├── LICENSE ├── README.md ├── geodesic_interpolate ├── .DS_Store ├── __init__.py ├── __main__.py ├── coord_utils.py ├── fileio.py ├── geodesic.py └── interpolation.py ├── setup.py └── test_cases ├── 2JOF-pH7.pdb ├── DielsAlder.log ├── DielsAlder.xyz ├── DielsAlder_interpolated.xyz ├── H+CH4_CH3+H2.log ├── H+CH4_CH3+H2.xyz ├── H+CH4_CH3+H2_interpolated.xyz ├── TrpCage_interpolated.xyz ├── TrpCage_unfold.xyz ├── calcium_binding.log ├── calcium_binding.xyz ├── calcium_binding_interpolated.pdb ├── calcium_binding_interpolated.xyz ├── collagen.log ├── collagen.xyz ├── collagen_interpolated.xyz ├── interpolated.xyz ├── raw.xyz └── trp_unfold.log /LICENSE: -------------------------------------------------------------------------------- 1 | MIT License 2 | 3 | Copyright (c) 2024 Xiaolei Zhu 4 | 5 | Permission is hereby granted, free of charge, to any person obtaining a copy 6 | of this software and associated documentation files (the "Software"), to deal 7 | in the Software without restriction, including without limitation the rights 8 | to use, copy, modify, merge, publish, distribute, sublicense, and/or sell 9 | copies of the Software, and to permit persons to whom the Software is 10 | furnished to do so, subject to the following conditions: 11 | 12 | The above copyright notice and this permission notice shall be included in all 13 | copies or substantial portions of the Software. 14 | 15 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 16 | IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 17 | FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE 18 | AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 19 | LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, 20 | OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE 21 | SOFTWARE. 22 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | Geodesic interpolations of reaction pathways 2 | ==== 3 | Constructing interpolation paths between molecular geometries to obtain reaction path. 4 | 5 | Traditional interpolation methods encounter difficulty when it comes to redundant internal coordinate spaces, because the feasible physical space compose only a very small and highly curved subspace. In this method, we avoid the problem of feasibility by operating strictly in feasible space, and bring in the benefit of internal coordinates through proper application of the corresponding metric tensor. With this new formulation, we view the configuration space as a Riemannian manifold with a metric generated from a set of internal coordinates. The interpolation paths are defined as geodesic curves on such manifolds. In other words the integrated total coordinate change is minimized. Such a definition ensures that the constructed paths are smooth and well behaved. The package is also used for smoothing discontinuous or noisy trajectories obtained from MD simulations. 6 | 7 | It has been shown that the method generate smooth paths with reasonable barrier height even for highly complex reactions, such as protein unfolding or concerted cycloaddition reactions with many simutaneous ring formations. The default coordinate system uses Morse scaled pair-wise distances. The lengths in such coordinate systems have the physical meaning of the total number of bond changes along the path. 8 | 9 | This is a pure python implementation, so it is not optimized for speed, but rather is intended to serve as a reference implementation of the algorithms described in the paper. Still, interpolating systems with ~1000 atoms should not be a problem. 10 | 11 | 12 | Directory Structure 13 | ---- 14 | - geodesic_interpolate Python package for interpolation and smoothing by finding geodesic curves with redundant internal metrics 15 | - `__init__.py` Python package file 16 | - `__main__.py` Standalone script for performing interpolation and smoothings. 17 | - `geodesic.py` Computation and minimization of path length in redundant internal metrics. This is used to optimize 18 | a path way to find a geodesic. Cannot change the number of images during optimization 19 | - `interpolation.py` Generating approximate interpolation points to be used as starting guess for the geodesic optimizations. 20 | Recursively attempt to perform bisections on largest segment in internal space. Generally will create path 21 | with discontinuities, so a smoothing process need to follow this. 22 | - `coord_utils.py` Coordinate utilities. A simplified version of Nanoreactor coordinates module which provide a scaled 23 | interatomic distance coordinate, pair screening based on threshold and connectivity, as well as trans-rotational 24 | alignment based on Kabsch algorithm. 25 | - `fileio.py` XYZ file reading and writing 26 | - setup.py Installation script. This will install both the Python package, which can be imported by name `geodesic_interpolate` 27 | and the standalone script, which is also named `geodesic_interpolate` 28 | - test_cases A few test cases used to check the performance of the code. Note that the large ones may take a few minutes 29 | thanks to Python. Especially need to run them when testing out alternative coordinate scaling methods. 30 | - `H+CH4_CH3+H2.xyz` A simple test case. Should always work 31 | - `DielsAlder.xyz` Dehydro-Diels-Alder reaction. This is an important test case because the initial structure is planar symmetric and 32 | could access both the final structure and its mirror image, which as exactly the same internal coordinates. Proper 33 | monitoring of geodesic length during the interpolation process is therefore crucial for this to work, without which 34 | the raw interpolated path will jump between mirror images and the optimized path would contain some flopping. 35 | Also tests the non-sweeping global path optimization algo in a relatively large system. 36 | - `TrpCage_unfold.xyz` Unfolding a Trp-cage mini-protein. Need at least 10 images to work. Folded geometry taken from Stefan''s test 37 | directory which is instead taken from Nathan. Unfolded structure is generated by force navigated MD for 1ns under 38 | 1nN on C and N terminal with ReaxFF, then optimizing without force at 6-31g/b3lyp level. For testing many 39 | simultaneous large amplitude motions. 40 | - `collagen.xyz` Interpolate between the solution and crystal structure of collagen Kunitz domain 1kun - 1kth. Solvents removed 41 | from the PDB structures. Tests collision avoidance for large movements in the core of folded protein. Other 42 | groups should slightly breath to create room for the part that changes. 43 | - `calcium_binding.xyz` Binding two Ca2+ ions to the yeast Calmodulin N terminal domain 1f54 -1f55. The apo structure did not have 44 | ions so two of which were added by hand at random locations away from the protein. It seem to be hard to avoid 45 | large movements of the Ca2+ cations when they are very far away from the protein but once in contact they should 46 | move smoothly. This is to test if the interpolater can correctly route and find the entry point and connect the 47 | path. 48 | 49 | 50 | Prerequisites 51 | ---- 52 | 53 | Python : >2.7 or >3.5 54 | 55 | Numpy : Tested with 1.13 56 | 57 | Scipy : Tested with 0.19 58 | 59 | 60 | Installation 61 | ---- 62 | The package can be used without installation from the package directory with 63 | 64 | python -m geodesic_interpolate filename ... 65 | 66 | To use the script from arbitrary location or to use the Python module, use setup tools: 67 | 68 | python setup.py install 69 | 70 | This will install a Python package `geodesic_interpolate` and a standalone script `geodesic_interpolate`. 71 | The package can be involved from arbitrary location using the aforementioned command line after installation, 72 | and a standalone script with the same signature can also be used 73 | 74 | geodesic_interpolate filename.xyz --output output.xyz --nimages 20 ... 75 | 76 | 77 | Usage 78 | ---- 79 | usage: geodesic_interpolate [-h] [--nimages NIMAGES] [--sweep] [--no-sweep] 80 | [--output OUTPUT] [--tol TOL] [--maxiter MAXITER] 81 | [--microiter MICROITER] [--scaling SCALING] 82 | [--friction FRICTION] [--dist-cutoff DIST_CUTOFF] 83 | [--logging {DEBUG,INFO,WARNING,ERROR}] 84 | [--save-raw SAVE_RAW] 85 | filename 86 | 87 | Interpolates between two geometries 88 | 89 | positional arguments: 90 | * filename XYZ file containing geometries. If the number of images is smaller than the desired number, 91 | interpolation points will be added. If the number is greater, subsampling will be performed. 92 | 93 | optional arguments: 94 | * `-h`, `--help` show this help message and exit 95 | * `--nimages NIMAGES` Number of images. (default: 17) 96 | * `--sweep` Sweep across the path optimizing one image at a time, instead of moving all images at the same time. 97 | Default is to perform sweeping updates if there are more than 30 atoms. (default: None) 98 | * `--no-sweep` Do not perform sweeping. (default: None) 99 | * `--output OUTPUT` Output filename. Default is interp.xyz (default: interpolated.xyz) 100 | * `--tol TOL` Convergence tolerance (default: 0.002) 101 | * `--maxiter MAXITER` Maximum number of minimization iterations (default: 15) 102 | * `--microiter MICROITER` Maximum number of micro iterations for sweeping algorithm. (default: 20) 103 | * `--scaling SCALING` Exponential parameter for morse potential (default: 1.7) 104 | * `--friction FRICTION` Size of friction term used to prevent very large change of geometry. (default: 0.01) 105 | * `--dist-cutoff DIST_CUTOFF` Cut-off value for the distance between a pair of atoms to be included in the coordinate system. (default: 3) 106 | * `--logging {DEBUG,INFO,WARNING,ERROR}` Logging level to adopt [ DEBUG | INFO | WARNING | ERROR ] (default: INFO) 107 | * `--save-raw SAVE_RAW` When specified, save the raw path after bisections be before smoothing. (default: None) 108 | 109 | -------------------------------------------------------------------------------- /geodesic_interpolate/.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/virtualzx-nad/geodesic-interpolate/a48c88bfbcabd1e2f883c368f49f2c81a5bc1173/geodesic_interpolate/.DS_Store -------------------------------------------------------------------------------- /geodesic_interpolate/__init__.py: -------------------------------------------------------------------------------- 1 | from .geodesic import Geodesic 2 | from .interpolation import redistribute -------------------------------------------------------------------------------- /geodesic_interpolate/__main__.py: -------------------------------------------------------------------------------- 1 | """Performing geodesic interpolation or smoothing. 2 | Optimize reaction path using geometric information by minimizing path length with metrics defined by 3 | redundant internal coordinates. Avoids the discontinuity and convergence problems of conventional 4 | interpolation methods by incorporating internal coordinate structure while operating in Cartesian, 5 | avoiding unfeasibility. 6 | 7 | Xiaolei Zhu et al, Martinez Group, Stanford University 8 | """ 9 | import logging 10 | import argparse 11 | 12 | import numpy as np 13 | 14 | from .fileio import read_xyz, write_xyz 15 | from .interpolation import redistribute 16 | from .geodesic import Geodesic 17 | 18 | 19 | logger = logging.getLogger(__name__) 20 | 21 | 22 | def main(): 23 | """Main entry point of the geodesic interpolation package. 24 | Parse command line arguments then activate the interpolators and smoothers.""" 25 | ps = argparse.ArgumentParser(description="Interpolates between two geometries", 26 | formatter_class=argparse.ArgumentDefaultsHelpFormatter) 27 | ps.add_argument("filename", type=str, help="XYZ file containing geometries. If the number of images " 28 | "is smaller than the desired number, interpolation points will be added. If the " 29 | "number is greater, subsampling will be performed.") 30 | ps.add_argument("--nimages", type=int, default=17, help="Number of images.") 31 | ps.add_argument("--sweep", action="store_true", help="Sweep across the path optimizing one image at " 32 | "a time, instead of moving all images at the same time. Default is to perform sweeping " 33 | "updates if there are more than 30 atoms.") 34 | ps.add_argument("--no-sweep", dest='sweep', action="store_false", help="Do not perform sweeping.") 35 | ps.set_defaults(sweep=None) 36 | ps.add_argument("--output", default="interpolated.xyz", type=str, help="Output filename. " 37 | "Default is interp.xyz") 38 | ps.add_argument("--tol", default=2e-3, type=float, help="Convergence tolerance") 39 | ps.add_argument("--maxiter", default=15, type=int, help="Maximum number of minimization iterations") 40 | ps.add_argument("--microiter", default=20, type=int, help="Maximum number of micro iterations for " 41 | "sweeping algorithm.") 42 | ps.add_argument("--scaling", default=1.7, type=float, help="Exponential parameter for morse potential") 43 | ps.add_argument("--friction", default=1e-2, type=float, help="Size of friction term used to prevent " 44 | "very large change of geometry.") 45 | ps.add_argument("--dist-cutoff", dest='dist_cutoff', default=3, type=float, help="Cut-off value for the " 46 | "distance between a pair of atoms to be included in the coordinate system.") 47 | ps.add_argument("--logging", default="INFO", choices=['DEBUG', 'INFO', 'WARNING', 'ERROR'], 48 | help="Logging level to adopt [ DEBUG | INFO | WARNING | ERROR ]") 49 | ps.add_argument("--save-raw", dest='save_raw', default=None, type=str, help="When specified, save the " 50 | "raw path after bisections be before smoothing.") 51 | args = ps.parse_args() 52 | 53 | # Setup logging based on designated logging level 54 | logging.basicConfig(format="[%(module)-12s]%(message)s", level=args.logging) 55 | 56 | # Read the initial geometries. 57 | symbols, X = read_xyz(args.filename) 58 | logger.info('Loaded %d geometries from %s', len(X), args.filename) 59 | if len(X) < 2: 60 | raise ValueError("Need at least two initial geometries.") 61 | 62 | # First redistribute number of images. Perform interpolation if too few and subsampling if too many 63 | # images are given 64 | raw = redistribute(symbols, X, args.nimages, tol=args.tol * 5) 65 | if args.save_raw is not None: 66 | write_xyz(args.save_raw, symbols, raw) 67 | 68 | # Perform smoothing by minimizing distance in Cartesian coordinates with redundant internal metric 69 | # to find the appropriate geodesic curve on the hyperspace. 70 | smoother = Geodesic(symbols, raw, args.scaling, threshold=args.dist_cutoff, friction=args.friction) 71 | if args.sweep is None: 72 | args.sweep = len(symbols) > 35 73 | try: 74 | if args.sweep: 75 | smoother.sweep(tol=args.tol, max_iter=args.maxiter, micro_iter=args.microiter) 76 | else: 77 | smoother.smooth(tol=args.tol, max_iter=args.maxiter) 78 | finally: 79 | # Save the smoothed path to output file. try block is to ensure output is saved if one ^C the 80 | # process, or there is an error 81 | logging.info('Saving final path to file %s', args.output) 82 | write_xyz(args.output, symbols, smoother.path) 83 | 84 | 85 | if __name__ == "__main__": 86 | main() 87 | -------------------------------------------------------------------------------- /geodesic_interpolate/coord_utils.py: -------------------------------------------------------------------------------- 1 | """Coordinate utilities used by the interpolation program""" 2 | import logging 3 | 4 | import numpy as np 5 | from scipy.spatial import KDTree 6 | 7 | 8 | logger = logging.getLogger(__name__) 9 | 10 | 11 | def align_path(path): 12 | """Rotate and translate images to minimize RMSD movements along the path. 13 | Also moves the geometric center of all images to the origin. 14 | """ 15 | path = np.array(path) 16 | path[0] -= np.mean(path[0], axis=0) 17 | max_rmsd = 0 18 | for g, nextg in zip(path, path[1:]): 19 | rmsd, nextg[:] = align_geom(g, nextg) 20 | max_rmsd = max(max_rmsd, rmsd) 21 | return max_rmsd, path 22 | 23 | 24 | def align_geom(refgeom, geom): 25 | """Find translation/rotation that moves a given geometry to maximally overlap 26 | with a reference geometry. Implemented with Kabsch algorithm. 27 | 28 | Args: 29 | refgeom: The reference geometry to be rotated to 30 | geom: The geometry to be rotated and shifted 31 | 32 | Returns: 33 | RMSD: Root-mean-squared difference between the rotated geometry 34 | and the reference 35 | new_geom: The rotated geometry that maximumally overal with the reference 36 | """ 37 | center = np.mean(refgeom, axis=0) # Find the geometric center 38 | ref2 = refgeom - center 39 | geom2 = geom - np.mean(geom, axis=0) 40 | cov = np.dot(geom2.T, ref2) 41 | v, sv, w = np.linalg.svd(cov) 42 | if np.linalg.det(v) * np.linalg.det(w) < 0: 43 | sv[-1] = -sv[-1] 44 | v[:, -1] = -v[:, -1] 45 | u = np.dot(v, w) 46 | new_geom = np.dot(geom2, u) + center 47 | rmsd = np.sqrt(np.mean((new_geom - refgeom) ** 2)) 48 | return rmsd, new_geom 49 | 50 | 51 | ATOMIC_RADIUS = dict(H=0.31, He=0.28, 52 | Li=1.28, Be=0.96, B=0.84, C=0.76, N=0.71, O=0.66, F=0.57, Ne=0.58, 53 | Na=1.66, Mg=1.41, Al=1.21, Si=1.11, P=1.07, S=1.05, Cl=1.02, Ar=1.06) 54 | 55 | 56 | def get_bond_list(geom, atoms=None, threshold=4, min_neighbors=4, snapshots=30, bond_threshold=1.8, 57 | enforce=()): 58 | """Get the list of all the important atom pairs. 59 | Samples a number of snapshots from a list of geometries to generate all 60 | distances that are below a given threshold in any of them. 61 | 62 | Args: 63 | atoms: Symbols for each atoms. 64 | geom: One or a list of geometries to check for pairs 65 | threshold: Threshold for including a bond in the bond list 66 | min_neighbors: Minimum number of neighbors to include for each atom. 67 | If an atom has smaller than this number of bonds, additional 68 | distances will be added to reach this number. 69 | snapshots: Number of snapshots to be used in the generation, useful 70 | for speeding up the process if the path is long and 71 | atoms numerous. 72 | 73 | Returns: 74 | List of all the included interatomic distance pairs. 75 | """ 76 | # Type casting and value checks on input parameters 77 | geom = np.asarray(geom) 78 | if len(geom.shape) < 3: 79 | # If there is only one geometry or it is flattened, promote to 3d 80 | geom = geom.reshape(1, -1, 3) 81 | min_neighbors = min(min_neighbors, geom.shape[1] - 1) 82 | 83 | # Determine which images to be used to determine distances 84 | snapshots = min(len(geom), snapshots) 85 | images = [0, len(geom) - 1] 86 | if snapshots > 2: 87 | images.extend(np.random.choice(range(1, snapshots - 1), snapshots - 2, replace=False)) 88 | # Get neighbor list for included geometry and merge them 89 | rijset = set(enforce) 90 | for image in images: 91 | tree = KDTree(geom[image]) 92 | pairs = tree.query_pairs(threshold) 93 | rijset.update(pairs) 94 | bonded = tree.query_pairs(bond_threshold) 95 | neighbors = {i: {i} for i in range(geom.shape[1])} 96 | for i, j in bonded: 97 | neighbors[i].add(j) 98 | neighbors[j].add(i) 99 | for i, j in bonded: 100 | for ni in neighbors[i]: 101 | for nj in neighbors[j]: 102 | if ni != nj: 103 | pair = tuple(sorted([ni, nj])) 104 | if pair not in rijset: 105 | rijset.add(pair) 106 | rijlist = sorted(rijset) 107 | # Check neighbor count to make sure `min_neighbors` is satisfied 108 | count = np.zeros(geom.shape[1], dtype=int) 109 | for i, j in rijlist: 110 | count[i] += 1 111 | count[j] += 1 112 | for idx, ct in enumerate(count): 113 | if ct < min_neighbors: 114 | _, neighbors = tree.query(geom[-1, idx], k=min_neighbors + 1) 115 | for i in neighbors: 116 | if i == idx: 117 | continue 118 | pair = tuple(sorted([i, idx])) 119 | if pair in rijset: 120 | continue 121 | else: 122 | rijset.add(pair) 123 | rijlist.append(pair) 124 | count[i] += 1 125 | count[idx] += 1 126 | if atoms is None: 127 | re = np.full(len(rijlist), 2.0) 128 | else: 129 | radius = np.array([ATOMIC_RADIUS.get(atom.capitalize(), 1.5) for atom in atoms]) 130 | re = np.array([radius[i] + radius[j] for i, j in rijlist]) 131 | logger.debug("Pair list contain %d pairs", len(rijlist)) 132 | return rijlist, re 133 | 134 | 135 | def compute_rij(geom, rij_list): 136 | """Calculate a list of distances and their derivatives 137 | 138 | Takes a set of cartesian geometries then calculate selected distances and their 139 | cartesian gradients given a list of atom pairs. 140 | 141 | Args: 142 | geom: Cartesian geometry of all the points. Must be 2d numpy array or list 143 | with shape (natoms, 3) 144 | rij_list: list of indexes of all the atom pairs 145 | 146 | Returns: 147 | rij (array): Array of all the distances. 148 | bmat (3d array): Cartesian gradients of all the distances.""" 149 | nrij = len(rij_list) 150 | rij = np.zeros(nrij) 151 | bmat = np.zeros((nrij, len(geom), 3)) 152 | for idx, (i, j) in enumerate(rij_list): 153 | dvec = geom[i] - geom[j] 154 | rij[idx] = r = np.sqrt(dvec[0] * dvec[0] + 155 | dvec[1] * dvec[1] + dvec[2] * dvec[2]) 156 | grad = dvec / r 157 | bmat[idx, i] = grad 158 | bmat[idx, j] = -grad 159 | return rij, bmat 160 | 161 | 162 | def compute_wij(geom, rij_list, func): 163 | """Calculate a list of scaled distances and their derivatives 164 | 165 | Takes a set of cartesian geometries then calculate selected distances and their 166 | cartesian gradients given a list of atom pairs. The distances are scaled with 167 | a given scaling function. 168 | 169 | Args: 170 | geom: Cartesian geometry of all the points. Must be 2d numpy array or list 171 | with shape (natoms, 3) 172 | rij_list: 2d numpy array of indexes of all the atom pairs 173 | func: A scaling function, which returns both the value and derivative. Must 174 | qualify as a numpy Ufunc in order to be broadcasted to array elements. 175 | 176 | Returns: 177 | wij (array): Array of all the scaled distances. 178 | bmat (2d array): Cartesian gradients of all the scaled distances, with the 179 | second dimension flattened (need this to be used in scipy.optimize).""" 180 | geom = np.asarray(geom).reshape(-1, 3) 181 | nrij = len(rij_list) 182 | rij, bmat = compute_rij(geom, rij_list) 183 | wij, dwdr = func(rij) 184 | for idx, grad in enumerate(dwdr): 185 | bmat[idx] *= grad 186 | return wij, bmat.reshape(nrij, -1) 187 | 188 | 189 | def morse_scaler(re=1.5, alpha=1.7, beta=0.01): 190 | """Returns a scaling function that determines the metric of the internal 191 | coordinates using morse potential 192 | 193 | Takes an internuclear distance, returns the scaled distance, and the 194 | derivative of the scaled distance with respect to the unscaled one. 195 | """ 196 | def scaler(x): 197 | ratio = x / re 198 | val1 = np.exp(alpha * (1 - ratio)) 199 | val2 = beta / ratio 200 | dval = -alpha / re * val1 - val2 / x 201 | return val1 + val2, dval 202 | return scaler 203 | 204 | 205 | def elu_scaler(re=2, alpha=2, beta=0.01): 206 | """Returns a scaling function that determines the metric of the internal 207 | coordinates using morse potential 208 | 209 | Takes an internuclear distance, returns the scaled distance, and the 210 | derivative of the scaled distance with respect to the unscaled one. 211 | """ 212 | def scaler(x): 213 | val1 = (1 - x / re) * alpha + 1 214 | dval = np.full(x.shape, -alpha / re) 215 | large = x > re 216 | v1l = np.exp(alpha * (1 - x[large] / re)) 217 | val1[large] = v1l 218 | dval[large] = -alpha / re * v1l 219 | val2 = beta * re / x 220 | return val1 + val2, dval - val2 / x 221 | return scaler 222 | -------------------------------------------------------------------------------- /geodesic_interpolate/fileio.py: -------------------------------------------------------------------------------- 1 | """File IO utilities""" 2 | import numpy as np 3 | 4 | 5 | def read_xyz(filename): 6 | """Read XYZ file and return atom names and coordinates 7 | 8 | Args: 9 | filename: Name of xyz data file 10 | 11 | Returns: 12 | atom_names: Element symbols of all the atoms 13 | coords: Cartesian coordinates for every frame. 14 | """ 15 | coords = [] 16 | with open(filename, 'r') as f: 17 | for line in f: 18 | try: 19 | natm = int(line) # Read number of atoms 20 | next(f) # Skip over comments 21 | atom_names = [] 22 | geom = np.zeros((natm, 3), float) 23 | for i in range(natm): 24 | line = next(f).split() 25 | atom_names.append(line[0]) 26 | geom[i] = line[1:4] # Numpy auto-converts str to float 27 | except (TypeError, IOError, IndexError, StopIteration): 28 | raise ValueError('Incorrect XYZ file format') 29 | coords.append(geom) 30 | if not coords: 31 | raise ValueError("File is empty") 32 | return atom_names, coords 33 | 34 | 35 | def write_xyz(filename, atoms, coords): 36 | """Write atom names and coordinate data to XYZ file 37 | 38 | Args: 39 | filename: Name of xyz data file 40 | atoms: Iterable of atom names 41 | coords: Coordinates, must be of shape nimages*natoms*3 42 | """ 43 | natoms = len(atoms) 44 | with open(filename, 'w') as f: 45 | for i, X in enumerate(np.atleast_3d(coords)): 46 | f.write("%d\n" % natoms) 47 | f.write("Frame %d\n" % i) 48 | for a, Xa in zip(atoms, X): 49 | f.write(" {:3} {:21.12f} {:21.12f} {:21.12f}\n".format(a, *Xa)) 50 | -------------------------------------------------------------------------------- /geodesic_interpolate/geodesic.py: -------------------------------------------------------------------------------- 1 | """Geodesic smoothing. Minimize the path length using redundant internal coordinate 2 | metric to find geodesics directly in Cartesian, to avoid feasibility problems associated 3 | with redundant internals. 4 | """ 5 | import logging 6 | 7 | import numpy as np 8 | from scipy.optimize import least_squares 9 | 10 | from .coord_utils import align_path, get_bond_list, morse_scaler, compute_wij 11 | 12 | 13 | logger = logging.getLogger(__name__) 14 | 15 | 16 | class Geodesic(object): 17 | """Optimizer to obtain geodesic in redundant internal coordinates. Core part is the calculation 18 | of the path length in the internal metric.""" 19 | def __init__(self, atoms, path, scaler=1.7, threshold=3, min_neighbors=4, log_level=logging.INFO, 20 | friction=1e-3): 21 | """Initialize the interpolater 22 | Args: 23 | atoms: Atom symbols, used to lookup radii 24 | path: Initial geometries of the path, must be of dimension `nimage * natoms * 3` 25 | scaler: Either the alpha parameter for morse potential, or an explicit scaling function. 26 | It is easier to get smoother paths with small number of data points using small 27 | scaling factors, as they have large range, but larger values usually give 28 | better energetics because they better represent the (sharp) energy landscape. 29 | threshold: Distance cut-off for constructing inter-nuclear distance coordinates. Note that 30 | any atoms linked by three or less bonds will also be added. 31 | min_neighbors: Minimum number of neighbors an atom must have in the atom pair list. 32 | log_level: Logging level to use. 33 | friction: Friction term in the target function which regularizes the optimization step 34 | size to prevent explosion. 35 | """ 36 | rmsd0, self.path = align_path(path) 37 | logger.log(log_level, "Maximum RMSD change in initial path: %10.2f", rmsd0) 38 | if self.path.ndim != 3: 39 | raise ValueError('The path to be interpolated must have 3 dimensions') 40 | self.nimages, self.natoms, _ = self.path.shape 41 | # Construct coordinates 42 | self.rij_list, self.re = get_bond_list(path, atoms, threshold=threshold, min_neighbors=min_neighbors) 43 | if isinstance(scaler, float): 44 | self.scaler = morse_scaler(re=self.re, alpha=1.7) 45 | else: 46 | self.scaler = scaler 47 | self.nrij = len(self.rij_list) 48 | self.friction = friction 49 | # Initalize interal storages for mid points, internal coordinates and B matrices 50 | logger.log(log_level, "Performing geodesic smoothing") 51 | logger.log(log_level, " Images: %4d Atoms %4d Rijs %6d", self.nimages, self.natoms, len(self.rij_list)) 52 | self.neval = 0 53 | self.w = [None] * len(path) 54 | self.dwdR = [None] * len(path) 55 | self.X_mid = [None] * (len(path) - 1) 56 | self.w_mid = [None] * (len(path) - 1) 57 | self.dwdR_mid = [None] * (len(path) - 1) 58 | self.disps = self.grad = self.segment = None 59 | self.conv_path = [] 60 | 61 | def update_intc(self): 62 | """Adjust unknown locations of mid points and compute missing values of internal coordinates 63 | and their derivatives. Any missing values will be marked with None values in internal storage, 64 | and this routine finds and calculates them. This is to avoid redundant evaluation of value and 65 | gradients of internal coordinates.""" 66 | for i, (X, w, dwdR) in enumerate(zip(self.path, self.w, self.dwdR)): 67 | if w is None: 68 | self.w[i], self.dwdR[i] = compute_wij(X, self.rij_list, self.scaler) 69 | for i, (X0, X1, w) in enumerate(zip(self.path, self.path[1:], self.w_mid)): 70 | if w is None: 71 | self.X_mid[i] = Xm = (X0 + X1) / 2 72 | self.w_mid[i], self.dwdR_mid[i] = compute_wij(Xm, self.rij_list, self.scaler) 73 | 74 | def update_geometry(self, X, start, end): 75 | """Update the geometry of a segment of the path, then set the corresponding internal 76 | coordinate, derivatives and midpoint locations to unknown""" 77 | X = X.reshape(self.path[start:end].shape) 78 | if np.array_equal(X, self.path[start:end]): 79 | return False 80 | self.path[start:end] = X 81 | for i in range(start, end): 82 | self.w_mid[i] = self.w[i] = None 83 | self.w_mid[start - 1] = None 84 | return True 85 | 86 | def compute_disps(self, start=1, end=-1, dx=None, friction=1e-3): 87 | """Compute displacement vectors and total length between two images. 88 | Only recalculate internal coordinates if they are unknown.""" 89 | if end < 0: 90 | end += self.nimages 91 | self.update_intc() 92 | # Calculate displacement vectors in each segment, and the total length 93 | vecs_l = [wm - wl for wl, wm in zip(self.w[start - 1:end], self.w_mid[start - 1:end])] 94 | vecs_r = [wr - wm for wr, wm in zip(self.w[start:end + 1], self.w_mid[start - 1:end])] 95 | self.length = np.sum(np.linalg.norm(vecs_l, axis=1)) + np.sum(np.linalg.norm(vecs_r, axis=1)) 96 | if dx is None: 97 | trans = np.zeros(self.path[start:end].size) 98 | else: 99 | trans = friction * dx # Translation from initial geometry. friction term 100 | self.disps = np.concatenate(vecs_l + vecs_r + [trans]) 101 | self.disps0 = self.disps[:len(vecs_l) * 2] 102 | 103 | def compute_disp_grad(self, start, end, friction=1e-3): 104 | """Compute derivatives of the displacement vectors with respect to the Cartesian coordinates""" 105 | # Calculate derivatives of displacement vectors with respect to image Cartesians 106 | l = end - start + 1 107 | self.grad = np.zeros((l * 2 * self.nrij + 3 * (end - start) * self.natoms, (end - start) * 3 * self.natoms)) 108 | self.grad0 = self.grad[:l * 2 * self.nrij] 109 | grad_shape = (l, self.nrij, end - start, 3 * self.natoms) 110 | grad_l = self.grad[:l * self.nrij].reshape(grad_shape) 111 | grad_r = self.grad[l * self.nrij:l * self.nrij * 2].reshape(grad_shape) 112 | for i, image in enumerate(range(start, end)): 113 | dmid1 = self.dwdR_mid[image - 1] / 2 114 | dmid2 = self.dwdR_mid[image] / 2 115 | grad_l[i + 1, :, i, :] = dmid2 - self.dwdR[image] 116 | grad_l[i, :, i, :] = dmid1 117 | grad_r[i + 1, :, i, :] = -dmid2 118 | grad_r[i, :, i, :] = self.dwdR[image] - dmid1 119 | for idx in range((end - start) * 3 * self.natoms): 120 | self.grad[l * self.nrij * 2 + idx, idx] = friction 121 | 122 | def compute_target_func(self, X=None, start=1, end=-1, log_level=logging.INFO, x0=None, friction=1e-3): 123 | """Compute the vectorized target function, which is then used for least 124 | squares minimization.""" 125 | if end < 0: 126 | end += self.nimages 127 | if X is not None and not self.update_geometry(X, start, end) and self.segment == (start, end): 128 | return 129 | self.segment = start, end 130 | dx = np.zeros(self.path[start:end].size) if x0 is None else self.path[start:end].ravel() - x0.ravel() 131 | self.compute_disps(start, end, dx=dx, friction=friction) 132 | self.compute_disp_grad(start, end, friction=friction) 133 | self.optimality = np.linalg.norm(np.einsum('i,i...', self.disps, self.grad), ord=np.inf) 134 | logger.log(log_level, " Iteration %3d: Length %10.3f |dL|=%7.3e", self.neval, self.length, self.optimality) 135 | self.conv_path.append(self.path[1].copy()) 136 | self.neval += 1 137 | 138 | def target_func(self, X, **kwargs): 139 | """Wrapper around `compute_target_func` to prevent repeated evaluation at 140 | the same geometry""" 141 | self.compute_target_func(X, **kwargs) 142 | return self.disps 143 | 144 | def target_deriv(self, X, **kwargs): 145 | """Wrapper around `compute_target_func` to prevent repeated evaluation at 146 | the same geometry""" 147 | self.compute_target_func(X, **kwargs) 148 | return self.grad 149 | 150 | def smooth(self, tol=1e-3, max_iter=50, start=1, end=-1, log_level=logging.INFO, friction=None, 151 | xref=None): 152 | """Minimize the path length as an overall function of the coordinates of all the images. 153 | This should in principle be very efficient, but may be quite costly for large systems with 154 | many images. 155 | 156 | Args: 157 | tol: Convergence tolerance of the optimality. (.i.e uniform gradient of target func) 158 | max_iter: Maximum number of iterations to run. 159 | start, end: Specify which section of the path to optimize. 160 | log_level: Logging level during the optimization 161 | 162 | Returns: 163 | The optimized path. This is also stored in self.path 164 | """ 165 | X0 = np.array(self.path[start:end]).ravel() 166 | if xref is None: 167 | xref= X0 168 | self.disps = self.grad = self.segment = None 169 | logger.log(log_level, " Degree of freedoms %6d: ", len(X0)) 170 | if friction is None: 171 | friction = self.friction 172 | # Configure the keyword arguments that will be sent to the target function. 173 | kwargs = dict(start=start, end=end, log_level=log_level, x0=xref, friction=friction) 174 | self.compute_target_func(**kwargs) # Compute length and optimality 175 | if self.optimality > tol: 176 | result = least_squares(self.target_func, X0, self.target_deriv, ftol=tol, gtol=tol, 177 | max_nfev=max_iter, kwargs=kwargs, loss='soft_l1') 178 | self.update_geometry(result['x'], start, end) 179 | logger.log(log_level, "Smoothing converged after %d iterations", result['nfev']) 180 | else: 181 | logger.log(log_level, "Skipping smoothing: path already optimal.") 182 | rmsd, self.path = align_path(self.path) 183 | logger.log(log_level, "Final path length: %12.5f Max RMSD in path: %10.2f", self.length, rmsd) 184 | return self.path 185 | 186 | def sweep(self, tol=1e-3, max_iter=50, micro_iter=20, start=1, end=-1): 187 | """Minimize the path length by adjusting one image at a time and sweeping the optimization 188 | side across the chain. This is not as efficient, but scales much more friendly with the 189 | size of the system given the slowness of scipy's optimizers. Also allows more detailed 190 | control and easy way of skipping nearly optimal points than the overall case. 191 | 192 | Args: 193 | tol: Convergence tolerance of the optimality. (.i.e uniform gradient of target func) 194 | max_iter: Maximum number of sweeps through the path. 195 | micro_iter: Number of micro-iterations to be performed when optimizing each image. 196 | start, end: Specify which section of the path to optimize. 197 | log_level: Logging level during the optimization 198 | 199 | Returns: 200 | The optimized path. This is also stored in self.path 201 | """ 202 | if end < 0: 203 | end = self.nimages + end 204 | self.neval = 0 205 | images = range(start, end) 206 | logger.info(" Degree of freedoms %6d: ", (end - start) * 3 * self.natoms) 207 | # Microiteration convergence tolerances are adjusted on the fly based on level of convergence. 208 | curr_tol = tol * 10 209 | self.compute_disps() # Compute and print the initial path length 210 | logger.info(" Initial length: %8.3f", self.length) 211 | for iteration in range(max_iter): 212 | max_dL = 0 213 | X0 = self.path.copy() 214 | for i in images[:-1]: # Use self.smooth() to optimize individual images 215 | xmid = (self.path[i - 1] + self.path[i + 1]) * 0.5 216 | self.smooth(curr_tol, max_iter=min(micro_iter, iteration + 6), 217 | start=i, end=i + 1, log_level=logging.DEBUG, 218 | friction=self.friction if iteration else 0.1, 219 | xref=xmid) 220 | max_dL = max(max_dL, self.optimality) 221 | self.compute_disps() # Compute final length after sweep 222 | logger.info("Sweep %3d: L=%7.2f dX=%7.2e tol=%7.3e dL=%7.3e", 223 | iteration, self.length, np.linalg.norm(self.path - X0), curr_tol, max_dL) 224 | if max_dL < tol: # Check for convergence. 225 | logger.info("Optimization converged after %d iteartions", iteration) 226 | break 227 | curr_tol = max(tol * 0.5, max_dL * 0.2) # Adjust micro-iteration threshold 228 | images = list(reversed(images)) # Alternate sweeping direction. 229 | else: 230 | logger.info("Optimization not converged after %d iteartions", iteration) 231 | rmsd, self.path = align_path(self.path) 232 | logger.info("Final path length: %12.5f Max RMSD in path: %10.2f", self.length, rmsd) 233 | return self.path 234 | -------------------------------------------------------------------------------- /geodesic_interpolate/interpolation.py: -------------------------------------------------------------------------------- 1 | """Simplified geodesic interpolations module, which uses geodesic lengths as criteria 2 | to add bisection points until point count meet desired number. 3 | Will need another following geodesic smoothing to get final path. 4 | """ 5 | import logging 6 | 7 | import numpy as np 8 | from scipy.optimize import least_squares, minimize 9 | 10 | from .geodesic import Geodesic 11 | from .coord_utils import get_bond_list, compute_wij, morse_scaler, align_geom, align_path 12 | 13 | 14 | logger = logging.getLogger(__name__) 15 | 16 | 17 | def mid_point(atoms, geom1, geom2, tol=1e-2, nudge=0.01, threshold=4): 18 | """Find the Cartesian geometry that has internal coordinate values closest to the average of 19 | two geometries. 20 | 21 | Simply perform a least-squares minimization on the difference between the current internal 22 | and the average of the two end points. This is done twice, using either end point as the 23 | starting guess. DON'T USE THE CARTESIAN AVERAGE AS GUESS, THINGS WILL BLOW UP. 24 | 25 | This is used to generate an initial guess path for the later smoothing routine. 26 | Genenrally, the added point may not be continuous with the both end points, but 27 | provides a good enough starting guess. 28 | 29 | Random nudges are added to the initial geometry, so running multiple times may not yield 30 | the same converged geometry. For larger systems, one will never get the same geometry 31 | twice. So one may want to perform multiple runs and check which yields the best result. 32 | 33 | Args: 34 | geom1, geom2: Cartesian geometry of the end points 35 | tol: Convergence tolarnce for the least-squares minimization process 36 | nudge: Random nudges added to the initial geometry, which helps to discover different 37 | solutions. Also helps in cases where optimal paths break the symmetry. 38 | threshold: Threshold for including an atom-pair in the coordinate system 39 | 40 | Returns: 41 | Optimized mid-point which bisects the two endpoints in internal coordinates 42 | """ 43 | # Process the initial geometries, construct coordinate system and obtain average internals 44 | geom1, geom2 = np.array(geom1), np.array(geom2) 45 | add_pair = set() 46 | geom_list = [geom1, geom2] 47 | # This loop is for ensuring a sufficient large coordinate system. The interpolated point may 48 | # have atom pairs in contact that are far away at both end-points, which may cause collision. 49 | # One can include all atom pairs, but this may blow up for large molecules. Here the compromise 50 | # is to use a screened list of atom pairs first, then add more if additional atoms come into 51 | # contant, then rerun the minimization until the coordinate system is consistant with the 52 | # interpolated geometry 53 | while True: 54 | rijlist, re = get_bond_list(geom_list, threshold=threshold + 1, enforce=add_pair) 55 | scaler = morse_scaler(alpha=0.7, re=re) 56 | w1, _ = compute_wij(geom1, rijlist, scaler) 57 | w2, _ = compute_wij(geom2, rijlist, scaler) 58 | w = (w1 + w2) / 2 59 | d_min, x_min = np.inf, None 60 | friction = 0.1 / np.sqrt(geom1.shape[0]) 61 | def target_func(X): 62 | """Squared difference with reference w0""" 63 | wx, dwdR = compute_wij(X, rijlist, scaler) 64 | delta_w = wx - w 65 | val, grad = 0.5 * np.dot(delta_w, delta_w), np.einsum('i,ij->j', delta_w, dwdR) 66 | logger.info("val=%10.3f ", val) 67 | return val, grad 68 | 69 | # The inner loop performs minimization using either end-point as the starting guess. 70 | for coef in [0.02, 0.98]: 71 | x0 = (geom1 * coef + (1 - coef) * geom2).ravel() 72 | x0 += nudge * np.random.random_sample(x0.shape) 73 | logger.debug('Starting least-squares minimization of bisection point at %7.2f.', coef) 74 | result = least_squares(lambda x: np.concatenate([compute_wij(x, rijlist, scaler)[0] - w, (x-x0)*friction]), x0, 75 | lambda x: np.vstack([compute_wij(x, rijlist, scaler)[1], np.identity(x.size) * friction]), ftol=tol, gtol=tol) 76 | x_mid = result['x'].reshape(-1, 3) 77 | # Take the interpolated geometry, construct new pair list and check for new contacts 78 | new_list = geom_list + [x_mid] 79 | new_rij, _ = get_bond_list(new_list, threshold=threshold, min_neighbors=0) 80 | extras = set(new_rij) - set(rijlist) 81 | if extras: 82 | logger.info(' Screened pairs came into contact. Adding reference point.') 83 | # Update pair list then go back to the minimization loop if new contacts are found 84 | geom_list = new_list 85 | add_pair |= extras 86 | break 87 | # Perform local geodesic optimization for the new image. 88 | smoother = Geodesic(atoms, [geom1, x_mid, geom2], 0.7, threshold=threshold, log_level=logging.DEBUG, friction=1) 89 | smoother.compute_disps() 90 | width = max([np.sqrt(np.mean((g - smoother.path[1]) ** 2)) for g in [geom1, geom2]]) 91 | dist, x_mid = width + smoother.length, smoother.path[1] 92 | logger.debug(' Trial path length: %8.3f after %d iterations', dist, result['nfev']) 93 | if dist < d_min: 94 | d_min, x_min = dist, x_mid 95 | else: # Both starting guesses finished without new atom pairs. Minimization successful 96 | break 97 | return x_min 98 | 99 | 100 | def redistribute(atoms, geoms, nimages, tol=1e-2): 101 | """Add or remove images so that the path length matches the desired number. 102 | 103 | If the number is too few, new points are added by bisecting the largest RMSD. If too numerous, 104 | one image is removed at a time so that the new merged segment has the shortest RMSD. 105 | 106 | Args: 107 | geoms: Geometry of the original path. 108 | nimages: The desired number of images 109 | tol: Convergence tolerance for bisection. 110 | 111 | Returns: 112 | An aligned and redistributed path with has the correct number of images. 113 | """ 114 | _, geoms = align_path(geoms) 115 | geoms = list(geoms) 116 | # If there are too few images, add bisection points 117 | while len(geoms) < nimages: 118 | dists = [np.sqrt(np.mean((g1 - g2) ** 2)) for g1, g2 in zip(geoms[1:], geoms)] 119 | max_i = np.argmax(dists) 120 | logger.info("Inserting image between %d and %d with Cartesian RMSD %10.3f. New length:%d", 121 | max_i, max_i + 1, dists[max_i], len(geoms) + 1) 122 | insertion = mid_point(atoms, geoms[max_i], geoms[max_i + 1], tol) 123 | _, insertion = align_geom(geoms[max_i], insertion) 124 | geoms.insert(max_i + 1, insertion) 125 | geoms = list(align_path(geoms)[1]) 126 | # If there are too many images, remove points 127 | while len(geoms) > nimages: 128 | dists = [np.sqrt(np.mean((g1 - g2) ** 2)) for g1, g2 in zip(geoms[2:], geoms)] 129 | min_i = np.argmin(dists) 130 | logger.info("Removing image %d. Cartesian RMSD of merged section %10.3f", 131 | min_i + 1, dists[min_i]) 132 | del geoms[min_i + 1] 133 | geoms = list(align_path(geoms)[1]) 134 | return geoms 135 | -------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- 1 | """Installer for geodesic interpolation package. 2 | Install the package into python environment, and provide an entry point for the 3 | main interpolation script. 4 | 5 | To run the package as standalone 6 | """ 7 | from setuptools import setup 8 | 9 | setup( 10 | name='geodesic_interpolate', 11 | version='1.0.0', 12 | description='Interpolation and smoothing of reaction paths with geodesics in ' 13 | 'redundant internal coordinates.', 14 | packages=['geodesic_interpolate'], 15 | entry_points = { 16 | 'console_scripts': [ 17 | 'geodesic_interpolate=geodesic_interpolate.__main__:main', 18 | ], 19 | }, 20 | ) 21 | -------------------------------------------------------------------------------- /test_cases/2JOF-pH7.pdb: -------------------------------------------------------------------------------- 1 | REMARK Created by http://biophysics.cs.vt.edu/H++ 2 | REMARK 3 | ATOM 1 N ASP 1 21.464 6.593 -4.077 0.0782 1.550 N 4 | ATOM 2 H1 ASP 1 20.922 7.447 -4.051 0.2200 1.200 H 5 | ATOM 3 H2 ASP 1 21.636 6.331 -5.037 0.2200 1.200 H 6 | ATOM 4 H3 ASP 1 20.951 5.859 -3.611 0.2200 1.200 H 7 | ATOM 5 CA ASP 1 22.746 6.821 -3.378 0.0292 1.700 C 8 | ATOM 6 HA ASP 1 23.278 7.615 -3.903 0.1141 1.200 H 9 | ATOM 7 CB ASP 1 22.484 7.311 -1.954 -0.0235 1.700 C 10 | ATOM 8 HB2 ASP 1 21.662 6.757 -1.497 -0.0169 1.200 H 11 | ATOM 9 HB3 ASP 1 23.383 7.186 -1.347 -0.0169 1.200 H 12 | ATOM 10 CG ASP 1 22.146 8.788 -2.063 0.8194 1.700 C 13 | ATOM 11 OD1 ASP 1 21.166 9.040 -2.800 -0.8084 1.500 O 14 | ATOM 12 OD2 ASP 1 22.939 9.598 -1.546 -0.8084 1.500 O 15 | ATOM 13 C ASP 1 23.653 5.606 -3.363 0.5621 1.700 C 16 | ATOM 14 O ASP 1 23.241 4.525 -2.949 -0.5889 1.500 O 17 | ATOM 15 N ALA 2 24.908 5.815 -3.770 -0.4157 1.550 N 18 | ATOM 16 H ALA 2 25.174 6.733 -4.097 0.2719 1.200 H 19 | ATOM 17 CA ALA 2 25.968 4.821 -3.656 0.0337 1.700 C 20 | ATOM 18 HA ALA 2 25.629 3.899 -4.131 0.0823 1.200 H 21 | ATOM 19 CB ALA 2 27.190 5.329 -4.430 -0.1825 1.700 C 22 | ATOM 20 HB1 ALA 2 27.995 4.595 -4.368 0.0603 1.200 H 23 | ATOM 21 HB2 ALA 2 26.928 5.475 -5.479 0.0603 1.200 H 24 | ATOM 22 HB3 ALA 2 27.533 6.277 -4.012 0.0603 1.200 H 25 | ATOM 23 C ALA 2 26.308 4.504 -2.188 0.5973 1.700 C 26 | ATOM 24 O ALA 2 26.485 3.336 -1.855 -0.5679 1.500 O 27 | ATOM 25 N TYR 3 26.357 5.511 -1.298 -0.4157 1.550 N 28 | ATOM 26 H TYR 3 26.204 6.458 -1.615 0.2719 1.200 H 29 | ATOM 27 CA TYR 3 26.691 5.317 0.123 -0.0014 1.700 C 30 | ATOM 28 HA TYR 3 27.658 4.814 0.157 0.0876 1.200 H 31 | ATOM 29 CB TYR 3 26.848 6.673 0.837 -0.0152 1.700 C 32 | ATOM 30 HB2 TYR 3 27.191 7.417 0.116 0.0295 1.200 H 33 | ATOM 31 HB3 TYR 3 25.880 7.010 1.211 0.0295 1.200 H 34 | ATOM 32 CG TYR 3 27.846 6.625 1.984 -0.0011 1.700 C 35 | ATOM 33 CD1 TYR 3 27.566 5.892 3.155 -0.1906 1.700 C 36 | ATOM 34 HD1 TYR 3 26.606 5.420 3.290 0.1699 1.200 H 37 | ATOM 35 CE1 TYR 3 28.548 5.753 4.154 -0.2341 1.700 C 38 | ATOM 36 HE1 TYR 3 28.340 5.175 5.041 0.1656 1.200 H 39 | ATOM 37 CZ TYR 3 29.815 6.351 3.989 0.3226 1.700 C 40 | ATOM 38 OH TYR 3 30.776 6.156 4.931 -0.5579 1.500 O 41 | ATOM 39 HH TYR 3 31.598 6.601 4.715 0.3992 1.200 H 42 | ATOM 40 CE2 TYR 3 30.079 7.132 2.843 -0.2341 1.700 C 43 | ATOM 41 HE2 TYR 3 31.040 7.609 2.713 0.1656 1.200 H 44 | ATOM 42 CD2 TYR 3 29.090 7.271 1.853 -0.1906 1.700 C 45 | ATOM 43 HD2 TYR 3 29.295 7.866 0.980 0.1699 1.200 H 46 | ATOM 44 C TYR 3 25.662 4.433 0.847 0.5973 1.700 C 47 | ATOM 45 O TYR 3 26.023 3.576 1.655 -0.5679 1.500 O 48 | ATOM 46 N ALA 4 24.375 4.599 0.516 -0.4157 1.550 N 49 | ATOM 47 H ALA 4 24.130 5.317 -0.150 0.2719 1.200 H 50 | ATOM 48 CA ALA 4 23.305 3.738 1.010 0.0337 1.700 C 51 | ATOM 49 HA ALA 4 23.253 3.846 2.094 0.0823 1.200 H 52 | ATOM 50 CB ALA 4 21.973 4.212 0.414 -0.1825 1.700 C 53 | ATOM 51 HB1 ALA 4 21.159 3.604 0.811 0.0603 1.200 H 54 | ATOM 52 HB2 ALA 4 21.798 5.254 0.684 0.0603 1.200 H 55 | ATOM 53 HB3 ALA 4 21.988 4.118 -0.671 0.0603 1.200 H 56 | ATOM 54 C ALA 4 23.596 2.264 0.685 0.5973 1.700 C 57 | ATOM 55 O ALA 4 23.537 1.409 1.571 -0.5679 1.500 O 58 | ATOM 56 N GLN 5 23.956 1.978 -0.573 -0.4157 1.550 N 59 | ATOM 57 H GLN 5 24.010 2.725 -1.251 0.2719 1.200 H 60 | ATOM 58 CA GLN 5 24.324 0.636 -1.015 -0.0031 1.700 C 61 | ATOM 59 HA GLN 5 23.525 -0.022 -0.678 0.0850 1.200 H 62 | ATOM 60 CB GLN 5 24.354 0.593 -2.550 -0.0036 1.700 C 63 | ATOM 61 HB2 GLN 5 23.620 1.309 -2.923 0.0171 1.200 H 64 | ATOM 62 HB3 GLN 5 25.332 0.896 -2.926 0.0171 1.200 H 65 | ATOM 63 CG GLN 5 23.988 -0.802 -3.090 -0.0645 1.700 C 66 | ATOM 64 HG2 GLN 5 24.899 -1.381 -3.243 0.0352 1.200 H 67 | ATOM 65 HG3 GLN 5 23.365 -1.337 -2.372 0.0352 1.200 H 68 | ATOM 66 CD GLN 5 23.210 -0.705 -4.398 0.6951 1.700 C 69 | ATOM 67 OE1 GLN 5 23.720 -0.958 -5.476 -0.6086 1.500 O 70 | ATOM 68 NE2 GLN 5 21.948 -0.314 -4.345 -0.9407 1.550 N 71 | ATOM 69 HE21 GLN 5 21.519 -0.113 -3.456 0.4251 1.200 H 72 | ATOM 70 HE22 GLN 5 21.419 -0.258 -5.202 0.4251 1.200 H 73 | ATOM 71 C GLN 5 25.638 0.157 -0.378 0.5973 1.700 C 74 | ATOM 72 O GLN 5 25.693 -0.963 0.117 -0.5679 1.500 O 75 | ATOM 73 N TRP 6 26.657 1.026 -0.296 -0.4157 1.550 N 76 | ATOM 74 H TRP 6 26.529 1.947 -0.684 0.2719 1.200 H 77 | ATOM 75 CA TRP 6 27.939 0.765 0.370 -0.0275 1.700 C 78 | ATOM 76 HA TRP 6 28.487 0.045 -0.239 0.1123 1.200 H 79 | ATOM 77 CB TRP 6 28.769 2.060 0.434 -0.0050 1.700 C 80 | ATOM 78 HB2 TRP 6 28.801 2.509 -0.560 0.0339 1.200 H 81 | ATOM 79 HB3 TRP 6 28.292 2.769 1.104 0.0339 1.200 H 82 | ATOM 80 CG TRP 6 30.176 1.872 0.902 -0.1415 1.700 C 83 | ATOM 81 CD1 TRP 6 31.203 1.507 0.110 -0.1638 1.700 C 84 | ATOM 82 HD1 TRP 6 31.135 1.348 -0.955 0.2062 1.200 H 85 | ATOM 83 NE1 TRP 6 32.335 1.325 0.876 -0.3418 1.550 N 86 | ATOM 84 HE1 TRP 6 33.219 1.035 0.490 0.3412 1.200 H 87 | ATOM 85 CE2 TRP 6 32.119 1.664 2.192 0.1380 1.700 C 88 | ATOM 86 CZ2 TRP 6 32.957 1.710 3.316 -0.2601 1.700 C 89 | ATOM 87 HZ2 TRP 6 33.993 1.413 3.240 0.1572 1.200 H 90 | ATOM 88 CH2 TRP 6 32.434 2.181 4.532 -0.1134 1.700 C 91 | ATOM 89 HH2 TRP 6 33.069 2.248 5.404 0.1417 1.200 H 92 | ATOM 90 CZ3 TRP 6 31.084 2.567 4.614 -0.1972 1.700 C 93 | ATOM 91 HZ3 TRP 6 30.687 2.932 5.550 0.1447 1.200 H 94 | ATOM 92 CE3 TRP 6 30.248 2.491 3.482 -0.2387 1.700 C 95 | ATOM 93 HE3 TRP 6 29.218 2.799 3.558 0.1700 1.200 H 96 | ATOM 94 CD2 TRP 6 30.744 2.042 2.239 0.1243 1.700 C 97 | ATOM 95 C TRP 6 27.748 0.150 1.763 0.5973 1.700 C 98 | ATOM 96 O TRP 6 28.319 -0.901 2.056 -0.5679 1.500 O 99 | ATOM 97 N LEU 7 26.896 0.768 2.593 -0.4157 1.550 N 100 | ATOM 98 H LEU 7 26.456 1.627 2.293 0.2719 1.200 H 101 | ATOM 99 CA LEU 7 26.513 0.223 3.896 -0.0518 1.700 C 102 | ATOM 100 HA LEU 7 27.428 0.010 4.449 0.0922 1.200 H 103 | ATOM 101 CB LEU 7 25.702 1.265 4.685 -0.1102 1.700 C 104 | ATOM 102 HB2 LEU 7 24.850 1.570 4.074 0.0457 1.200 H 105 | ATOM 103 HB3 LEU 7 25.312 0.796 5.590 0.0457 1.200 H 106 | ATOM 104 CG LEU 7 26.509 2.517 5.087 0.3531 1.700 C 107 | ATOM 105 HG LEU 7 27.000 2.933 4.208 -0.0361 1.200 H 108 | ATOM 106 CD1 LEU 7 25.559 3.581 5.640 -0.4121 1.700 C 109 | ATOM 107 HD11 LEU 7 24.827 3.854 4.879 0.1000 1.200 H 110 | ATOM 108 HD12 LEU 7 25.039 3.200 6.520 0.1000 1.200 H 111 | ATOM 109 HD13 LEU 7 26.120 4.474 5.917 0.1000 1.200 H 112 | ATOM 110 CD2 LEU 7 27.569 2.212 6.153 -0.4121 1.700 C 113 | ATOM 111 HD21 LEU 7 28.075 3.131 6.449 0.1000 1.200 H 114 | ATOM 112 HD22 LEU 7 27.100 1.767 7.031 0.1000 1.200 H 115 | ATOM 113 HD23 LEU 7 28.316 1.524 5.760 0.1000 1.200 H 116 | ATOM 114 C LEU 7 25.751 -1.109 3.777 0.5973 1.700 C 117 | ATOM 115 O LEU 7 26.102 -2.047 4.490 -0.5679 1.500 O 118 | ATOM 116 N LYS 8 24.754 -1.222 2.879 -0.3479 1.550 N 119 | ATOM 117 H LYS 8 24.540 -0.428 2.292 0.2747 1.200 H 120 | ATOM 118 CA LYS 8 23.983 -2.465 2.653 -0.2400 1.700 C 121 | ATOM 119 HA LYS 8 23.462 -2.702 3.582 0.1426 1.200 H 122 | ATOM 120 CB LYS 8 22.933 -2.300 1.533 -0.0094 1.700 C 123 | ATOM 121 HB2 LYS 8 23.226 -1.510 0.848 0.0362 1.200 H 124 | ATOM 122 HB3 LYS 8 22.886 -3.226 0.956 0.0362 1.200 H 125 | ATOM 123 CG LYS 8 21.515 -2.036 2.055 0.0187 1.700 C 126 | ATOM 124 HG2 LYS 8 20.808 -2.182 1.237 0.0103 1.200 H 127 | ATOM 125 HG3 LYS 8 21.281 -2.758 2.839 0.0103 1.200 H 128 | ATOM 126 CD LYS 8 21.346 -0.612 2.592 -0.0479 1.700 C 129 | ATOM 127 HD2 LYS 8 22.130 -0.403 3.321 0.0621 1.200 H 130 | ATOM 128 HD3 LYS 8 21.412 0.094 1.766 0.0621 1.200 H 131 | ATOM 129 CE LYS 8 19.985 -0.454 3.270 -0.0143 1.700 C 132 | ATOM 130 HE2 LYS 8 19.201 -0.480 2.511 0.1135 1.200 H 133 | ATOM 131 HE3 LYS 8 19.833 -1.285 3.962 0.1135 1.200 H 134 | ATOM 132 NZ LYS 8 19.917 0.819 4.024 -0.3854 1.550 N 135 | ATOM 133 HZ1 LYS 8 18.984 0.954 4.390 0.3400 1.200 H 136 | ATOM 134 HZ2 LYS 8 20.573 0.793 4.793 0.3400 1.200 H 137 | ATOM 135 HZ3 LYS 8 20.153 1.590 3.415 0.3400 1.200 H 138 | ATOM 136 C LYS 8 24.869 -3.673 2.342 0.7341 1.700 C 139 | ATOM 137 O LYS 8 24.636 -4.741 2.900 -0.5894 1.500 O 140 | ATOM 138 N ASP 9 25.877 -3.512 1.480 -0.5163 1.550 N 141 | ATOM 139 H ASP 9 26.007 -2.617 1.031 0.2936 1.200 H 142 | ATOM 140 CA ASP 9 26.833 -4.578 1.163 0.0381 1.700 C 143 | ATOM 141 HA ASP 9 26.272 -5.465 0.865 0.0880 1.200 H 144 | ATOM 142 CB ASP 9 27.701 -4.147 -0.031 -0.0303 1.700 C 145 | ATOM 143 HB2 ASP 9 28.099 -3.147 0.149 -0.0122 1.200 H 146 | ATOM 144 HB3 ASP 9 28.551 -4.826 -0.112 -0.0122 1.200 H 147 | ATOM 145 CG ASP 9 26.954 -4.169 -1.372 0.7994 1.700 C 148 | ATOM 146 OD1 ASP 9 26.283 -3.172 -1.707 -0.8014 1.500 O 149 | ATOM 147 OD2 ASP 9 27.192 -5.111 -2.163 -0.8014 1.500 O 150 | ATOM 148 C ASP 9 27.727 -4.980 2.357 0.5366 1.700 C 151 | ATOM 149 O ASP 9 28.298 -6.067 2.328 -0.5819 1.500 O 152 | ATOM 150 N GLY 10 27.852 -4.139 3.398 -0.4157 1.550 N 153 | ATOM 151 H GLY 10 27.331 -3.273 3.378 0.2719 1.200 H 154 | ATOM 152 CA GLY 10 28.693 -4.383 4.580 -0.0252 1.700 C 155 | ATOM 153 HA2 GLY 10 28.047 -4.345 5.457 0.0698 1.200 H 156 | ATOM 154 HA3 GLY 10 29.128 -5.381 4.529 0.0698 1.200 H 157 | ATOM 155 C GLY 10 29.832 -3.374 4.791 0.5973 1.700 C 158 | ATOM 156 O GLY 10 30.691 -3.605 5.650 -0.5679 1.500 O 159 | ATOM 157 N GLY 11 29.855 -2.277 4.020 -0.4157 1.550 N 160 | ATOM 158 H GLY 11 29.126 -2.185 3.326 0.2719 1.200 H 161 | ATOM 159 CA GLY 11 30.828 -1.185 4.062 -0.0252 1.700 C 162 | ATOM 160 HA2 GLY 11 30.677 -0.565 3.180 0.0698 1.200 H 163 | ATOM 161 HA3 GLY 11 30.611 -0.567 4.929 0.0698 1.200 H 164 | ATOM 162 C GLY 11 32.288 -1.659 4.054 0.5973 1.700 C 165 | ATOM 163 O GLY 11 32.721 -2.217 3.042 -0.5679 1.500 O 166 | ATOM 164 N PRO 12 33.058 -1.476 5.151 -0.2548 1.550 N 167 | ATOM 165 CD PRO 12 32.669 -0.823 6.394 0.0192 1.700 C 168 | ATOM 166 HD2 PRO 12 32.073 -1.513 6.993 0.0391 1.200 H 169 | ATOM 167 HD3 PRO 12 32.114 0.097 6.219 0.0391 1.200 H 170 | ATOM 168 CG PRO 12 33.973 -0.502 7.119 0.0189 1.700 C 171 | ATOM 169 HG2 PRO 12 33.840 -0.480 8.201 0.0213 1.200 H 172 | ATOM 170 HG3 PRO 12 34.368 0.449 6.759 0.0213 1.200 H 173 | ATOM 171 CB PRO 12 34.895 -1.636 6.682 -0.0070 1.700 C 174 | ATOM 172 HB2 PRO 12 34.731 -2.497 7.333 0.0253 1.200 H 175 | ATOM 173 HB3 PRO 12 35.943 -1.336 6.711 0.0253 1.200 H 176 | ATOM 174 CA PRO 12 34.440 -1.955 5.252 -0.0266 1.700 C 177 | ATOM 175 HA PRO 12 35.050 -1.386 4.549 0.0641 1.200 H 178 | ATOM 176 C PRO 12 34.601 -3.454 4.962 0.5896 1.700 C 179 | ATOM 177 O PRO 12 35.633 -3.863 4.436 -0.5748 1.500 O 180 | ATOM 178 N SER 13 33.573 -4.260 5.264 -0.4157 1.550 N 181 | ATOM 179 H SER 13 32.747 -3.849 5.676 0.2719 1.200 H 182 | ATOM 180 CA SER 13 33.561 -5.719 5.076 -0.0249 1.700 C 183 | ATOM 181 HA SER 13 34.369 -6.152 5.667 0.0843 1.200 H 184 | ATOM 182 CB SER 13 32.228 -6.321 5.552 0.2117 1.700 C 185 | ATOM 183 HB2 SER 13 31.469 -6.182 4.781 0.0352 1.200 H 186 | ATOM 184 HB3 SER 13 32.361 -7.391 5.718 0.0352 1.200 H 187 | ATOM 185 OG SER 13 31.759 -5.715 6.741 -0.6546 1.500 O 188 | ATOM 186 HG SER 13 31.318 -4.891 6.505 0.4275 1.200 H 189 | ATOM 187 C SER 13 33.760 -6.106 3.608 0.5973 1.700 C 190 | ATOM 188 O SER 13 34.434 -7.083 3.299 -0.5679 1.500 O 191 | ATOM 189 N SER 14 33.152 -5.326 2.710 -0.4157 1.550 N 192 | ATOM 190 H SER 14 32.629 -4.532 3.054 0.2719 1.200 H 193 | ATOM 191 CA SER 14 33.098 -5.543 1.266 -0.0249 1.700 C 194 | ATOM 192 HA SER 14 32.938 -6.603 1.066 0.0843 1.200 H 195 | ATOM 193 CB SER 14 31.926 -4.734 0.697 0.2117 1.700 C 196 | ATOM 194 HB2 SER 14 32.264 -3.716 0.525 0.0352 1.200 H 197 | ATOM 195 HB3 SER 14 31.596 -5.166 -0.248 0.0352 1.200 H 198 | ATOM 196 OG SER 14 30.845 -4.656 1.602 -0.6546 1.500 O 199 | ATOM 197 HG SER 14 30.401 -5.509 1.642 0.4275 1.200 H 200 | ATOM 198 C SER 14 34.360 -5.073 0.537 0.5973 1.700 C 201 | ATOM 199 O SER 14 34.556 -5.413 -0.626 -0.5679 1.500 O 202 | ATOM 200 N GLY 15 35.169 -4.214 1.172 -0.4157 1.550 N 203 | ATOM 201 H GLY 15 34.933 -3.959 2.121 0.2719 1.200 H 204 | ATOM 202 CA GLY 15 36.410 -3.643 0.636 -0.0252 1.700 C 205 | ATOM 203 HA2 GLY 15 36.943 -3.166 1.459 0.0698 1.200 H 206 | ATOM 204 HA3 GLY 15 37.027 -4.462 0.265 0.0698 1.200 H 207 | ATOM 205 C GLY 15 36.255 -2.613 -0.497 0.5973 1.700 C 208 | ATOM 206 O GLY 15 37.211 -1.898 -0.792 -0.5679 1.500 O 209 | ATOM 207 N ARG 16 35.070 -2.497 -1.115 -0.3479 1.550 N 210 | ATOM 208 H ARG 16 34.334 -3.132 -0.842 0.2747 1.200 H 211 | ATOM 209 CA ARG 16 34.727 -1.465 -2.108 -0.2637 1.700 C 212 | ATOM 210 HA ARG 16 35.376 -1.640 -2.963 0.1560 1.200 H 213 | ATOM 211 CB ARG 16 33.284 -1.656 -2.618 -0.0007 1.700 C 214 | ATOM 212 HB2 ARG 16 33.061 -0.894 -3.366 0.0327 1.200 H 215 | ATOM 213 HB3 ARG 16 33.252 -2.624 -3.120 0.0327 1.200 H 216 | ATOM 214 CG ARG 16 32.198 -1.623 -1.527 0.0390 1.700 C 217 | ATOM 215 HG2 ARG 16 32.616 -1.941 -0.575 0.0285 1.200 H 218 | ATOM 216 HG3 ARG 16 31.848 -0.605 -1.404 0.0285 1.200 H 219 | ATOM 217 CD ARG 16 31.013 -2.537 -1.856 0.0486 1.700 C 220 | ATOM 218 HD2 ARG 16 31.382 -3.486 -2.248 0.0687 1.200 H 221 | ATOM 219 HD3 ARG 16 30.481 -2.743 -0.926 0.0687 1.200 H 222 | ATOM 220 NE ARG 16 30.046 -1.926 -2.789 -0.5295 1.550 N 223 | ATOM 221 HE ARG 16 29.985 -0.920 -2.774 0.3456 1.200 H 224 | ATOM 222 CZ ARG 16 29.054 -2.590 -3.371 0.8076 1.700 C 225 | ATOM 223 NH1 ARG 16 29.096 -3.892 -3.506 -0.8627 1.550 N 226 | ATOM 224 HH11 ARG 16 29.894 -4.407 -3.172 0.4478 1.200 H 227 | ATOM 225 HH12 ARG 16 28.262 -4.392 -3.784 0.4478 1.200 H 228 | ATOM 226 NH2 ARG 16 27.977 -1.966 -3.776 -0.8627 1.550 N 229 | ATOM 227 HH21 ARG 16 27.888 -0.972 -3.648 0.4478 1.200 H 230 | ATOM 228 HH22 ARG 16 27.190 -2.505 -4.107 0.4478 1.200 H 231 | ATOM 229 C ARG 16 34.980 -0.047 -1.551 0.7341 1.700 C 232 | ATOM 230 O ARG 16 34.467 0.259 -0.472 -0.5894 1.500 O 233 | ATOM 231 N PRO 17 35.751 0.821 -2.239 -0.2548 1.550 N 234 | ATOM 232 CD PRO 17 36.478 0.550 -3.472 0.0192 1.700 C 235 | ATOM 233 HD2 PRO 17 35.784 0.567 -4.313 0.0391 1.200 H 236 | ATOM 234 HD3 PRO 17 37.003 -0.404 -3.429 0.0391 1.200 H 237 | ATOM 235 CG PRO 17 37.495 1.678 -3.617 0.0189 1.700 C 238 | ATOM 236 HG2 PRO 17 37.715 1.891 -4.663 0.0213 1.200 H 239 | ATOM 237 HG3 PRO 17 38.407 1.418 -3.076 0.0213 1.200 H 240 | ATOM 238 CB PRO 17 36.808 2.853 -2.927 -0.0070 1.700 C 241 | ATOM 239 HB2 PRO 17 36.130 3.334 -3.635 0.0253 1.200 H 242 | ATOM 240 HB3 PRO 17 37.531 3.575 -2.545 0.0253 1.200 H 243 | ATOM 241 CA PRO 17 36.016 2.191 -1.791 -0.0266 1.700 C 244 | ATOM 242 HA PRO 17 36.661 2.123 -0.917 0.0641 1.200 H 245 | ATOM 243 C PRO 17 34.725 2.977 -1.472 0.5896 1.700 C 246 | ATOM 244 O PRO 17 33.816 2.988 -2.306 -0.5748 1.500 O 247 | ATOM 245 N PRO 18 34.610 3.631 -0.297 -0.2548 1.550 N 248 | ATOM 246 CD PRO 18 35.518 3.563 0.837 0.0192 1.700 C 249 | ATOM 247 HD2 PRO 18 36.553 3.719 0.531 0.0391 1.200 H 250 | ATOM 248 HD3 PRO 18 35.408 2.595 1.328 0.0391 1.200 H 251 | ATOM 249 CG PRO 18 35.091 4.680 1.787 0.0189 1.700 C 252 | ATOM 250 HG2 PRO 18 35.635 5.593 1.538 0.0213 1.200 H 253 | ATOM 251 HG3 PRO 18 35.260 4.409 2.830 0.0213 1.200 H 254 | ATOM 252 CB PRO 18 33.607 4.882 1.490 -0.0070 1.700 C 255 | ATOM 253 HB2 PRO 18 33.305 5.918 1.655 0.0253 1.200 H 256 | ATOM 254 HB3 PRO 18 33.014 4.227 2.124 0.0253 1.200 H 257 | ATOM 255 CA PRO 18 33.451 4.462 0.024 -0.0266 1.700 C 258 | ATOM 256 HA PRO 18 32.559 3.848 -0.063 0.0641 1.200 H 259 | ATOM 257 C PRO 18 33.346 5.686 -0.904 0.5896 1.700 C 260 | ATOM 258 O PRO 18 34.365 6.311 -1.205 -0.5748 1.500 O 261 | ATOM 259 N PRO 19 32.128 6.060 -1.341 -0.2548 1.550 N 262 | ATOM 260 CD PRO 19 30.873 5.361 -1.093 0.0192 1.700 C 263 | ATOM 261 HD2 PRO 19 30.671 5.284 -0.024 0.0391 1.200 H 264 | ATOM 262 HD3 PRO 19 30.918 4.367 -1.541 0.0391 1.200 H 265 | ATOM 263 CG PRO 19 29.779 6.176 -1.778 0.0189 1.700 C 266 | ATOM 264 HG2 PRO 19 29.287 6.822 -1.055 0.0213 1.200 H 267 | ATOM 265 HG3 PRO 19 29.054 5.522 -2.257 0.0213 1.200 H 268 | ATOM 266 CB PRO 19 30.530 7.025 -2.802 -0.0070 1.700 C 269 | ATOM 267 HB2 PRO 19 30.013 7.963 -3.011 0.0253 1.200 H 270 | ATOM 268 HB3 PRO 19 30.655 6.451 -3.721 0.0253 1.200 H 271 | ATOM 269 CA PRO 19 31.901 7.248 -2.156 -0.0266 1.700 C 272 | ATOM 270 HA PRO 19 32.655 7.317 -2.942 0.0641 1.200 H 273 | ATOM 271 C PRO 19 31.946 8.519 -1.291 0.5896 1.700 C 274 | ATOM 272 O PRO 19 31.097 8.703 -0.420 -0.5748 1.500 O 275 | ATOM 273 N SER 20 32.938 9.384 -1.532 -0.3821 1.550 N 276 | ATOM 274 H SER 20 33.620 9.148 -2.237 0.2681 1.200 H 277 | ATOM 275 CA SER 20 33.016 10.745 -0.974 -0.2722 1.700 C 278 | ATOM 276 HA SER 20 32.681 10.726 0.063 0.1304 1.200 H 279 | ATOM 277 CB SER 20 34.451 11.264 -1.011 0.1123 1.700 C 280 | ATOM 278 HB2 SER 20 34.876 11.124 -2.006 0.0813 1.200 H 281 | ATOM 279 HB3 SER 20 34.455 12.328 -0.770 0.0813 1.200 H 282 | ATOM 280 OG SER 20 35.229 10.579 -0.048 -0.6514 1.500 O 283 | ATOM 281 HG SER 20 34.788 10.661 0.800 0.4474 1.200 H 284 | ATOM 282 C SER 20 32.120 11.723 -1.734 0.8113 1.700 C 285 | ATOM 283 O SER 20 32.254 11.771 -2.977 -0.8132 1.500 O 286 | ATOM 284 OXT SER 20 31.362 12.441 -1.049 -0.8132 1.500 O 287 | TER 288 | END 289 | 290 | -------------------------------------------------------------------------------- /test_cases/DielsAlder.log: -------------------------------------------------------------------------------- 1 | [__main__ ]Loaded 2 geometries from test_cases/DielsAlder.xyz 2 | [interpolation]Inserting image between 0 and 1 with Cartesian RMSD 2.119. New length:3 3 | [interpolation]Inserting image between 0 and 1 with Cartesian RMSD 1.806. New length:4 4 | [interpolation]Inserting image between 0 and 1 with Cartesian RMSD 1.639. New length:5 5 | [interpolation]Inserting image between 0 and 1 with Cartesian RMSD 1.513. New length:6 6 | [interpolation]Inserting image between 0 and 1 with Cartesian RMSD 1.443. New length:7 7 | [interpolation]Inserting image between 0 and 1 with Cartesian RMSD 1.394. New length:8 8 | [interpolation]Inserting image between 0 and 1 with Cartesian RMSD 1.348. New length:9 9 | [interpolation]Inserting image between 0 and 1 with Cartesian RMSD 1.306. New length:10 10 | [interpolation]Inserting image between 0 and 1 with Cartesian RMSD 1.266. New length:11 11 | [interpolation]Inserting image between 0 and 1 with Cartesian RMSD 1.230. New length:12 12 | [interpolation]Inserting image between 0 and 1 with Cartesian RMSD 1.197. New length:13 13 | [interpolation]Inserting image between 0 and 1 with Cartesian RMSD 1.166. New length:14 14 | [interpolation]Inserting image between 0 and 1 with Cartesian RMSD 1.138. New length:15 15 | [interpolation]Inserting image between 0 and 1 with Cartesian RMSD 1.111. New length:16 16 | [interpolation]Inserting image between 1 and 2 with Cartesian RMSD 1.091. New length:17 17 | [geodesic ]Maximum RMSD change in initial path: 1.07 18 | [geodesic ]Performing geodesic smoothing 19 | [geodesic ] Images: 17 Atoms 31 Rijs 171 20 | [geodesic ] Degree of freedoms 1395: 21 | [geodesic ] Iteration 0: Length 5.273 |dL|=5.965e-01 22 | [geodesic ] Iteration 1: Length 11.551 |dL|=3.833e+00 23 | [geodesic ] Iteration 2: Length 3.953 |dL|=1.308e-01 24 | [geodesic ] Iteration 3: Length 4.914 |dL|=2.413e-01 25 | [geodesic ] Iteration 4: Length 2.946 |dL|=1.134e-01 26 | [geodesic ] Iteration 5: Length 2.749 |dL|=5.641e-02 27 | [geodesic ] Iteration 6: Length 2.960 |dL|=8.823e-02 28 | [geodesic ] Iteration 7: Length 2.505 |dL|=3.120e-02 29 | [geodesic ] Iteration 8: Length 2.422 |dL|=3.621e-02 30 | [geodesic ] Iteration 9: Length 2.636 |dL|=3.709e-02 31 | [geodesic ] Iteration 10: Length 2.329 |dL|=1.205e-02 32 | [geodesic ] Iteration 11: Length 2.341 |dL|=1.716e-02 33 | [geodesic ] Iteration 12: Length 2.239 |dL|=5.393e-03 34 | [geodesic ] Iteration 13: Length 2.195 |dL|=8.426e-03 35 | [geodesic ] Iteration 14: Length 2.226 |dL|=2.472e-02 36 | [geodesic ]Smoothing converged after 15 iterations 37 | [geodesic ]Final path length: 2.22629 Max RMSD in path: 0.28 38 | [__main__ ]Saving final path to file test_cases/DielsAlder_interpolated.xyz 39 | -------------------------------------------------------------------------------- /test_cases/DielsAlder.xyz: -------------------------------------------------------------------------------- 1 | 31 2 | -9.1724809262591930e+02 frame 22 xyz file generated by TeraChem 3 | C -1.3634783960 0.7418380125 1.0392532252 4 | C 0.0207544828 0.9108367950 1.0728825806 5 | C 0.8580949149 -0.0023509023 0.4186123183 6 | C 0.3072131055 -1.0898755883 -0.2719488038 7 | C -1.0757694088 -1.2682499876 -0.3114873120 8 | C -1.9278645918 -0.3518807718 0.3449707141 9 | C -3.3401800505 -0.5268816618 0.3045973410 10 | C -4.5495162564 -0.6752116833 0.2655192991 11 | C -5.9543040906 -0.8904794567 0.1893027587 12 | O 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1.448153724703 561 | H -0.785565186428 0.095552186511 1.987296871524 562 | -------------------------------------------------------------------------------- /test_cases/H+CH4_CH3+H2.log: -------------------------------------------------------------------------------- 1 | [__main__ ]Loaded 2 geometries from test_cases/H+CH4_CH3+H2.xyz 2 | [interpolation]Inserting image between 0 and 1 with Cartesian RMSD 0.711. New length:3 3 | [interpolation]Inserting image between 1 and 2 with Cartesian RMSD 0.380. New length:4 4 | [interpolation]Inserting image between 0 and 1 with Cartesian RMSD 0.349. New length:5 5 | [interpolation]Inserting image between 3 and 4 with Cartesian RMSD 0.212. New length:6 6 | [interpolation]Inserting image between 0 and 1 with Cartesian RMSD 0.180. New length:7 7 | [interpolation]Inserting image between 3 and 4 with Cartesian RMSD 0.178. New length:8 8 | [interpolation]Inserting image between 2 and 3 with Cartesian RMSD 0.173. New length:9 9 | [interpolation]Inserting image between 7 and 8 with Cartesian RMSD 0.115. New length:10 10 | [interpolation]Inserting image between 0 and 1 with Cartesian RMSD 0.101. New length:11 11 | [interpolation]Inserting image between 7 and 8 with Cartesian RMSD 0.099. New length:12 12 | [interpolation]Inserting image between 6 and 7 with Cartesian RMSD 0.091. New length:13 13 | [interpolation]Inserting image between 3 and 4 with Cartesian RMSD 0.090. New length:14 14 | [interpolation]Inserting image between 6 and 7 with Cartesian RMSD 0.090. New length:15 15 | [interpolation]Inserting image between 5 and 6 with Cartesian RMSD 0.083. New length:16 16 | [interpolation]Inserting image between 2 and 3 with Cartesian RMSD 0.079. New length:17 17 | [geodesic ]Maximum RMSD change in initial path: 0.07 18 | [geodesic ]Performing geodesic smoothing 19 | [geodesic ] Images: 17 Atoms 6 Rijs 14 20 | [geodesic ] Degree of freedoms 270: 21 | [geodesic ] Iteration 0: Length 1.507 |dL|=4.479e-02 22 | [geodesic ] Iteration 1: Length 1.995 |dL|=9.878e-02 23 | [geodesic ] Iteration 2: Length 1.347 |dL|=1.882e-02 24 | [geodesic ] Iteration 3: Length 1.511 |dL|=1.274e-01 25 | [geodesic ] Iteration 4: Length 1.314 |dL|=1.806e-02 26 | [geodesic ] Iteration 5: Length 1.319 |dL|=9.342e-02 27 | [geodesic ] Iteration 6: Length 1.300 |dL|=2.455e-02 28 | [geodesic ] Iteration 7: Length 1.284 |dL|=1.956e-02 29 | [geodesic ] Iteration 8: Length 1.356 |dL|=1.052e-01 30 | [geodesic ] Iteration 9: Length 1.280 |dL|=2.287e-02 31 | [geodesic ] Iteration 10: Length 1.275 |dL|=1.884e-02 32 | [geodesic ] Iteration 11: Length 1.271 |dL|=1.670e-02 33 | [geodesic ] Iteration 12: Length 1.268 |dL|=2.056e-02 34 | [geodesic ] Iteration 13: Length 1.264 |dL|=2.304e-03 35 | [geodesic ] Iteration 14: Length 1.263 |dL|=4.275e-03 36 | [geodesic ]Smoothing converged after 15 iterations 37 | [geodesic ]Final path length: 1.26274 Max RMSD in path: 0.11 38 | [__main__ ]Saving final path to file test_cases/H+CH4_CH3+H2_interpolated.xyz 39 | -------------------------------------------------------------------------------- /test_cases/H+CH4_CH3+H2.xyz: -------------------------------------------------------------------------------- 1 | 6 2 | Frame 1 3 | C 0.63304144726145573 -0.1087864399671382 -0.56719035628535563 4 | H 0.32211844158744957 0.73940868963550133 0.028233702151437438 5 | H 0.22314828480594268 -1.0162149828075975 -0.14431891709099165 6 | H 0.27351378480348959 0.010954265382729918 -1.5807812527838665 7 | H 1.7132780565470138 -0.16922154133995207 -0.57278318217663571 8 | H 2.0978400000000001 0.35783999999999999 2.2104199999999996 9 | 6 10 | Frame 1 11 | C 0.88562473811384212 0.97416578530588571 1.0453399509875991 12 | H 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2.3150372327 6.0209025892 541 | H 39.8156734600 2.6845910459 6.9909725647 542 | H 39.6296568456 1.3809793809 5.8049772745 543 | C 39.8887900558 3.3350238652 4.8799952776 544 | H 38.9248775214 3.1659509975 4.3961385730 545 | C 39.9708248864 4.7813835947 5.3881354696 546 | O 41.0607429371 5.4239828615 5.3845271094 547 | N 38.8341811212 5.3224616854 5.8929616497 548 | C 37.5187800183 4.6464220302 6.0437657285 549 | H 37.6153258046 3.7761938247 6.7001444289 550 | H 37.1525224217 4.3075299341 5.0698647665 551 | C 36.5943138589 5.7169175780 6.6717950210 552 | H 36.3455800112 5.4480034048 7.7020194303 553 | H 35.6567367145 5.7964328958 6.1148759377 554 | C 37.3797035998 7.0515951684 6.6210707565 555 | H 37.1849833944 7.6783939332 7.4956889565 556 | H 37.1090453195 7.6288656988 5.7314358334 557 | C 38.8720152970 6.6484614941 6.5266566590 558 | H 39.4388222470 7.3370732282 5.8950526921 559 | C 39.5398142569 6.5711652838 7.9049573292 560 | O 39.4142621489 5.5193838294 8.6162661920 561 | N 40.1963782587 7.6721885206 8.2923789120 562 | H 40.2924882505 8.4849768565 7.6760120649 563 | C 40.7776845924 7.9572346319 9.6120583870 564 | H 39.9826917615 7.9827521527 10.3703152482 565 | C 41.8203247338 6.9299683682 10.0791881255 566 | H 42.5015086529 6.7002738958 9.2467667203 567 | H 42.3938111656 7.3809555632 10.8905631883 568 | O 41.2214193021 5.7193961808 10.6189943684 569 | H 40.5159344216 5.4355445523 9.9751139861 570 | C 41.3898587291 9.3942833047 9.5224549625 571 | O 41.2128588196 10.0298250719 8.4173548405 572 | O 42.0012177043 9.8178817643 10.5597018566 573 | -------------------------------------------------------------------------------- /test_cases/calcium_binding.log: -------------------------------------------------------------------------------- 1 | [__main__ ]Loaded 2 geometries from calcium_binding.xyz 2 | [interpolation]Inserting image between 0 and 1 with Cartesian RMSD 3.645. New length:3 3 | [interpolation] Screened pairs came into contact. Adding reference point. 4 | [interpolation] Screened pairs came into contact. Adding reference point. 5 | [interpolation] Screened pairs came into contact. Adding reference point. 6 | [interpolation]Inserting image between 0 and 1 with Cartesian RMSD 2.693. New length:4 7 | [interpolation] Screened pairs came into contact. Adding reference point. 8 | [interpolation] Screened pairs came into contact. Adding reference point. 9 | [interpolation] Screened pairs came into contact. Adding reference point. 10 | [interpolation]Inserting image between 0 and 1 with Cartesian RMSD 1.684. New length:5 11 | [interpolation] Screened pairs came into contact. Adding reference point. 12 | [interpolation] Screened pairs came into contact. Adding reference point. 13 | [interpolation]Inserting image between 2 and 3 with Cartesian RMSD 1.546. New length:6 14 | [interpolation]Inserting image between 4 and 5 with Cartesian RMSD 1.525. New length:7 15 | [interpolation]Inserting image between 0 and 1 with Cartesian RMSD 1.339. New length:8 16 | [interpolation]Inserting image between 0 and 1 with Cartesian RMSD 1.039. New length:9 17 | [interpolation]Inserting image between 2 and 3 with Cartesian RMSD 1.004. New length:10 18 | [interpolation]Inserting image between 1 and 2 with Cartesian RMSD 0.938. New length:11 19 | [interpolation]Inserting image between 1 and 2 with Cartesian RMSD 0.959. New length:12 20 | [interpolation]Inserting image between 4 and 5 with Cartesian RMSD 0.936. New length:13 21 | [interpolation] Screened pairs came into contact. Adding reference point. 22 | [interpolation] Screened pairs came into contact. Adding reference point. 23 | [interpolation]Inserting image between 2 and 3 with Cartesian RMSD 0.921. New length:14 24 | [interpolation]Inserting image between 2 and 3 with Cartesian RMSD 0.954. New length:15 25 | [interpolation]Inserting image between 2 and 3 with Cartesian RMSD 0.974. New length:16 26 | [interpolation]Inserting image between 2 and 3 with Cartesian RMSD 1.008. New length:17 27 | [geodesic ]Maximum RMSD change in initial path: 0.99 28 | [geodesic ]Performing geodesic smoothing 29 | [geodesic ] Images: 17 Atoms 600 Rijs 2729 30 | [geodesic ] Degree of freedoms 27000: 31 | [geodesic ] Initial length: 36.839 32 | [geodesic ]Sweep 0: L= 17.15 dX=4.15e+01 tol=2.000e-02 dL=2.758e-01 33 | [geodesic ]Sweep 1: L= 12.48 dX=2.27e+01 tol=5.517e-02 dL=1.579e-01 34 | [geodesic ]Sweep 2: L= 10.57 dX=1.55e+01 tol=3.158e-02 dL=3.759e-02 35 | [geodesic ]Sweep 3: L= 9.46 dX=9.36e+00 tol=7.517e-03 dL=3.484e-02 36 | [geodesic ]Sweep 4: L= 8.91 dX=7.99e+00 tol=6.968e-03 dL=2.569e-02 37 | [geodesic ]Sweep 5: L= 8.44 dX=7.21e+00 tol=5.137e-03 dL=1.411e-02 38 | [geodesic ]Sweep 6: L= 8.15 dX=6.07e+00 tol=2.821e-03 dL=2.977e-02 39 | [geodesic ]Sweep 7: L= 7.88 dX=5.43e+00 tol=5.955e-03 dL=3.423e-02 40 | [geodesic ]Sweep 8: L= 7.66 dX=1.01e+01 tol=6.846e-03 dL=1.983e-02 41 | [geodesic ]Sweep 9: L= 7.45 dX=7.54e+00 tol=3.965e-03 dL=2.950e-02 42 | [geodesic ]Sweep 10: L= 7.29 dX=7.93e+00 tol=5.900e-03 dL=8.818e-03 43 | [geodesic ]Sweep 11: L= 7.12 dX=8.32e+00 tol=1.764e-03 dL=6.121e-03 44 | [geodesic ]Sweep 12: L= 7.00 dX=1.15e+01 tol=1.224e-03 dL=3.120e-03 45 | [geodesic ]Sweep 13: L= 6.87 dX=7.37e+00 tol=1.000e-03 dL=7.086e-03 46 | [geodesic ]Sweep 14: L= 6.77 dX=8.87e+00 tol=1.417e-03 dL=2.483e-03 47 | [geodesic ]Optimization not converged after 14 iteartions 48 | [geodesic ]Final path length: 6.77003 Max RMSD in path: 0.62 49 | [__main__ ]Saving final path to file interpolated.xyz 50 | -------------------------------------------------------------------------------- /test_cases/calcium_binding.xyz: -------------------------------------------------------------------------------- 1 | 600 2 | Frame 1 3 | N -13.8970 1.1470 -22.4980 4 | C -12.5990 1.1110 -21.7650 5 | C -12.4240 -0.2380 -21.0650 6 | O -13.3690 -0.9780 -20.8760 7 | C -12.6940 2.2390 -20.7380 8 | O -11.9550 1.8820 -19.5780 9 | N -11.2200 -0.5660 -20.6790 10 | C -10.9860 -1.8680 -19.9910 11 | C -11.0760 -1.6880 -18.4730 12 | O -11.4010 -0.6240 -17.9830 13 | C -9.5730 -2.2820 -20.3990 14 | O -8.9490 -2.9520 -19.3120 15 | N -10.7910 -2.7190 -17.7260 16 | C -10.8610 -2.6060 -16.2410 17 | C -10.4380 -3.9260 -15.5880 18 | O -10.4610 -4.9710 -16.2070 19 | C -12.3290 -2.3030 -15.9350 20 | C -12.4410 -1.6720 -14.5460 21 | O -12.0710 -2.2760 -13.5590 22 | N -12.9400 -0.4720 -14.4270 23 | N -10.0520 -3.8850 -14.3430 24 | C -9.6270 -5.1370 -13.6520 25 | C -10.7000 -6.2180 -13.8140 26 | O -11.6730 -6.0400 -14.5190 27 | C -9.4770 -4.7450 -12.1810 28 | C -8.0710 -5.1020 -11.6980 29 | C -7.0350 -4.5340 -12.6710 30 | C -7.8440 -4.5020 -10.3080 31 | N -10.5300 -7.3380 -13.1660 32 | C -11.5390 -8.4280 -13.2840 33 | C -11.4200 -9.3890 -12.0980 34 | O -10.9570 -9.0240 -11.0350 35 | C -11.1970 -9.1450 -14.5910 36 | O -10.6240 -8.2170 -15.5020 37 | C -12.4700 -9.7400 -15.1980 38 | N -11.8340 -10.6140 -12.2700 39 | C -11.7430 -11.5950 -11.1510 40 | C -10.2970 -12.0640 -10.9760 41 | O -9.7170 -11.9350 -9.9160 42 | C -12.6380 -12.7620 -11.5730 43 | C -14.0210 -12.6000 -10.9410 44 | C -15.0910 -12.6470 -12.0340 45 | O -14.8320 -12.1360 -13.1120 46 | O -16.1500 -13.1930 -11.7760 47 | N -9.7100 -12.6080 -12.0070 48 | C -8.3010 -13.0830 -11.8980 49 | C -7.3500 -11.8920 -11.7570 50 | O -6.3310 -11.9740 -11.1010 51 | C -8.0340 -13.8330 -13.2030 52 | C -9.0180 -14.9960 -13.3360 53 | C -9.2000 -15.3460 -14.8140 54 | O -8.3670 -14.9380 -15.6060 55 | O -10.1710 -16.0150 -15.1290 56 | N -7.6750 -10.7840 -12.3670 57 | C -6.7870 -9.5910 -12.2620 58 | C -6.7590 -9.0860 -10.8180 59 | O -5.7340 -9.0980 -10.1650 60 | C -7.4110 -8.5470 -13.1860 61 | C -6.3180 -7.8970 -14.0350 62 | C -5.9990 -8.7960 -15.2320 63 | O -4.8470 -9.0410 -15.5320 64 | N -6.9770 -9.3020 -15.9310 65 | N -7.8780 -8.6470 -10.3120 66 | C -7.9140 -8.1470 -8.9080 67 | C -7.2950 -9.1850 -7.9700 68 | O -6.6660 -8.8500 -6.9840 69 | C -9.3970 -7.9550 -8.5920 70 | C -9.9870 -6.9070 -9.5370 71 | C -9.5540 -7.4820 -7.1450 72 | C -11.4570 -6.6700 -9.1840 73 | N -7.4660 -10.4430 -8.2700 74 | C -6.8860 -11.5040 -7.3990 75 | C -5.3640 -11.3520 -7.3300 76 | O -4.8040 -11.0880 -6.2850 77 | C -7.2650 -12.8230 -8.0760 78 | N -4.6910 -11.5150 -8.4370 79 | C -3.2070 -11.3770 -8.4310 80 | C -2.8070 -10.0740 -7.7350 81 | O -1.7650 -9.9830 -7.1160 82 | C -2.8070 -11.3420 -9.9060 83 | C -2.6000 -12.7710 -10.4130 84 | C -2.6360 -12.7820 -11.9420 85 | O -3.5820 -12.2470 -12.4960 86 | O -1.7170 -13.3240 -12.5330 87 | N -3.6290 -9.0640 -7.8290 88 | C -3.2980 -7.7680 -7.1700 89 | C -3.2990 -7.9380 -5.6490 90 | O -2.3840 -7.5210 -4.9680 91 | C -4.4060 -6.8080 -7.6030 92 | C -4.1070 -6.2790 -8.9850 93 | C -3.8390 -7.1680 -10.0330 94 | C -4.0990 -4.8980 -9.2180 95 | C -3.5630 -6.6750 -11.3140 96 | C -3.8240 -4.4070 -10.4990 97 | C -3.5560 -5.2940 -11.5470 98 | N -4.3190 -8.5490 -5.1110 99 | C -4.3740 -8.7460 -3.6350 100 | C -3.1320 -9.5040 -3.1620 101 | O -2.3950 -9.0390 -2.3150 102 | C -5.6360 -9.5750 -3.3900 103 | C -5.8500 -9.7480 -1.8850 104 | C -7.0220 -8.8760 -1.4320 105 | C -7.7060 -9.5250 -0.2260 106 | N -7.9310 -8.4100 0.7340 107 | N -2.8920 -10.6660 -3.7050 108 | C -1.6920 -11.4460 -3.2880 109 | C -0.4520 -10.5490 -3.3170 110 | O 0.4160 -10.6440 -2.4730 111 | C -1.5680 -12.5680 -4.3190 112 | C -1.7610 -13.9190 -3.6290 113 | C -2.7280 -14.7780 -4.4470 114 | O -3.8580 -14.3550 -4.6260 115 | O -2.3220 -15.8430 -4.8800 116 | N -0.3690 -9.6740 -4.2820 117 | C 0.8090 -8.7650 -4.3670 118 | C 0.7390 -7.7130 -3.2580 119 | O 1.5020 -7.7400 -2.3130 120 | C 0.7000 -8.1040 -5.7410 121 | N -0.1720 -6.7860 -3.3640 122 | C -0.2960 -5.7320 -2.3170 123 | C -0.1570 -6.3500 -0.9230 124 | O 0.5790 -5.8630 -0.0870 125 | C -1.6970 -5.1530 -2.5090 126 | C -1.9020 -3.9990 -1.5580 127 | C -1.4710 -2.7140 -1.9110 128 | C -2.5260 -4.2130 -0.3240 129 | C -1.6650 -1.6450 -1.0290 130 | C -2.7190 -3.1440 0.5590 131 | C -2.2880 -1.8590 0.2060 132 | N -0.8600 -7.4180 -0.6640 133 | C -0.7730 -8.0640 0.6770 134 | C 0.5990 -8.7190 0.8690 135 | O 1.0450 -8.9310 1.9780 136 | C -1.8750 -9.1230 0.6780 137 | N 1.2700 -9.0440 -0.2020 138 | C 2.6100 -9.6880 -0.0730 139 | C 3.5870 -8.7480 0.6400 140 | O 4.6060 -9.1690 1.1480 141 | C 3.0660 -9.9490 -1.5090 142 | C 3.4180 -11.4280 -1.6710 143 | C 3.5270 -11.7670 -3.1590 144 | C 4.7570 -11.7120 -0.9860 145 | N 3.2860 -7.4780 0.6820 146 | C 4.2020 -6.5200 1.3650 147 | C 3.4480 -5.7460 2.4500 148 | O 3.8960 -4.7170 2.9170 149 | C 4.6790 -5.5680 0.2660 150 | C 5.0660 -6.3620 -0.9600 151 | C 4.0850 -6.7370 -1.8860 152 | C 6.4020 -6.7190 -1.1720 153 | C 4.4410 -7.4710 -3.0240 154 | C 6.7580 -7.4530 -2.3100 155 | C 5.7770 -7.8280 -3.2360 156 | N 2.3070 -6.2320 2.8550 157 | C 1.5270 -5.5240 3.9090 158 | C 2.0610 -5.8860 5.2980 159 | O 1.7870 -6.9490 5.8210 160 | C 0.0910 -6.0190 3.7410 161 | C -0.8820 -4.9340 4.2040 162 | O -0.9150 -4.6650 5.3940 163 | O -1.5760 -4.3890 3.3620 164 | N 2.8200 -5.0120 5.8980 165 | C 3.3690 -5.3070 7.2540 166 | C 2.2450 -5.3030 8.2920 167 | O 2.2640 -6.0570 9.2450 168 | C 4.3610 -4.1770 7.5320 169 | C 4.9060 -4.3140 8.9560 170 | C 5.4240 -2.9580 9.4380 171 | C 6.6100 -2.5270 8.5720 172 | N 6.6310 -1.0400 8.6630 173 | N 1.2650 -4.4590 8.1150 174 | C 0.1390 -4.4090 9.0920 175 | C -0.7700 -5.6260 8.9160 176 | O -1.6540 -5.8740 9.7110 177 | C -0.6170 -3.1210 8.7580 178 | C 0.1620 -1.9180 9.2920 179 | O 1.0600 -1.4650 8.6000 180 | O -0.1520 -1.4680 10.3820 181 | N -0.5600 -6.3900 7.8780 182 | C -1.4130 -7.5920 7.6510 183 | C -2.8910 -7.2350 7.8310 184 | O -3.6770 -8.0260 8.3120 185 | C -0.9700 -8.5980 8.7150 186 | C -0.0550 -9.6450 8.0770 187 | O -0.4490 -10.3350 7.1580 188 | N 1.1600 -9.7940 8.5310 189 | N -3.2740 -6.0470 7.4480 190 | C -4.7010 -5.6400 7.5970 191 | C -5.2630 -5.1800 6.2490 192 | O -6.4480 -4.9540 6.1040 193 | C -4.6800 -4.4810 8.5940 194 | C -3.7410 -3.3860 8.0830 195 | O -3.0330 -3.5780 7.1150 196 | N -3.7060 -2.2350 8.6990 197 | N -4.4210 -5.0380 5.2620 198 | C -4.9070 -4.5920 3.9260 199 | C -4.2870 -3.2370 3.5830 200 | O -4.7510 -2.5360 2.7060 201 | N -3.2420 -2.8620 4.2680 202 | C -2.5930 -1.5510 3.9780 203 | C -1.0730 -1.7200 3.8980 204 | O -0.4770 -2.4360 4.6770 205 | C -2.9720 -0.6540 5.1560 206 | O -2.8030 -1.3750 6.3690 207 | N -0.4440 -1.0660 2.9600 208 | C 1.0360 -1.1900 2.8310 209 | C 1.6780 0.1980 2.7430 210 | O 1.0160 1.1830 2.4870 211 | C 1.2570 -1.9650 1.5310 212 | C 0.9620 -1.0530 0.3370 213 | C 0.3200 -3.1740 1.4910 214 | C 1.1650 -1.8310 -0.9640 215 | N 2.9640 0.2800 2.9520 216 | C 3.6450 1.6040 2.8770 217 | C 3.9410 1.9590 1.4180 218 | O 4.1670 1.0960 0.5930 219 | C 4.9450 1.4240 3.6600 220 | O 5.1930 2.5930 4.4310 221 | N 3.9400 3.2220 1.0910 222 | C 4.2200 3.6270 -0.3170 223 | C 5.3930 2.8180 -0.8750 224 | O 5.2870 2.1810 -1.9050 225 | C 4.5770 5.1100 -0.2390 226 | O 5.6780 5.3730 -1.1010 227 | N 6.5130 2.8390 -0.2050 228 | C 7.6910 2.0690 -0.7000 229 | C 7.2660 0.6550 -1.1040 230 | O 7.8100 0.0700 -2.0180 231 | C 8.6570 2.0210 0.4830 232 | O 9.8030 2.8080 0.1840 233 | N 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-8.1110 266 | C 2.4820 -4.3250 -4.8920 267 | C 2.8230 -4.8080 -3.4820 268 | C 2.3940 -2.7980 -4.8960 269 | N 3.5630 -3.0440 -7.5590 270 | C 3.2900 -2.4910 -8.9160 271 | C 4.0360 -3.2980 -9.9820 272 | O 3.4360 -3.8880 -10.8580 273 | C 3.8150 -1.0540 -8.8650 274 | C 3.3360 -0.2890 -10.1000 275 | S 1.5270 -0.3200 -10.1680 276 | C 1.3220 1.0270 -11.3590 277 | N 5.3390 -3.3290 -9.9160 278 | C 6.1200 -4.0970 -10.9300 279 | C 5.9060 -5.6020 -10.7400 280 | O 6.1560 -6.3910 -11.6280 281 | C 7.5790 -3.7270 -10.6650 282 | C 8.4860 -4.5240 -11.6050 283 | C 9.1680 -5.6500 -10.8240 284 | N 10.2120 -4.9720 -10.0070 285 | C 11.2630 -5.6370 -9.6100 286 | N 12.2470 -5.8600 -10.4380 287 | N 11.3300 -6.0800 -8.3840 288 | N 5.4510 -6.0050 -9.5850 289 | C 5.2280 -7.4580 -9.3350 290 | C 4.0490 -7.9700 -10.1660 291 | O 4.0230 -9.1110 -10.5840 292 | C 4.9140 -7.5590 -7.8430 293 | O 5.9690 -6.9590 -7.1010 294 | N 3.0720 -7.1410 -10.4070 295 | C 1.8980 -7.5930 -11.2100 296 | C 2.3230 -7.8970 -12.6490 297 | O 1.7260 -8.7130 -13.3230 298 | C 0.9110 -6.4240 -11.1770 299 | C 0.1260 -6.4440 -9.8620 300 | C -1.0010 -5.4110 -9.9260 301 | C -0.4760 -7.8340 -9.6430 302 | N 3.3500 -7.2500 -13.1280 303 | C 3.8080 -7.5110 -14.5240 304 | C 4.0520 -6.1830 -15.2430 305 | O 3.7940 -6.0490 -16.4230 306 | N 4.5520 -5.2010 -14.5450 307 | C 4.8160 -3.8840 -15.1950 308 | C 6.1250 -3.2890 -14.6700 309 | O 6.7740 -3.8540 -13.8120 310 | C 3.6300 -2.9960 -14.8090 311 | C 3.2820 -3.2090 -13.3340 312 | C 2.7210 -1.9120 -12.7490 313 | C 2.2310 -4.3150 -13.2150 314 | N 6.5190 -2.1540 -15.1790 315 | C 7.7870 -1.5270 -14.7080 316 | C 7.8890 -0.0880 -15.2200 317 | O 8.4570 0.1620 -16.2640 318 | C 8.8990 -2.3870 -15.3040 319 | O 9.2140 -3.4400 -14.4020 320 | N 7.3310 0.8140 -14.4580 321 | C 7.3560 2.2500 -14.8310 322 | C 8.7680 2.8190 -14.6630 323 | O 9.7410 2.0920 -14.6430 324 | C 6.3870 2.8930 -13.8420 325 | C 6.3690 1.9700 -12.6650 326 | C 6.6320 0.5830 -13.1900 327 | N 8.8890 4.1130 -14.5440 328 | C 10.2400 4.7220 -14.3790 329 | C 10.2710 5.6130 -13.1340 330 | O 9.2470 6.0250 -12.6280 331 | C 10.4530 5.5570 -15.6410 332 | O 9.6020 5.0750 -16.6720 333 | N 11.4410 5.9130 -12.6370 334 | C 11.5350 6.7780 -11.4270 335 | C 10.5600 7.9520 -11.5400 336 | O 9.6300 8.0750 -10.7680 337 | C 12.9800 7.2800 -11.4090 338 | C 13.8730 6.2430 -10.7260 339 | C 14.4480 6.8340 -9.4380 340 | O 15.1130 7.8540 -9.5230 341 | O 14.2150 6.2580 -8.3880 342 | N 10.7620 8.8140 -12.4990 343 | C 9.8420 9.9760 -12.6610 344 | C 8.3900 9.5200 -12.4990 345 | O 7.6060 10.1440 -11.8100 346 | C 10.0900 10.4840 -14.0810 347 | N 8.0270 8.4340 -13.1230 348 | C 6.6280 7.9350 -13.0010 349 | C 6.3220 7.5910 -11.5410 350 | O 5.2250 7.7980 -11.0610 351 | C 6.5770 6.6790 -13.8710 352 | C 5.2970 6.6900 -14.7100 353 | C 5.6470 6.4410 -16.1780 354 | O 6.3760 5.4990 -16.4420 355 | O 5.1800 7.1960 -17.0140 356 | N 7.2850 7.0710 -10.8330 357 | C 7.0530 6.7160 -9.4030 358 | C 6.9140 7.9870 -8.5630 359 | O 6.0490 8.0930 -7.7160 360 | C 8.2950 5.9290 -8.9800 361 | C 8.0070 5.1820 -7.6770 362 | C 8.6600 4.9210 -10.0730 363 | N 7.7590 8.9540 -8.7910 364 | C 7.6770 10.2200 -8.0070 365 | C 6.2600 10.7960 -8.0800 366 | O 5.6570 11.1160 -7.0750 367 | C 8.6750 11.1650 -8.6750 368 | C 9.4400 11.9430 -7.6020 369 | O 8.8730 12.7710 -6.9150 370 | N 10.7120 11.7120 -7.4280 371 | N 5.7230 10.9270 -9.2630 372 | C 4.3460 11.4810 -9.3990 373 | C 3.3190 10.4810 -8.8570 374 | O 2.3690 10.8500 -8.1960 375 | C 4.1500 11.6910 -10.9000 376 | C 5.1360 12.7490 -11.4000 377 | O 6.3140 12.4430 -11.4730 378 | O 4.6960 13.8450 -11.7030 379 | N 3.5050 9.2200 -9.1330 380 | C 2.5420 8.1970 -8.6340 381 | C 2.5290 8.1850 -7.1020 382 | O 1.5070 7.9680 -6.4820 383 | C 3.0590 6.8660 -9.1770 384 | C 2.2470 5.7170 -8.5760 385 | C 0.9300 5.5690 -9.3390 386 | C 3.0470 4.4180 -8.6840 387 | N 3.6580 8.4180 -6.4890 388 | C 3.7100 8.4190 -4.9990 389 | C 3.2340 9.7690 -4.4540 390 | O 2.3290 9.8390 -3.6460 391 | C 5.1820 8.1910 -4.6540 392 | C 5.5900 6.7770 -5.0700 393 | S 5.1110 5.6040 -3.7770 394 | C 3.9070 4.6700 -4.7520 395 | N 3.8360 10.8410 -4.8920 396 | C 3.4180 12.1850 -4.3980 397 | C 1.8980 12.3400 -4.5120 398 | O 1.2870 13.1080 -3.7970 399 | C 4.1280 13.1820 -5.3140 400 | C 5.2420 13.8860 -4.5360 401 | O 6.4070 13.7320 -4.8470 402 | N 4.9320 14.6560 -3.5300 403 | N 1.2850 11.6140 -5.4070 404 | C -0.1940 11.7190 -5.5670 405 | C -0.9020 10.9900 -4.4220 406 | O -2.0850 11.1610 -4.2010 407 | C -0.4980 11.0430 -6.9030 408 | C -0.8140 12.1080 -7.9550 409 | C -1.9970 11.6460 -8.8100 410 | O -2.6530 10.6970 -8.4140 411 | O -2.2260 12.2490 -9.8440 412 | N -0.1890 10.1770 -3.6920 413 | C -0.8220 9.4370 -2.5630 414 | C 0.0130 9.6000 -1.2890 415 | O -0.5140 9.7660 -0.2070 416 | C -0.8400 7.9760 -3.0070 417 | C -1.6200 7.1430 -1.9870 418 | C 0.5930 7.4520 -3.1030 419 | C -1.4030 5.6550 -2.2680 420 | N 1.3120 9.5560 -1.4100 421 | C 2.1780 9.7090 -0.2060 422 | C 1.9950 11.1010 0.4030 423 | O 2.2790 12.1040 -0.2200 424 | C 3.6070 9.5320 -0.7200 425 | C 4.4710 8.9070 0.3770 426 | O 4.4410 9.4120 1.4870 427 | O 5.1470 7.9330 0.0880 428 | N 1.5220 11.1700 1.6180 429 | C 1.3220 12.4990 2.2660 430 | C 2.2600 12.6480 3.4670 431 | O 2.4570 13.7310 3.9810 432 | C -0.1370 12.5000 2.7220 433 | C -0.4080 13.7460 3.5660 434 | C -1.0540 12.5060 1.4960 435 | N 2.8390 11.5690 3.9180 436 | C 3.7630 11.6510 5.0850 437 | C 5.0370 10.8490 4.8080 438 | O 5.7770 10.5100 5.7100 439 | C 2.9860 11.0380 6.2500 440 | C 1.5610 11.5940 6.2630 441 | O 1.3920 12.7280 6.6830 442 | O 0.6620 10.8790 5.8530 443 | N 5.3000 10.5440 3.5670 444 | C 6.5260 9.7640 3.2340 445 | C 6.2170 8.2690 3.3080 446 | O 6.2650 7.5650 2.3190 447 | N 5.8990 7.7770 4.4740 448 | C 5.5880 6.3240 4.6120 449 | C 4.1230 6.1330 5.0130 450 | O 3.7980 5.3020 5.8360 451 | C 6.5170 5.8230 5.7180 452 | C 7.8670 5.4340 5.1140 453 | O 8.4580 6.1970 4.3740 454 | N 8.3850 4.2710 5.4000 455 | N 3.2350 6.8960 4.4350 456 | C 1.7920 6.7580 4.7840 457 | C 1.3540 5.2970 4.6490 458 | O 2.0340 4.4880 4.0510 459 | C 1.0540 7.6370 3.7740 460 | C 1.0940 6.9860 2.4190 461 | N 1.9870 5.9710 2.1130 462 | C 0.3590 7.1960 1.2780 463 | C 1.7670 5.6090 0.8350 464 | N 0.7850 6.3250 0.2800 465 | N 0.2200 4.9550 5.1980 466 | C -0.2600 3.5460 5.0990 467 | C -1.2450 3.4050 3.9350 468 | O -2.3930 3.7900 4.0300 469 | C -0.9600 3.2710 6.4300 470 | C -2.1780 4.1860 6.5660 471 | C -2.2330 4.7550 7.9850 472 | O -1.3540 4.5100 8.7850 473 | N -3.2390 5.5110 8.3330 474 | N -0.8030 2.8560 2.8360 475 | C -1.7140 2.6910 1.6670 476 | C -2.7720 1.6250 1.9660 477 | O -2.7180 0.9490 2.9740 478 | C -0.8080 2.2380 0.5220 479 | C 0.2240 3.3300 0.2280 480 | C -1.6520 1.9860 -0.7300 481 | C 1.0710 2.9210 -0.9780 482 | N -3.7340 1.4720 1.0980 483 | C -4.7950 0.4490 1.3320 484 | C -5.0890 -0.3120 0.0370 485 | O -5.3170 0.2760 -1.0020 486 | C -6.0220 1.2460 1.7780 487 | C -6.4670 0.7700 3.1610 488 | C -7.4250 -0.4130 3.0090 489 | O -6.9550 -1.4960 2.7010 490 | O -8.6130 -0.2160 3.2050 491 | N -5.0850 -1.6160 0.0890 492 | C -5.3640 -2.4120 -1.1400 493 | C -6.5360 -1.7990 -1.9120 494 | O -6.5120 -1.7010 -3.1220 495 | C -5.7250 -3.8090 -0.6360 496 | C -5.8850 -4.7420 -1.8120 497 | C -4.8980 -4.7950 -2.8030 498 | C -7.0200 -5.5550 -1.9120 499 | C -5.0460 -5.6590 -3.8940 500 | C -7.1690 -6.4210 -3.0020 501 | C -6.1810 -6.4720 -3.9940 502 | N -7.5630 -1.3860 -1.2200 503 | C -8.7350 -0.7800 -1.9140 504 | C -8.2860 0.4110 -2.7660 505 | O -8.0790 0.2920 -3.9570 506 | C -9.6640 -0.3180 -0.7930 507 | O -10.4970 0.7290 -1.2760 508 | N -8.1330 1.5600 -2.1640 509 | C -7.6970 2.7550 -2.9390 510 | C -6.5460 2.3830 -3.8790 511 | O -6.5070 2.7920 -5.0220 512 | C -7.2290 3.7610 -1.8880 513 | C -5.9240 3.2700 -1.2560 514 | C -5.5160 4.2170 -0.1270 515 | O -5.9710 5.3490 -0.1350 516 | O -4.7550 3.7940 0.7280 517 | N -5.6090 1.6090 -3.4040 518 | C -4.4620 1.2090 -4.2710 519 | C -4.9640 0.8140 -5.6610 520 | O -4.5830 1.3950 -6.6580 521 | C -3.8320 0.0100 -3.5620 522 | C -2.9150 -0.7200 -4.5150 523 | C -2.2640 -0.0160 -5.5360 524 | C -2.7180 -2.0990 -4.3790 525 | C -1.4150 -0.6930 -6.4190 526 | C -1.8700 -2.7750 -5.2630 527 | C -1.2180 -2.0720 -6.2830 528 | N -5.8170 -0.1720 -5.7360 529 | C -6.3420 -0.6050 -7.0630 530 | C -7.4090 0.3770 -7.5540 531 | O -7.5010 0.6700 -8.7300 532 | C -6.9530 -1.9850 -6.8160 533 | C -5.9310 -3.0670 -7.1700 534 | C -4.5830 -2.7290 -6.5310 535 | C -6.4180 -4.4180 -6.6430 536 | N -8.2130 0.8880 -6.6640 537 | C -9.2710 1.8520 -7.0810 538 | C -8.6540 2.9960 -7.8900 539 | O -9.3120 3.6290 -8.6910 540 | C -9.8650 2.3780 -5.7740 541 | N -7.3930 3.2660 -7.6850 542 | C -6.7330 4.3670 -8.4410 543 | C -5.8010 3.7920 -9.5090 544 | O -5.6500 4.3460 -10.5810 545 | C -5.9340 5.1440 -7.3940 546 | C -6.8470 6.1590 -6.7040 547 | C -8.0860 5.4460 -6.1600 548 | C -6.0910 6.8200 -5.5490 549 | N -5.1740 2.6820 -9.2270 550 | C -4.2520 2.0710 -10.2280 551 | C -4.9810 1.8550 -11.5560 552 | O -4.3800 1.8520 -12.6120 553 | C -3.8390 0.7310 -9.6190 554 | C -2.3910 0.8160 -9.1320 555 | S -2.2220 2.1980 -7.9760 556 | C -0.4420 2.4470 -8.1790 557 | N -6.2720 1.6750 -11.5130 558 | C -7.0390 1.4590 -12.7740 559 | C -6.7540 2.5910 -13.7660 560 | O -6.9870 2.4630 -14.9510 561 | C -8.5070 1.4720 -12.3520 562 | O -8.8650 2.7840 -11.9370 563 | N -6.2520 3.6970 -13.2890 564 | C -5.9550 4.8350 -14.2050 565 | C -5.1150 4.3530 -15.3920 566 | O -5.4710 4.5500 -16.5360 567 | C -5.1620 5.8300 -13.3570 568 | C -6.0170 7.0700 -13.0880 569 | C -5.2010 8.3280 -13.3910 570 | N -5.3050 9.1590 -12.1590 571 | C -4.7140 10.3200 -12.1030 572 | N -3.4140 10.3940 -12.1770 573 | N -5.4220 11.4080 -11.9730 574 | N -4.0030 3.7240 -15.1270 575 | C -3.1430 3.2300 -16.2410 576 | C -2.1870 2.1480 -15.7310 577 | O -1.2660 2.4200 -14.9880 578 | C -2.3600 4.4580 -16.7110 579 | C -2.1630 4.3880 -18.2270 580 | C -0.8390 5.0570 -18.6000 581 | O -0.1080 5.5070 -17.7400 582 | N -0.4970 5.1450 -19.8570 583 | N -2.4010 0.9220 -16.1260 584 | C -1.5050 -0.1760 -15.6630 585 | C -0.3670 -0.3890 -16.6650 586 | O 0.7610 -0.6470 -16.2940 587 | C -2.3980 -1.4150 -15.5960 588 | C -1.9650 -2.2930 -14.4210 589 | C -2.8200 -1.9650 -13.1950 590 | C -2.1530 -3.7660 -14.7920 591 | N -0.6540 -0.2810 -17.9340 592 | C 0.4120 -0.4770 -18.9590 593 | C 0.4530 0.7180 -19.9140 594 | O 1.5230 1.2760 -20.0880 595 | C 0.0120 -1.7490 -19.7070 596 | C 0.7780 -2.9420 -19.1310 597 | C -0.1580 -4.1480 -19.0280 598 | C 0.6680 -5.4220 -18.8330 599 | N 0.0730 -6.0860 -17.6400 600 | O -0.5880 1.0550 -20.4550 601 | Ca 30.0 0.00 0.00 602 | Ca -30.0 0.00 0.00 603 | 600 604 | Frame 2 605 | N -11.0780 0.5790 -24.3620 606 | C -12.3670 -0.0770 -24.7230 607 | C -13.5350 0.8830 -24.4860 608 | O -13.3530 2.0780 -24.3660 609 | C -12.4700 -1.2870 -23.7940 610 | O -11.4130 -2.1910 -24.0830 611 | N -14.7330 0.3710 -24.4170 612 | C -15.9100 1.2560 -24.1870 613 | C -16.6600 0.8210 -22.9250 614 | O -17.7510 1.2810 -22.6490 615 | C -16.7910 1.0730 -25.4220 616 | O -18.1470 1.3190 -25.0730 617 | N -16.0830 -0.0610 -22.1550 618 | C -16.7640 -0.5230 -20.9110 619 | C -15.7580 -0.6100 -19.7590 620 | O -14.8850 -1.4560 -19.7470 621 | C -17.3110 -1.9100 -21.2520 622 | C -18.6460 -1.7660 -21.9840 623 | O -19.5220 -1.0490 -21.5420 624 | N -18.8410 -2.4240 -23.0940 625 | N -15.8740 0.2580 -18.7910 626 | C -14.9250 0.2240 -17.6420 627 | C -15.6760 -0.1110 -16.3460 628 | O -16.1170 -1.2260 -16.1510 629 | C -14.3180 1.6280 -17.5880 630 | C -15.4220 2.6720 -17.7640 631 | C -15.0760 3.9240 -16.9570 632 | C -15.5440 3.0390 -19.2450 633 | N -15.8310 0.8360 -15.4570 634 | C -16.5580 0.5500 -14.1850 635 | C -16.0020 -0.7200 -13.5340 636 | O -14.8210 -0.9940 -13.5970 637 | C -18.0260 0.3490 -14.5860 638 | O -18.2210 -0.9860 -15.0340 639 | C -18.4000 1.3250 -15.7060 640 | N -16.8470 -1.4960 -12.9110 641 | C -16.3710 -2.7500 -12.2570 642 | C -15.3610 -3.4650 -13.1570 643 | O -14.4560 -4.1270 -12.6920 644 | C -17.6310 -3.5970 -12.0750 645 | C -18.0420 -4.2090 -13.4170 646 | C -19.2470 -5.1290 -13.2120 647 | O -19.1980 -5.9430 -12.3060 648 | O -20.1980 -5.0020 -13.9640 649 | N -15.5100 -3.3290 -14.4440 650 | C -14.5610 -3.9910 -15.3800 651 | C -13.1890 -3.3290 -15.2700 652 | O -12.1760 -3.9870 -15.1410 653 | C -15.1540 -3.7740 -16.7720 654 | C -15.3500 -5.1270 -17.4610 655 | C -16.4450 -5.9140 -16.7380 656 | O -17.5850 -5.4820 -16.7800 657 | O -16.1240 -6.9360 -16.1540 658 | N -13.1510 -2.0240 -15.3030 659 | C -11.8420 -1.3230 -15.1830 660 | C -11.3410 -1.4520 -13.7430 661 | O -10.1960 -1.7700 -13.4980 662 | C -12.1270 0.1400 -15.5610 663 | C -12.5360 0.9480 -14.3240 664 | C -12.6710 2.4250 -14.7010 665 | O -11.9990 2.8990 -15.5960 666 | N -13.5170 3.1770 -14.0530 667 | N -12.2030 -1.2210 -12.7910 668 | C -11.7940 -1.3440 -11.3670 669 | C -11.1620 -2.7130 -11.1330 670 | O -9.9980 -2.8210 -10.8110 671 | C -13.0900 -1.2200 -10.5720 672 | C -13.6990 0.1650 -10.7980 673 | C -12.7920 -1.4110 -9.0850 674 | C -15.2130 0.0940 -10.5980 675 | N -11.9200 -3.7630 -11.2980 676 | C -11.3540 -5.1250 -11.0900 677 | C -9.9730 -5.2150 -11.7430 678 | O -9.0100 -5.6480 -11.1360 679 | C -12.3370 -6.0760 -11.7740 680 | N -9.8690 -4.7970 -12.9750 681 | C -8.5510 -4.8460 -13.6680 682 | C -7.5410 -3.9830 -12.9110 683 | O -6.3960 -4.3520 -12.7390 684 | C -8.8120 -4.2720 -15.0610 685 | C -9.4000 -5.3620 -15.9600 686 | C -8.3610 -5.7830 -16.9990 687 | O -7.9140 -4.9250 -17.7440 688 | O -8.0280 -6.9570 -17.0340 689 | N -7.9620 -2.8370 -12.4490 690 | C -7.0360 -1.9510 -11.6940 691 | C -6.6270 -2.6260 -10.3830 692 | O -5.4600 -2.7060 -10.0520 693 | C -7.8410 -0.6790 -11.4240 694 | C -7.9870 0.1010 -12.7100 695 | C -6.8620 0.3420 -13.5070 696 | C -9.2410 0.5810 -13.1070 697 | C -6.9900 1.0640 -14.6990 698 | C -9.3690 1.3040 -14.2990 699 | C -8.2440 1.5440 -15.0960 700 | N -7.5800 -3.1210 -9.6390 701 | C -7.2500 -3.8010 -8.3560 702 | C -6.0340 -4.7040 -8.5580 703 | O -5.0400 -4.5860 -7.8700 704 | C -8.4880 -4.6320 -8.0150 705 | C -9.6010 -3.7090 -7.5170 706 | C -10.7950 -4.5500 -7.0590 707 | C -10.5440 -5.0610 -5.6390 708 | N -11.3230 -6.3270 -5.5430 709 | N -6.0990 -5.5950 -9.5100 710 | C -4.9340 -6.4870 -9.7620 711 | C -3.6930 -5.6300 -10.0220 712 | O -2.6220 -5.8900 -9.5060 713 | C -5.3070 -7.2900 -11.0080 714 | C -5.8900 -8.6410 -10.5890 715 | C -5.2270 -9.7570 -11.3970 716 | O -4.8780 -9.5080 -12.5390 717 | O -5.0780 -10.8430 -10.8600 718 | N -3.8360 -4.6000 -10.8110 719 | C -2.6740 -3.7130 -11.0990 720 | C -2.2240 -3.0170 -9.8130 721 | O -1.0610 -3.0300 -9.4640 722 | C -3.1960 -2.6910 -12.1100 723 | N -3.1390 -2.4150 -9.1000 724 | C -2.7530 -1.7300 -7.8340 725 | C -1.8120 -2.6300 -7.0340 726 | O -0.6730 -2.2880 -6.7810 727 | C -4.0600 -1.5170 -7.0700 728 | C -3.7420 -1.1020 -5.6530 729 | C -3.3550 0.2160 -5.3790 730 | C -3.8290 -2.0360 -4.6130 731 | C -3.0560 0.6000 -4.0660 732 | C -3.5280 -1.6520 -3.3000 733 | C -3.1420 -0.3350 -3.0270 734 | N -2.2770 -3.7840 -6.6390 735 | C -1.4040 -4.7080 -5.8640 736 | C -0.0200 -4.7640 -6.5120 737 | O 0.9910 -4.6240 -5.8520 738 | C -2.0930 -6.0710 -5.9440 739 | N 0.0330 -4.9550 -7.8020 740 | C 1.3540 -5.0060 -8.4900 741 | C 2.2310 -3.8530 -7.9990 742 | O 3.3970 -4.0260 -7.7050 743 | C 1.0350 -4.8470 -9.9770 744 | C 1.5340 -6.0750 -10.7400 745 | C 0.7720 -6.2000 -12.0610 746 | C 3.0300 -5.9220 -11.0280 747 | N 1.6740 -2.6760 -7.8980 748 | C 2.4690 -1.5120 -7.4150 749 | C 2.8350 -1.7140 -5.9430 750 | O 3.9810 -1.5970 -5.5560 751 | C 1.5470 -0.3020 -7.5760 752 | C 1.1340 -0.1630 -9.0230 753 | C 1.9990 -0.5800 -10.0420 754 | C -0.1130 0.3870 -9.3440 755 | C 1.6160 -0.4480 -11.3820 756 | C -0.4960 0.5190 -10.6840 757 | C 0.3690 0.1010 -11.7040 758 | N 1.8690 -2.0210 -5.1220 759 | C 2.1560 -2.2380 -3.6760 760 | C 2.9260 -3.5490 -3.4860 761 | O 2.4480 -4.6130 -3.8250 762 | C 0.7830 -2.3200 -3.0080 763 | C 0.9530 -2.6830 -1.5320 764 | O 2.0840 -2.8740 -1.1150 765 | O -0.0500 -2.7660 -0.8420 766 | N 4.1140 -3.4800 -2.9520 767 | C 4.9120 -4.7230 -2.7480 768 | C 4.5590 -5.3700 -1.4040 769 | O 5.2210 -6.2840 -0.9540 770 | C 6.3690 -4.2630 -2.7550 771 | C 6.7630 -3.8400 -4.1730 772 | C 7.4820 -4.9970 -4.8690 773 | C 8.8980 -4.5620 -5.2530 774 | N 9.7390 -5.7770 -5.0590 775 | N 3.5250 -4.9020 -0.7620 776 | C 3.1350 -5.4930 0.5520 777 | C 1.6730 -5.9500 0.5170 778 | O 1.2180 -6.6680 1.3850 779 | C 3.3170 -4.3610 1.5620 780 | C 4.6500 -3.6550 1.3100 781 | O 5.6550 -4.3420 1.2270 782 | O 4.6430 -2.4400 1.2030 783 | N 0.9360 -5.5400 -0.4780 784 | C -0.4960 -5.9500 -0.5670 785 | C -1.2770 -5.4070 0.6310 786 | O -2.2980 -5.9450 1.0130 787 | C -0.4860 -7.4790 -0.5380 788 | C 0.6750 -8.0100 -1.3820 789 | O 0.5830 -8.0740 -2.5910 790 | N 1.7710 -8.3980 -0.7900 791 | N -0.8120 -4.3440 1.2270 792 | C -1.5370 -3.7700 2.3970 793 | C -2.6240 -2.8040 1.9190 794 | O -3.0390 -1.9170 2.6370 795 | C -0.4750 -3.0150 3.2000 796 | C 0.7990 -3.8570 3.2930 797 | O 1.8830 -3.3260 3.4300 798 | N 0.7130 -5.1580 3.2240 799 | N -3.0840 -2.9650 0.7080 800 | C -4.1350 -2.0490 0.1850 801 | C -3.5910 -0.6200 0.1740 802 | O -4.3280 0.3370 0.0490 803 | N -2.3010 -0.4740 0.3050 804 | C -1.6980 0.8880 0.3060 805 | C -0.3580 0.8670 -0.4330 806 | O 0.3110 -0.1460 -0.4970 807 | C -1.4930 1.2250 1.7820 808 | O -0.2040 1.7960 1.9600 809 | N 0.0400 1.9750 -0.9950 810 | C 1.3340 2.0120 -1.7320 811 | C 2.1850 3.1940 -1.2600 812 | O 1.7110 4.3070 -1.1470 813 | C 0.9420 2.1880 -3.1990 814 | C 0.3800 0.8720 -3.7350 815 | C 2.1720 2.5870 -4.0150 816 | C -0.4600 1.1530 -4.9810 817 | N 3.4390 2.9600 -0.9850 818 | C 4.3220 4.0690 -0.5230 819 | C 5.1770 4.5830 -1.6840 820 | O 5.0100 4.1770 -2.8170 821 | C 5.2050 3.4470 0.5590 822 | O 4.4110 2.6130 1.3910 823 | N 6.0900 5.4750 -1.4110 824 | C 6.9530 6.0150 -2.5010 825 | C 7.7180 4.8790 -3.1850 826 | O 7.5390 4.6130 -4.3550 827 | C 7.9220 6.9680 -1.8010 828 | O 7.8760 8.2370 -2.4410 829 | N 8.5720 4.2060 -2.4610 830 | C 9.3480 3.0890 -3.0700 831 | C 8.3990 2.0490 -3.6730 832 | O 8.6060 1.5690 -4.7690 833 | C 10.1420 2.4820 -1.9130 834 | O 10.3800 1.1060 -2.1790 835 | N 7.3600 1.7000 -2.9670 836 | C 6.3970 0.6920 -3.5000 837 | C 6.1020 0.9710 -4.9770 838 | O 6.4600 0.2020 -5.8470 839 | C 5.1340 0.8660 -2.6580 840 | C 5.3830 0.3350 -1.2450 841 | C 4.0840 -0.2340 -0.6740 842 | O 3.3010 0.5420 -0.1500 843 | O 3.8920 -1.4360 -0.7700 844 | N 5.4510 2.0650 -5.2660 845 | C 5.1350 2.3890 -6.6870 846 | C 6.4260 2.5830 -7.4850 847 | O 6.4400 2.4840 -8.6960 848 | C 4.3390 3.6930 -6.6280 849 | C 2.8880 3.4240 -7.0310 850 | C 2.0170 4.6170 -6.6330 851 | C 2.8080 3.2190 -8.5460 852 | N 7.5130 2.8610 -6.8170 853 | C 8.8020 3.0610 -7.5390 854 | C 9.3810 1.7120 -7.9750 855 | O 10.0260 1.6050 -8.9980 856 | C 9.7240 3.7370 -6.5230 857 | N 9.1560 0.6830 -7.2050 858 | C 9.6950 -0.6570 -7.5770 859 | C 9.0000 -1.1750 -8.8390 860 | O 9.4230 -2.1430 -9.4390 861 | C 9.3790 -1.5570 -6.3820 862 | O 7.9800 -1.5470 -6.1400 863 | C 10.1180 -1.0460 -5.1440 864 | N 7.9360 -0.5370 -9.2460 865 | C 7.2150 -0.9930 -10.4680 866 | C 8.0540 -0.7010 -11.7160 867 | O 7.8670 -1.3000 -12.7560 868 | C 5.9200 -0.1810 -10.4910 869 | C 5.0620 -0.6180 -11.6790 870 | C 5.1490 -0.4190 -9.1910 871 | N 8.9780 0.2150 -11.6180 872 | C 9.8300 0.5450 -12.7970 873 | C 11.3030 0.2780 -12.4780 874 | O 12.1360 0.2050 -13.3590 875 | C 9.5970 2.0350 -13.0480 876 | C 9.2920 2.2630 -14.5300 877 | S 8.0750 3.5920 -14.6980 878 | C 7.8230 3.4450 -16.4840 879 | N 11.6300 0.1290 -11.2230 880 | C 13.0500 -0.1330 -10.8480 881 | C 13.5040 -1.4810 -11.4140 882 | O 14.5720 -1.5980 -11.9810 883 | C 13.0560 -0.1640 -9.3200 884 | C 14.4640 0.1520 -8.8080 885 | C 14.7710 -0.7180 -7.5870 886 | N 14.4300 0.1340 -6.4140 887 | C 13.7760 -0.3750 -5.4060 888 | N 13.8860 -1.6460 -5.1310 889 | N 13.0120 0.3870 -4.6730 890 | N 12.7010 -2.4990 -11.2650 891 | C 13.0890 -3.8380 -11.7950 892 | C 13.1690 -3.7990 -13.3240 893 | O 13.8770 -4.5710 -13.9380 894 | C 11.9750 -4.7800 -11.3410 895 | O 12.0680 -5.9990 -12.0660 896 | N 12.4480 -2.9030 -13.9420 897 | C 12.4840 -2.8140 -15.4300 898 | C 13.8230 -2.2340 -15.8930 899 | O 14.3950 -2.6730 -16.8720 900 | C 11.3360 -1.8740 -15.7980 901 | C 10.2520 -2.6580 -16.5390 902 | C 10.7920 -3.1220 -17.8930 903 | C 9.8470 -3.8770 -15.7080 904 | N 14.3260 -1.2500 -15.1990 905 | C 15.6260 -0.6440 -15.6000 906 | C 15.5140 0.8810 -15.5580 907 | O 15.6600 1.5520 -16.5610 908 | N 15.2570 1.4350 -14.4050 909 | C 15.1360 2.9180 -14.3010 910 | C 15.7090 3.4030 -12.9660 911 | O 16.4130 4.3920 -12.9050 912 | C 13.6350 3.1990 -14.3730 913 | C 13.3870 4.7000 -14.2130 914 | C 13.5540 5.3930 -15.5660 915 | C 11.9650 4.9280 -13.6960 916 | N 15.4150 2.7150 -11.8970 917 | C 15.9430 3.1390 -10.5690 918 | C 15.7530 4.6460 -10.3800 919 | O 16.7110 5.3890 -10.3070 920 | C 17.4290 2.7860 -10.6030 921 | O 17.9290 2.7270 -9.2740 922 | N 14.5130 5.0450 -10.3100 923 | C 14.1820 6.4800 -10.1310 924 | C 14.4630 6.9160 -8.6890 925 | O 14.5000 6.1080 -7.7820 926 | C 12.6890 6.5440 -10.4360 927 | C 12.1740 5.1670 -10.1590 928 | C 13.3130 4.2060 -10.3910 929 | N 14.6600 8.1880 -8.4720 930 | C 14.9370 8.6730 -7.0900 931 | C 13.6530 9.2080 -6.4510 932 | O 12.6780 9.4640 -7.1280 933 | C 15.9590 9.7970 -7.2620 934 | O 16.8980 9.4270 -8.2630 935 | N 13.6490 9.3700 -5.1520 936 | C 12.4340 9.8830 -4.4480 937 | C 11.7000 10.9130 -5.3110 938 | O 10.4970 10.8550 -5.4730 939 | C 12.9640 10.5370 -3.1710 940 | C 14.0770 11.5260 -3.5270 941 | C 14.9120 11.8240 -2.2810 942 | O 15.4460 10.8860 -1.7110 943 | O 15.0050 12.9840 -1.9170 944 | N 12.4110 11.8530 -5.8720 945 | C 11.7430 12.8760 -6.7260 946 | C 10.7610 12.1930 -7.6820 947 | O 9.5840 12.4950 -7.6990 948 | C 12.8760 13.5430 -7.5050 949 | N 11.2360 11.2700 -8.4730 950 | C 10.3310 10.5610 -9.4240 951 | C 9.4690 9.5460 -8.6670 952 | O 8.3110 9.3470 -8.9730 953 | C 11.2660 9.8480 -10.4010 954 | C 12.2270 10.8640 -11.0220 955 | C 11.4950 11.6680 -12.0980 956 | O 10.4170 12.1620 -11.8100 957 | O 12.0240 11.7770 -13.1910 958 | N 10.0280 8.9110 -7.6740 959 | C 9.2490 7.9130 -6.8870 960 | C 8.0800 8.6070 -6.1880 961 | O 6.9280 8.3970 -6.5150 962 | C 10.2370 7.3720 -5.8510 963 | C 9.6240 6.1750 -5.1270 964 | C 11.5240 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| O -2.4610 4.4700 -21.5190 1184 | N -1.5050 6.3640 -21.0090 1185 | N -6.1900 7.8190 -22.3060 1186 | C -6.7310 8.4190 -23.5600 1187 | C -7.8990 7.5810 -24.0860 1188 | O -9.0490 7.9460 -23.9490 1189 | C -5.5640 8.3940 -24.5460 1190 | C -4.7010 9.6410 -24.3500 1191 | C -3.2540 9.2250 -24.0760 1192 | C -4.7520 10.5000 -25.6160 1193 | N -7.6120 6.4580 -24.6870 1194 | C -8.7070 5.5990 -25.2220 1195 | C -8.4900 4.1420 -24.8010 1196 | O -8.2340 3.3260 -25.6700 1197 | C -8.6120 5.7360 -26.7420 1198 | C -7.1500 5.6070 -27.1770 1199 | C -7.0450 5.8160 -28.6880 1200 | C -7.0910 4.4600 -29.3960 1201 | N -6.6460 4.7400 -30.7900 1202 | O -8.5840 3.8690 -23.6150 1203 | Ca 2.0100 -1.4740 1.3090 1204 | Ca -3.1630 7.9200 0.2600 1205 | -------------------------------------------------------------------------------- /test_cases/collagen.xyz: -------------------------------------------------------------------------------- 1 | 460 2 | Frame 1 3 | N -4.3180 -16.2500 3.9130 4 | C -4.3140 -14.7930 4.2910 5 | C 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-5.0050 13.5480 -4.7820 135 | C -6.7650 12.7010 -2.8530 136 | C -6.3590 13.5170 -5.0450 137 | C -7.2400 13.0930 -4.0790 138 | N -0.3660 12.0460 -1.9210 139 | C 1.1360 11.9200 -1.8820 140 | C 1.5520 10.8900 -2.9580 141 | O 0.6860 10.2950 -3.5690 142 | C 1.5250 11.4900 -0.4090 143 | C 3.0670 11.6210 -0.1480 144 | C 1.0270 10.0600 -0.0470 145 | C 3.8810 10.2980 -0.3150 146 | N 2.8140 10.6640 -3.1870 147 | C 3.1940 9.6570 -4.2480 148 | C 3.4440 8.2310 -3.6750 149 | O 4.1300 8.0200 -2.6850 150 | C 4.4860 10.1540 -4.9900 151 | C 4.1850 11.2510 -6.0830 152 | C 5.4730 11.6360 -6.8160 153 | C 3.2280 10.7310 -7.1760 154 | N 2.8650 7.2400 -4.2870 155 | C 3.0550 5.8240 -3.8030 156 | C 3.1980 4.8280 -4.9950 157 | O 2.9540 5.2180 -6.1220 158 | C 1.8060 5.4610 -2.9040 159 | C 1.5090 6.5330 -1.7920 160 | C 1.7480 6.0350 -0.3280 161 | C 3.0250 5.2320 -0.1080 162 | N 4.1490 5.8770 -0.8600 163 | N 3.5650 3.5960 -4.7400 164 | C 3.7010 2.6040 -5.8580 165 | C 2.4800 1.7140 -5.6270 166 | O 2.1520 1.4560 -4.4910 167 | C 5.0030 1.7480 -5.7300 168 | C 6.2430 2.5730 -6.0790 169 | C 6.8950 3.3800 -5.2070 170 | C 6.8470 2.6270 -7.2850 171 | N 7.8680 3.8910 -5.9510 172 | C 7.9260 3.4970 -7.2090 173 | C 6.5650 1.9820 -8.4930 174 | C 8.7290 3.7260 -8.3220 175 | C 7.3650 2.2060 -9.6130 176 | C 8.4520 3.0780 -9.5330 177 | N 1.8310 1.2720 -6.6480 178 | C 0.6380 0.4030 -6.4550 179 | C 0.7870 -0.8440 -7.3240 180 | O 1.4670 -0.7820 -8.3330 181 | C -0.5900 1.2750 -6.8390 182 | C -1.1730 0.9500 -8.2240 183 | C -0.6400 1.4420 -9.4010 184 | C -2.2800 0.1400 -8.2820 185 | C -1.2330 1.1140 -10.6200 186 | C -2.8580 -0.1790 -9.4940 187 | C -2.3440 0.3070 -10.6590 188 | O -2.9870 -0.0030 -11.8310 189 | N 0.1570 -1.9070 -6.9250 190 | C 0.2480 -3.1610 -7.7180 191 | C -0.8340 -3.1870 -8.8100 192 | O -2.0010 -2.9530 -8.5490 193 | C 0.0450 -4.3410 -6.7870 194 | C 0.3600 -5.6080 -7.5930 195 | C 1.6510 -5.9100 -7.9690 196 | C -0.6590 -6.4530 -7.9770 197 | C 1.9180 -7.0360 -8.7240 198 | C -0.3860 -7.5770 -8.7310 199 | C 0.8980 -7.8710 -9.1080 200 | O 1.1530 -8.9890 -9.8740 201 | N -0.3830 -3.4910 -9.9820 202 | C -1.2470 -3.5740 -11.1760 203 | C -1.4530 -5.0780 -11.5820 204 | O -0.6710 -5.6680 -12.3070 205 | C -0.4930 -2.6880 -12.1630 206 | C -1.2280 -2.6070 -13.4670 207 | O -1.3710 -3.6650 -14.0430 208 | O -1.5870 -1.5050 -13.7990 209 | N -2.4990 -5.7080 -11.0960 210 | C -2.8440 -7.0930 -11.5270 211 | C -2.7450 -7.4190 -13.0360 212 | O -2.5390 -8.5820 -13.3360 213 | C -4.2650 -7.2920 -10.9280 214 | C -4.7450 -5.8380 -10.6630 215 | C -3.4860 -5.1760 -10.1100 216 | N -2.8690 -6.4210 -13.8690 217 | C -2.8140 -6.5400 -15.3720 218 | C -1.3760 -6.6700 -15.9360 219 | O -1.1340 -7.3850 -16.8860 220 | C -3.5460 -5.2840 -15.9130 221 | C -5.0060 -5.3110 -15.5060 222 | O -5.3860 -5.4800 -14.3730 223 | N -5.9190 -5.1440 -16.3910 224 | N -0.4660 -5.9720 -15.3350 225 | C 0.9970 -5.9950 -15.7580 226 | C 1.6840 -7.0430 -14.8870 227 | O 2.5860 -7.7480 -15.2850 228 | C 1.6970 -4.6640 -15.4830 229 | O 1.4690 -4.4270 -14.1020 230 | C 1.0410 -3.4850 -16.1610 231 | N 1.1900 -7.0540 -13.6880 232 | C 1.5560 -7.9170 -12.5380 233 | C 2.7960 -7.4890 -11.7760 234 | O 3.4640 -8.2720 -11.1240 235 | C 1.6790 -9.3990 -13.0690 236 | C 0.3240 -9.7730 -13.7350 237 | C -0.2050 -11.1870 -13.2350 238 | C -0.2980 -11.2430 -11.7100 239 | N -1.0170 -10.0120 -11.2800 240 | N 3.0320 -6.2230 -11.8870 241 | C 4.1850 -5.5610 -11.2270 242 | C 3.6250 -4.2940 -10.5120 243 | O 2.4640 -4.2580 -10.1470 244 | C 5.2080 -5.2100 -12.3220 245 | O 6.3040 -4.6400 -11.6030 246 | N 4.4150 -3.2790 -10.3360 247 | C 3.9530 -2.0350 -9.6490 248 | C 4.2180 -0.7370 -10.4490 249 | O 5.2060 -0.5950 -11.1420 250 | C 4.6680 -2.0800 -8.3030 251 | S 4.4260 -3.6130 -7.3750 252 | N 3.3250 0.1980 -10.3290 253 | C 3.4340 1.5050 -11.0340 254 | C 3.3200 2.6170 -9.9730 255 | O 3.0680 2.3450 -8.8250 256 | C 2.2960 1.5210 -12.0750 257 | N 3.4840 3.8300 -10.3750 258 | C 3.4030 5.0000 -9.4430 259 | C 2.1340 5.8630 -9.5620 260 | O 1.6550 6.1160 -10.6480 261 | C 4.6510 5.8660 -9.6940 262 | C 5.6330 5.6850 -8.5070 263 | C 6.9430 6.4460 -8.7290 264 | N 7.4820 5.9080 -10.0290 265 | C 7.8280 6.6480 -10.9910 266 | N 6.9280 7.2950 -11.5720 267 | N 9.0390 6.6860 -11.2970 268 | N 1.6320 6.2920 -8.4410 269 | C 0.3900 7.1440 -8.4400 270 | C 0.3220 8.1940 -7.2980 271 | O 1.0520 8.1170 -6.3290 272 | C -0.8140 6.1560 -8.3840 273 | C -1.0850 5.6020 -6.9760 274 | C -0.2520 4.6630 -6.4160 275 | C -2.1880 6.0190 -6.2590 276 | C -0.5140 4.1450 -5.1630 277 | C -2.4500 5.4990 -5.0060 278 | C -1.6130 4.5620 -4.4580 279 | N -0.5680 9.1330 -7.4590 280 | C -0.7740 10.2310 -6.4400 281 | C -1.7680 9.8200 -5.3240 282 | O -2.8140 10.4120 -5.1600 283 | C -1.3190 11.4820 -7.1880 284 | C -0.2580 12.4300 -7.6820 285 | C -0.2020 12.7650 -8.9670 286 | C 0.7010 13.0680 -6.9810 287 | N 0.8110 13.6120 -9.0180 288 | C 1.4190 13.8580 -7.8700 289 | C 1.0400 13.0660 -5.6230 290 | C 2.4690 14.6460 -7.4290 291 | C 2.0980 13.8600 -5.1760 292 | C 2.8130 14.6500 -6.0770 293 | N -1.3960 8.8280 -4.5720 294 | C -2.2810 8.3270 -3.4610 295 | C -3.7570 8.0690 -3.8930 296 | O -4.1490 8.0490 -5.0410 297 | C -2.2230 9.3910 -2.3240 298 | C -3.0800 9.0750 -1.0680 299 | C -2.6530 8.1280 -0.1670 300 | C -4.2770 9.7360 -0.8020 301 | C -3.3760 7.8530 0.9770 302 | C -4.9880 9.4490 0.3490 303 | C -4.5380 8.5160 1.2340 304 | O -5.2440 8.2620 2.3790 305 | N -4.4790 7.8350 -2.8520 306 | C -5.9110 7.5590 -2.7610 307 | C -6.1070 6.7090 -1.5560 308 | O -5.2410 5.9030 -1.2560 309 | N -7.1940 6.8790 -0.8760 310 | C -7.3910 6.0180 0.3200 311 | C -7.1400 6.3670 1.7710 312 | O -6.2080 5.7560 2.2560 313 | N -7.8500 7.2560 2.4310 314 | C -7.6080 7.5850 3.9130 315 | C -6.9690 6.3330 4.5990 316 | O -6.0110 6.3430 5.3430 317 | C -8.9660 7.9140 4.5860 318 | S -10.2110 8.9070 3.7290 319 | N -7.6450 5.2670 4.2450 320 | C -7.3530 3.8490 4.6670 321 | C -7.2000 2.9950 3.3800 322 | O -6.1250 2.5680 3.0080 323 | N -8.2910 2.7720 2.6820 324 | C -8.2560 1.9380 1.3980 325 | C -7.5340 0.5990 1.6340 326 | O -7.5350 0.1470 2.7550 327 | N -6.9470 -0.0150 0.6450 328 | C -6.2380 -1.3330 0.9180 329 | C -4.6720 -1.3410 0.7920 330 | O -4.0380 -0.3910 0.3570 331 | C -6.8580 -2.3520 -0.0520 332 | C -6.2350 -2.1340 -1.4020 333 | O -5.2770 -2.7790 -1.7650 334 | N -6.7000 -1.2410 -2.1880 335 | N -4.1280 -2.4440 1.1920 336 | C -2.6600 -2.7650 1.1980 337 | C -1.8020 -2.1750 0.0530 338 | O -0.7740 -1.5700 0.2580 339 | C -2.5110 -4.3150 1.1940 340 | C -3.6330 -5.0320 2.0340 341 | C -4.0570 -4.2770 3.2810 342 | O -3.2170 -4.1410 4.1450 343 | O -5.2120 -3.8910 3.2440 344 | N -2.2920 -2.3890 -1.1390 345 | C -1.6590 -1.9410 -2.4380 346 | C -0.8110 -0.6030 -2.4490 347 | O -0.0160 -0.3840 -3.3380 348 | C -2.8850 -1.9470 -3.4470 349 | C -2.4770 -1.7310 -4.8890 350 | O -1.8380 -0.7890 -5.2630 351 | N -2.8060 -2.5780 -5.7980 352 | N -0.9740 0.2520 -1.4770 353 | C -0.2070 1.5600 -1.4120 354 | C 1.2650 1.4090 -0.8930 355 | O 1.5380 1.4900 0.2900 356 | C -0.9750 2.5280 -0.4770 357 | C -2.4760 2.6070 -0.7920 358 | C -3.0900 3.4840 0.3420 359 | C -4.5990 3.4480 0.3240 360 | N -4.9850 2.0330 0.5500 361 | N 2.2020 1.2510 -1.7810 362 | C 3.6390 1.0760 -1.3820 363 | C 4.5820 2.3100 -1.4470 364 | O 4.3030 3.3670 -1.9990 365 | C 4.1550 -0.0680 -2.2920 366 | C 3.3980 -1.3750 -2.0290 367 | C 3.6550 -2.0750 -0.8790 368 | C 2.4760 -1.8720 -2.9260 369 | C 3.0090 -3.2590 -0.6080 370 | C 1.8250 -3.0590 -2.6640 371 | C 2.0880 -3.7540 -1.5080 372 | N 5.7130 2.1250 -0.8400 373 | C 6.8240 3.1480 -0.7530 374 | C 7.7580 3.0880 -1.9720 375 | O 8.0920 4.1190 -2.5180 376 | N 8.1300 1.9050 -2.3620 377 | C 9.0490 1.6520 -3.5410 378 | C 8.6090 0.5440 -4.5150 379 | O 7.9210 -0.3820 -4.1430 380 | C 10.4570 1.2930 -3.0520 381 | O 10.9750 2.5500 -2.6380 382 | N 9.0240 0.6210 -5.7540 383 | C 8.6290 -0.4270 -6.7580 384 | C 8.9770 -1.8400 -6.2680 385 | O 8.1470 -2.6820 -6.0170 386 | C 9.3700 -0.1600 -8.0900 387 | C 8.9580 -1.2740 -9.1400 388 | C 10.0130 -1.4410 -10.2190 389 | O 10.3840 -0.5330 -10.9190 390 | N 10.5710 -2.5790 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-5.1670 -8.8860 423 | O 11.4160 -6.8190 -7.7810 424 | N 8.1010 -7.2270 -4.3330 425 | C 8.3040 -8.3820 -3.4070 426 | C 7.1420 -8.6540 -2.4020 427 | O 7.2530 -9.5170 -1.5550 428 | C 9.6640 -8.1200 -2.6710 429 | C 10.6150 -9.3180 -2.9880 430 | C 11.9330 -8.8930 -3.7170 431 | C 11.7370 -7.9610 -4.9170 432 | N 10.8000 -8.5660 -5.8860 433 | N 6.0640 -7.9230 -2.5070 434 | C 4.8850 -8.1180 -1.6030 435 | C 3.8690 -8.9530 -2.4300 436 | O 3.2110 -9.8300 -1.9070 437 | C 4.3670 -6.7210 -1.2300 438 | C 3.0490 -6.8850 -0.4510 439 | C 5.3610 -6.0720 -0.2520 440 | N 3.7660 -8.6370 -3.6970 441 | C 2.8330 -9.3830 -4.6230 442 | C 3.6010 -10.2700 -5.6400 443 | O 3.2530 -11.4110 -5.8690 444 | C 1.9640 -8.4320 -5.4470 445 | S 1.0870 -9.3650 -6.7270 446 | N 4.6370 -9.7470 -6.2430 447 | C 5.4270 -10.5510 -7.2410 448 | C 6.5360 -11.4280 -6.5430 449 | O 7.6040 -10.9310 -6.2470 450 | C 6.0340 -9.5290 -8.2320 451 | N 6.2730 -12.6990 -6.2960 452 | C 7.0780 -13.5320 -5.3280 453 | C 8.5010 -14.0110 -5.7970 454 | O 8.8110 -15.1880 -5.7550 455 | C 6.0970 -14.6710 -5.0370 456 | C 5.5230 -14.9160 -6.4620 457 | C 5.1680 -13.4920 -6.9210 458 | N 9.2830 -13.0650 -6.2190 459 | C 10.6880 -13.2370 -6.7200 460 | C 11.4810 -11.9700 -6.2340 461 | O 10.9050 -11.2300 -5.4600 462 | O 12.6150 -11.7420 -6.6180 463 | 460 464 | Frame 1 465 | N -8.7920 7.2090 17.1930 466 | C -7.7490 8.2450 17.2910 467 | C -7.1900 8.5830 15.9140 468 | O -7.9970 8.5240 14.9760 469 | C -6.6840 7.8160 18.2960 470 | C -5.6410 6.8520 17.7880 471 | C -6.1590 5.5400 17.2530 472 | O -5.6850 4.4880 17.7280 473 | O -7.0160 5.5010 16.3430 474 | N -5.9340 8.9630 15.6820 475 | C -5.6240 9.4070 14.2990 476 | C -5.6290 8.2480 13.3170 477 | O -5.1830 7.1580 13.7350 478 | C -4.2680 10.1220 14.2070 479 | O -3.7980 10.0730 12.8700 480 | C -3.1890 9.4410 15.0520 481 | N -6.0350 8.4760 12.0740 482 | C -6.1780 7.4740 11.0270 483 | C -4.8090 6.8630 10.6130 484 | O -4.7980 5.7100 10.1500 485 | C -6.9700 7.8680 9.7960 486 | C -7.4280 6.6720 9.0270 487 | O -6.9430 5.5630 9.3390 488 | O -8.2610 6.7820 8.0970 489 | N -3.6610 7.4800 10.8840 490 | C -2.3790 6.7880 10.7290 491 | C -2.3990 5.4780 11.5350 492 | O -1.8680 4.4500 11.0640 493 | C -1.2170 7.6740 11.2150 494 | C -1.0280 8.9660 10.3760 495 | C 0.1070 6.9250 11.3260 496 | C -0.8730 8.7710 8.8960 497 | N -2.9860 5.4720 12.7230 498 | C -2.9650 4.2600 13.5520 499 | C -3.8530 3.1180 13.0240 500 | O -3.7220 1.9830 13.4830 501 | C -3.5140 4.6190 14.9300 502 | S -2.5040 5.7980 15.8670 503 | N -4.7120 3.4660 12.0570 504 | C -5.5980 2.4560 11.4470 505 | C -5.0640 1.9860 10.1100 506 | O -5.7160 1.1270 9.5070 507 | C -6.9910 3.0800 11.2630 508 | C -7.6140 3.3390 12.6210 509 | C -9.0730 3.7550 12.5730 510 | C -9.2080 5.2410 12.6050 511 | N -10.5870 5.7090 12.2810 512 | N -3.9110 2.5050 9.6380 513 | C -3.3190 1.9960 8.4090 514 | C -2.9110 0.5420 8.5800 515 | O -2.5430 0.1490 9.6750 516 | C -2.0810 2.8400 8.0160 517 | C -2.3570 4.2930 7.5880 518 | C -1.0650 5.0890 7.6040 519 | C -3.0370 4.3060 6.2090 520 | N -2.9440 -0.2250 7.5190 521 | C -2.5310 -1.6290 7.6550 522 | C -1.0640 -1.7850 7.9390 523 | O -0.2500 -0.9550 7.5210 524 | C -2.8500 -2.2070 6.2730 525 | C -2.8120 -1.0220 5.3570 526 | C -3.3480 0.1320 6.1520 527 | N -0.7280 -2.8860 8.6010 528 | C 0.6850 -3.2800 8.7040 529 | C 1.2660 -3.3560 7.2880 530 | O 0.6660 -4.0580 6.4360 531 | C 0.7210 -4.6740 9.3360 532 | C 2.1180 -5.2860 9.5190 533 | C 1.9970 -6.8200 9.7800 534 | C 1.8880 -7.4790 8.4170 535 | N 1.8580 -8.9600 8.4990 536 | N 2.4140 -2.7340 7.0620 537 | C 3.0210 -2.7290 5.7330 538 | C 4.5010 -3.0640 5.8680 539 | O 5.3490 -2.2500 6.1640 540 | C 2.8140 -1.3590 5.1030 541 | C 3.3270 -1.1810 3.7020 542 | O 3.8670 -2.1850 3.1690 543 | O 3.1730 -0.0190 3.1990 544 | N 4.8120 -4.3440 5.5900 545 | C 6.1820 -4.8100 5.6290 546 | C 7.0390 -4.1450 4.5860 547 | O 8.2740 -4.1870 4.6750 548 | C 6.2080 -6.3430 5.4370 549 | C 5.6720 -7.0980 6.5960 550 | C 5.6380 -8.6180 6.3980 551 | O 5.6490 -9.0620 5.2580 552 | O 5.5210 -9.3000 7.4030 553 | N 6.4160 -3.5520 3.5600 554 | C 7.2370 -2.8600 2.5590 555 | C 8.1050 -3.8110 1.7760 556 | O 7.7880 -5.0000 1.5780 557 | N 9.1970 -3.2530 1.2410 558 | C 10.0990 -3.9810 0.3640 559 | C 11.5070 -3.4950 0.7560 560 | O 11.6630 -2.7310 1.7330 561 | C 9.8040 -3.7180 -1.1160 562 | O 9.7280 -2.2620 -1.2740 563 | C 8.4500 -4.2410 -1.5650 564 | N 12.5000 -3.9590 -0.0320 565 | C 13.8930 -3.7740 0.2710 566 | C 14.3200 -4.7710 1.3610 567 | O 13.5150 -5.4700 1.9800 568 | C 14.3160 -2.3410 0.5860 569 | S 14.0140 -1.2500 -0.8350 570 | N 15.6210 -4.7780 1.5650 571 | C 16.2060 -5.8560 2.3670 572 | C 17.0900 -5.2650 3.4550 573 | O 18.0360 -5.8910 3.9270 574 | C 16.9600 -6.8870 1.5350 575 | C 16.2250 -7.5060 0.3650 576 | C 15.1160 -8.4380 0.9190 577 | N 14.2850 -8.9900 -0.1440 578 | C 14.4990 -10.0950 -0.7910 579 | N 15.5750 -10.8490 -0.4470 580 | N 13.6780 -10.5090 -1.7750 581 | N 16.7110 -4.0590 3.9210 582 | C 17.3060 -3.4360 5.0490 583 | C 16.3960 -3.5490 6.2760 584 | O 15.7620 -2.6100 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