molSimplify 1.7.4__py3-none-any.whl

molSimplify/Classes/rundiag.py

@@ -0,0 +1,151 @@
+# @file rundiag.py
+#  Contains run_diag class for ANN
+#
+#  Written by Kulik group
+#
+#  Department of Chemical Engineering, MIT
+
+
+class run_diag:
+    """Class of run diagnostic information to automated decision making and property prediction
+    """
+
+    # Constructor
+    #  @param self The object pointer
+    def __init__(self):
+        self.sanity_is_set = False  # flag to indicate if properties
+        # have been written to this file
+        self.ANN_is_set = False
+        self.bl_is_set = False
+        self.mol_is_set = False
+        self.catalysis_is_set = False
+        self.sanity = False
+        self.min_dist = False
+        self.ANN_flag = False  # ANN value has been set?
+        self.ANN_reason = " not set"  # Reason ANN not set
+        self.ANN_attributes = dict()  # placeholder for
+        # predicted properties
+        self.catalysis_flag = False
+        self.catalysis_reason = " not activated"
+        self.dict_bondl = False  # stores the ML-dict bond dist
+        self.mol = False  # stores a mol3D representation of the mol.
+
+    ########################################
+    ### class methods needed to populate ###
+    ########################################
+
+    def set_sanity(self, sanity, min_distance):
+        """Set the sanity of predictions.
+
+        Parameters
+        ----------
+            sanity : bool
+                Flag for whether the ANN variables exist.
+            min_distance : float
+                Minimum distance to train
+        """
+        if not self.sanity_is_set:
+            self.sanity_is_set = True
+        self.sanity = sanity
+        self.min_dist = min_distance
+
+    def set_ANN(self, ANN_flag, ANN_reason=False, ANN_dict=False, catalysis_flag=False, catalysis_reason=False):
+        """Set the ANN properties.
+
+        Parameters
+        ----------
+            ANN_flag : bool
+                Flag for whether the ANN variables exist.
+            ANN_reason : str, optional
+                Reasoning for why ANN failed if failed. Default is False.
+            ANN_dict : dict, optional
+                Dictionary with ANN values and uncertainty.
+            catalysis_flag : bool, optional
+                Whether or not catalytic properties are set.
+            catalysis_reason : str, optional
+                Reasoning for why catalytic ANN failed if failed. Default is False.
+        """
+        if not self.ANN_is_set:
+            self.ANN_is_set = True
+        self.ANN_flag = ANN_flag
+        if not ANN_flag:
+            self.ANN_reason = ANN_reason
+        elif ANN_flag:
+            self.ANN_attributes = ANN_dict
+        if not self.catalysis_is_set:
+            self.catalysis_is_set = True
+        self.catalysis_flag = catalysis_flag
+        if not catalysis_flag:
+            self.catalysis_reason = catalysis_reason
+        elif catalysis_flag:
+            self.ANN_attributes = ANN_dict
+
+    def set_dict_bl(self, dict_bl):
+        """Set the ANN properties.
+
+        Parameters
+        ----------
+            dict_bl : dict, optional
+                Dictionary with ANN bond lengths.
+
+        """
+        if not self.bl_is_set:
+            self.bl_is_set = True
+        self.dict_bondl = dict_bl
+
+    def set_mol(self, mol):
+        """Set the ANN molecule.
+
+        Parameters
+        ----------
+            mol : mol3D
+                mol3D class instance for optimized molecule.
+
+        """
+        if not self.mol_is_set:
+            self.mol_is_set = True
+        self.mol = mol
+
+    ########################################
+    ### class methods needed to report  ####
+    ########################################
+    def write_report(self, path):
+        """Write report of molecule with ANN properties.
+
+        Parameters
+        ----------
+            path : str
+                Path for location to write the report.
+
+        """
+        report = []
+        if (not self.sanity_is_set) and (not self.ANN_is_set) and (not self.bl_is_set):
+            report.append('No diagnostic set')
+        else:
+            if self.sanity_is_set:
+                report.append('Bad structure?, ' + str(self.sanity))
+                if not self.sanity:
+                    report.append('Min_dist (A), ' + str(self.min_dist))
+            if self.ANN_is_set:
+                report.append('Was ANN used?, '+str(self.ANN_flag))
+                if not self.ANN_flag:
+                    report.append('ANN reason, ' + str(self.ANN_reason))
+                else:
+                    for keys in list(self.ANN_attributes.keys()):
+                        report.append(str(keys) + ', ' +
+                                      str(self.ANN_attributes[keys]))
+            if self.catalysis_is_set:
+                report.append('Was Catalytic ANN used?, ' +
+                              str(self.catalysis_flag))
+                if not self.catalysis_flag:
+                    report.append('Catalytic ANN reason, ' +
+                                  str(self.catalysis_reason))
+                else:
+                    for keys in list(self.ANN_attributes.keys()):
+                        report.append(str(keys) + ', ' +
+                                      str(self.ANN_attributes[keys]))
+            if self.bl_is_set:
+                report.append('ML-bl (database, A), ' + str(self.dict_bondl))
+        with open(path, 'w') as f:
+            for lines in report:
+                f.write(lines + '\n')

molSimplify/Data/ML.dat

@@ -0,0 +1,212 @@
+# Default data for bond lengths (in A) between metal, connection atom and ligand
+# keys are metal, ox state, spin multiplicity, connection atom of ligand, ligand
+Co	-	-	N	-		2.15
+Co	-	-	C	-		1.96
+Co	-	-	O	-		2.01
+Co	-	-	N	ammonia		2.23
+Co	2	2	N	ammonia		2.10	# tpss def2TZVP
+Co	2	4	N	ammonia		2.20	# tpss def2TZVP
+Co	3	1	N	ammonia		2.00	# tpss def2TZVP
+Co	3	3	N	ammonia		2.09	# tpss def2TZVP
+Co	3	5	N	ammonia		2.17	# tpss def2TZVP
+Co	-	-	C	carbonyl	1.96
+Co	2	2	C	carbonyl	2.00	# tpss def2TZVP
+Co	2	4	C	carbonyl	2.17	# tpss def2TZVP
+Co	3	1	C	carbonyl	1.93	# tpss def2TZVP
+Co	3	3	C	carbonyl	2.08	# tpss def2TZVP
+Co	3	5	C	carbonyl	2.21	# tpss def2TZVP
+Co	-	-	O	water		2.01
+Co	2	2	O	water		2.04	# tpss def2TZVP
+Co	2	4	O	water		2.32	# tpss def2TZVP
+Co	3	1	O	water		1.92	# tpss def2TZVP
+Co	3	3	O	water		1.97	# tpss def2TZVP
+Co	3	5	O	water		2.01	# tpss def2TZVP
+Co	-	-	N	hydrocyanide	2.14
+Co	-	-	N	bipy		2.09
+Co	4	2	O	oxo		1.65
+Co	4	4	O	oxo		1.65
+Co	4	6	O	oxo		1.65
+Co	5	1	O	oxo		1.65
+Co	5	3	O	oxo		1.65
+Co	5	5	O	oxo		1.65
+Cr	-	-	N	-		2.20
+Cr	-	-	C	-		2.09
+Cr	-	-	O	-		2.09
+Cr	-	-	N	ammonia		2.20
+Cr	2	1	N	ammonia		2.20	# tpss def2TZVP
+Cr	2	3	N	ammonia		2.16	# tpss def2TZVP
+Cr	2	5	N	ammonia		2.32	# tpss def2TZVP
+Cr	3	2	N	ammonia		2.14	# tpss def2TZVP
+Cr	3	4	N	ammonia		2.15	# tpss def2TZVP
+Cr	-	-	C	carbonyl	2.09
+Cr	2	1	C	carbonyl	2.05	# tpss def2TZVP
+Cr	2	3	C	carbonyl	2.05	# tpss def2TZVP
+Cr	2	5	C	carbonyl	2.27	# tpss def2TZVP
+Cr	3	2	C	carbonyl	2.13	# tpss def2TZVP
+Cr	3	4	C	carbonyl	2.15	# tpss def2TZVP
+Cr	-	-	O	water		2.09
+Cr	2	1	O	water		2.07	# tpss def2TZVP
+Cr	2	3	O	water		2.09	# tpss def2TZVP
+Cr	2	5	O	water		2.19	# tpss def2TZVP
+Cr	3	2	O	water		1.99	# tpss def2TZVP
+Cr	3	4	O	water		2.00	# tpss def2TZVP
+Cr	4	1	O	oxo		1.65
+Cr	4	3	O	oxo		1.65
+Cr	5	2	O	oxo		1.65
+Cu	-	-	N	-		2.14
+Cu	-	-	C	-		2.12
+Cu	-	-	O	-		2.28
+Cu	-	-	N	ammonia		2.14
+Cu	2	2	N	ammonia		2.19	# tpss def2TZVP
+Cu	3	1	N	ammonia		2.11	# tpss def2TZVP
+Cu	3	3	N	ammonia		2.11	# tpss def2TZVP
+Cu	-	-	C	carbonyl	2.12
+Cu	3	1	C	carbonyl	2.13	# tpss def2TZVP
+Cu	3	3	C	carbonyl	2.13	# tpss def2TZVP
+Cu	-	-	O	water		2.28
+Cu	2	2	O	water		2.28	# tpss def2TZVP
+Fe	-	-	N	-		2.10
+Fe	-	-	C	-		2.03
+Fe	-	-	O	-		2.08
+Fe	-	-	N	ammonia		2.03
+Fe	2	1	N	ammonia		2.10	# b3lyp lacvps
+Fe	2	3	N	ammonia		2.43	# tpss def2TZVP
+Fe	2	5	N	ammonia		2.29	# b3lyp lacvps
+Fe	3	2	N	ammonia		2.06	# b3lyp lacvps
+Fe	3	4	N	ammonia		2.13	# tpss def2TZVP
+Fe	3	6	N	ammonia		2.23	# b3lyp lacvps
+Fe	-	-	C	carbonyl	1.94
+Fe	1	1	C	carbonyl	1.94	# b3lyp lacvps
+Fe	2	3	C	carbonyl	2.06	# tpss def2TZVP
+Fe	2	5	C	carbonyl	2.33	# b3lyp lacvps
+Fe	3	2	C	carbonyl	2.02	# b3lyp lacvps
+Fe	3	4	C	carbonyl	2.14	# tpss def2TZVP
+Fe	3	6	C	carbonyl	2.30	# b3lyp lacvps
+Fe	-	-	O	water		2.08
+Fe	2	1	O	water		1.98	# tpss def2TZVP
+Fe	2	3	O	water		2.08	# tpss def2TZVP
+Fe	2	5	O	water		2.12	# tpss def2TZVP
+Fe	3	2	O	water		1.93	# tpss def2TZVP
+Fe	3	4	O	water		1.99	# tpss def2TZVP
+Fe	3	6	O	water		2.05	# tpss def2TZVP
+Fe	2	1	C	cyanide		2.03	# b3lyp lacvps
+Fe	2	5	C	cyanide		2.46	# b3lyp lacvps
+Fe	3	2	C	cyanide		1.99	# b3lyp lacvps
+Fe	3	6	C	cyanide		2.24	# b3lyp lacvps
+Fe	-	-	C	hydrocyanide	2.20
+Fe	2	1	C	hydrocyanide	1.92	# b3lyp lacvps
+Fe	2	5	C	hydrocyanide	2.27	# b3lyp lacvps
+Fe	3	2	C	hydrocyanide	1.97	# b3lyp lacvps
+Fe	3	6	C	hydrocyanide	2.22	# b3lyp lacvps
+Fe	-	-	N	hydroisocyanide	1.95
+Fe	-	-	N	terpy		2.17
+Fe	2	1	N	terpy		1.89	# b3lyp lacvps
+Fe	2	5	N	terpy		2.17	# b3lyp lacvps
+Fe	3	2	N	terpy		1.98	# b3lyp lacvps
+Fe	3	6	N	terpy		2.14	# b3lyp lacvps
+Fe	-	-	N	bipy		2.01
+Fe	2	1	N	bipy		2.02	# b3lyp lacvps
+Fe	2	5	N	bipy		2.23	# b3lyp lacvps
+Fe	3	2	N	bipy		2.00	# b3lyp lacvps
+Fe	3	6	N	bipy		2.15	# b3lyp lacvps
+Fe	2	5	O	oxo		1.61
+Fe	4	1	O	oxo		1.65
+Fe	4	3	O	oxo		1.65
+Fe	4	5	O	oxo		1.65
+Fe	5	2	O	oxo		1.65
+Fe	5	4	O	oxo		1.65
+Fe	-	-	N	isothiocyanate	2.06
+Mn	-	-	N	-		2.19
+Mn	-	-	C	-		2.01
+Mn	-	-	O	-		2.10
+Mn	-	-	N	ammonia		2.19
+Mn	2	2	N	ammonia		2.09	# tpss def2TZVP
+Mn	2	4	N	ammonia		2.23	# tpss def2TZVP
+Mn	2	6	N	ammonia		2.33	# tpss def2TZVP
+Mn	3	1	N	ammonia		2.09	# tpss def2TZVP
+Mn	3	3	N	ammonia		2.08	# tpss def2TZVP
+Mn	-	-	C	carbonyl	2.01
+Mn	2	2	C	carbonyl	1.96	# tpss def2TZVP
+Mn	2	4	C	carbonyl	2.16	# tpss def2TZVP
+Mn	2	6	C	carbonyl	2.35	# tpss def2TZVP
+Mn	3	1	C	carbonyl	2.05	# tpss def2TZVP
+Mn	3	3	C	carbonyl	2.05	# tpss def2TZVP
+Mn	3	5	C	carbonyl	2.22	# tpss def2TZVP
+Mn	-	-	O	water		2.10
+Mn	2	2	O	water		2.06	# tpss def2TZVP
+Mn	2	4	O	water		2.32	# tpss def2TZVP
+Mn	2	6	O	water		2.18	# tpss def2TZVP
+Mn	3	1	O	water		1.97	# tpss def2TZVP
+Mn	3	3	O	water		1.95	# tpss def2TZVP
+Mn	3	5	O	water		2.02	# tpss def2TZVP
+Mn	4	2	O	oxo		1.65
+Mn	4	4	O	oxo		1.65
+Mn	5	1	O	oxo		1.65
+Mn	5	3	O	oxo		1.65
+Mo	0	7	O	water		2.40	# b3lyp lacvps
+Mo	2	5	O	water		2.20	# b3lyp lacvps
+Mo	2	5	O	hydroxyl	2.10	# b3lyp lacvps
+Mo	4	3	O	water		2.39	# b3lyp lacvps
+Mo	4	3	O	hydroxyl	1.97	# b3lyp lacvps
+Mo	6	1	O	hydroxyl	1.89	# b3lyp lacvps
+Ni	-	-	N	-		2.14
+Ni	-	-	C	-		2.14
+Ni	-	-	O	-		2.00
+Ni	-	-	N	ammonia		2.14
+Ni	2	1	N	ammonia		2.13	# tpss def2TZVP
+Ni	2	3	N	ammonia		2.14	# tpss def2TZVP
+Ni	3	4	N	ammonia		2.14	# tpss def2TZVP
+Ni	-	-	C	carbonyl	2.14
+Ni	2	1	C	carbonyl	2.08	# tpss def2TZVP
+Ni	2	3	C	carbonyl	2.09	# tpss def2TZVP
+Ni	3	4	C	carbonyl	2.17	# tpss def2TZVP
+Ni	-	-	O	water		2.00
+Ni	2	1	O	water		2.04	# tpss def2TZVP
+Ni	2	3	O	water		2.04	# tpss def2TZVP
+Ni	3	2	O	water		1.96	# tpss def2TZVP
+Ni	3	4	O	water		1.99	# tpss def2TZVP
+Sc	-	-	N	-		2.36
+Sc	-	-	C	-		2.42
+Sc	-	-	O	-		2.19
+Sc	-	-	N	ammonia		2.36
+Sc	2	2	N	ammonia		2.42	# tpss def2TZVP
+Sc	3	1	N	ammonia		2.33	# tpss def2TZVP
+Sc	-	-	C	carbonyl	2.42
+Sc	2	2	C	carbonyl	2.41	# tpss def2TZVP
+Sc	3	1	C	carbonyl	2.44	# tpss def2TZVP
+Sc	-	-	O	water		2.19
+Sc	2	2	O	water		2.26	# tpss def2TZVP
+Sc	3	1	O	water		2.14	# tpss def2TZVP
+Ti	-	-	N	-		2.28
+Ti	-	-	C	-		2.29
+Ti	-	-	O	-		2.14
+Ti	-	-	N	ammonia		2.28
+Ti	2	1	N	ammonia		2.33	# tpss def2TZVP
+Ti	2	3	N	ammonia		2.34	# tpss def2TZVP
+Ti	3	2	N	ammonia		2.25	# tpss def2TZVP
+Ti	-	-	C	carbonyl	2.29
+Ti	2	1	C	carbonyl	2.26	# tpss def2TZVP
+Ti	2	3	C	carbonyl	2.27	# tpss def2TZVP
+Ti	3	2	C	carbonyl	2.32	# tpss def2TZVP
+Ti	-	-	O	water		2.14
+Ti	2	1	O	water		2.19	# tpss def2TZVP
+Ti	2	3	O	water		2.14	# tpss def2TZVP
+Ti	3	2	O	water		2.09	# tpss def2TZVP
+V	-	-	N	-		2.22
+V	-	-	C	-		2.19
+V	-	-	O	-		2.08
+V	-	-	N	ammonia		2.22
+V	2	2	N	ammonia		2.25	# tpss def2TZVP
+V	2	4	N	ammonia		2.26	# tpss def2TZVP
+V	3	1	N	ammonia		2.19	# tpss def2TZVP
+V	3	3	N	ammonia		2.20	# tpss def2TZVP
+V	-	-	C	carbonyl	2.19
+V	2	2	C	carbonyl	2.15	# tpss def2TZVP
+V	2	4	C	carbonyl	2.16	# tpss def2TZVP
+V	3	1	C	carbonyl	2.21	# tpss def2TZVP
+V	3	3	C	carbonyl	2.22	# tpss def2TZVP
+V	-	-	O	water		2.08
+V	2	2	O	water		2.13	# tpss def2TZVP
+V	2	4	O	water		2.14	# tpss def2TZVP
+V	3	1	O	water		2.03	# tpss def2TZVP
+V	3	3	O	water		2.04	# tpss def2TZVP

molSimplify/Data/MLS_FSR_for_inter.dat

@@ -0,0 +1,23 @@
+# Default data for bond lengths (in A) between metal, connection atom and ligand
+# keys are sym, val, bo, ox state, spin multiplicity,
+# returns are MLS: bangle_m3D/bangle_m3Dsub/bangle_core3D/bangle_sub,
+# MLSS: bdihedral_m3D/bdihedral_m3Dsub/bdihedral_core3D/bdihedral_sub (angle from norm)
+# main group
+# octet = 2
+H 0 - - 180 0
+H 1 - - 180 0
+# octet = 8
+#C 0 - - 180 0
+#N 0 - - 180 0
+#O 0 - - 180 0
+C 1 - - 103 90
+N 1 - - 120 90
+O 1 - - 120 90
+C 2 - - 120 90
+N 2 - - 180 90
+O 2 - - 109 90
+C 3 - - 109 20
+N 3 - - 109 20
+# metals
+Cu -5 - - 90 90
+#Cu -5 - - 109 90

molSimplify/Data/MLS_FSR_for_inter2.dat

@@ -0,0 +1,23 @@
+# Default data for bond lengths (in A) between metal, connection atom and ligand
+# keys are sym, val, bo, ox state, spin multiplicity,
+# returns are MLS: bangle_m3D/bangle_m3Dsub/bangle_core3D/bangle_sub,
+# MLSS: bdihedral_m3D/bdihedral_m3Dsub/bdihedral_core3D/bdihedral_sub (angle from norm)
+# main group
+# octet = 2
+H 0 - - 180 0
+H 1 - - 180 0
+# octet = 8
+#C 0 - - 180 0
+#N 0 - - 180 0
+#O 0 - - 180 0
+C 1 - - 47 90
+N 1 - - 120 90
+O 1 - - 120 90
+C 2 - - 120 90
+N 2 - - 120 90
+O 2 - - 109 90
+C 3 - - 109 20
+N 3 - - 109 20
+# metals
+Cu -5 - - 90 90
+#Cu 3 - - 109 20

molSimplify/Data/MLS_angle_for_click.dat

@@ -0,0 +1,8 @@
+# Default data for bond lengths (in A) between metal, connection atom and ligand
+# keys are metal, ox state, spin multiplicity, substrate, C-M-cpoint angle, rO-C-Ca angle
+# Default
+Cu - - - 90
+## azide
+# DOI = 10.1021/om700573h
+Cu - - N-quinolinylbutyramidate 90
+Cu 1 1 N-quinolinylbutyramidate 90

molSimplify/Data/MLS_angle_for_inter.dat

@@ -0,0 +1,23 @@
+# Default data for bond lengths (in A) between metal, connection atom and ligand
+# keys are sym, val, bo, ox state, spin multiplicity,
+# returns are MLS: bangle_m3D/bangle_m3Dsub/bangle_core3D/bangle_sub,
+# MLSS: bdihedral_m3D/bdihedral_m3Dsub/bdihedral_core3D/bdihedral_sub (angle from norm)
+# main group
+# octet = 2
+H 0 - - 180 0
+H 1 - - 180 0
+# octet = 8
+#C 0 - - 180 0
+#N 0 - - 180 0
+#O 0 - - 180 0
+C 1 - - 180 90
+N 1 - - 120 90
+O 1 - - 120 90
+C 2 - - 120 90
+N 2 - - 180 90
+O 2 - - 109 90
+C 3 - - 109 20
+N 3 - - 109 20
+# metals
+Cu 2 - - 120 90
+Cu 3 - - 109 20

molSimplify/Data/MLS_angle_for_inter2.dat

@@ -0,0 +1,48 @@
+# Default data for bond lengths (in A) between metal, connection atom and ligand
+# keys are metal, ox state, reacting atom, spin multiplicity, bangle_m3D, bangle_m3Dsub, bangle_core3D, bangle_sub
+# hat, reacting atom = H
+Co - - H 115 180 109
+Co 4 2 H 111 180 109
+Co 4 4 H 121 180 109
+Cr - - H 120 180 109
+Cr 4 3 H 120 180 109
+Fe - - H 120 180 109
+Fe 4 3 H 122 180 109
+Fe 4 5 H 127 180 109
+Fe 5 2 H 115 180 109
+Fe 5 4 H 115 180 109
+Mn - - H 120 180 109
+Mn 4 2 H 121 180 109
+Mn 4 4 H 118 180 109
+Mn 5 3 H 115 180 109
+# nat, reacting atom = N
+Co - - N 130 120 120
+Co 4 2 N 123 114 120
+Co 4 4 N 135 125 120
+Cr - - N 126 121 120
+Cr 4 3 N 126 121 120
+Fe - - N 135 135 120
+Fe 4 3 N 130 130 120
+Fe 4 5 N 137 130 120
+Fe 5 2 N 142 122 120
+Fe 5 4 N 140 125 120
+Mn - - N 137 126 120
+Mn 4 4 N 130 124 120
+Mn 5 3 N 143 128 120
+Cu - - N 106 121 143 138
+# cat, reacting atom = C
+Co - - C 105 103 120
+Co 4 2 C 105 103 120
+Co 4 4 C 105 103 120
+Cr - - C 105 103 120
+Cr 4 3 C 105 103 120
+Cr 5 2 C 105 103 120
+Fe - - C 105 103 120
+Fe 4 3 C 105 103 120
+Fe 4 5 C 105 103 120
+Fe 5 2 C 105 103 120
+Fe 5 4 C 105 103 120
+Mn - - C 105 103 120
+Mn 4 2 C 105 103 120
+Mn 4 4 C 105 103 120
+Mn 5 3 C 105 103 120

molSimplify/Data/MLS_angle_for_intra.dat

@@ -0,0 +1,10 @@
+# Default data for bond angle (in degree) between metal, connection atom and ligand
+# keys are metal, ox state, spin multiplicity, bangle_m3D, bangle_m3Dsub, bangle_core3D
+# hat, reacting atom = H
+# DOI = 10.1021/om700573h
+Pd - - H 35 35 35
+Pd 1 1 H 35 35 35
+# cat, reacting atom = C
+Pd - - C 63 116 120
+# DOI = 10.1021/ja0471525
+Cu - - N 84 121 143

molSimplify/Data/MLS_angle_for_intra2.dat

@@ -0,0 +1,6 @@
+# Default data for bond lengths (in A) between metal, connection atom and ligand
+# keys are metal, ox state, spin multiplicity, substrate, C-L-M angle, rO-C-Ca angle
+# cat, reacting atom = C
+# DOI = 10.1021/om700573h
+Pd - - C 35
+Pd 1 1 C 35

molSimplify/Data/MLS_angle_for_oa.dat

@@ -0,0 +1,18 @@
+# Default data for bond lengths (in A) between metal, connection atom and ligand
+# keys are metal, ox state, spin multiplicity, substrate, C-M-cpoint angle, rO-C-Ca angle
+# Default
+Cu - - - 145 94
+## aryl halides
+# DOI = 10.1021/om700573h
+Cu - - bromobenzene 145 94
+Cu 1 1 bromobenzene 145 94
+## triazoles
+# DOI = 10.1021/ja0471525
+Cu - - triazole 180 70
+Cu 1 1 triazole 180 70
+## Default
+Pd - - - 157 87
+# aryl halides
+# DOI = 10.1021/om049963n
+Pd - - bromobenzene 157 87
+Pd 1 1 bromobenzene 157 87

molSimplify/Data/ML_FSR_for_inter.dat

@@ -0,0 +1,112 @@
+# Default data for bond lengths (in A) between metal, connection atom and ligand
+# keys are sym1_valency, sym2_valency, ox state, spin multiplicity, fsr
+# usually, fsr_bondl_m3D and fsr_bondl_sub
+C0 H0 - - 1.14
+N0 H0 - - 1.1
+O0 H0 - - 1.26
+C0 C0 - - 1.1
+N0 C0 - - 1.1
+O0 C0 - - 1.27
+N0 N0 - - 1.1
+O0 N0 - - 1.27
+O0 O0 - - 1.27
+C1 H0 - - 1.14
+N1 H0 - - 1.1
+O1 H0 - - 1.20 1.20
+C1 C0 - - 1.1
+N1 C0 - - 1.1
+O1 C0 - - 1.27
+N1 N0 - - 1.1
+O1 N0 - - 1.27
+O1 O0 - - 1.27
+C1 C1 - - 0.90
+C1 O1 - - 1.36 1.36
+N1 C1 - - 1.1
+O1 C1 - - 1.27 1.36
+N1 N1 - - 0.80
+O1 N1 - - 1.27
+O1 O1 - - 1.27
+C2 H0 - - 1.14
+N2 H0 - - 1.1
+O2 H0 - - 1.26
+C2 C0 - - 1.1
+N2 C0 - - 1.1
+O2 C0 - - 1.27
+N2 N0 - - 1.1
+O2 N0 - - 1.27
+O2 O0 - - 1.27
+C2 C1 - - 1.1
+N2 C1 - - 1.1
+O2 C1 - - 1.27
+N2 N1 - - 0.80
+O2 N1 - - 1.27
+O2 O1 - - 1.27
+C2 C2 - - 0.82
+N2 C2 - - 1.1 1.1
+O2 C2 - - 1.27
+N2 N2 - - 0.85
+O2 N2 - - 1.27
+O2 O2 - - 1.27
+C3 H0 - - 1.14
+N3 H0 - - 1.1
+C3 C0 - - 1.1
+C3 N0 - - 1.1
+C3 O0 - - 1.1
+N3 C0 - - 1.1
+N3 N0 - - 1.1
+N3 O0 - - 1.1
+C3 C1 - - 1.1
+C3 N1 - - 1.1
+C3 O1 - - 1.1
+N3 C1 - - 1.1
+N3 N1 - - 1.1
+N3 O1 - - 1.1
+C3 C2 - - 1.1
+C3 N2 - - 1.1
+C3 O2 - - 1.1
+N3 C2 - - 1.1
+N3 N2 - - 1.1
+N3 O2 - - 1.1
+C3 C3 - - 1.1
+C3 N3 - - 1.1
+N3 N3 - - 1.1
+C4 H0 - - 1.14
+C4 C0 - - 1.1
+C4 N0 - - 1.1
+C4 O0 - - 1.1
+C4 C1 - - 1.1
+C4 N1 - - 1.1
+C4 O1 - - 1.1
+C4 C2 - - 1.1
+C4 N2 - - 1.1
+C4 O2 - - 1.1
+C4 C3 - - 1.1
+C4 N3 - - 1.1
+C4 C4 - - 1.1
+# usually, fsr_bondl_core3D
+Ti O1 - - 0.9
+V O1 - - 0.9
+Cr O1 - - 0.9
+Mn O1 - - 0.9
+Fe O1 - - 0.9
+Co O1 - - 0.9
+Ni O1 - - 0.9
+Cu O1 - - 0.9
+Ti N1 - - 1.1
+V N1 - - 1.1
+Cr N1 - - 1.1
+Mn N1 - - 1.1
+Fe N1 - - 1.1
+Co N1 - - 1.1
+Ni N1 - - 1.1
+Cu N1 - - 1.1
+Ti C1 - - 1.1
+V C1 - - 1.1
+Cr C1 - - 1.1
+Mn C1 - - 1.1
+Fe C1 - - 1.1
+Co C1 - - 1.1
+Ni C1 - - 1.1
+Cu C1 - - 0.8
+Cu-5 C2 - - 0.86
+Cu-5 N2 - - 0.97 0.97