Remove unused code, add unit test for paddle wheel

mofa/assemble.py

@@ -1,6 +1,6 @@
 """Functions for assembling a MOF structure"""
+from pathlib import Path
 from typing import Sequence
-from .model import NodeDescription, LigandDescription, MOFRecord
 import os
 import io
 import itertools
@@ -9,6 +9,8 @@
 import pymatgen.core as mg
 from rdkit import Chem
 
+from .model import NodeDescription, LigandDescription, MOFRecord
+
 
 def readPillaredPaddleWheelXYZ(fpath, dummyElementCOO="At", dummyElementPillar="Fr"):
     """Read xyz file of a paddlewheel node
@@ -139,31 +141,6 @@ def rotmat2align(vec1, vec2):
     return rotation_matrix
 
 
-def assemble_COO_pcuMOF_multiProc(inputDict):
-    """multiprocessing wrapper for assemble_COO_pcuMOF
-
-    Args:
-        inputDict: input of many structures to assemble in the format of dictionary
-
-    Returns:
-        returnValue a file path if assembly succeeded, None if failed
-    """
-    nodePath = inputDict["nodePath"]
-    linkerPaths = inputDict["linkerPaths"]
-    newMOFdir = inputDict["newMOFdir"]
-    if "dummyElement" in inputDict.keys():
-        dummyElement = inputDict["dummyElement"]
-    else:
-        dummyElement = "At"
-
-    returnValue = None
-    try:
-        returnValue = assemble_COO_pcuMOF(nodePath, linkerPaths, newMOFdir, dummyElement=dummyElement)
-    except Exception as e:
-        print(e)
-    return returnValue
-
-
 def assemble_COO_pcuMOF(nodePath, linkerPaths, newMOFpath, dummyElement="At"):
     """assembly code for -COO only MOF with pcu topology
 
@@ -262,7 +239,7 @@ def assemble_COO_pcuMOF(nodePath, linkerPaths, newMOFpath, dummyElement="At"):
 def assemble_pillaredPaddleWheel_pcuMOF(nodePath,
                                         COOLinkerPaths,
                                         PillarLinkerPath,
-                                        newMOFpath,
+                                        newMOFpath: Path,
                                         dummyElementCOO="At",
                                         dummyElementPillar="Fr"):
     """assembly code for -COO and -N ligands MOF with pcu topology
@@ -278,8 +255,12 @@ def assemble_pillaredPaddleWheel_pcuMOF(nodePath,
     Returns:
         returnValue a cif file path if assembly succeeded, None if failed
     """
-    MOFRootdir = os.path.split(newMOFpath)[0]
-    os.makedirs(MOFRootdir, exist_ok=True)
+
+    # Ensure the output directory exists
+    MOFRootdir = newMOFpath.parent
+    MOFRootdir.mkdir(exist_ok=True, parents=True)
+
+    # Make sure the dummy atoms are valid elements
     Chem.rdchem.Atom(dummyElementCOO).GetAtomicNum()
     Chem.rdchem.Atom(dummyElementPillar).GetAtomicNum()
 
@@ -397,65 +378,6 @@ def assemble_pillaredPaddleWheel_pcuMOF(nodePath,
         return ""
 
 
-def assemble_PillarPaddle_pcuMOF_multiProc(inputDict):
-    """multiprocessing wrapper for assemble_PillarPaddle_pcuMOF
-
-    Args:
-        inputDict: input of many structures to assemble in the format of dictionary
-
-    Returns:
-        returnValue a file path if assembly succeeded, None if failed
-    """
-    nodePath = inputDict["nodePath"]
-    COOLinkerPaths = inputDict["COOLinkerPaths"]
-    PillarLinkerPath = inputDict["PillarLinkerPath"]
-    newMOFdir = inputDict["newMOFdir"]
-    if "dummyElementCOO" in inputDict.keys():
-        dummyElementCOO = inputDict["dummyElementCOO"]
-    else:
-        dummyElementCOO = "At"
-
-    if "dummyElementPillar" in inputDict.keys():
-        dummyElementPillar = inputDict["dummyElementPillar"]
-    else:
-        dummyElementPillar = "Fr"
-
-    returnValue = None
-    try:
-        returnValue = assemble_pillaredPaddleWheel_pcuMOF(nodePath,
-                                                          COOLinkerPaths,
-                                                          PillarLinkerPath,
-                                                          newMOFdir,
-                                                          dummyElementCOO=dummyElementCOO,
-                                                          dummyElementPillar=dummyElementPillar)
-    except Exception as e:
-        print(e)
-    return returnValue
-
-
-def testPillarMOF():
-    linker_base = "inferred_linkers/molGAN-batch512-Linkers"
-    linker_folders = os.listdir(linker_base)
-    # chosen_linker_folders
-    clf = [os.path.join(linker_base, x) for x in linker_folders[0:3]]
-    COOLinkers = [os.path.join(clf[0], y) for y in os.listdir(clf[0]) if y.endswith(".xyz") and y.startswith(
-        "linker-COO")] + [os.path.join(clf[1], y) for y in os.listdir(clf[1]) if y.endswith(".xyz") and y.startswith("linker-COO")]
-    PillarLinker = [os.path.join(clf[2], y) for y in os.listdir(clf[2])
-                    if y.endswith(".xyz") and y.startswith("linker-") and "COO" not in y][0]
-
-    nodePath = "nodes/zinc_paddle_pillar.xyz"
-    COOLinkerPaths = COOLinkers
-    PillarLinkerPath = PillarLinker
-    comb_name = "L" + "".join(list(reversed(os.path.split(COOLinkers[0])[-1].replace(".xyz", "").replace("linker-", "").split("-")))) + "-" + \
-        "L" + "".join(list(reversed(os.path.split(COOLinkers[1])[-1].replace(".xyz", "").replace("linker-", "").split("-")))) + "-" + \
-        "L" + "".join(list(reversed(os.path.split(PillarLinker)[-1].replace(".xyz", "").replace("linker-", "").split("-"))))
-    newMOFdir = "newMOFs/molGAN-MOF-" + comb_name
-    return assemble_pillaredPaddleWheel_pcuMOF(nodePath,
-                                               COOLinkerPaths,
-                                               PillarLinkerPath,
-                                               newMOFdir)
-
-
 def assemble_mof(nodes: Sequence[NodeDescription], ligands: Sequence[LigandDescription], topology: str) -> MOFRecord:
     """Generate a new MOF from the description of the nodes, ligands and toplogy
 
@@ -467,4 +389,10 @@ def assemble_mof(nodes: Sequence[NodeDescription], ligands: Sequence[LigandDescr
     Returns:
         A new MOF record
     """
-    raise NotImplementedError()
+
+    # Step 1: Detect which node type, use that to pick the assembly
+    if 'Zn' in nodes[0].xyz and topology == 'pcu':
+        # Step 2: Gather the XYZ files for the node and linker(s).
+        raise NotImplementedError()  # Waiting on code from Xiaoli about how to go from "generated linker->ligands"
+    else:
+        raise NotImplementedError('No assembly methods for this linker/topology pair')

tests/files/assemble/linkers/molGAN-batch512-Linker-400/linker-COO-400.xyz

@@ -0,0 +1,46 @@
+44
+
+C      4.901243    2.336638    0.255723
+C      3.650010    2.931033    0.312459
+C      2.497499    2.160472    0.205546
+C      2.565080    0.749789    0.081203
+C      3.855778    0.144786    0.007902
+C      3.949784   -1.252742   -0.095028
+C      2.816533   -2.062186   -0.199978
+C      3.013910   -3.554785   -0.337240
+C      1.529574   -1.476919   -0.150841
+C      0.372405   -2.279350   -0.198384
+C     -0.907093   -1.717370   -0.132282
+C     -2.018130   -2.556317   -0.040539
+C     -3.295936   -2.039968    0.175684
+N     -4.360885   -2.974602    0.419292
+C     -3.500453   -0.634928    0.130371
+C     -4.790414   -0.082290    0.283237
+C     -3.954492    2.119728   -0.214784
+C     -2.670487    1.604012   -0.435807
+C     -1.706776    2.518855   -1.157715
+C     -2.391276    0.235101   -0.117226
+C     -1.070394   -0.319715   -0.083930
+C      0.084741    0.464237    0.110981
+C      1.393144   -0.071253    0.009694
+H      5.779871    2.968395    0.313287
+H      3.571617    4.005618    0.420256
+H      1.571617    2.709129    0.212835
+H      4.913848   -1.738587   -0.075274
+H      2.589446   -4.073511    0.547985
+H      4.087453   -3.830979   -0.409272
+H      2.515993   -3.918807   -1.260554
+H      0.451933   -3.357237   -0.257575
+H     -1.880647   -3.632190   -0.046934
+H     -4.212204   -3.994420    0.248401
+H     -5.242556   -2.720449    0.911325
+H     -5.645107   -0.707010    0.480528
+H     -4.141038    3.171440   -0.401006
+H     -2.251735    3.157917   -1.885697
+H     -0.968398    1.947177   -1.756473
+H     -1.199336    3.191997   -0.435778
+H     -0.057639    1.472252    0.437153
+C      5.027895    0.955912    0.069936
+At     6.401478    0.425395   -0.091886
+C     -5.012517    1.292876    0.165861
+At    -6.368948    1.854212    0.372352

tests/files/assemble/linkers/molGAN-batch512-Linker-400/linker-Cyano-400.xyz

@@ -0,0 +1,50 @@
+48
+
+C      3.723864    1.399083   -3.865589
+C      2.380070    1.743223   -3.810625
+C      1.580353    1.300032   -2.759965
+C      2.107879    0.477214   -1.732277
+C      3.497398    0.165720   -1.772988
+C      4.068675   -0.578564   -0.728860
+C      3.309180   -1.020701    0.357016
+C      4.007252   -1.798680    1.448527
+C      1.919568   -0.752393    0.396335
+C      1.119566   -1.249285    1.443829
+C     -0.257360   -1.003462    1.488884
+C     -1.027377   -1.612605    2.481396
+C     -2.416381   -1.488564    2.495522
+N     -3.143143   -2.167959    3.532177
+C     -3.055234   -0.664074    1.535999
+C     -4.461781   -0.594850    1.461838
+C     -5.088120    0.294604    0.592366
+C     -6.525855    0.345447    0.524010
+N     -7.729145    0.388597    0.467176
+Fr    -9.488540    0.452906    0.384586
+C     -4.326021    1.183446   -0.157649
+C     -2.925032    1.148189   -0.110059
+C     -2.209871    2.332423   -0.718075
+C     -2.268576    0.104025    0.621035
+C     -0.870963   -0.193406    0.511734
+C     -0.094380    0.183303   -0.602769
+C      1.306894   -0.015571   -0.653748
+C      4.294868    0.622172   -2.856115
+C      5.704335    0.316569   -2.960187
+N      6.879303    0.061382   -3.046429
+Fr     8.596789   -0.313452   -3.168822
+H      4.325850    1.754323   -4.693989
+H      1.953896    2.366531   -4.586670
+H      0.560163    1.645223   -2.769681
+H      5.125755   -0.812433   -0.746022
+H      3.846989   -1.302248    2.428744
+H      3.611401   -2.835461    1.483477
+H      5.104038   -1.859655    1.282885
+H      1.553898   -1.858921    2.225765
+H     -0.547761   -2.231509    3.231899
+H     -2.669258   -2.889346    4.120692
+H     -4.094940   -1.873432    3.837675
+H     -5.091043   -1.244076    2.053666
+H     -4.827876    1.938532   -0.753618
+H     -2.091070    2.190944   -1.812470
+H     -2.800481    3.260793   -0.561213
+H     -1.229086    2.513160   -0.232126
+H     -0.611896    0.534729   -1.470698

tests/files/assemble/linkers/molGAN-batch512-Linker-400/linker-Pyridine-400.xyz

@@ -0,0 +1,66 @@
+64
+
+C     -4.452313    2.005762    2.102416
+C     -3.115032    2.239146    2.388190
+C     -2.116814    1.551197    1.704441
+C     -2.433532    0.621387    0.681922
+C     -3.809922    0.365237    0.413899
+C     -4.155789   -0.569210   -0.574896
+C     -3.186459   -1.288286   -1.277293
+C     -3.648435   -2.294063   -2.306738
+C     -1.814878   -1.044241   -1.028073
+C     -0.819219   -1.710987   -1.768655
+C      0.540590   -1.469493   -1.543629
+C      1.486119   -2.044798   -2.393064
+C      2.837607   -1.713173   -2.297437
+N      3.722492   -2.216690   -3.312532
+C      3.287816   -0.915042   -1.212539
+C      4.657693   -0.619068   -1.048692
+C      4.221429    0.445987    1.065392
+C      2.862577    0.117096    0.973464
+C      2.066532    0.241515    2.253006
+C      2.348057   -0.440333   -0.242820
+C      0.950098   -0.595330   -0.518000
+C     -0.045475    0.175094    0.116001
+C     -1.428295   -0.076524   -0.061131
+H     -5.210722    2.543663    2.659207
+H     -2.847869    2.951341    3.158747
+H     -1.108271    1.759997    2.018200
+H     -5.195584   -0.748589   -0.812967
+H     -4.754659   -2.392858   -2.328768
+H     -3.316871   -1.976793   -3.317857
+H     -3.230209   -3.295589   -2.071563
+H     -1.090006   -2.406407   -2.552789
+H      1.159917   -2.691071   -3.200806
+H      3.393464   -2.953530   -3.976170
+H      4.640097   -1.778976   -3.537087
+H      5.396246   -0.967875   -1.751778
+H      4.588033    0.941348    1.957341
+H      1.695204    1.280127    2.376985
+H      2.706324    0.007990    3.131438
+H      1.231756   -0.488084    2.289504
+H      0.273991    1.034049    0.667160
+C     -4.818075    1.061513    1.138200
+C     -6.264050    0.813457    0.937931
+C     -7.087162    1.823699    0.416534
+C     -8.455722    1.596506    0.243297
+N     -9.012630    0.362338    0.596699
+Fr   -10.764493    0.072456    0.372813
+C     -8.198807   -0.643720    1.129125
+C     -6.830017   -0.418552    1.304302
+C      5.120503    0.102470    0.055229
+C      6.563487    0.432338    0.184251
+C      7.232096    0.268151    1.412024
+C      8.590280    0.579567    1.526173
+N      9.296445    1.058436    0.418604
+Fr    11.034940    1.456745    0.568010
+C      8.642605    1.223744   -0.806106
+C      7.284835    0.912387   -0.924656
+H     -6.667490    2.782955    0.139636
+H     -9.080800    2.380139   -0.165494
+H     -8.625220   -1.598807    1.408584
+H     -6.210042   -1.201978    1.723168
+H      6.709882   -0.117961    2.278276
+H      9.092846    0.444795    2.475600
+H      9.183889    1.596289   -1.666532
+H      6.794236    1.061221   -1.878621

tests/files/assemble/linkers/molGAN-batch512-Linker-402/linker-COO-402.xyz

@@ -0,0 +1,19 @@
+17
+
+C      0.069719   -1.558622   -0.045561
+C      0.932503    0.700713    0.199745
+C      2.047116    1.691189    0.420054
+C     -0.361038    1.194011   -0.037610
+C     -1.212739   -1.062715   -0.315689
+N     -2.245718   -1.991843   -0.673625
+H      0.224758   -2.631135   -0.055158
+H      2.318132    1.718034    1.496039
+H      2.933283    1.415156   -0.189166
+H      1.748836    2.716781    0.114334
+H     -0.530923    2.264504   -0.017763
+H     -2.090769   -3.019780   -0.571568
+H     -3.112146   -1.691951   -1.170050
+C      1.148173   -0.700148    0.230242
+At     2.472338   -1.303982    0.533859
+C     -1.442098    0.332068   -0.277295
+At    -2.788373    0.926369   -0.444685

tests/files/assemble/linkers/molGAN-batch512-Linker-402/linker-Cyano-402.xyz

@@ -0,0 +1,23 @@
+21
+
+C      0.994485    1.078221   -0.296693
+C     -0.338074    1.075137   -0.727444
+C     -0.825966    2.200646   -1.488337
+N     -1.234682    3.139981   -2.123614
+Fr    -1.833475    4.513038   -3.052059
+C     -1.176153   -0.015514   -0.415321
+C     -2.613235   -0.044941   -0.865839
+C     -0.657688   -1.088525    0.327318
+C      0.675531   -1.084568    0.757779
+C      1.161953   -2.209839    1.518009
+N      1.566989   -3.150977    2.153176
+Fr     2.159582   -4.526750    3.081644
+C      1.511784    0.006782    0.444823
+N      2.881642    0.045023    0.868841
+H      1.635099    1.918721   -0.538828
+H     -3.156785    0.825021   -0.440792
+H     -3.129244   -0.971636   -0.535934
+H     -2.659148    0.002104   -1.974267
+H     -1.293682   -1.931914    0.572472
+H      3.488814    0.860461    0.629302
+H      3.310035   -0.729181    1.422329

tests/files/assemble/linkers/molGAN-batch512-Linker-402/linker-Pyridine-402.xyz

@@ -0,0 +1,39 @@
+37
+
+C      0.668103    1.203568   -0.488988
+C     -0.732920    1.128634   -0.509704
+C     -1.516754    2.316676   -1.004728
+C     -0.589997   -1.135864    0.367349
+C      0.809564   -1.070585    0.359384
+N      1.560510   -2.233104    0.736833
+H      1.158695    2.116426   -0.807917
+H     -0.901593    2.946096   -1.682662
+H     -2.408475    1.988819   -1.579222
+H     -1.838499    2.937223   -0.143041
+H     -1.076416   -2.045633    0.700089
+H      2.593086   -2.293023    0.601157
+H      1.074032   -3.085586    1.093938
+C      1.447287    0.121355   -0.051556
+C      2.918977    0.274819   -0.015714
+C      3.619701    0.132866    1.193841
+C      5.007332    0.299863    1.228403
+N      5.705040    0.618676    0.058423
+Fr     7.481395    0.832621    0.104463
+C      5.011675    0.774441   -1.146729
+C      3.623973    0.607776   -1.184119
+C     -1.370434   -0.045147   -0.044608
+C     -2.844967   -0.168015    0.010564
+C     -3.603605    0.701277    0.811891
+C     -4.994681    0.573726    0.868700
+N     -5.638215   -0.427325    0.133150
+Fr    -7.419093   -0.589479    0.207375
+C     -4.887288   -1.303832   -0.657526
+C     -3.496026   -1.178361   -0.716073
+H      3.090428   -0.103042    2.108985
+H      5.537655    0.184106    2.165105
+H      5.545788    1.024797   -2.054539
+H      3.099804    0.730481   -2.124053
+H     -3.117724    1.469374    1.400399
+H     -5.569745    1.250105    1.488270
+H     -5.379358   -2.082608   -1.226242
+H     -2.926796   -1.862264   -1.333759