(!:{{ cid }}) @CA&(!:CA)&(!:{{ cid }}) out {{ tmp_rmsdfile }}
+rms ToREF ref [REF] @CA&(!:CA)&(!:{{ cid }}) @CA&(!:CA)&(!:{{ cid }}) out {{ basedir }}/{{ rmsdfile }}
 
 {% for MAP in maps %}
 grid {{ basedir }}/{{ prefix }}_{{ MAP.suffix }}.dx {{ map_voxel }} :{{ cid }}&{{ MAP.selector }}

diff --git a/script/utilities/util.py b/script/utilities/util.py
@@ -132,17 +132,32 @@ def parse_yaml(yamlpath: str) -> dict:
         setting["input"]["probe"]["pdb"] \
             = setting["input"]["probe"]["cid"] + ".pdb"
 
+    setting["general"]["workdir"] = expandpath(setting["general"]["workdir"])
     setting["general"]["workdir"] = setting["general"]["workdir"] \
         if setting["general"]["workdir"].startswith("/") \
+           or setting["general"]["workdir"].startswith("$HOME") \
+           or setting["general"]["workdir"].startswith("~") \
         else YAML_DIR_PATH + "/" + setting["general"]["workdir"]
+
+    setting["input"]["protein"]["pdb"] = expandpath(setting["input"]["protein"]["pdb"])
     setting["input"]["protein"]["pdb"] = setting["input"]["protein"]["pdb"] \
         if setting["input"]["protein"]["pdb"].startswith("/") \
+           or setting["input"]["protein"]["pdb"].startswith("$HOME") \
+           or setting["input"]["protein"]["pdb"].startswith("~") \
         else YAML_DIR_PATH + "/" + setting["input"]["protein"]["pdb"]
+
+    setting["input"]["probe"]["pdb"] = expandpath(setting["input"]["probe"]["pdb"])
     setting["input"]["probe"]["pdb"] = setting["input"]["probe"]["pdb"] \
         if setting["input"]["probe"]["pdb"].startswith("/") \
+           or setting["input"]["probe"]["pdb"].startswith("$HOME") \
+           or setting["input"]["probe"]["pdb"].startswith("~") \
         else YAML_DIR_PATH + "/" + setting["input"]["probe"]["pdb"]
+
+    setting["input"]["probe"]["mol2"] = expandpath(setting["input"]["probe"]["mol2"])
     setting["input"]["probe"]["mol2"] = setting["input"]["probe"]["mol2"] \
         if setting["input"]["probe"]["mol2"].startswith("/") \
+           or setting["input"]["probe"]["mol2"].startswith("$HOME") \
+           or setting["input"]["probe"]["mol2"].startswith("~") \
         else YAML_DIR_PATH + "/" + setting["input"]["probe"]["mol2"]
 
     if setting["input"]["protein"]["ssbond"] is None: