rdworks 0.53.1__py3-none-any.whl → 0.54.2__py3-none-any.whl

rdworks/__init__.py

@@ -1,4 +1,4 @@
-__version__ = '0.53.1'
+__version__ = '0.54.2'
 
 from rdworks.conf    import Conf
 from rdworks.mol     import Mol

rdworks/microstates.py

@@ -1,12 +1,16 @@
 import numpy as np
 import math
 import itertools
+import logging
 
 from types import SimpleNamespace
 from rdworks import Conf, Mol
 from rdworks.xtb.wrapper import GFN2xTB
 
 
+logger = logging.getLogger(__name__)
+
+
 kT = 0.001987 * 298.0 # (kcal/mol K), standard condition
 C = math.log(10) * kT
 
@@ -23,9 +27,10 @@ class Microstates():
         self.mols = []
         self.reference = None
     
-        # read QupKake results
+
+    def enumerate(self) -> None:
+        # Qu pKake results must be stored at .confs
         for conf in self.origin:
-            print(conf.props)
             pka = conf.props.get('pka', None)
             if pka is None:
                 # no protonation/deprotonation sites
@@ -49,7 +54,7 @@ class Microstates():
         
         for (p, d) in PD:
             conf = self.origin.confs[0].copy()
-            conf = conf.protonate(p).deprotonate(d).optimize(calculator=calculator)
+            conf = conf.protonate(p).deprotonate(d).optimize(calculator=self.calculator)
             charge = len(p) - len(d)
             self.states.append(SimpleNamespace(
                 charge=charge, 
@@ -83,7 +88,7 @@ class Microstates():
         return float(np.dot(p, pe_array))
 
 
-    def potential_energy(self) -> None:
+    def populate(self) -> None:
         for microstate in self.states:
             mol = Mol(microstate.conf).make_confs(n=4).optimize_confs()
             # mol = mol.drop_confs(similar=True, similar_rmsd=0.3, verbose=True)
@@ -94,23 +99,21 @@ class Microstates():
                 conf = conf.optimize(calculator=self.calculator, verbose=True)
                 # GFN2xTB requires 3D coordinates
                 # xtb = GFN2xTB(conf.rdmol).singlepoint(water='cpcmx', verbose=True)
-                xtb = GFN2xTB(conf.rdmol).singlepoint(verbose=True)
-                PE.append(xtb.PE)
+                PE.append(conf.potential_energy(calculator=self.calculator))
+                # xtb = GFN2xTB(conf.rdmol).singlepoint(verbose=True)
                 # SimpleNamespace(
                 #             PE = datadict['total energy'] * hartree2kcalpermol,
                 #             Gsolv = Gsolv,
                 #             charges = datadict['partial charges'],
                 #             wbo = Wiberg_bond_orders,
                 #             )
-            print("PE=", PE)
             microstate.PE = self.Boltzmann_weighted_average(PE)
-            print("Boltzmann weighted=", microstate.PE)
-            
+            logger.info(f"PE= {PE}")
+            logger.info(f"Boltzmann weighted= {microstate.PE}")            
             self.mols.append(mol)
-            print("microstate.energy", microstate)
 
 
-    def populations(self, pH: float) -> list[tuple]:
+    def get_populations(self, pH: float) -> list[tuple]:
         # set the lowest dG as the reference
         self.reference = self.states[np.argmin([microstate.PE for microstate in self.states])]
         for microstate in self.states:
@@ -120,7 +123,7 @@ class Microstates():
             dG.append((microstate.PE - self.reference.PE) + microstate.delta_m * C * pH)
         dG = np.array(dG)
 
-        print("dG=", dG)
+        logger.info(f"dG= {dG}")
         Boltzmann_factors = np.exp(-dG/kT)
         Z = np.sum(Boltzmann_factors)
         p = Boltzmann_factors/Z
@@ -128,11 +131,16 @@ class Microstates():
         # [(0, p0), (1, p1), ...]
 
         return idx_p
+
+
+    def get_ensemble(self) -> list[Mol]:
+        return self.mols
+
+
+    def get_mol(self, idx: int) -> Mol:
+        return self.mols[idx]
     
 
     def count(self) -> int:
         return len(self.states)
     
-
-    def get_mol(self, idx: int) -> Mol:
-        return self.mols[idx]

rdworks/xtb/wrapper.py

@@ -79,7 +79,8 @@ class GFN2xTB:
                 proc = subprocess.run(['xtb', test_geometry, '--opt'],
                                       cwd=temp_dir,
                                       capture_output=True, 
-                                      text=True)
+                                      text=True,
+                                      encoding='utf-8')
                 assert proc.returncode == 0
 
             return True
@@ -122,7 +123,7 @@ $ cp -r xtb-dist/share      /usr/local/ """)
         if GFN2xTB.is_xtb_ready():
             with tempfile.TemporaryDirectory() as temp_dir: # tmpdir is a string
                 cmd = ['xtb', '--cpcmx']
-                proc = subprocess.run(cmd, cwd=temp_dir, capture_output=True, text=True)
+                proc = subprocess.run(cmd, cwd=temp_dir, capture_output=True, text=True, encoding='utf-8')
                 # we are expecting an error because no input file is given
                 assert proc.returncode != 0
                 for line in proc.stdout.split('\n'):
@@ -156,7 +157,7 @@ $ cp -r xtb-dist/share      /usr/local/ """)
         if GFN2xTB.is_xtb_ready():
             with tempfile.TemporaryDirectory() as temp_dir: # tmpdir is a string
                 cmd = ['xtb', '--version']
-                proc = subprocess.run(cmd, cwd=temp_dir, capture_output=True, text=True)
+                proc = subprocess.run(cmd, cwd=temp_dir, capture_output=True, text=True, encoding='utf-8')
                 assert proc.returncode == 0, "GFN2xTB() Error: xtb not available"
                 match = re.search('xtb\s+version\s+(?P<version>[\d.]+)', proc.stdout)
                 if match:
@@ -358,7 +359,7 @@ $ cp -r xtb-dist/share      /usr/local/ """)
 
             # 'xtbout.json', 'xtbrestart', 'xtbtopo.mol', 'charges', and 'wbo' files will be 
             # created in the current working directory.
-            proc = subprocess.run(cmd + options, cwd=temp_dir, capture_output=True, text=True)
+            proc = subprocess.run(cmd + options, cwd=temp_dir, capture_output=True, text=True, encoding='utf-8')
             # if proc.returncode == 0:
             #     print("Standard Output:")
             #     print(proc.stdout)
@@ -461,7 +462,7 @@ $ cp -r xtb-dist/share      /usr/local/ """)
             if verbose:
                 logger.info(f"optimize() {' '.join(cmd+options)}")
 
-            proc = subprocess.run(cmd + options, cwd=temp_dir, capture_output=True, text=True)
+            proc = subprocess.run(cmd + options, cwd=temp_dir, capture_output=True, text=True, encoding='utf-8')
 
             if proc.returncode == 0 and xtbout_path.is_file():
                 with open(xtbout_path, 'r') as f:
@@ -527,7 +528,7 @@ $ cp -r xtb-dist/share      /usr/local/ """)
                 elif water == 'alpb':
                     options += ['--alpb', 'water']
 
-            proc = subprocess.run(cmd + options, cwd=temp_dir, capture_output=True, text=True)
+            proc = subprocess.run(cmd + options, cwd=temp_dir, capture_output=True, text=True, encoding='utf-8')
             # output files: xtb_esp.cosmo, xtb_esp.dat, xtb_esp_profile.dat
 
             if proc.returncode == 0 and xtb_esp_dat.is_file():

{rdworks-0.53.1.dist-info → rdworks-0.54.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rdworks
-Version: 0.53.1
+Version: 0.54.2
 Summary: Routine tasks built on RDKit and other tools
 Author-email: Sung-Hun Bae <sunghun.bae@gmail.com>
 Maintainer-email: Sung-Hun Bae <sunghun.bae@gmail.com>

{rdworks-0.53.1.dist-info → rdworks-0.54.2.dist-info}/RECORD

@@ -1,10 +1,10 @@
-rdworks/__init__.py,sha256=iKipZN3E7INKDKEGeK2CbjgwyGu8Vu5a3THRaKNU_NE,1358
+rdworks/__init__.py,sha256=wn52g1WQn_aTo2WLF-sBenvSluTfnH2dgZRIB3cjDVI,1358
 rdworks/conf.py,sha256=eH_a3ywmmJiPtnvgk86ykurYOx879AHg80-Dn8z1X70,36379
 rdworks/descriptor.py,sha256=34T_dQ6g8v3u-ym8TLKbQtxIIV5TEo-d3pdedq3o-cg,2106
 rdworks/display.py,sha256=JR0gR26UpH-JCxVOaqXZCUj2MiGZSrx9Me87FncspVI,13469
 rdworks/ionized.py,sha256=_t-Ajssv1rytV4Y_KsSbxfnsBKqy-EusbhNUtaWcV6o,7681
 rdworks/matchedseries.py,sha256=A3ON4CUpQV159mu9VqgNiJ8uoQ9ePOry9d3ra4NCAgc,10377
-rdworks/microstates.py,sha256=T206JgeB3d23MX3sRCrxVj2arxlSILYecBTKaD1VcoE,5109
+rdworks/microstates.py,sha256=V1xhMPxAB06_WrB71NEMJjKHI9pPMUuZVswpSmdnSBM,5285
 rdworks/mol.py,sha256=4gNjs_ryNNWThMekV794uwjjBE-JLGGWcdyMaS9-xP8,71369
 rdworks/mollibr.py,sha256=X4UBO6Ga-QmNS7RwUiaDYAx0Q5hnWs71yTkEpH02Qb4,37696
 rdworks/pka.py,sha256=NVJVfpcNEMlX5QRyLBgUM7GIT7VMjO-llAR4LWc8J2c,1656
@@ -66,9 +66,9 @@ rdworks/predefined/misc/reactive-part-2.xml,sha256=0vNTMwWrrQmxBpbgbyRHx8sVs83cq
 rdworks/predefined/misc/reactive-part-3.xml,sha256=LgWHSEbRTVmgBoIO45xbTo1xQJs0Xu51j3JnIapRYo4,3094
 rdworks/predefined/misc/reactive.xml,sha256=syedoQ6VYUfRLnxy99ObuDniJ_a_WhrWAJbTKFfJ6VY,11248
 rdworks/xtb/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-rdworks/xtb/wrapper.py,sha256=p_ddunnjtxe3F2yN7RC2mvSUDnw7fNBhGm1bZVMAWAE,21901
-rdworks-0.53.1.dist-info/licenses/LICENSE,sha256=UOkJSBqYyQUvtCp7a-vdCANeEcLE2dnTie_eB1By5SY,1074
-rdworks-0.53.1.dist-info/METADATA,sha256=kErcEEj-I1D5jI8ZTSr3D1jVXfZ-cGRlV_z1bsG7vLA,1967
-rdworks-0.53.1.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-rdworks-0.53.1.dist-info/top_level.txt,sha256=05C98HbvBK2axUBogC_hAT_CdpOeQYGnQ6vRAgawr8s,8
-rdworks-0.53.1.dist-info/RECORD,,
+rdworks/xtb/wrapper.py,sha256=YpZY8SJ9Lrp3I3_GAVawSb_4_Zc8hcJtF5l7-I-Wbys,22048
+rdworks-0.54.2.dist-info/licenses/LICENSE,sha256=UOkJSBqYyQUvtCp7a-vdCANeEcLE2dnTie_eB1By5SY,1074
+rdworks-0.54.2.dist-info/METADATA,sha256=qwcHC-qMQQQwes5UKUJtbwpFRUr9aEr5wdBuCJ5HWOQ,1967
+rdworks-0.54.2.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+rdworks-0.54.2.dist-info/top_level.txt,sha256=05C98HbvBK2axUBogC_hAT_CdpOeQYGnQ6vRAgawr8s,8
+rdworks-0.54.2.dist-info/RECORD,,