1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38 package ffx.xray.parsers;
39
40 import ffx.crystal.Crystal;
41 import ffx.crystal.HKL;
42 import ffx.crystal.ReflectionList;
43 import ffx.crystal.Resolution;
44 import ffx.crystal.SpaceGroupDefinitions;
45 import ffx.crystal.SpaceGroupInfo;
46 import ffx.xray.DiffractionRefinementData;
47 import org.apache.commons.configuration2.CompositeConfiguration;
48
49 import java.io.BufferedReader;
50 import java.io.File;
51 import java.io.FileReader;
52 import java.io.IOException;
53 import java.util.logging.Level;
54 import java.util.logging.Logger;
55
56 import static ffx.crystal.SpaceGroupInfo.spaceGroupNames;
57 import static java.lang.Double.parseDouble;
58 import static java.lang.Integer.parseInt;
59 import static java.lang.String.format;
60 import static org.apache.commons.math3.util.FastMath.min;
61
62
63
64
65
66
67
68 public class CNSFilter implements DiffractionFileFilter {
69
70 private static final Logger logger = Logger.getLogger(CNSFilter.class.getName());
71
72 private final double[] cell = {-1.0, -1.0, -1.0, -1.0, -1.0, -1.0};
73 private double resHigh = -1.0;
74 private String spaceGroupName = null;
75 private int spaceGroupNum = -1;
76
77
78 public CNSFilter() {
79 }
80
81
82 @Override
83 public ReflectionList getReflectionList(File cnsFile) {
84 return getReflectionList(cnsFile, null);
85 }
86
87
88 @Override
89 public ReflectionList getReflectionList(File cnsFile, CompositeConfiguration properties) {
90 try (BufferedReader br = new BufferedReader(new FileReader(cnsFile))) {
91 String string;
92 while ((string = br.readLine()) != null) {
93 String[] strArray = string.split("\\s+");
94 if (strArray[0].equalsIgnoreCase("{")) {
95 if (strArray[1].toLowerCase().startsWith("sg=")) {
96 spaceGroupName = strArray[1].substring(3);
97 cell[0] = parseDouble(strArray[2].substring(2));
98 cell[1] = parseDouble(strArray[3].substring(2));
99 cell[2] = parseDouble(strArray[4].substring(2));
100 cell[3] = parseDouble(strArray[5].substring(6));
101 cell[4] = parseDouble(strArray[6].substring(5));
102 cell[5] = parseDouble(strArray[7].substring(6));
103 }
104 } else if (strArray[0].equalsIgnoreCase("CRYST1")) {
105 cell[0] = parseDouble(strArray[1]);
106 cell[1] = parseDouble(strArray[2]);
107 cell[2] = parseDouble(strArray[3]);
108 cell[3] = parseDouble(strArray[4]);
109 cell[4] = parseDouble(strArray[5]);
110 cell[5] = parseDouble(strArray[6]);
111 spaceGroupName = SpaceGroupInfo.pdb2ShortName(string.substring(55, 65));
112 } else if (strArray[0].toLowerCase().startsWith("inde")) {
113 break;
114 }
115 }
116 } catch (IOException e) {
117 String message = " CNS IO Exception.";
118 logger.log(Level.WARNING, message, e);
119 return null;
120 }
121
122 Resolution resolution = null;
123 if (properties != null) {
124 resolution = Resolution.checkProperties(properties);
125 resHigh = resolution.resolution;
126 }
127
128 if (spaceGroupName != null) {
129 spaceGroupNum = SpaceGroupDefinitions.spaceGroupNumber(spaceGroupName);
130 }
131
132 if (spaceGroupNum < 0 || cell[0] < 0 || resolution == null) {
133 logger.info(
134 " The CNS file contains insufficient information to generate the reflection list.");
135 return null;
136 }
137
138 if (logger.isLoggable(Level.INFO)) {
139 StringBuilder sb = new StringBuilder();
140 sb.append(format("\n Opening %s\n", cnsFile.getName()));
141 sb.append(" Setting up Reflection List based on CNS:\n");
142 sb.append(format(" Spacegroup #: %d (name: %s)\n",
143 spaceGroupNum, spaceGroupNames[spaceGroupNum - 1]));
144 sb.append(format(" Resolution: %8.3f\n", resHigh));
145 sb.append(format(" Cell: %8.3f %8.3f %8.3f %8.3f %8.3f %8.3f\n",
146 cell[0], cell[1], cell[2], cell[3], cell[4], cell[5]));
147 logger.info(sb.toString());
148 }
149
150 Crystal crystal = new Crystal(cell[0], cell[1], cell[2],
151 cell[3], cell[4], cell[5], spaceGroupNames[spaceGroupNum - 1]);
152
153 return new ReflectionList(crystal, resolution, properties);
154 }
155
156
157 @Override
158 public double getResolution(File cnsFile, Crystal crystal) {
159 double res = Double.POSITIVE_INFINITY;
160
161 try (BufferedReader br = new BufferedReader(new FileReader(cnsFile))) {
162 HKL hkl = new HKL();
163 String string;
164 while ((string = br.readLine()) != null) {
165 String[] strArray = string.split("\\s+");
166 for (int i = 0; i < strArray.length; i++) {
167 if (strArray[i].toLowerCase().startsWith("inde")) {
168 if (i < strArray.length - 3) {
169 int ih = parseInt(strArray[i + 1]);
170 int ik = parseInt(strArray[i + 2]);
171 int il = parseInt(strArray[i + 3]);
172 hkl.setH(ih);
173 hkl.setK(ik);
174 hkl.setL(il);
175 res = min(res, crystal.res(hkl));
176 }
177 }
178 }
179 }
180 } catch (IOException e) {
181 String message = " CNS IO Exception.";
182 logger.log(Level.WARNING, message, e);
183 return -1.0;
184 }
185
186 return res;
187 }
188
189
190 @Override
191 public boolean readFile(
192 File cnsFile,
193 ReflectionList reflectionList,
194 DiffractionRefinementData refinementData,
195 CompositeConfiguration properties) {
196
197 int nRead, nRes, nIgnore, nFriedel, nCut;
198 boolean transpose = false;
199
200 StringBuilder sb = new StringBuilder();
201 sb.append(format("\n Opening %s\n", cnsFile.getName()));
202
203 if (refinementData.rFreeFlag < 0) {
204 refinementData.setFreeRFlag(1);
205 sb.append(format(" Setting R free flag to CNS default: %d\n", refinementData.rFreeFlag));
206 }
207
208
209 String foString = null;
210 String sigFoString = null;
211 String rFreeString = null;
212 int ih, ik, il, free;
213 double fo, sigFo;
214
215 try (BufferedReader br = new BufferedReader(new FileReader(cnsFile))) {
216 ih = ik = il = free = -1;
217 fo = sigFo = -1.0;
218
219
220 HKL mate = new HKL();
221 int nPosIgnore = 0;
222 int nTransIgnore = 0;
223
224 String string;
225 while ((string = br.readLine()) != null) {
226 String[] strArray = string.split("\\s+");
227
228 for (int i = 0; i < strArray.length; i++) {
229 if (strArray[i].toLowerCase().startsWith("inde")) {
230 if (i < strArray.length - 3) {
231 ih = parseInt(strArray[i + 1]);
232 ik = parseInt(strArray[i + 2]);
233 il = parseInt(strArray[i + 3]);
234 reflectionList.findSymHKL(ih, ik, il, mate, false);
235 HKL hklpos = reflectionList.getHKL(mate);
236 if (hklpos == null) {
237 nPosIgnore++;
238 }
239
240 reflectionList.findSymHKL(ih, ik, il, mate, true);
241 HKL hkltrans = reflectionList.getHKL(mate);
242 if (hkltrans == null) {
243 nTransIgnore++;
244 }
245 }
246 }
247 }
248 }
249 if (nPosIgnore > nTransIgnore) {
250 transpose = true;
251 }
252
253 if (properties != null) {
254 foString = properties.getString("fostring", null);
255 sigFoString = properties.getString("sigfostring", null);
256 rFreeString = properties.getString("rfreestring", null);
257 }
258 } catch (IOException e) {
259 String message = "CNS IO Exception.";
260 logger.log(Level.WARNING, message, e);
261 return false;
262 }
263
264 boolean hasHKL, hasFo, hasSigFo, hasFree;
265 hasHKL = hasFo = hasSigFo = hasFree = false;
266
267
268 try (BufferedReader br = new BufferedReader(new FileReader(cnsFile))) {
269
270
271 double[][] anofSigF = new double[refinementData.n][4];
272 for (int i = 0; i < refinementData.n; i++) {
273 anofSigF[i][0] = anofSigF[i][1] = anofSigF[i][2] = anofSigF[i][3] = Double.NaN;
274 }
275 nRead = nRes = nIgnore = nFriedel = nCut = 0;
276
277 String string;
278 HKL mate = new HKL();
279 while ((string = br.readLine()) != null) {
280 String[] strArray = string.split("\\s+");
281 for (int i = 0; i < strArray.length; i++) {
282 if (strArray[i].toLowerCase().startsWith("inde")) {
283 if (hasHKL && hasFo && hasSigFo && hasFree) {
284 boolean friedel = reflectionList.findSymHKL(ih, ik, il, mate, transpose);
285 HKL hkl = reflectionList.getHKL(mate);
286 if (hkl != null) {
287 if (refinementData.fSigFCutoff > 0.0 && (fo / sigFo) < refinementData.fSigFCutoff) {
288 nCut++;
289 } else if (friedel) {
290 anofSigF[hkl.getIndex()][2] = fo;
291 anofSigF[hkl.getIndex()][3] = sigFo;
292 nFriedel++;
293 } else {
294 anofSigF[hkl.getIndex()][0] = fo;
295 anofSigF[hkl.getIndex()][1] = sigFo;
296 }
297 refinementData.setFreeR(hkl.getIndex(), free);
298 nRead++;
299 } else {
300 HKL tmp = new HKL(ih, ik, il);
301 if (!reflectionList.resolution.inInverseResSqRange(
302 reflectionList.crystal.invressq(tmp))) {
303 nRes++;
304 } else {
305 nIgnore++;
306 }
307 }
308 }
309 hasHKL = false;
310 hasFo = false;
311 hasSigFo = false;
312 hasFree = false;
313 if (i < strArray.length - 3) {
314 ih = parseInt(strArray[i + 1]);
315 ik = parseInt(strArray[i + 2]);
316 il = parseInt(strArray[i + 3]);
317 hasHKL = true;
318 }
319 }
320 if (strArray[i].toLowerCase().startsWith("fobs=")
321 || strArray[i].equalsIgnoreCase(foString + "=")) {
322 fo = parseDouble(strArray[i + 1]);
323 hasFo = true;
324 }
325 if (strArray[i].toLowerCase().startsWith("sigma=")
326 || strArray[i].equalsIgnoreCase(sigFoString + "=")) {
327 sigFo = parseDouble(strArray[i + 1]);
328 hasSigFo = true;
329 }
330 if (strArray[i].toLowerCase().startsWith("test=")
331 || strArray[i].equalsIgnoreCase(rFreeString + "=")) {
332 free = parseInt(strArray[i + 1]);
333 hasFree = true;
334 }
335 }
336 }
337
338 refinementData.generateFsigFfromAnomalousFsigF(anofSigF);
339 } catch (IOException e) {
340 String message = "CNS IO Exception.";
341 logger.log(Level.WARNING, message, e);
342 return false;
343 }
344
345 if (logger.isLoggable(Level.INFO)) {
346 sb.append(format(" HKL read in: %d\n", nRead));
347 sb.append(format(" HKL read as friedel mates: %d\n", nFriedel));
348 sb.append(format(" HKL not read in (too high resolution): %d\n", nRes));
349 sb.append(format(" HKL not read in (not in internal list?): %d\n", nIgnore));
350 sb.append(format(" HKL not read in (F/sigF cutoff): %d\n", nCut));
351 sb.append(
352 format(" HKL in internal list: %d\n", reflectionList.hklList.size()));
353 logger.info(sb.toString());
354 }
355
356 return true;
357 }
358 }