- initial work to put the Trajectory code into a separate object

Code/ForceField/ForceField.cpp

@@ -13,7 +13,6 @@
 
 #include <RDGeneral/Invariant.h>
 #include <Numerics/Optimizer/BFGSOpt.h>
-#include <Geometry/Trajectory.h>
 
 namespace ForceFieldsHelper {
 class calcEnergy {
@@ -186,7 +185,7 @@ int ForceField::minimize(unsigned int maxIts, double forceTol,
   return minimize(0, NULL, maxIts, forceTol, energyTol);
 }
 
-int ForceField::minimize(unsigned int trajEverySteps, RDGeom::Trajectory *traj,
+int ForceField::minimize(unsigned int trajEverySteps, std::vector<double *> *traj,
                          unsigned int maxIts, double forceTol, double energyTol) {
   PRECONDITION(df_init, "not initialized");
   PRECONDITION(static_cast<unsigned int>(d_numPoints) == d_positions.size(),

Code/ForceField/ForceField.h

@@ -131,7 +131,7 @@ class ForceField {
       - 0: indicates success
       - 1: the minimization did not converge in \c maxIts iterations.
   */
-  int minimize(unsigned int trajEverySteps, RDGeom::Trajectory *traj,
+  int minimize(unsigned int trajEverySteps, std::vector<double *> *traj,
                unsigned int maxIts = 200, double forceTol = 1e-4,
                double energyTol = 1e-6);
 
@@ -144,7 +144,7 @@ class ForceField {
                              will be stored after as many steps as indicated
                              through this parameter; defaults to 0 (no
                              trajectory stored)
-    \param traj              the pointer to the Trajectory object where
+    \param traj              a pointer to a std::vector<double *> where
                              coordinates will be stored
 
     \return an integer value indicating whether or not the convergence

Code/Geometry/CMakeLists.txt

@@ -1,6 +1,6 @@
 rdkit_library(RDGeometryLib 
               point.cpp Transform2D.cpp Transform3D.cpp 
-              Trajectory.cpp UniformGrid3D.cpp GridUtils.cpp
+              UniformGrid3D.cpp GridUtils.cpp
               LINK_LIBRARIES DataStructs RDGeneral)
 
 rdkit_headers(Grid3D.h
@@ -9,12 +9,10 @@ rdkit_headers(Grid3D.h
               Transform2D.h
               Transform3D.h
               Transform.h
-              Trajectory.h
               UniformGrid3D.h
               Utils.h DEST Geometry)
 
 rdkit_test(testTransforms testTransforms.cpp LINK_LIBRARIES RDGeometryLib DataStructs RDGeneral )
 rdkit_test(testGrid testGrid.cpp LINK_LIBRARIES RDGeometryLib DataStructs RDGeneral )
-rdkit_test(testTrajectory testTrajectory.cpp LINK_LIBRARIES RDGeometryLib RDGeneral )
 
 add_subdirectory(Wrap)

Code/Geometry/Wrap/CMakeLists.txt

@@ -1,5 +1,5 @@
 rdkit_python_extension(rdGeometry
-                       Point.cpp Trajectory.cpp UniformGrid3D.cpp rdGeometry.cpp
+                       Point.cpp UniformGrid3D.cpp rdGeometry.cpp
                        DEST Geometry
                        LINK_LIBRARIES RDGeometryLib DataStructs RDGeneral RDBoost)
 

Code/Geometry/Wrap/testGeometry.py

@@ -406,241 +406,6 @@ class TestCase(unittest.TestCase):
         self.assertEqual(yi,2)
         self.assertEqual(zi,1)
 
-    def testSnapshot(self):
-      s = geom.Snapshot([])
-      e = False
-      try:
-        s.GetPoint2D(12)
-      except:
-        e = True
-      self.assertTrue(e)
-      s = geom.Snapshot([0.0, 0.0, 0.0])
-      e = False
-      try:
-        s.GetPoint2D(0)
-      except:
-        e = True
-      self.assertTrue(e)
-
-    def testTrajectory2D(self):
-      dim = 2
-      np = 10
-      ns = 5
-      traj = geom.Trajectory(dim, np)
-      self.assertEqual(traj.Dimension(), dim)
-      self.assertEqual(traj.NumPoints(), np)
-      c = []
-      for i in range(np * dim):
-        c.append(float(i))
-      for i in range(ns):
-        traj.AddSnapshot(geom.Snapshot(c, float(i)))
-      self.assertEqual(len(traj), ns)
-      e = False
-      try:
-        traj.GetSnapshot(ns)
-      except:
-        e = True
-      self.assertTrue(e)
-      e = False
-      try:
-        traj.GetSnapshot(0).GetPoint2D(np)
-      except:
-        e = True
-      self.assertTrue(e)
-      for i in range(np):
-        self.assertAlmostEqual(traj.GetSnapshot(0).GetPoint2D(i).x, float(i * dim))
-        self.assertAlmostEqual(traj.GetSnapshot(0).GetPoint2D(i).y, float(i * dim + 1))
-        e = False
-        try:
-          self.assertAlmostEqual(traj.GetSnapshot(0).GetPoint3D(i).z, 0.0)
-        except:
-          e = True;
-        self.assertFalse(e)
-      for i in range(ns):
-        self.assertAlmostEqual(traj.GetSnapshot(i).GetEnergy(), float(i))
-      traj.RemoveSnapshot(0)
-      self.assertEqual(len(traj), ns - 1)
-      for i in range(ns - 1):
-        self.assertAlmostEqual(traj.GetSnapshot(i).GetEnergy(), float(i + 1))
-      traj.InsertSnapshot(0, geom.Snapshot(c, 999.0))
-      self.assertEqual(len(traj), ns)
-      copySnapshot = geom.Snapshot(traj.GetSnapshot(0))
-      traj.AddSnapshot(copySnapshot)
-      self.assertEqual(len(traj), ns + 1)
-      self.assertAlmostEqual(traj.GetSnapshot(0).GetEnergy(), 999.0)
-      self.assertAlmostEqual(traj.GetSnapshot(1).GetEnergy(), 1.0)
-      self.assertAlmostEqual(traj.GetSnapshot(len(traj) - 1).GetEnergy(), 999.0)
-      traj2 = geom.Trajectory(traj);
-      self.assertEqual(len(traj), len(traj2))
-
-    def testTrajectory3D(self):
-      dim = 3
-      np = 10
-      ns = 5
-      traj = geom.Trajectory(dim, np)
-      self.assertEqual(traj.Dimension(), dim)
-      self.assertEqual(traj.NumPoints(), np)
-      c = []
-      for i in range(np * dim):
-        c.append(float(i))
-      for i in range(ns):
-        traj.AddSnapshot(geom.Snapshot(c, float(i)))
-      self.assertEqual(len(traj), ns)
-      e = False
-      try:
-        traj.GetSnapshot(ns)
-      except:
-        e = True
-      self.assertTrue(e)
-      e = False
-      try:
-        traj.GetSnapshot(0).GetPoint2D(np)
-      except:
-        e = True
-      self.assertTrue(e)
-      for i in range(np):
-        self.assertAlmostEqual(traj.GetSnapshot(0).GetPoint3D(i).x, float(i * dim))
-        self.assertAlmostEqual(traj.GetSnapshot(0).GetPoint3D(i).y, float(i * dim + 1))
-        self.assertAlmostEqual(traj.GetSnapshot(0).GetPoint3D(i).z, float(i * dim + 2))
-        if (not i):
-          e = False
-          try:
-            traj.GetSnapshot(0).GetPoint2D(i)
-          except:
-            e = True
-          self.assertTrue(e)
-      for i in range(ns):
-        self.assertAlmostEqual(traj.GetSnapshot(i).GetEnergy(), float(i))
-      traj.RemoveSnapshot(0)
-      self.assertEqual(len(traj), ns - 1)
-      for i in range(ns - 1):
-        self.assertAlmostEqual(traj.GetSnapshot(i).GetEnergy(), float(i + 1))
-      traj.InsertSnapshot(0, geom.Snapshot(c, 999.0))
-      self.assertEqual(len(traj), ns)
-      copySnapshot = geom.Snapshot(traj.GetSnapshot(0))
-      traj.AddSnapshot(copySnapshot)
-      self.assertEqual(len(traj), ns + 1)
-      self.assertAlmostEqual(traj.GetSnapshot(0).GetEnergy(), 999.0)
-      self.assertAlmostEqual(traj.GetSnapshot(1).GetEnergy(), 1.0)
-      self.assertAlmostEqual(traj.GetSnapshot(len(traj) - 1).GetEnergy(), 999.0)
-      traj2 = geom.Trajectory(traj);
-      self.assertEqual(len(traj), len(traj2))
-
-    def testReadAmber(self):
-      rdbase = os.environ['RDBASE']
-      fName = os.path.join(rdbase, 'Code', 'Geometry', 'testData', 'water_coords_bad.trx')
-      traj = geom.Trajectory(2, 0)
-      ok = False
-      try:
-        geom.ReadAmberTrajectory(fName, traj)
-      except:
-        ok = True
-      self.assertTrue(ok)
-      traj = geom.Trajectory(3, 3)
-      ok = False
-      try:
-        geom.ReadAmberTrajectory(fName, traj)
-      except:
-        ok = True
-      self.assertTrue(ok)
-      fName = os.path.join(rdbase, 'Code', 'Geometry', 'testData', 'water_coords_bad2.trx')
-      ok = False
-      try:
-        traj = geom.Trajectory(3, 3)
-        geom.ReadAmberTrajectory(fName, traj)
-      except:
-        ok = True
-      self.assertTrue(ok)
-      fName = os.path.join(rdbase, 'Code', 'Geometry', 'testData', 'water_coords.trx')
-      traj = geom.Trajectory(3, 3)
-      geom.ReadAmberTrajectory(fName, traj)
-      self.assertEqual(len(traj), 1)
-      fName = os.path.join(rdbase, 'Code', 'Geometry', 'testData', 'water_coords2.trx')
-      traj = geom.Trajectory(3, 3)
-      geom.ReadAmberTrajectory(fName, traj)
-      self.assertEqual(len(traj), 2)
-
-    def testReadAmberPython(self):
-      # reimplemented the Amber trajectory reader in Python
-      # let's check we get the same data as the C++ reader
-      # (test for building a trajectory out of Snapshots from Python)
-      rdbase = os.environ['RDBASE']
-      fName = os.path.join(rdbase, 'Code', 'Geometry', 'testData', 'water_coords2.trx')
-      traj = geom.Trajectory(3, 3)
-      nCoords = traj.NumPoints() * 3
-      nSnapshots = 0
-      hnd = open(fName, 'r')
-      line = hnd.readline()
-      lineNum = 0
-      c = []
-      i = 0
-      while (line):
-        lineNum += 1
-        if (lineNum > 1):
-          tok = line.strip().split()
-          j = 0
-          while ((i < nCoords) and (j < len(tok))):
-            c.append(float(tok[j]))
-            j += 1
-            i += 1
-          if (i == nCoords):
-            nSnapshots += 1
-            traj.AddSnapshot(geom.Snapshot(c))
-            c = []
-            i = 0
-            line = ' '.join(tok[j:]) + ' '
-          else:
-            line = ''
-        else:
-          line = ''
-        line += hnd.readline()
-      hnd.close()
-      self.assertEqual(i, 0)
-      self.assertEqual(nSnapshots, 2)
-      traj2 = geom.Trajectory(3, 3)
-      geom.ReadAmberTrajectory(fName, traj2)
-      self.assertEqual(len(traj), len(traj2))
-      self.assertEqual(traj.NumPoints(), traj2.NumPoints())
-      for snapshotNum in range(len(traj)):
-        for pointNum in range(traj.NumPoints()):
-          for i in range(3):
-            self.assertEqual(traj.GetSnapshot(snapshotNum).GetPoint3D(pointNum)[i],
-              traj2.GetSnapshot(snapshotNum).GetPoint3D(pointNum)[i])
-
-    def testReadGromos(self):
-      rdbase = os.environ['RDBASE']
-      fName = os.path.join(rdbase, 'Code', 'Geometry', 'testData', 'water_coords_bad.trc')
-      traj = geom.Trajectory(2, 0)
-      ok = False
-      try:
-        geom.ReadGromosTrajectory(fName, traj)
-      except:
-        ok = True
-      self.assertTrue(ok)
-      traj = geom.Trajectory(3, 3)
-      ok = False
-      try:
-        geom.ReadGromosTrajectory(fName, traj)
-      except:
-        ok = True
-      self.assertTrue(ok)
-      fName = os.path.join(rdbase, 'Code', 'Geometry', 'testData', 'water_coords_bad2.trc')
-      ok = False
-      try:
-        traj = geom.Trajectory(3, 3)
-        geom.ReadGromosTrajectory(fName, traj)
-      except:
-        ok = True
-      self.assertTrue(ok)
-      fName = os.path.join(rdbase, 'Code', 'Geometry', 'testData', 'water_coords.trc')
-      traj = geom.Trajectory(3, 3)
-      geom.ReadGromosTrajectory(fName, traj)
-      self.assertEqual(len(traj), 1)
-      fName = os.path.join(rdbase, 'Code', 'Geometry', 'testData', 'water_coords2.trc')
-      traj = geom.Trajectory(3, 3)
-      geom.ReadGromosTrajectory(fName, traj)
-      self.assertEqual(len(traj), 2)
-
 if __name__=='__main__':
     print("Testing Geometry wrapper")
     unittest.main()

Code/GraphMol/CMakeLists.txt

@@ -74,6 +74,7 @@ add_subdirectory(MMPA)
 
 
 add_subdirectory(ReducedGraphs)
+add_subdirectory(Trajectory)
 
 if(RDK_BUILD_SLN_SUPPORT AND NOT CMAKE_COMPILER_IS_CLANG)
 add_subdirectory(SLNParse)
@@ -110,3 +111,6 @@ rdkit_test(graphmolMemTest1 memtest1.cpp LINK_LIBRARIES SmilesParse GraphMol RDG
 
 rdkit_test(resMolSupplierTest resMolSupplierTest.cpp
            LINK_LIBRARIES SmilesParse GraphMol RDGeometryLib RDGeneral SubstructMatch FileParsers)
+
+rdkit_test(trajectoryTest resMolSupplierTest.cpp
+           LINK_LIBRARIES SmilesParse GraphMol RDGeometryLib RDGeneral SubstructMatch FileParsers)

Code/GraphMol/Trajectory/Trajectory.cpp

@@ -15,7 +15,7 @@
 #include <set>
 #include "Trajectory.h"
 
-namespace RDGeom {
+namespace RDKit {
 
 Snapshot::Snapshot(boost::shared_array<double> pos, double energy) :
   d_trajectory(NULL),

Code/GraphMol/Trajectory/Trajectory.h

@@ -12,11 +12,11 @@
 #define __RD_TRAJECTORY_H__
 #include <vector>
 #include <map>
-#include "point.h"
+#include "Geometry/point.h"
 #include "boost/shared_ptr.hpp"
 #include "boost/shared_array.hpp"
 
-namespace RDGeom {
+namespace RDKit {
 
 class Trajectory;
 

Code/GraphMol/Trajectory/trajectoryTest.cpp

@@ -1,6 +1,6 @@
 //  $Id$
 //
-//   Copyright (C) 2005-2013 Greg Landrum and Rational Discovery LLC
+//   Copyright (C) 2016 Sereina Riniker, Paolo Tosco
 //
 //   @@ All Rights Reserved @@
 //  This file is part of the RDKit.
@@ -8,11 +8,11 @@
 //  which is included in the file license.txt, found at the root
 //  of the RDKit source tree.
 //
+
 #include "Trajectory.h"
-#include "point.h"
+#include "Geometry/point.h"
 #include <RDGeneral/Invariant.h>
 
-using namespace RDGeom;
 using namespace RDKit;
 
 void testSnapshot() {
@@ -180,7 +180,7 @@ void testReadAmber() {
   BOOST_LOG(rdErrorLog) << "testReadAmber" << std::endl;
 
   std::string rdbase = getenv("RDBASE");
-  std::string fName = rdbase + "/Code/Geometry/testData/water_coords_bad.trx";
+  std::string fName = rdbase + "/Code/GraphMol/testData/water_coords_bad.trx";
   {
     Trajectory traj(2, 0);
     bool ok = false;
@@ -204,7 +204,7 @@ void testReadAmber() {
     }
     TEST_ASSERT(ok);
   }
-  fName = rdbase + "/Code/Geometry/testData/water_coords_bad2.trx";
+  fName = rdbase + "/Code/GraphMol/testData/water_coords_bad2.trx";
   {
     bool ok = false;
     try {
@@ -217,13 +217,13 @@ void testReadAmber() {
     }
     TEST_ASSERT(ok);
   }
-  fName = rdbase + "/Code/Geometry/testData/water_coords.trx";
+  fName = rdbase + "/Code/GraphMol/testData/water_coords.trx";
   {
     Trajectory traj(3, 3);
     readAmberTrajectory(fName, traj);
     TEST_ASSERT(traj.size() == 1);
   }
-  fName = rdbase + "/Code/Geometry/testData/water_coords2.trx";
+  fName = rdbase + "/Code/GraphMol/testData/water_coords2.trx";
   {
     Trajectory traj(3, 3);
     readAmberTrajectory(fName, traj);
@@ -238,7 +238,7 @@ void testReadGromos() {
   BOOST_LOG(rdErrorLog) << "testReadGromos" << std::endl;
 
   std::string rdbase = getenv("RDBASE");
-  std::string fName = rdbase + "/Code/Geometry/testData/water_coords_bad.trc";
+  std::string fName = rdbase + "/Code/GraphMol/testData/water_coords_bad.trc";
   {
     Trajectory traj(2, 0);
     bool ok = false;
@@ -262,7 +262,7 @@ void testReadGromos() {
     }
     TEST_ASSERT(ok);
   }
-  fName = rdbase + "/Code/Geometry/testData/water_coords_bad2.trc";
+  fName = rdbase + "/Code/GraphMol/testData/water_coords_bad2.trc";
   {
     bool ok = false;
     try {
@@ -275,13 +275,13 @@ void testReadGromos() {
     }
     TEST_ASSERT(ok);
   }
-  fName = rdbase + "/Code/Geometry/testData/water_coords.trc";
+  fName = rdbase + "/Code/GraphMol/testData/water_coords.trc";
   {
     Trajectory traj(3, 3);
     readGromosTrajectory(fName, traj);
     TEST_ASSERT(traj.size() == 1);
   }
-  fName = rdbase + "/Code/Geometry/testData/water_coords2.trc";
+  fName = rdbase + "/Code/GraphMol/testData/water_coords2.trc";
   {
     Trajectory traj(3, 3);
     readGromosTrajectory(fName, traj);

Code/GraphMol/Wrap/Trajectory.cpp

@@ -15,7 +15,7 @@
 
 namespace python = boost::python;
 
-namespace RDGeom {
+namespace RDKit {
 
 Snapshot *getSnapshot_wrap(Trajectory *traj, unsigned int snapshotNum) {
   return new Snapshot(traj->getSnapshot(snapshotNum));

Code/GraphMol/Wrap/testTrajectory.py

@@ -0,0 +1,251 @@
+from __future__ import print_function
+import os,sys
+import unittest
+
+from rdkit import RDConfig
+
+def feq(v1, v2, tol=1.0e-4):
+    return abs(v1-v2) < tol
+
+class TestCase(unittest.TestCase):
+    def setUp(self) :
+        pass
+
+    def testSnapshot(self):
+      s = Snapshot([])
+      e = False
+      try:
+        s.GetPoint2D(12)
+      except:
+        e = True
+      self.assertTrue(e)
+      s = Snapshot([0.0, 0.0, 0.0])
+      e = False
+      try:
+        s.GetPoint2D(0)
+      except:
+        e = True
+      self.assertTrue(e)
+
+    def testTrajectory2D(self):
+      dim = 2
+      np = 10
+      ns = 5
+      traj = Trajectory(dim, np)
+      self.assertEqual(traj.Dimension(), dim)
+      self.assertEqual(traj.NumPoints(), np)
+      c = []
+      for i in range(np * dim):
+        c.append(float(i))
+      for i in range(ns):
+        traj.AddSnapshot(Snapshot(c, float(i)))
+      self.assertEqual(len(traj), ns)
+      e = False
+      try:
+        traj.GetSnapshot(ns)
+      except:
+        e = True
+      self.assertTrue(e)
+      e = False
+      try:
+        traj.GetSnapshot(0).GetPoint2D(np)
+      except:
+        e = True
+      self.assertTrue(e)
+      for i in range(np):
+        self.assertAlmostEqual(traj.GetSnapshot(0).GetPoint2D(i).x, float(i * dim))
+        self.assertAlmostEqual(traj.GetSnapshot(0).GetPoint2D(i).y, float(i * dim + 1))
+        e = False
+        try:
+          self.assertAlmostEqual(traj.GetSnapshot(0).GetPoint3D(i).z, 0.0)
+        except:
+          e = True;
+        self.assertFalse(e)
+      for i in range(ns):
+        self.assertAlmostEqual(traj.GetSnapshot(i).GetEnergy(), float(i))
+      traj.RemoveSnapshot(0)
+      self.assertEqual(len(traj), ns - 1)
+      for i in range(ns - 1):
+        self.assertAlmostEqual(traj.GetSnapshot(i).GetEnergy(), float(i + 1))
+      traj.InsertSnapshot(0, Snapshot(c, 999.0))
+      self.assertEqual(len(traj), ns)
+      copySnapshot = Snapshot(traj.GetSnapshot(0))
+      traj.AddSnapshot(copySnapshot)
+      self.assertEqual(len(traj), ns + 1)
+      self.assertAlmostEqual(traj.GetSnapshot(0).GetEnergy(), 999.0)
+      self.assertAlmostEqual(traj.GetSnapshot(1).GetEnergy(), 1.0)
+      self.assertAlmostEqual(traj.GetSnapshot(len(traj) - 1).GetEnergy(), 999.0)
+      traj2 = Trajectory(traj);
+      self.assertEqual(len(traj), len(traj2))
+
+    def testTrajectory3D(self):
+      dim = 3
+      np = 10
+      ns = 5
+      traj = Trajectory(dim, np)
+      self.assertEqual(traj.Dimension(), dim)
+      self.assertEqual(traj.NumPoints(), np)
+      c = []
+      for i in range(np * dim):
+        c.append(float(i))
+      for i in range(ns):
+        traj.AddSnapshot(Snapshot(c, float(i)))
+      self.assertEqual(len(traj), ns)
+      e = False
+      try:
+        traj.GetSnapshot(ns)
+      except:
+        e = True
+      self.assertTrue(e)
+      e = False
+      try:
+        traj.GetSnapshot(0).GetPoint2D(np)
+      except:
+        e = True
+      self.assertTrue(e)
+      for i in range(np):
+        self.assertAlmostEqual(traj.GetSnapshot(0).GetPoint3D(i).x, float(i * dim))
+        self.assertAlmostEqual(traj.GetSnapshot(0).GetPoint3D(i).y, float(i * dim + 1))
+        self.assertAlmostEqual(traj.GetSnapshot(0).GetPoint3D(i).z, float(i * dim + 2))
+        if (not i):
+          e = False
+          try:
+            traj.GetSnapshot(0).GetPoint2D(i)
+          except:
+            e = True
+          self.assertTrue(e)
+      for i in range(ns):
+        self.assertAlmostEqual(traj.GetSnapshot(i).GetEnergy(), float(i))
+      traj.RemoveSnapshot(0)
+      self.assertEqual(len(traj), ns - 1)
+      for i in range(ns - 1):
+        self.assertAlmostEqual(traj.GetSnapshot(i).GetEnergy(), float(i + 1))
+      traj.InsertSnapshot(0, Snapshot(c, 999.0))
+      self.assertEqual(len(traj), ns)
+      copySnapshot = Snapshot(traj.GetSnapshot(0))
+      traj.AddSnapshot(copySnapshot)
+      self.assertEqual(len(traj), ns + 1)
+      self.assertAlmostEqual(traj.GetSnapshot(0).GetEnergy(), 999.0)
+      self.assertAlmostEqual(traj.GetSnapshot(1).GetEnergy(), 1.0)
+      self.assertAlmostEqual(traj.GetSnapshot(len(traj) - 1).GetEnergy(), 999.0)
+      traj2 = Trajectory(traj);
+      self.assertEqual(len(traj), len(traj2))
+
+    def testReadAmber(self):
+      rdbase = os.environ['RDBASE']
+      fName = os.path.join(rdbase, 'Code', 'GraphMol', 'test_data', 'water_coords_bad.trx')
+      traj = Trajectory(2, 0)
+      ok = False
+      try:
+        ReadAmberTrajectory(fName, traj)
+      except:
+        ok = True
+      self.assertTrue(ok)
+      traj = Trajectory(3, 3)
+      ok = False
+      try:
+        ReadAmberTrajectory(fName, traj)
+      except:
+        ok = True
+      self.assertTrue(ok)
+      fName = os.path.join(rdbase, 'Code', 'GraphMol', 'test_data', 'water_coords_bad2.trx')
+      ok = False
+      try:
+        traj = Trajectory(3, 3)
+        ReadAmberTrajectory(fName, traj)
+      except:
+        ok = True
+      self.assertTrue(ok)
+      fName = os.path.join(rdbase, 'Code', 'GraphMol', 'test_data', 'water_coords.trx')
+      traj = Trajectory(3, 3)
+      ReadAmberTrajectory(fName, traj)
+      self.assertEqual(len(traj), 1)
+      fName = os.path.join(rdbase, 'Code', 'GraphMol', 'test_data', 'water_coords2.trx')
+      traj = Trajectory(3, 3)
+      ReadAmberTrajectory(fName, traj)
+      self.assertEqual(len(traj), 2)
+
+    def testReadAmberPython(self):
+      # reimplemented the Amber trajectory reader in Python
+      # let's check we get the same data as the C++ reader
+      # (test for building a trajectory out of Snapshots from Python)
+      rdbase = os.environ['RDBASE']
+      fName = os.path.join(rdbase, 'Code', 'GraphMol', 'test_data', 'water_coords2.trx')
+      traj = Trajectory(3, 3)
+      nCoords = traj.NumPoints() * 3
+      nSnapshots = 0
+      hnd = open(fName, 'r')
+      line = hnd.readline()
+      lineNum = 0
+      c = []
+      i = 0
+      while (line):
+        lineNum += 1
+        if (lineNum > 1):
+          tok = line.strip().split()
+          j = 0
+          while ((i < nCoords) and (j < len(tok))):
+            c.append(float(tok[j]))
+            j += 1
+            i += 1
+          if (i == nCoords):
+            nSnapshots += 1
+            traj.AddSnapshot(Snapshot(c))
+            c = []
+            i = 0
+            line = ' '.join(tok[j:]) + ' '
+          else:
+            line = ''
+        else:
+          line = ''
+        line += hnd.readline()
+      hnd.close()
+      self.assertEqual(i, 0)
+      self.assertEqual(nSnapshots, 2)
+      traj2 = Trajectory(3, 3)
+      ReadAmberTrajectory(fName, traj2)
+      self.assertEqual(len(traj), len(traj2))
+      self.assertEqual(traj.NumPoints(), traj2.NumPoints())
+      for snapshotNum in range(len(traj)):
+        for pointNum in range(traj.NumPoints()):
+          for i in range(3):
+            self.assertEqual(traj.GetSnapshot(snapshotNum).GetPoint3D(pointNum)[i],
+              traj2.GetSnapshot(snapshotNum).GetPoint3D(pointNum)[i])
+
+    def testReadGromos(self):
+      rdbase = os.environ['RDBASE']
+      fName = os.path.join(rdbase, 'Code', 'GraphMol', 'test_data', 'water_coords_bad.trc')
+      traj = Trajectory(2, 0)
+      ok = False
+      try:
+        ReadGromosTrajectory(fName, traj)
+      except:
+        ok = True
+      self.assertTrue(ok)
+      traj = Trajectory(3, 3)
+      ok = False
+      try:
+        ReadGromosTrajectory(fName, traj)
+      except:
+        ok = True
+      self.assertTrue(ok)
+      fName = os.path.join(rdbase, 'Code', 'GraphMol', 'test_data', 'water_coords_bad2.trc')
+      ok = False
+      try:
+        traj = Trajectory(3, 3)
+        ReadGromosTrajectory(fName, traj)
+      except:
+        ok = True
+      self.assertTrue(ok)
+      fName = os.path.join(rdbase, 'Code', 'GraphMol', 'test_data', 'water_coords.trc')
+      traj = Trajectory(3, 3)
+      ReadGromosTrajectory(fName, traj)
+      self.assertEqual(len(traj), 1)
+      fName = os.path.join(rdbase, 'Code', 'GraphMol', 'test_data', 'water_coords2.trc')
+      traj = Trajectory(3, 3)
+      ReadGromosTrajectory(fName, traj)
+      self.assertEqual(len(traj), 2)
+
+if __name__=='__main__':
+    print("Testing Trajectory wrapper")
+    unittest.main()

Code/GraphMol/test1.cpp

@@ -22,7 +22,6 @@
 #include <GraphMol/ForceFieldHelpers/MMFF/AtomTyper.h>
 #include <GraphMol/ForceFieldHelpers/MMFF/Builder.h>
 #include <ForceField/ForceField.h>
-#include <Geometry/Trajectory.h>
 #include <sstream>
 #include <iostream>
 
@@ -932,6 +931,7 @@ void test1() {
   }
 }
 
+#if 0
 void testAddConformersFromTrajectory() {
   BOOST_LOG(rdInfoLog) << "-----------------------\n";
   BOOST_LOG(rdInfoLog) << "Testing adding conformers from a trajectory" << std::endl;
@@ -1187,6 +1187,7 @@ void testAddConformersFromGromosTrajectory() {
   delete mol;
   BOOST_LOG(rdErrorLog) << "done" << std::endl;
 }
+#endif
 
 void testPeriodicTable() {
   BOOST_LOG(rdInfoLog) << "-----------------------\n";
@@ -1523,9 +1524,6 @@ int main() {
 // boost::logging::enable_logs("rdApp.info");
 #if 1
   test1();
-  testAddConformersFromTrajectory();
-  testAddConformersFromAmberTrajectory();
-  testAddConformersFromGromosTrajectory();
   testPropLeak();
   testMolProps();
   testAtomProps();
@@ -1535,6 +1533,10 @@ int main() {
   testIssue1993296();
   testIssue2381580();
   testIssue2840217();
+#else
+  testAddConformersFromTrajectory();
+  testAddConformersFromAmberTrajectory();
+  testAddConformersFromGromosTrajectory();
 #endif
   testPeriodicTable();
   testAddAtomWithConf();